Gene Expression Regulation, Bacterial
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Promoter Regions, Genetic
Artificial Gene Fusion
Oligonucleotide Array Sequence Analysis
Gene Expression Profiling
Cyclic AMP Receptor Protein
A transcriptional regulator in prokaryotes which, when activated by binding cyclic AMP, acts at several promoters. Cyclic AMP receptor protein was originally identified as a catabolite gene activator protein. It was subsequently shown to regulate several functions unrelated to catabolism, and to be both a negative and a positive regulator of transcription. Cell surface cyclic AMP receptors are not included (CYCLIC AMP RECEPTORS), nor are the eukaryotic cytoplasmic cyclic AMP receptor proteins, which are the regulatory subunits of CYCLIC AMP-DEPENDENT PROTEIN KINASES.
SOS Response (Genetics)
An error-prone mechanism or set of functions for repairing damaged microbial DNA. SOS functions (a concept reputedly derived from the SOS of the international distress signal) are involved in DNA repair and mutagenesis, in cell division inhibition, in recovery of normal physiological conditions after DNA repair, and possibly in cell death when DNA damage is extensive.
Electrophoretic Mobility Shift Assay
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
Operator Regions, Genetic
RNA Polymerase Sigma 54
Genetic Complementation Test
A whiplike motility appendage present on the surface cells. Prokaryote flagella are composed of a protein called FLAGELLIN. Bacteria can have a single flagellum, a tuft at one pole, or multiple flagella covering the entire surface. In eukaryotes, flagella are threadlike protoplasmic extensions used to propel flagellates and sperm. Flagella have the same basic structure as CILIA but are longer in proportion to the cell bearing them and present in much smaller numbers. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Genes that show rapid and transient expression in the absence of de novo protein synthesis. The term was originally used exclusively for viral genes where immediate-early referred to transcription immediately following virus integration into the host cell. It is also used to describe cellular genes which are expressed immediately after resting cells are stimulated by extracellular signals such as growth factors and neurotransmitters.
Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
... of which 30 genes are members of the OxyR regulon. The genes include many genes coding for metabolic enzymes and antioxidant ... SoxRS regulon genes can be regulated by additional factors. At least three known genes including xthA and katE are regulated by ... The structural genes under this regulon include sodA (Mn-superoxide dismutase(SOD)), zwf (glucose-6-phosphate dehydrogenase( ... The oxidized form of this factor specifically binds to the promoters of constituent genes of OxyR regulon, including katG ( ...
Qin, N (2007). "Analysis of LuxR regulon gene expression during quorum sensing in Vibrio fischeri". J Bacteriol. 189 (11): 4127 ... The bacterial luciferin-luciferase system is encoded by a set of genes labelled the lux operon. In A. fischeri, five such genes ... and specific proteins that regulate transcription of genes bind to these autoinducers and alter gene expression. This system ... This operon has a known gene sequence of luxCDAB(F)E, where luxA and luxB code for the protein subunits of the luciferase ...
Sudarsan, N. (16 October 2003). "An mRNA structure in bacteria that controls gene expression by binding lysine". Genes & ... Grundy, F. J.; Lehman, S. C.; Henkin, T. M. (1 October 2003). "The L box regulon: Lysine sensing by leader RNAs of bacterial ... lysine biosynthesis genes". Proceedings of the National Academy of Sciences. 100 (21): 12057-12062. doi:10.1073/pnas.2133705100 ...
"Inverse regulation in the metabolic genes pckA and metE revealed by proteomic analysis of the Salmonella RcsCDB regulon". J ... "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli". ... The majority of genes downregulated by FnrS are required for aerobic metabolism or the oxidative stress response. Some of the ... MarA activates genes involved in the resistance to superoxide, which might not be necessary at the anaerobic conditions where ...
Grundy, FJ; Lehman SC; Henkin TM (2003). "The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis ... Serganov A, Huang L, Patel DJ (2008). "Structural insights into amino acid binding and gene control by a lysine riboswitch". ... Lysine riboswitch are most abundant in Firmicutes and Gammaproteobacteria where they are found upstream of a number of genes ... Sudarsan, N; Wickiser JK; Nakamura S; Ebert MS; Breaker RR (2003). "An mRNA structure in bacteria that controls gene expression ...
Amino acid synthesis
The genes required for the synthesis of cysteine are coded for on the cys regulon. The integration of sulfur is positively ... They are coded for by the genes AsnA and AsnB. AsnC is autogenously regulated, which is where the product of a structural gene ... Steiert JG, Rolfes RJ, Zalkin H, Stauffer GV (1990). "Regulation of the Escherichia coli glyA gene by the purR gene product". J ... Arginine synthesis also utilizes negative feedback as well as repression through a repressor encoded by the gene argR. The gene ...
Doug Cameron (engineer)
1,3-Propanediol production by Escherichia coli expressing genes from the Klebsiella pneumoniae dha regulon. , Applied and ...
... to 4-fold change in protein expression of their target genes. Individual miRNAs often repress several hundred target genes. ... Keene JD (2007). "RNA regulons: coordination of post-transcriptional events". Nature Reviews Genetics. 8 (7): 533-543. doi: ... In order for gene expression to proceed, regulatory proteins must bind to the RNA chain and remove the attenuation, which is ... ISBN 978-0-12-498264-2. Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J, Do L, Gorospe M, Becker KG (2005). "Control of gene ...
Jack D. Keene
He formalized the posttranscriptional operon and regulon (PTRO) model to describe global gene regulation, and proposed the RNA ... By 2007, Keene proposed the RNA regulon hypothesis, "that mRNAs encoded by functionally related genes may be coordinately ... In 2001-2002, Keene formalized the posttranscriptional operon and regulon (PTRO) model for global gene regulation. ... Keene, J. D. (January 2007). "Biological Clocks and the Coordination Theory of RNA Operons and Regulons". Cold Spring Harbor ...
"In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon". ... SOS box is the region in the promoter of various genes to which the LexA repressor binds to repress the transcription of SOS- ... SOS response SOS gene LexA RecA Walker, GC (October 1995). "SOS-regulated proteins in translesion DNA synthesis and mutagenesis ... Davis EO, Dullaghan EM, Rand L (June 2002). "Definition of the Mycobacterial SOS Box and Use To Identify LexA-Regulated Genes ...
Uptake hexose phosphate
Hoffer, Sally; Uden, Nathalie; Tommassen, Jan (2001). "Expression of the pho regulon interferes with induction of the uhpT gene ...
... also models the organization of the genes in transcription units, operons and regulons. A total of 120 sRNAs with 231 ... A transcription unit is a set of one or more genes transcribed from a single promoter. A TU may also include regulatory protein ... A transcription unit must include all the genes in an operon. A promoter is defined in RegulonDB as the nucleotide sequence 60 ... The graphic display of an operon contains all the genes of its different transcription units, as well as all the regulatory ...
"Gene expression analysis of the Streptococcus pneumoniae competence regulons by use of DNA microarrays". J. Bacteriol. 182 (21 ... has identified an excitable core module of genes which can explain entry into and exit from competence when cellular noise is ... Other differences between competence and sex have been considered in models of the evolution of genes causing competence; these ... Claverys, JP; Prudhomme, M; Martin, B (2006). "Induction of competence regulons as a general response to stress in gram- ...
Sxy 5′ UTR element
When the sxy gene is deleted the bacterium loses the ability to express genes in the competence regulon. Cameron et al. ... The Sxy 5′ UTR element is an RNA element that controls expression of the sxy gene in H. influenzae. The sxy gene is a ... Gene. 457 (1-2): 42-49. doi:10.1016/j.gene.2010.03.003. PMID 20302923. Yamamoto, S; Izumiya, H; Mitobe, J; Morita, M; Arakawa, ... recently showed that mutations in the 5′ end of the sxy gene lead to hypercompetance. They showed that this region formed an ...
There are specific genes that were found to be crucial in the different biofilm growth stages. Two of these genes include rocD ... ComK1 and ComK2 regulons by transcriptome sequencing". Molecular Microbiology. 94 (3): 557-79. doi:10.1111/mmi.12767. PMID ... The genes encoding the components of PVL are encoded on a bacteriophage found in community-associated MRSA strains.[citation ... In fact, studies involving mutation of genes coding for protein A resulted in a lowered virulence of S. aureus as measured by ...
Culjkovic B, Topisirovic I, Borden KL (2007). "Controlling gene expression through RNA regulons: the role of the eukaryotic ... "Entrez Gene: eIF4E Eukaryotic translation initiation factor 4E". Duncan, R.; Milburn, S. C.; Hershey, J. W. (1987-01-05). " ... Eukaryotic translation initiation factor 4E, also known as eIF4E, is a protein that in humans is encoded by the EIF4E gene. ... Jones RM, MacDonald ME, Branda J, Altherr MR, Louis DN, Schmidt EV (May 1997). "Assignment of the human gene encoding ...
Other names in common use include gene hpd protein, glycerophosphoryl diester phosphodiesterase, and IgD-binding protein D. ... a new enzyme of the glp regulon". J. Biol. Chem. 258 (9): 5428-32. doi:10.1016/S0021-9258(20)81908-5. PMID 6304089. Biology ...
Martin Turner (scientist)
His work has included research the fundamental mechanisms regulating gene expression by cells of the immune system. Turner ... PMID 29348497 Galloway A, and Turner M. (2017) Cell cycle RNA regulons coordinating early lymphocyte development. Wiley ... 2018) "RNA-binding proteins control gene expression and cell fate in the immune system." Nature Immunology 19(2):120-129. ... "Regulation of expression of human interleukin 1 alpha and beta genes." J. Immunol. 143:3556-3561. Hirano, T., Matsuda, T., ...
Genes Dev. 15 (13): 1637-1651. doi:10.1101/gad.901001. PMC 312727. PMID 11445539. Papenfort, K; Pfeiffer V; Mika F; Lucchini S ... "Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins". J Mol ... Genes Dev. 26 (7): 726-739. doi:10.1101/gad.182493.111. PMC 3323883. PMID 22474262. Johansen J, Rasmussen AA, Overgaard M, ... RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon". ...
... candidates are also consistently located in the 5' UTRs of protein-coding genes, and these genes are suggestive of ... Grundy FJ, Henkin TM (November 1998). "The S box regulon: a new global transcription termination control system for methionine ... The expression platform is what regulates gene expression. Expression platforms typically turn off gene expression in response ... cyclic di-GMP riboswitches bind the signaling molecule cyclic di-GMP in order to regulate a variety of genes controlled by this ...
SAM riboswitch (S-box leader)
"The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram ... The SAM riboswitch (also known as the S-box leader and the SAM-I riboswitch) is found upstream of a number of genes which code ... Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR (2003). "An mRNA structure that controls gene expression by binding S- ... However, many SAM riboswitches are likely to regulate gene expression at the level of translation. The structure of the SAM ...
McIver KS, Myles RL (March 2002). "Two DNA-binding domains of Mga are required for virulence gene activation in the group A ... Hondorp ER, McIver KS (December 2007). "The Mga virulence regulon: infection where the grass is greener". Molecular ... Mga is a wide-reaching regulator, affecting gene expression in over 10% of the S. pyrogenes genome. The other large regulator ... Churchward G (April 2007). "The two faces of Janus: virulence gene regulation by CovR/S in group A streptococci". Molecular ...
PTS L-Ascorbate Family
Campos E, Aguilar J, Baldoma L, Badia J (November 2002). "The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), ... This gene product, as well as SgaB and SgaA, are all essential for anaerobic L-ascorbate utilization, transport and ...
The yop genes, yadA, ylpA, and the virC operon are considered the "Yop regulon" since they are coregulated by pYV-encoded VirF ... A 26-kb "core region" in the pYV contains the ysc genes, which regulate the expression and secretion of Yops. Many Ysc proteins ... In contrast to the ysc and yop genes listed above, the Yops that act directly on host cells to cause cytopathologic effects - " ... The core region also includes yopN, yopB, yopD, tyeA, lcrG, and lcrV, which also regulate Yops gene expression and help to ...
Cia-dependent small RNAs
"Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in ... These RNAs are part of the regulon of the CiaRH two-component regulatory system. Two of these RNAs, csRNA4 and csRNA5, have ... Bacterial small RNA Halfmann, A; Kovács, M; Hakenbeck, R; Brückner, R (October 2007). "Identification of the genes directly ...
Genes and Development 16: 1696-1706. 10. Sarker, R. I., Ogawa, W., Shimamoto, T., Shimamoto, T., and Tsuchiya, T. (1996). ... The cAMP-CRP complex activates the gal regulon and is responsible for upregulation of GalP (Figure 2) (9,11). GalP is also ... The GalP/H+ symporter is the galactose permease from the galP gene of the Escherichia coli genome. Galactose is an alternate ... The two proteins responsible for inhibiting transcription from the gal regulon are GalR and GalS (Figure 4) (11). GalR and GalS ...
GalR is a transcriptional regulator of the galactose regulon composed of genes encoding enzymes for transport and metabolism of ... Consequently, many genes were repressed, and many quiescent genes were expressed. Besides, there are many specific cases in ... A null strain of topA, the gene encoding Topo I, survives only because of the presence of suppressor mutations in the genes ... According to the twin supercoiling domain model, transcription of a gene can influence transcription of other nearby genes ...
Bacterial morphological plasticity
The event to inactivate ftsl gene product requires the SOS-promoting recA and lexA genes as well as dpiA and transiently ... The LexA regulon includes a cell division inhibitor, SulA, that prevent the transmission of mutant DNA to the daughter cells. ... The ftsl gene is a group of filamentous temperature-sensitive genes implicated in cell division. In addition, it is a membrane ... encoded by nfo gene) and exonuclease III (encoded by xth gene). Under this mechanism, daughter cells are protected from ...
... by variation in the number of SSRs in the mod gene. Multiple different mod genes have been identified. Each Mod methylates a ... In bacteria, phasevarions (also known as phase variable regulons) mediate a coordinated change in the expression of multiple ... Switching of mod genes is selected for under certain disease states or within specific host niches: for example, the non- ... Mod genes are the methyltransferase component of type III restriction modification (R-M) systems in bacteria, and serve to ...
Reporter genes can be used as markers, such as the lacZ gene which codes for β-galactosidase used in blue-white screening. This ... Claverys JP, Prudhomme M, Martin B (2006). "Induction of competence regulons as a general response to stress in gram-positive ... By removing the genes in the plasmid that caused the tumor and adding in novel genes, researchers were able to infect plants ... The progeny of the infected plants is virus-free and also free of the inserted gene. Some vector-less methods include: Gene gun ...
It has a core set of 1553 genes, plus 154 genes in its virulome, which contribute to virulence and 176 genes that maintain a ... Claverys JP, Prudhomme M, Martin B (2006). "Induction of competence regulons as a general response to stress in gram-positive ... For instance, the Xisco gene was recently described as a biomarker for PCR-based detection of S. pneumoniae and differentiation ... In S. pneumoniae, at least 23 genes are required for transformation. For a bacterium to bind, take up, and recombine exogenous ...
... the mutant phenotype implies that a broad range of genes is involved in secreted antimicrobials associated with the clp regulon ... A clp gene homologue belonging to the crp gene family globally regulates lytic enzyme production, antimicrobial activity, and ... making mutation effects of non-related genes difficult or nearly impossible to evaluate. However, strains harboring clp gene ... including mutants affected in structural genes encoding enzyme activities, the regulatory clp gene and various combinations ...
In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and inhibit transcriptional ... "A novel transcriptional regulation mechanism in the flagellar regulon of Salmonella typhimurium: an antisigma factor inhibits ... From the same study it can be concluded that every anti-sigma factor has a specific gene location to act and affect in the cell ... As a negative feedback interaction, anti-sigma factor in E-coli, help the cell or allow it to control the gene expression in a ...
Walkerton E. coli outbreak
Genes. *CPS operon. *DnaG. *Fis. *FNR regulon. *OmpT. *RecBCD. *RpoE. *RpoF. *RpoN ...
Bacillus anthracis bahasa Indonesia, ensiklopedia bebas
"PlcR is a pleiotropic regulator of extracellular virulence factor gene expression in Bacillus thuringiensis". Molecular ... "A cell-cell signaling peptide activates the PlcR virulence regulon in bacteria of the Bacillus cereus group". The EMBO Journal ... "Sequence analysis of three Bacillus cereus loci carrying PIcR-regulated genes encoding degradative enzymes and enterotoxin". ...
Escherichia coli in molecular biology
Considered a very versatile host for the production of heterologous proteins, researchers can introduce genes into the ... Cornelis P (2000). "Expressing genes in different Escherichia coli compartments". Current Opinion in Biotechnology. 11 (5): 450 ... coli and phage T4 to understand the topography of gene structure. Prior to Benzer's research, it was not known whether the ... "Gene recombination in E. coli" (PDF). Nature. 158 (4016): 558. Bibcode:1946Natur.158..558L. doi:10.1038/158558a0. PMID ...
... genes, which inactivate the kil genes. The kil and kor genes together are suspected to play a role in the broad host range of ... J A Kornacki, C H Chang, and D H Figurski: "kil-kor regulon of promiscuous plasmid RK2: structure, products, and regulation of ... In addition, RK2 contains a set of potentially lethal (to the cell) genes, called kil genes, and a set of complementary ... The essential replication system in RK2 consists of an origin of replication, oriV, and a gene, trfA, whose gene product, the ...
CsrC RNA family
Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H, Altuvia S (June 2001). "Novel small RNA-encoding genes in ... "A direct link between the global regulator PhoP and the Csr regulon in Y. pseudotuberculosis through the small regulatory RNA ... The gene called SraK, was highly abundant in stationary phase, but low levels could be detected in exponentially growing cells ...
The gene for tissue-nonspecific alkaline phosphatase is located on chromosome 1, and the genes for the other three isoforms are ... evidence for multiple positive regulators of the phosphate regulon in Escherichia coli". Genetics. 96 (2): 353-66. PMC 1214304 ... When multiple copies of a polypeptide encoded by a gene form an aggregate, this protein structure is referred to as a multimer ... The human body has multiple types of alkaline phosphatase present, which are determined by a minimum of three gene loci. Each ...
These genes play a variety of roles in the developmental cycle. For example, in experiments where the fbFA gene was deactivated ... Silakowski, B.; Kunze, B.; Nordsiek, G.; Blöcker, H.; Höfle, G.; Müller, R. (2000). "The myxochelin iron transport regulon of ... Most of the 95 known M. xanthus development-specific genes are highly conserved in S. aurantiaca. Genes for entire signal ... a gene encoding a putative galactose oxidase, various genes including those encoding tRNAAsp and tRNAVal located at the attB ...
HOX genes are important developmental regulatory genes. Tissue repair and maintenance are important parts of the life cycle of ... Png, K. J.; Halberg, N.; Yoshida, M.; Tavazoie, S. F. (2011). "A microRNA regulon that mediates endothelial recruitment and ... Epigenetic regulation of the host gene by accumulation of methylation and gene silencing nucleosomes reduces expression of ... One of the main targets of mir-126 is the host gene EGFL7. Transcription of both occur, however mature mir-126 binds to a ...
Cyclin-dependent kinase 1
It has been highly studied in the budding yeast S. cerevisiae, and the fission yeast S. pombe, where it is encoded by genes ... allowing for transcription of the G1/S regulon, which includes the G1/S cyclins Cln1,2. G1/S cyclin-Cdk1 activity leads to ... In humans, Cdk1 is encoded by the CDC2 gene. With its cyclin partners, Cdk1 forms complexes that phosphorylate a variety of ... Nazarenko SA, Ostroverhova NV, Spurr NK (1991). "Regional assignment of the human cell cycle control gene CDC2 to chromosome ...
In bacterial genetics, the mal regulon is a regulon - or group of genes under common regulation - associated with the ... Genes under the control of malT include ATP-binding cassette transporter components, maltoporin, maltose binding protein, and ... Other Gram-negative bacteria such as Klebsiella pneumoniae have additional genes under the control of malT. In many Gram- ... where it is classically described as a group of ten genes in multiple operons whose expression is regulated by a single ...
The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding ... "Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of ... Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. A deletion of GcvB RNA ... lifting the GcvB-mediated mRNA repression of its target genes. GcvB has been shown to regulate a large number of genes in E. ...
Natália Pasternak Taschner
She presented a paper entitled The Xanthomonas axonopodis citri PHO regulon. Most media relating to Taschner can be found on ... Galbiati, Heloisa F.; Taschner, Natalia P.; Spira, Beny (27 May 2014). "The effect of the rpoSam allele on gene expression and ...
Tryptophan-rich sensory protein
... functioning as a negative regulator of the expression of some photosynthesis genes (PpsR/AppA repressor/antirepressor regulon ... Yeliseev AA, Kaplan S (July 1999). "A novel mechanism for the regulation of photosynthesis gene expression by the TspO outer ... thereby causing the accumulation of a biosynthetic intermediate that serves as a corepressor for the regulated genes. A ... negatively affecting transcription of specific photosynthesis genes. This suggests that PBR may function as an oxygen sensor, ...
The link to P-bodies comes by the fact that many, if not most, of the proteins necessary for miRNA gene silencing are localized ... "P-Body Purification Reveals the Condensation of Repressed mRNA Regulons". Molecular Cell. 68 (1): 144-157.e5. doi:10.1016/j. ... The evidence being that GW182 and Ago2, both associated with miRNA gene silencing, are found exclusively in multivesicular ... Anderson, P.; Kedersha, N. (2009). "RNA granules: post-transcriptional and epigenetic modulators of gene expression". Nature ...
DdrO could be the global regulator of the RDR regulon, because it is the only induced and conserved regulator gene preceded by ... The irrE gene is essential for radiation resistance and required for the radiation-induced expression of recA and other genes ... including various DNA repair genes such as recA, gyrA, uvrB and ssb, strongly suggesting the presence of an RDR regulon that is ... the five most highly radio-induced genes were the Deinococcus-specific genes ddrA, ddrB, ddrC, ddrD, and pprA. Their homologs ...
The plcR gene is part of a two-gene operon with papR. The papR gene encodes a small protein which is secreted from the cell and ... Slamti, L.; Lereclus, D (2 September 2002). "A cell-cell signaling peptide activates the PlcR virulence regulon in bacteria of ... both of which regulate the expression of the anthrax toxin genes. pXO2 encodes a five-gene operon (capBCADE) which synthesizes ... The genes encoding these proteins are commonly located on plasmids which can be lost from the organism, making it ...
2015-07-15). "Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose". PLOS ONE. 10 (7 ... Bhat PJ (2 March 2008). Galactose Regulon of Yeast: From Genetics to Systems Biology. Springer Science & Business Media. ISBN ...
"GntP is the Escherichia coli Fructuronic acid transporter and belongs to the UxuR regulon". Journal of Bacteriology. 186 (22): ... "Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism". ...
Gene Expression: RNA regulons
Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... Narrow Roads of Gene Land 1. Narrow Roads of Gene Land 2. Narrow Roads of Gene Land 3. Statistical Methods in Molecular ... The idea of RNA regulons is nice, but how much can you predict knowing that your gene of interest is part of one? RNAs ... RNA regulons posted by amnestic @ 8/23/2007 10:59:00 PM RNA regulons ...
A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae. - PubMed - NCBI
... and eight genes of unknown function. Competence-induced transcription of genes in the CRE regulon is strongly dependent on cAMP ... This CRE regulon contains 25 genes in 13 transcription units, only about half of which have been previously associated with ... A novel CRP-dependent regulon controls expression of competence genes in Haemophilus influenzae.. Redfield RJ1, Cameron AD, ... gene sxy is induced early in competence development and is required for competence-induced transcription of CRE-regulon genes ...
Aspergillus nidulans genes encoding reverse transsulfuration enzymes belong to homocysteine regulon | SpringerLink
We call this group of genes the "homocysteine regulon".. Keywords. Aspergillus nidulans Transsulfuration Cystathionine β- ... On the basis of the mode of mecA and mecB regulation by homocysteine, these genes may be classified in a group of genes ... metR gene encodes a bZIP protein which activates transcription of sulphur metabolism genes. Mol Microbiol 49:1081-1094CrossRef ... Nucleotide sequence and expression of the glucoamylase-encoding gene (glaA) from Aspergillus oryzae. Gene 108:145-150CrossRef ...
Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon
We have cloned the soxR locus, which is positioned near the uvrA gene at 92.2 min on the genetic map, by monitoring complement ... The soxR locus of Escherichia coli K12 mediates transcriptional activation of a complex oxidative stress regulon in response to ... Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon Nucleic Acids ... DNA sequence analysis revealed the presence of two genes involved in activating the soxR regulon. These genes, named soxR and ...
phoB - Phosphate regulon transcriptional regulatory protein PhoB - Escherichia coli (strain K12) - phoB gene & protein
This protein is a positive regulator for the phosphate regulon. Transcription of this operon is positively regulated by PhoB ... Phosphate regulon transcriptional regulatory protein PhoBAdd BLAST. 229. Amino acid modifications. Feature key. Position(s). ... p>This subsection of the Names and taxonomy section indicates the name(s) of the gene(s) that code for the protein sequence(s ... p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source ...
The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram...
This set of genes is proposed to form a new regulon controlled by a global termination control system, which we designate the S ... The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram ... Analysis of the yitJ gene, which is homologous to Escherichia coli metH and metF, revealed that expression was induced by ... The molecular mechanisms for regulation of the genes involved in the biosynthesis of methionine and cysteine are poorly ...
Transcription of the yop regulon from Y. enterocolitica requires trans acting pYV and chromosomal genes
These genes appear to be scattered on pYV, outside the calcium region and to constitute a regulon. Transcription of these yop ... Transcription of the yop regulon from Y. enterocolitica requires trans acting pYV and chromosomal genes Microb Pathog. 1987 May ... Transcription of the yop genes was very poor in E. coli K12, even in the presence of a fully functional calcium region. ... we localized plasmid genes encoding POMPs of 84, 51, 30 and 25 kDa. ...
The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3 | Journal of...
b Genes with names in bold belong to the FeuPQ regulon (77). Genes with names in italics belong to the motility and chemotaxis ... The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3. Melanie J. Barnett, ... Venn diagram of genes whose expression changed when syrM, syrA, or nodD3 was overexpressed. syrM- and syrA-dependent gene ... The Sinorhizobium meliloti SyrM Regulon: Effects on Global Gene Expression Are Mediated by syrA and nodD3 ...
The Gonococcal Fur Regulon: Identification of Additional Genes Involved in Major Catabolic, Recombination, and Secretory...
Fur regulon of Salmonella typhimurium: identification of new iron-regulated genes. J. Bacteriol. 177:4628-4637. ... Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a ... Furthermore, the gonococcal Fur regulon is not well defined; the only genes that appear to be regulated by Fur are those ... The Gonococcal Fur Regulon: Identification of Additional Genes Involved in Major Catabolic, Recombination, and Secretory ...
Frontiers | Mycobacterium tuberculosis DosR Regulon Gene Rv2004c Encodes a Novel Antigen with Pro-inflammatory Functions and...
In this study, we investigated the role of Rv2004c, a member of DosR regulon (exclusive to Mtb complex), in host pathogen ... In this study, we investigated the role of Rv2004c, a member of DosR regulon (exclusive to Mtb complex), in host pathogen ... DosR regulon antigens of Mtb might serve as attractive targets for LTBI diagnosis or vaccine development as they are ... DosR regulon antigens of Mtb might serve as attractive targets for LTBI diagnosis or vaccine development as they are ...
The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon...
Previously, the gene cg0156 was shown to belong to the regulon of McbR, a global transcriptional repressor of sulphur ... The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon ... Among the genes positively controlled by CysR were the gene cluster involved in sulphate reduction, fpr2 cysIXHDNYZ, and ssuR. ... In both bacteria, gene duplication events seem to have taken place which resulted in the evolution of dedicated regulators for ...
Frontiers | The Role of OmpR in the Expression of Genes of the KdgR Regulon Involved in the Uptake and Depolymerization of...
... which might positively affect the expression of genes of the KdgR regulon. Binding of OmpR to the promoter regions of the kdgM2 ... which might positively affect the expression of genes of the KdgR regulon. Binding of OmpR to t... ... Reporter gene fusion and real-time PCR analysis confirmed that the expression of kdgM2 is repressed by OmpR. We also found that ... Reporter gene fusion and real-time PCR analysis confirmed that the expression of kdgM2 is repressed by OmpR. We also found that ...
Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas...
We demonstrated that the size and composition of the HrpL regulon varies among strains, and explored how genes are recruited ... Here we overlaid transcriptome profiling of genes onto their phylogenetic distribution by characterizing the HrpL regulon ... HrpL controls the activation of virulence factor genes, including those encoding the type III secretion system which ... into, or lost from, the virulence regulon. Overall, our work widens the understanding of P. syringae pathogenicity and presents ...
Xylan Utilization Regulon in Xanthomonas citri pv. citri Strain 306: Gene Expression and Utilization of Oligoxylosides |...
Xylan Utilization Regulon in Xanthomonas citri pv. citri Strain 306: Gene Expression and Utilization of Oligoxylosides. V. Chow ... Xylan utilization regulon in Xanthomonas citri pv. citri strain 306: gene expression and utilization of oligoxylosides. Appl ... Xylan Utilization Regulon in Xanthomonas citri pv. citri Strain 306: Gene Expression and Utilization of Oligoxylosides ... Xylan Utilization Regulon in Xanthomonas citri pv. citri Strain 306: Gene Expression and Utilization of Oligoxylosides ...
Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. |...
Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization.. K M ... Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. ... Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. ... Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. ...
DNA REPAIR - approximate positions of some of the genes of the SOS regulon are shown SOS RESPONSE 20 Trans-lesion synthesis by...
approximate positions of some of the genes of the SOS regulon are shown. SOS RESPONSE 20 Trans-lesion synthesis by DNA POL V (A ... Regulation of the SOS response regulon in E. coli. (A) About 30 genes around the E. coli chromosome are normally repressed by ... Unformatted text preview: approximate positions of some of the genes of the SOS regulon are shown. SOS RESPONSE 20 Trans-lesion ... The cleaved repressor can no longer bind to the operators of the genes, and the genes are induced as indicated by two arrows. ...
Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon | BMC Microbiology |...
... and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in ... fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon. ... Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of ... A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for ...
Interleukin 12 gene therapy - Regulon - AdisInsight
Interleukin 12 gene therapy - Regulon Alternative Names: LipoVIL12 Latest Information Update: 30 Sep 2015 ... Class Antineoplastics; Cytokine genes; Gene therapies; Interleukins * Mechanism of Action Immunomodulators; Interleukin 12 ... 08 Dec 2014 Interleukin 12 gene therapy licensed to In Ovations Holdings ...
Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and characterization of the AmtR regulon
" The AmtR regulon was characterized in this study by a combination of bioinformatics, transcriptome and proteome analyses. At ... Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation.. ... AmtR, the master regulator of nitrogen control in Corynebacterium glutamicum, represses transcription of a number of genes ... G. Beckers, et al., "Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and ...
Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle | PNAS
Functional Distribution of the Genes in the CtrA Cell Cycle Regulon.. The 95 CtrA cell cycle regulon genes were classified by ... Regulatory genes directly controlled by CtrA. The 14 regulatory genes in the CtrA cell cycle regulon are listed below the cell ... Regulatory Genes.. Among the members of the CtrA cell cycle regulon are 14 genes encoding regulatory proteins, including ... Of the 55 genes that are adjacent to an intergenic region bound by CtrA, 34 are single genes, and 21 are the first genes in ...
Exposure to Glycolytic Carbon Sources Reveals a Novel Layer of Regulation for the MalT Regulon
A. Hartmann and W. Boos, "Mutations in phoB, the positive gene activator of the pho regulon in Escherichia coli, affect the ... MalT is the central regulator of all mal genes [6, 7] (Figure 1). The mal genes encode proteins involved in transport and ... we asked if exposure to maltose reduces MalT regulon transcription. First, we monitored MalT regulon expression of an ompR malT ... b) Effect of glycolytic carbon sources on mal gene transcription. β-galactoside activity was determined in ompR malT con ...
The Streptococcus sanguinis Competence Regulon Is Not Required for Infective Endocarditis Virulence in a Rabbit Model
Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the ,100-gene com regulon ... Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes ... We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be ... Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction ...
Signals, Switches, Regulons, and Cascad... | WHSmith Books
Regulons, and Cascades: Control of Bacterial Gene Expression (Society for General Microbiology Symposia 61) by From WHSmith ... Signals, Switches, Regulons, and Cascades: Control of Bacterial Gene Expression (Society for General Microbiology Symposia 61) ... Gene variation and gene regulation in bacterial pathogenesis D. Hood and R. Moxon; 3. DNA topology and regulation of bacterial ... The use of DNA arrays and proteomics will transform the scale of our ability to describe the patterns of gene expression as ...
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli | Genome Biology...
One example of such a connector gene is the SodA gene product, manganese superoxide dismutase [33-35]. The gene sodA is present ... Chen G, Jensen ST, Stoeckert CJ: Clustering of genes into regulons using integrated modeling-COGRIM. Genome Biol. 2007, 8: R4- ... All genes of module 1 share two motifs, MarA and SoxS, and are co-expressed in a subset of conditions. For module 2 all genes ... In contrast, of the total of 663 interactions in RegulonDB that belong to simple regulons of at least four genes, 398 ...
Regulon - Wikipedia
Regulons can sometimes be pathogenicity islands. The Ada regulon in E. coli is a well-characterized example of a group of genes ... the term refers to any group of non-contiguous genes controlled by the same regulatory gene. A modulon is a set of regulons or ... a regulon is a group of genes that are regulated as a unit, generally controlled by the same regulatory gene that expresses a ... the genes contained within a regulon are usually organized into more than one operon at disparate locations on the chromosome. ...
Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development | Nature Communications
... expansion is controlled by the KUA1 transcription factor that acts in a circadian manner and modulates the expression of genes ... Furthermore, KUA1 directly represses the expression of a set of genes encoding for peroxidases that control reactive oxygen ... Indentification of KUA1 regulon. Genes differentially expressed upon induction of KUA1. Results are based on two biological ... Figure 3: Identification of KUA1-regulated genes.. (a) Enriched gene ontology (GO) categories among genes that are negatively ...
Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and characterization of the AmtR regulon
Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding ... " The AmtR regulon was characterized in this study by a combination of bioinformatics, transcriptome and proteome analyses. At ... Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon.. Baichoo N, Wang T, Ye R, Helmann JD., ... The alcohol dehydrogenase gene adhA in Corynebacterium glutamicum is subject to carbon catabolite repression.. Arndt A, ...
A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis
... ... Our analysis shows that there are pairs of divergent genes where one gene in the pair is up-regulated before the other, ... tuberculosis to hypoxia and controls a regulon of approximately 50 genes that are induced under this condition. The aim of this ... A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis. ...
Salt-triggered expression of the ANAC092-dependent senescence regulon in Arabidopsis thaliana
Left: The currently known ANAC092 senescence regulon includes 78 genes of which 36 genes are induced by long-term salt stress. ... Table 1), representing ~40% of the ANAC092 salt-dependent senescence regulon. However, five genes were repressed by H2O2- ... representing 36 genes (46%) of the senescence regulon of ANAC092, are significantly induced by long-term salt stress (4 days), ... of the currently known 78 genes of the ANAC092 senescence regulon, suggesting that it constitutes an important element of the ...
Transcriptional Repressor Gal80 Recruits Corepressor Complex Cyc8-Tup1 to Structural Genes of the Saccharomyces Cerevisiae GAL...
... yeast structural genes of the GAL regulon are repressed by Gal80, preventing interaction of Gal4 bound to UASGAL promoter ... Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, ... Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, ... Corepressor interaction and in vivo gene repression could be mapped to a Gal80 minimal domain of 65 amino acids (aa 81-145). ...
ProteinsRegulatorRegulationEscherichiaTarget genesPromotersPromoterUpstreamOperonsExpression of GeOperonAntibiotic resistanceSaccharomycesMutationsUptakeMetabolismDosRProteinRegulatory genesOxidative stressReactive oxygenCharacterizationIdentification of novel genesEnzymesCompetence regulonRepressionDirectly or indirectlyMolecularRegulatorsStructural genesBacillusPneumoniaeMotifsPhosphateBacteriaLate genesEarly genesMRNA levelsStrainsColiVirulence geneFunctionalRequired for virulenceRegulateToxRGeneticStrainSynthesisTranscription of the genesHomeostasisYeastDeletionBiosynthesisGroups of genesGenome-wideActivates
- Subclones from the soxR region in the delta soxR strain simultaneously restored cellular resistance to the redox-cycling agent phenazine methosulfate and inducibility of at least two of the regulon proteins, glucose-6-phosphate dehydrogenase and endonuclease IV, by paraquat, another redox-cycling agent. (nih.gov)
- The predicted 12.9-kDa SoxS protein is related to the AraC family of one-component gene regulators, but corresponds only to the putative DNA-binding regions of these proteins. (nih.gov)
- SoxS is evidently the proximal activator of the regulon genes: antibiotic resistance and high-level expression of at least three of the regulon proteins was effected in vivo by the individual expression of SoxS, but not of SoxR, whether or not the cells were exposed to paraquat. (nih.gov)
- 173, 2864-2871), indicate that SoxR and SoxS may constitute a novel type of two-component regulatory system in which the two proteins act sequentially to activate transcription of the various regulon genes in response to superoxide stress. (nih.gov)
- P trp-syrM induces nod gene expression in the absence of all three NodD proteins. (asm.org)
- While gonococcal Fur was demonstrated to bind to the promoter regions of all 11 opa genes ( opaA through - K ), we did not detect binding of purified E. coli Fur with 8 of the 11 opa members, indicating that target DNA sequence specificities between these two closely related proteins exist. (asm.org)
- This is the first report that definitively demonstrates the binding of gonococcal Fur to its own promoter/operator region, as well as to the opa family of genes that encode surface proteins. (asm.org)
- We found that deletion of the gene encoding response regulator OmpR causes the porin KdgM2 to become one of the most abundant proteins in the outer membrane of the human enteropathogen Yersinia enterocolitica . (frontiersin.org)
- phoA) fusions to genes encoding secreted proteins that are apparently coordinately regulated with cholera toxin. (asm.org)
- A time course experiment (2, 8 and 12 hours) of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. (biomedcentral.com)
- Also among the genes in this notably large regulon are 14 that encode regulatory proteins, including 10 two-component signal transduction regulatory proteins. (pnas.org)
- The comC gene encodes a precursor peptide that is cleaved and exported by the ComA and ComB proteins. (plos.org)
- The mal genes encode proteins involved in transport and metabolism of maltose and maltodextrins. (hindawi.com)
- In this work we show that Gal80 is also able to interact with histone deacetylase-recruiting corepressor proteins Cyc8 and Tup1, indicating an additional mechanism of gene repression. (researchsquare.com)
- Strain persistence or extinction between epidemics was strongly associated with presence or absence, respectively, of the prophage encoding streptococcal pyrogenic exotoxin A. A serotype M3 clone significantly underrepresented among necrotizing fasciitis cases has a unique frameshift mutation that truncates MtsR, a transcriptional regulator controlling expression of genes encoding iron-acquisition proteins. (pnas.org)
- Expression microarray analysis of this clone confirmed significant alteration in expression of genes encoding iron metabolism proteins. (pnas.org)
- To translate genes into functional proteins, the gene-DNA is first copied to messenger RNA (mRNA) during a process called transcription, and subsequently the mRNA is translated to proteins. (uva.nl)
- It is already known that during this process a very important role is played by transcription factors, which are proteins that bind small specific stretches of DNA (called motifs) to enable transcription of genes. (uva.nl)
- Two of these CpHistone H3 proteins are constitutively expressed histone H3 variants which are suggested to be involved in gene regulation via histone modification. (deepdyve.com)
- As 14-3-3 proteins are key regulators of signal transduction processes, we investigated the effect of deletion of the 14-3-3 genes BMH1 or BMH2 on gene expression during potassium starvation and focused especially on the expression of genes involved in phosphate uptake. (biomedcentral.com)
- Our data indicate that that yeast cells can be in either of two states, expressing or not expressing genes required for high-affinity phosphate uptake and that 14-3-3 proteins are involved in the process(es) that establish the activation state of the PHO regulon. (biomedcentral.com)
- When this occurs, phosphate starvation-inducible (psi) genes activate other proteins that aid in the transport of inorganic phosphate. (wikipedia.org)
- These proteins bind to upstream promoters in the pho regulon in order to induce a general change in gene transcription. (wikipedia.org)
- These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA) genes or transfer RNA (tRNA) genes, the product is a functional RNA. (wikibooks.org)
- Genes encoding proteins that are involved in DNA uptake and transformation, as well as virulence, are upregulated. (prolekare.cz)
- For many years, proteins were considered the master regulators of gene expression, and RNA was seen only as the "intermediate" between the genetic code DNA, and proteins, the functional moieties of the cell. (mdpi.com)
- cAMP activates cAMP-dependent protein kinase (PKA), which can directly modulate effector proteins by phosphorylation at PKA-specific serine or threonine residues or can alter the levels of the effector proteins themselves by modulating gene expression. (jneurosci.org)
- Another group of target genes includes membrane-associated stress response proteins (CsgB, NanC, OmpA, PgaA, YbjJ, YehA, and YoeA) and stress response cytoplasmic proteins (Asr and YdeI), among others  RcdA exhibits strong cooperative DNA binding and produces aggregates of RcdA-DNA complexes. (unam.mx)
- We argue that while such heterogeneity in ribosome composition likely exists in different tissues, such complex explanations may not be needed to explain the differences in gene expression that result from losses of specific ribosomal proteins. (sciencemag.org)
- however, a small number of those genes encode global regulatory proteins with extensive regulons. (osti.gov)
- The FlhD and FlhC proteins are transcriptional activators for the class 2 promoters upstream of the middle gene operons. (asm.org)
- The Reg regulon from Rhodobacter capsulatus and Rhodobacter sphaeroides encodes proteins involved in numerous energy-generating and energy-utilizing processes such as photosynthesis, carbon fixation, nitrogen fixation, hydrogen utilization, aerobic and anaerobic respiration, denitrification, electron transport, and aerotaxis. (asm.org)
- A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. (hindawi.com)
- Moreover, small molecules from the environment can also be either toxic inhibitors or activatiors of particular activities in different organisms, and in many cases they might be used as effectors of the expression some genes, and the production or action of particular proteins. (bifi.es)
- Repressor proteins bind to DNA in such a way that they interfere with RNA Polymerase action and prevent gene expression. (syvum.com)
- Introns allow for alternative splicing of a gene, so that several different proteins that share some common DNA sections can be produced from a single gene. (syvum.com)
- Repressors are regulator proteins that inhibit transcription initiation at gene promoters in order to modulate gene expression in response to variations in environmental conditions. (els.net)
- This suggests that SoxR could be a metal-binding gene regulator that acts as the intracellular sensor for superoxide. (nih.gov)
- This protein is a positive regulator for the phosphate regulon. (uniprot.org)
- In several gram-negative pathogens, the ferric uptake regulator protein (Fur) functions as a general global regulator and controls the expression of not only genes required for iron transport but also genes required for virulence. (asm.org)
- In some organisms, Fur may also act as a positive regulator in controlling gene expression. (asm.org)
- The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules. (sigmaaldrich.com)
- This gene encodes a putative ROK-type regulator, a paralogue of the activator of sulphonate utilisation, SsuR. (sigmaaldrich.com)
- The EnvZ/OmpR regulatory system of non-pathogenic Escherichia coli K-12 is the most well characterized TCS, consisting of the transmembrane histidine kinase EnvZ and response regulator OmpR, which acts to modulate gene transcription ( Kenney, 2002 ). (frontiersin.org)
- AmtR, the master regulator of nitrogen control in Corynebacterium glutamicum, represses transcription of a number of genes during nitrogen surplus. (uni-bielefeld.de)
- Studies of the genetic network that controls the Caulobacter cell cycle have identified a response regulator, CtrA, that controls, directly or indirectly, one-quarter of the 553 cell cycle-regulated genes. (pnas.org)
- A single regulatory factor, the CtrA response regulator ( 5 ), controls, directly or indirectly, at least 25% of the cell cycle-regulated genes ( 4 ). (pnas.org)
- MalT is the central regulator of all mal genes [ 6 , 7 ] (Figure 1 ). (hindawi.com)
- The two component sensor/regulator dosRS is a major mediator in the transcriptional response of M. tuberculosis to hypoxia and controls a regulon of approximately 50 genes that are induced under this condition. (cam.ac.uk)
- DISTILLER is a data integration framework that searches for condition-dependent transcriptional modules by combining expression data with information on the direct interaction between a regulator and its corresponding target genes. (biomedcentral.com)
- The Pho regulon is controlled by a two-component regulatory system composed of a histidine kinase sensor protein (PhoR) within the inner membrane and a transcriptional response regulator (PhoB/PhoR) on the cytoplasmic side of the membrane. (wikipedia.org)
- This occurs when the cell senses low concentrations of phosphate within its internal environment causing the response regulator to be phosphorylated inducing an overall decrease in gene transcription. (wikipedia.org)
- Under phosphate-starved conditions B. subtilis binds its transcription regulator, PhoP and the histidine kinase, PhoR to the Pho-regulon gene which induces a production of teichuronic acid. (wikipedia.org)
- The authors also showed, that the sigma-54 activator protein FleQ is the master regulator of the flagellar regulon. (asmscience.org)
- Upon binding of CSP to its membrane-associated receptor kinase ComD, a cascade of signaling events is initiated, leading to activation of the competence regulon by the response regulator ComE. (prolekare.cz)
- RcdA, also known as YbjK, belongs to the TetR family and is involved in the regulation of a number of stress response genes, biofilm formation, and transcription regulator genes  Genomic SELEX analysis showed that RcdA can bind to the upstream regions of 27 genes. (unam.mx)
- In one LacI regulator termed GlyR3 inC. thermocellumATCC 27405 we identified a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). (osti.gov)
- Global gene expression patterns from time course analyses identified glycoside hydrolase genes encoding hemicellulases, including cellulosomal enzymes, that were highly upregulated (5- to 100-fold) in the absence of each LacI regulator, suggesting that these were repressed under wild-type conditions and that relatively few genes were controlled by each regulator under the conditions tested. (osti.gov)
- The E3 ubiquitin ligase HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) functions as a cold signaling attenuator by degrading the INDUCER OF CBF EXPRESSION 1 transcription factor, which is a key regulator of the cold-induced transcriptome and freezing tolerance in plants. (biomedsearch.com)
- Both phosphorylated and unphosphorylated forms of the cognate response regulator RegA are capable of activating or repressing a variety of genes in the regulon. (asm.org)
- PCR amplification of the complete acrR (regulator/repressor) gene of eight isolates revealed amino acid changes in four isolates, a 9-bp deletion in another, and a 22-bp duplication in a sixth strain. (asm.org)
- In Neurospora crassa, the transcriptional regulator, CLR-2, is required for cellulolytic gene expression and cellulose deconstruction. (biomedsearch.com)
- At any rate, I'm expecting that RNA regulons will be increasingly important in understanding the translational regulation that must take place in dendrites to produce persistent memories. (gnxp.com)
- Competence-induced transcription of genes in the CRE regulon is strongly dependent on cAMP, consistent with the known role of catabolite regulation in competence. (nih.gov)
- On the basis of the mode of mecA and mecB regulation by homocysteine, these genes may be classified in a group of genes upregulated directly or indirectly by this amino acid. (springer.com)
- The molecular mechanisms for regulation of the genes involved in the biosynthesis of methionine and cysteine are poorly characterized in Bacillus subtilis. (nih.gov)
- We also found that kdgM2 expression is subject to negative regulation by KdgR, a specific repressor of genes involved in the uptake and metabolism of pectin derivatives in plant pathogens. (frontiersin.org)
- In addition, our data showed that OmpR is responsible for up regulation of the kdgM1 gene encoding the second specific oligogalacturonide porin KdgM1. (frontiersin.org)
- Over 600 PhoA+ strains were isolated and then tested for regulation of their gene fusions in broth media that permitted high or low expression of cholera toxin. (asm.org)
- Regulation of the SOS response regulon in E. coli. (coursehero.com)
- In this species, a number of "early" com genes are essential for induction and regulation of this cascade  . (plos.org)
- Regulation of MalT and its regulon. (hindawi.com)
- The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops. (plantphysiol.org)
- Changes in the regulation of gene networks are a common mechanism for prokaryotic evolution. (wikipedia.org)
- Conidiation in A. nidulans involves many common developmental themes including spatial and temporal regulation of gene expression, specialized cellular differentiation, and intercellular communication. (genetics.org)
- Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism. (wikibooks.org)
- Gene regulation may also serve as a substrate for evolutionary change, since control of the timing, location, and amount of gene expression can have a profound effect on the functions (actions) of the gene in a cell or in a multicellular organism. (wikibooks.org)
- To analyze the cascade of flagellar gene regulation, the authors identified, cloned and characterized the regulators which may be involved in flaA regulation. (asmscience.org)
- The Bacillus subtilis ResD-ResE two-component system is responsible for the regulation of a number of genes involved in cytochrome c biogenesis and haem A biosynthesis, and it is required for anaerobic respiration in this organism. (wiley.com)
- In this study, we analyzed the regulation of pear DAM genes by CBFs in further detail. (springer.com)
- Considering all these results, we propose that the PpCBF1 - PpDAM2 regulon mainly responds to low temperature during endodormancy regulation, with further post-translational regulation by PpICE3. (springer.com)
- Bielenberg DG, Wang Y, Li ZG, Zhebentyayeva T, Fan SH, Reighard GL, Scorza R, Abbott AG (2008) Sequencing and annotation of the evergrowing locus in peach [ Prunus persica (L.) Batsch] reveals a cluster of six MADS-box transcription factors as candidate genes for regulation of terminal bud formation. (springer.com)
- Control of Escherichia coli superoxide dismutase (sodA and sodB) genes by the ferric uptake regulation (fur) locus. (semanticscholar.org)
- The effects of fur on the transcriptional and post-transcriptional regulation of MnSOD gene (sodA) in Escherichia coli. (semanticscholar.org)
- Brain gene regulation by natural stimuli is well documented in songbirds. (jneurosci.org)
- In particular, we seek to address whether fundamental aspects of gene regulation are controlled by ribosomes harboring a unique activity or composition that are tuned to translating specific transcripts by virtue of RNA regulatory elements embedded within their 5'UTRs. (stanford.edu)
- Finally, the identification of LacI repressor activity for hemicellulase gene expression is a key result of this work and will add to the small body of existing literature on the area of gene regulation inC. thermocellum. (osti.gov)
- Regulation of these two genes is complex, involving 2 activators and 3 repressors of transcription. (rochester.edu)
- In addition to regulation at the level of gene transcription, regulating RNA stability offers the potential to control mRNA abundance, but whether such a mechanism existed for the physiological regulation of gene expression was uncertain. (jimmunol.org)
- The Shaw and Kamen paper provided the foundation for understanding a fundamental mechanism of gene regulation relevant to many different cell types. (jimmunol.org)
- The tails of histones H3 and H4 are important for transcriptional regulation of numerous genes, because mutations in these histone tails result in both derepression and diminished activation ( 15 , 44 ). (asm.org)
- To assess conservation and divergence of cellulase gene regulation between fungi from different ecological niches, we compared clr-2 function with its ortholog (clrB) in the distantly related species, Aspergillus nidulans. (biomedsearch.com)
- The soxR locus of Escherichia coli K12 mediates transcriptional activation of a complex oxidative stress regulon in response to superoxide-generating (redox-cycling) agents. (nih.gov)
- Analysis of the yitJ gene, which is homologous to Escherichia coli metH and metF, revealed that expression was induced by starvation for methionine and that induction was independent of the promoter and dependent on the leader region terminator. (nih.gov)
- The virulence-associated genes include those for the Shigella Shiga toxin, Escherichia coli hemolysin, the fimbriae of enterotoxigenic E. coli , and exotoxin A of Pseudomonas aeruginosa ( 8 , 19 , 21 , 27 , 41 ). (asm.org)
- Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. (uni-bielefeld.de)
- Mapping of two ugp genes coding for the pho regulon-dependent sn-glycerol-3-phosphate transport system of Escherichia coli. (cngb.org)
- Characterization of TetD as a transcriptional activator of a subset of genes of the Escherichia coli SoxS/MarA/Rob regulon. (umass.edu)
- In Escherichia coli, SoxS, MarA and Rob form a closely related subset of the AraC/XylS family of positive regulators, sharing approximately 42% amino acid sequence identity over the length of SoxS and the ability to activate transcription of a common set of target genes that provide resistance to redox-cycling compounds and antibiotics. (umass.edu)
- Although the Pho regulon system is most widely studied in Escherichia coli it is found in other bacterial species such as Pseudomonas fluorescens and Bacillus subtilis. (wikipedia.org)
- The Escherichia coli Fur protein, with its iron(II) cofactor, represses iron assimilation and manganese superoxide dismutase (MnSOD) genes, thus coupling iron metabolism to protection against oxygen toxicity. (semanticscholar.org)
- Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay. (semanticscholar.org)
- The GadX regulon affects virulence gene expression and adhesion of porcine enteropathogenic Escherichia coli in vitro . (uni-giessen.de)
- The cell cycle-regulated expression of these CtrA target genes is effected by changes in active CtrA levels during the cell cycle (Fig. 1 ). (pnas.org)
- Positioning of the PhoP transcription factor relative to the RNA polymerase and its target genes measured as the most probable values from ChIP-seq data. (bifi.es)
- C . PhoP binding motifs elucidated from ChIP-seq data shown in panel B. Distance to the start codon of target genes is also indicated. (bifi.es)
- In this work we analyse and model the transcription dynamics in the XlnR regulon from time-course data of the messenger RNA levels for some XlnR target genes, obtained by reverse transcription quantitative PCR (RT-qPCR). (wur.nl)
- We show that perturbing the XlnR regulon with Xyl in low and high concentrations results in different expression levels and transcription dynamics of the target genes. (wur.nl)
- Distinct profiles of REST interactions with its target genes at different stages of neuronal development. (google.com)
- A more complete picture of the σ 54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ 54 -dependent promoters, using a position weight matrix approach. (biomedcentral.com)
- Electrophoretic mobility shift assays have confirmed LacI transcription factor binding to specific regions of gene promoters. (osti.gov)
- These genes were previously referred to as class 1, class 2, and class 3, but recent findings that many genes are transcribed from multiple promoters added confusion to this nomenclature. (asm.org)
- In this review we will refer to the genes as early, middle, and late and the promoters as class 1, class 2, and class 3. (asm.org)
- The factors controlling gene expression at the molecular level were only starting to be understood (e.g., the identification of promoters and enhancers that regulate gene transcription in tissue-specific and inducible manners). (jimmunol.org)
- B . ChIP-seq reads from representative promoters of PhoP-regulated genes. (bifi.es)
- We demonstrated that the differential rcsD and rcsB expression is due to the activity of two promoters to transcribe the rcsB gene: (1) P rcsDB located upstream of rcsD and (2) P rcsB located within the rcsD coding region. (wiley.com)
- This analysis confirmed the existence of a postulated competence regulon, characterized by a promoter-associated 22 bp competence regulatory element (CRE) closely related to the cAMP receptor protein (CRP) binding consensus. (nih.gov)
- Gonococcal Fur was found to bind to the promoter/operator region of a gene encoding the previously identified Fur-regulated periplasmic binding protein (FbpA) in a metal ion-dependent fashion, demonstrating that purified Fur is functional. (asm.org)
- Binding of OmpR to the promoter regions of the kdgM2-pelP-sghX operon, and kdgM1 and kdgR genes was confirmed using the electrophoretic mobility shift assay, suggesting that OmpR can directly regulate their transcription. (frontiersin.org)
- One of these σ 54 -predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase), was validated by primer extension assays, confirming that this gene has a σ 54 -dependent promoter. (biomedcentral.com)
- Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, preventing interaction of Gal4 bound to UAS GAL promoter motifs with general factors of the transcriptional machinery. (researchsquare.com)
- 21 ]. The latter approach searches simultaneously for biclusters and de novo motifs in the promoter region of the bicluster genes by using cMonkey [ 22 ], and subsequently applies a regression strategy [ 21 ], to associate a regulatory program with the inferred biclusters. (biomedcentral.com)
- We show that mutations in the putative TetD binding site of a TetD-activatable promoter and a mutation in the protein's N-terminal DNA recognition helix interfere with transcription activation, thereby indicating that TetD directly activates target gene transcription. (umass.edu)
- 1 , 3 Age-dependent and salt-promoted expression of ANAC092 is controlled at the promoter level as shown by reporter gene fusion. (pubmedcentralcanada.ca)
- Identification of a dehydration and ABA-responsive promoter regulon and isolation of. (deepdyve.com)
- The CpC2 promoter was analysed and a core promoter region (CPR) was identified which is critical for the responsiveness of the gene to dehydration and the plant hormone ABA. (deepdyve.com)
- Furthermore the promoter of these genes is less active after deletion of BMH1 . (biomedcentral.com)
- It could be activated by other signals in the environment, but it has been shown that PhoB directly inhibits the toxins production by binding to the tcpPH promoter and stopping the ToxR regulon from being activated. (wikipedia.org)
- thus 0 represents the beginning of the gene or the promoter, respectively. (unam.mx)
- An integron is characterized by (i) an intI gene encoding a site-specific recombinase of the tyrosine recombinase family, (ii) an adjacent primary recombination site attI [ 1 ] and (iii) an array of gene cassettes, downstream of a constitutive promoter (Pc). (mdpi.com)
- The integrated gene cassettes can be expressed from the Pc promoter located upstream of the attI site in the integron platform [ 4 ]. (mdpi.com)
- The class 1 promoter is a single promoter that transcribes the two early genes in the flhDC operon. (asm.org)
- Genes repressed by targeted recruitment of the Sin3-Rpd3 histone deacetylase complex contain deacetylated histones in their promoter region ( 31 , 54 ), and the histone deacetylase activity of Rpd3 is essential for repression ( 30 ). (asm.org)
- In the present work we performed in silico analysis on promoter sequences of protein-coding genes from this phytopathogen, including those involved in virulence and pathogenic mechanisms, in an attempt to better understand the underlying transcriptional regulatory dynamics. (usp.br)
- c) Autorepression of the promoter of the bacteriophage λ cI gene by its own protein product. (els.net)
- In all cases, this motif was located in the leader region of putative transcriptional units, upstream of coding sequences that included genes involved in methionine or cysteine biosynthesis. (nih.gov)
- A computational analysis of potential binding sites upstream of the DosR-controlled genes shows how the transcriptional responses of these genes are influenced by the affinity of these binding sites to DosR. (cam.ac.uk)
- This is supported by our demonstration that a lexA-Gal80 fusion efficiently mediates repression of a reporter gene with an upstream lexA operator sequence. (researchsquare.com)
- In the figure, each line represents an upstream region of a given gene, with different binding sites. (unam.mx)
- Orthology information is introduced by phylogenetic footprinting which is based on the assumption that among phylogenetically related species, the regulating sequences in the upstream regions of orthologous genes are selectively conserved by evolution. (biomedcentral.com)
- Both sequences are upstream of the actual gene. (syvum.com)
- Operons in prokaryotes are groups of genes whose protein products all function in the same biochemical pathway. (gnxp.com)
- Furthermore, the transcriptional organization of AmtR-regulated genes and operons was characterized. (uni-bielefeld.de)
- A modulon is a set of regulons or operons that are collectively regulated in response to changes in overall conditions or stresses, but may be under the control of different or overlapping regulatory molecules. (wikipedia.org)
- The synthesis and function of the flagellar and chemotaxis system require the expression of more than 50 genes which are divided among at least 17 operons (Fig. 1 ) that constitute the large, coordinately regulated flagellar regulon ( 85 ). (asm.org)
- Within the regulon, the operons are divided into three temporally regulated, hierarchical transcriptional classes: early, middle, and late. (asm.org)
- Chromosomal locations of the operons that make up the flagellar regulon of S. enterica serovar Typhimurium. (asm.org)
Expression of Ge4
- Moreover, we demonstrated the negative impact of OmpR on kdgR transcription, which might positively affect the expression of genes of the KdgR regulon. (frontiersin.org)
- The yeast Saccharomyces cerevisiae has two paralogous iron-responsive transcription activators, Aft1 and Aft2, that play key roles in the response to a lack of iron in the environment by increasing the expression of genes involved in iron transport and its subcellular distribution and use ( 28 ). (asm.org)
- The integrase IntI recognizes attC and attI recombination sites and respectively catalyzes excision ( attC × attC recombination) and integration ( attI × attC recombination) of the cassettes, generating combinations that allow the expression of genes that have been positioned close to Pc [ 2 ]. (mdpi.com)
- These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. (hindawi.com)
- One of my favorite recent ideas wondering through the literature is that of an RNA regulon or post-transcriptional operon. (gnxp.com)
- We confirmed that kdgM2 occurs in an operon with the pelP gene, encoding the periplasmic pectate lyase PelP. (frontiersin.org)
- Many of these insertions were located in one of the two cholera toxin operon copies of strain O395, as well as a large gene cluster involved in the biogenesis of the toxin-coregulated pilus colonization factor. (asm.org)
- the genes contained within a regulon are usually organized into more than one operon at disparate locations on the chromosome. (wikipedia.org)
- The uxuAB operon is composed of two genes coding for enzymes involved in hexuronate degradation. (bireme.br)
- This operon is negatively controlled by the uxuR and exuR regulatory gene products. (bireme.br)
- The uxuAB operon is under the dual control of uxuR- and exuR-encoded repressors whereas the exu regulon genes are regulated by the sole ExuR repressor. (bireme.br)
- As discussed below, the flhD and flhC genes encode transcriptional activators, and transcription of the flhDC operon responds to many environmental cues. (asm.org)
- The rcsC gene is convergently transcribed toward rcsB , which follows rcsD in what appears to be a two-gene operon. (wiley.com)
- Furthermore, CSP1-E1A attenuated the acquisition of an antibiotic resistance gene and a capsule gene in vivo . (prolekare.cz)
- These results demonstrate the applicability of generating competitive analogues of CSPs as drugs to control horizontal transfer of antibiotic resistance and virulence genes, and to attenuate virulence during infection by S. pneumoniae . (prolekare.cz)
- The acquisition and spread of antibiotic resistance genes in S. pneumoniae is at least partly due to genetic transformation, which occurs when the bacteria enter the competent state  -  . (prolekare.cz)
- In this review, we focus on factors leading to integron rearrangements and gene capture facilitating antibiotic resistance acquisition, maintenance and spread. (mdpi.com)
- Other secondary mechanisms, such as those that affect the regulatory gene marA (multiple antibiotic resistance) ( 9 , 10 ) or soxS (superoxide) ( 2 ), generally cause decreased expression of the OmpF porin ( 11 ) and overexpression of the AcrAB efflux pump ( 40 ). (asm.org)
- After all, the yeast ( Saccharomyces cerevisiae ) genome has been sequenced since 1996 and the precise number of genes is not yet confirmed. (genomicglossaries.com)
- p>Describes annotations that are concluded from looking at variations or changes in a gene product such as mutations or abnormal levels and includes techniques such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors. (uniprot.org)
- Careful reading and/or listening will often reveal that people use the word gene and a number of related words and phrases (mutations and other variants) very loosely and interchangeably. (genomicglossaries.com)
- It is simpler to hypothesize that differences in mRNA-specific rates of initiation and changes in ribosome concentration can adequately explain much (if not all) of the diversity of gene expression changes in different tissues as a result of ribosomal mutations. (sciencemag.org)
- Mutations affecting the two exuR and uxuR regulatory genes were selected to investigate the relationship between the two repressors. (bireme.br)
- The origins of resistance are intensively studied and many mechanisms involved in resistance have been identified, such as exogenous gene acquisition by horizontal gene transfer (HGT), mutations in the targeted functions, and more recently, antibiotic tolerance through persistence. (mdpi.com)
- This plasticity is a consequence not only of spontaneous mutations or genome rearrangements that can occur during the bacterial life cycle, but also of exogenous gene acquisition through genetic exchange between bacteria and gene capture in integrons. (mdpi.com)
- PCR sequence analysis of the quinolone resistance-determining region of the topoisomerase genes ( gyrA/B, parC ) revealed three to five mutations known to be associated with fluoroquinolone resistance. (asm.org)
- In this study, we sought to determine whether the regulatory genes ( marA, soxS, acrR ), in addition to the structural genes ( gyrA/B, parC ), contained mutations which contribute to the high-level fluoroquinolone resistance of clinical E. coli isolates from China. (asm.org)
- The new CRE genes encode a periplasmic ATP-dependent DNA ligase, homologs of SSB, RadC and the Bacillus subtilis DNA uptake protein ComEA, and eight genes of unknown function. (nih.gov)
- 100-gene com regulon in addition to DNA uptake, including virulence. (plos.org)
- ComX serves as an alternative sigma factor, directing the expression of "late" genes required for uptake and incorporation of DNA. (plos.org)
- In this yeast genes involved in high-affinity phosphate uptake ( PHO genes) are strongly induced during both phosphate and potassium starvation, indicating a link between phosphate and potassium homeostasis. (biomedcentral.com)
- Consistent with this phenotype, Aft1 activates the transcription of genes involved in iron uptake at the plasma membrane. (asm.org)
- This set of genes is proposed to form a new regulon controlled by a global termination control system, which we designate the S box system, as most of the genes are involved in sulphur metabolism and biosynthesis of methionine and cysteine. (nih.gov)
- Previously, the gene cg0156 was shown to belong to the regulon of McbR, a global transcriptional repressor of sulphur metabolism in C. glutamicum. (sigmaaldrich.com)
- In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. (biomedcentral.com)
- The total group of CtrA-regulated genes includes those involved in polar morphogenesis, DNA replication initiation, DNA methylation, cell division, and cell wall metabolism. (pnas.org)
- SeqA remains bound to some targets after replication has ceased, and these targets locate to genes encoding factors involved in nucleotide metabolism, chromosome replication, and methyl transfer. (asm.org)
- oryzicola annotates one uncharacterized gene, XOC _ 3841 , only one ORF in this strain is annotated to encode Phosphohexose mutase (XanA), which reversibly converts glucose 1-phosphate to glucose 6-phosphate that implicates in the carbon metabolism pathways. (springer.com)
- DosR regulon antigens of Mtb might serve as attractive targets for LTBI diagnosis or vaccine development as they are specifically expressed and are upregulated during latent phase. (frontiersin.org)
- In this study, we investigated the role of Rv2004c , a member of DosR regulon (exclusive to Mtb complex), in host-pathogen interaction and its immunogenic potential in LTBI, active TB, and healthy control cohorts. (frontiersin.org)
- The aim of this study was to determine whether the induction of the entire DosR regulon is triggered as a synchronous event or if induction can unfold as a cascade of events as the differential expression of subsets of genes is stimulated by different oxygen availabilities. (cam.ac.uk)
- Our study also indicates that a subgroup of DosR-controlled genes is regulated indirectly. (cam.ac.uk)
- Conclusion The majority of the dosR-dependent genes were up-regulated at 0.2% DOT, which confirms previous findings that these genes are triggered by hypoxic environments. (cam.ac.uk)
- Our results demonstrate that the gonococcal Fur protein binds to the regulatory regions of a broad array of genes and indicates that the gonococcal Fur regulon is larger than originally proposed. (asm.org)
- The P. aeruginosa Fur protein has been demonstrated to control the expression of other regulatory genes that encode transcriptional activators, which, in turn, regulate the expression of the toxA gene ( 1 , 24 , 27 , 40 , 41 ). (asm.org)
- Most of these genes are transcribed by the RNA polymerase containing the sigma factor RpoN (σ 54 ) and activated by the nitrogen regulatory protein C (NtrC). (biomedcentral.com)
- We have performed in vivo genomic binding site analysis of the CtrA protein to identify which of these genes have regulatory regions bound directly by CtrA. (pnas.org)
- In molecular genetics, a regulon is a group of genes that are regulated as a unit, generally controlled by the same regulatory gene that expresses a protein acting as a repressor or activator. (wikipedia.org)
- Suppressor analyses of fluG led to the identification of the sfgA gene encoding a novel protein with the Gal4-type Zn(II) 2 Cys 6 binuclear cluster DNA-binding motif at the N terminus. (genetics.org)
- Biology term index Related glossaries include Gene categories , Nomenclature Genomics and Proteomics are also key, since it is the gene's protein products which are ultimately of interest. (genomicglossaries.com)
- About 60% of our genes exhibit alternative splicing, making the number of protein products close to 100,000, not a very different number from the more recent estimates. (genomicglossaries.com)
- p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
- section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (uniprot.org)
- Several steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-translational modification of a protein. (wikibooks.org)
- Genes are expressed by being transcribed into RNA, and this transcript may then be translated into protein. (wikibooks.org)
- If the gene transcribed encodes a protein, the result of transcription is messenger RNA (mRNA), which will then be used to create that protein via the process of translation. (wikibooks.org)
- Alternatively, the transcribed gene may encode for either ribosomal RNA (rRNA) or transfer RNA (tRNA), other components of the protein-assembly process, or other ribozymes. (wikibooks.org)
- Bacterial toxin-antitoxin loci consist of two genes: one encodes a potentially toxic protein, and the second, an antitoxin to repress its function or expression. (mdpi.com)
- cAMP can stimulate the transcription of many activity-dependent genes via activation of the transcription factor, cAMP response element-binding protein (CREB). (jneurosci.org)
- In Bacillus subtillis (gram positive) dinR protein is homologous to lexA (Repressor of din-damage inducible genes).din genes include uvrA, uvrB, dinB, dinC dinR and recA. (igem.org)
- Fur has also been demonstrated to repress the transcription of genes induced in response to oxidative stress, including the E. coli and P. aeruginosa sodA (superoxide dismutase) genes ( 13 , 35 ). (asm.org)
- Furthermore, KUA1 directly represses the expression of a set of genes encoding for peroxidases that control reactive oxygen species (ROS) homeostasis in the apoplast. (nature.com)
- Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization. (asm.org)
- This report also demonstrates a new approach for the identification of bacterial virulence factors, based on the characterization of genes that are regulated by the same environmental signals that control the expression of a known virulence factor. (asm.org)
- We are seeking an individual who has interests in prokaryotic molecular genetics/biochemistry with an emphasis on DNA sequencing, and gene product characterization. (bio.net)
Identification of novel genes1
- A promising new approach involves the identification of novel genes whose expression is regulated by zinc status. (genetics.org)
- Organisms regulate gene expression in response to the environment to coordinate metabolic reactions.Clostridium thermocellumexpresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. (osti.gov)
- Approximately 50% of the cellulose-responsive genes showed strict dependence on functional clr-2/clrB, with a subset of 28 genes encoding plant biomass degrading enzymes that were conserved between N. crassa and A. nidulans. (biomedsearch.com)
- Background: Transcription of genes coding for xylanolytic and cellulolytic enzymes in Aspergillus niger is controlled by the transactivator XlnR. (wur.nl)
- Previous studies have shown that disruption of key components in the competence regulon inhibits DNA transformation and attenuates virulence. (prolekare.cz)
- Corepressor interaction and in vivo gene repression could be mapped to a Gal80 minimal domain of 65 amino acids (aa 81-145). (researchsquare.com)
- Site-directed mutagenesis of selected residues within this domain showed that a cluster of aromatic-hydrophobic amino acids (YLFV, aa 118-121) is important, although not solely responsible, for gene repression. (researchsquare.com)
- Expression of a GAL1-lacZ fusion was elevated in a tup1 mutant (but not in a cyc8 mutant) grown in derepressing medium, indicating that Tup1 may be mainly responsible for this second mechanism of Gal80-dependent gene repression. (researchsquare.com)
- Histone acetylation is also involved in transcriptional repression and activation at the single-gene level. (asm.org)
Directly or indirectly2
- Introduction of a toxR null mutation into 10 of these fusion strains confirmed that these TnphoA gene fusions are controlled either directly or indirectly by the cholera toxin transcriptional activator encoded by toxR. (asm.org)
- Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ 54 -dependent manner. (biomedcentral.com)
- These temporal expression patterns revealed that cell cycle-regulated genes are maximally induced immediately before or coincident with the time of execution of the cell cycle event in which they participate, and genes that encode subunits of molecular complexes or that function in the same cellular process are coexpressed. (pnas.org)
- The book covers almost all relevant areas in molecular breeding of forage and turf as well as biofuel crops, from gene discovery to the development of improved cultivars. (springer.com)
- The third lineage, lineage III, can be subdivided into lineages IIIA/C and IIIB (lineage IIIB has recently been classified as lineage IV [ 65 ]), based on results obtained with a number of molecular subtyping strategies, including pulsed-field gel electrophoresis (PFGE) ( 20 ) and virulence gene sequencing ( 20 , 68 ). (asm.org)
- With the identification of their gene sequences, it was possible to examine how the expression of cytokines was regulated at the molecular level. (jimmunol.org)
- In both bacteria, gene duplication events seem to have taken place which resulted in the evolution of dedicated regulators for the control of sulphonate utilisation. (sigmaaldrich.com)
- 4 Blocking the function of these genes individually delays senescence, 2 - 4 establishing both NAC TFs as positive regulators of senescence. (pubmedcentralcanada.ca)
- Specific mutants of the identified regulators were generated and analyzed for flagellar gene expression. (asmscience.org)
- This indicates that a large number of genes must be regulated indirectly by these regulators. (unam.mx)
- Accordingly, the publication of the paper we highlight in this commentary coincided with the discovery of NF-κB and predated the identification of NFAT and STAT transcription factors, which are among the most often encountered regulators of cytokine gene transcription. (jimmunol.org)
- In addition to studies revealing the extent of the RegB/RegA regulon, there has been a substantial amount of biochemical research on mechanistic functions of these regulators. (asm.org)
- The MocR regulators are widespread among eubacteria [ 2 , 4 ] and can occur within different species as single orthologous or multiple paralogous genes. (hindawi.com)
- Since the MocR discovery, studies have been intensified and in several cases the regulons under the control of MocR regulators have been experimentally determined and characterized, although many details of their action mechanism remain obscure. (hindawi.com)
- In Bacillus subtilis and Staphylococcus aureus , signermycin B preferentially controlled the WalR regulon, thereby inhibiting cell division. (asm.org)
- We propose that the different roles of the S. sanguinis , S. pneumoniae , and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species. (plos.org)
- Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. (biomedcentral.com)
- To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. (biomedcentral.com)
- Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates. (biomedcentral.com)
- We developed an approach that can reliably identify multiple regulatory motifs lacking a high degree of overrepresentation in a set of coexpressed genes (motifs belonging to sparsely connected hubs in the regulatory network) by exploiting the advantages of using both coexpression and phylogenetic information. (biomedcentral.com)
- The rationale behind these methodologies is that a set of genes regulated by the same transcription factor should contain in their intergenic regions motifs that are statistically overrepresented as compared to their occurrences in unrelated sequences. (biomedcentral.com)
- an often-studied example is the phosphate regulon in E. coli, which couples phosphate homeostasis to pathogenicity through a two-component system. (wikipedia.org)
- The Phosphate (Pho) regulon is a bacterial regulatory mechanism used for the conservation and management of inorganic phosphate within the cell. (wikipedia.org)
- Under low nutrient availability, the Pho regulon helps the cell survive and thrive despite a depletion of phosphate within the environment. (wikipedia.org)
- Depletion of inorganic phosphate within the cell is required for activation of the Pho regulon in most prokaryotes. (wikipedia.org)
- Although inorganic phosphate is primarily used in the Pho regulon system, there are several species of bacteria that can utilize varying forms of phosphate. (wikipedia.org)
- The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. (nih.gov)
- The use of DNA arrays and proteomics will transform the scale of our ability to describe the patterns of gene expression as bacteria respond to their environments. (whsmith.co.uk)
- Commonly studied regulons in bacteria are those involved in response to stress such as heat shock. (wikipedia.org)
- Because bacteria use the Pho regulon to maintain homeostasis of Pi, it has the added effect of being used to control other genes. (wikipedia.org)
- The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea) and viruses - to generate the macromolecular machinery for life. (wikibooks.org)
- Fur regulon in gram-negative bacteria. (semanticscholar.org)
- Highly conserved homologues of RegB and RegA have been found in a wide number of photosynthetic and nonphotosynthetic bacteria, with evidence suggesting that RegB/RegA plays a fundamental role in the transcription of redox-regulated genes in many bacterial species. (asm.org)
- Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. (plos.org)
- Despite considerable knowledge about the early components of this response, little is known about late components (i.e., genes regulated 2-6 h after stimulation) and the relationship between early and late genes. (jneurosci.org)
- In general, late genes are downregulated in strains defective in early or middle genes, and neither middle nor late genes are expressed in strains defective in early class genes. (asm.org)
- Global analysis of expression profiles during the Caulobacter cell cycle showed that the mRNA levels of approximately 19% of the genes (553 of 2,966 assayed) are cell cycle-regulated ( 4 ). (pnas.org)
- Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast growth. (uv.es)
- In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. (uv.es)
- Genome-wide analysis of the effect of disruption of either BMH1 or BMH2 revealed that the mRNA levels of the PHO genes PHO84 and SPL2 are greatly reduced in the mutant strains compared to the levels in wild type strains. (biomedcentral.com)
- Genes included in the diagram showed expression changes of at least 2-fold in one or more of the overexpression strains. (asm.org)
- By combining these data with previous global analysis of cell cycle transcription patterns and gene expression profiles of mutant ctrA strains, we have determined that CtrA directly regulates at least 95 genes. (pnas.org)
- Genetic diversity in the strains was indexed by pulsed-field gel electrophoresis, DNA-DNA microarray, whole-genome PCR scanning, prophage genotyping, targeted gene sequencing, and SNP genotyping. (pnas.org)
- different total numbers of genes were positively regulated by σ B in the strains. (asm.org)
- To enhance the research capabilities of investigators interested in Staphylococcus aureus , the Nebraska Center for Staphylococcal Research (CSR) has generated a sequence-defined transposon mutant library consisting of 1,952 strains, each containing a single mutation within a nonessential gene of the epidemic community-associated methicillin-resistant S. aureus (CA-MRSA) isolate USA300. (asm.org)
- Transcription of the yop genes was very poor in E. coli K12, even in the presence of a fully functional calcium region. (nih.gov)
- A) About 30 genes around the E. coli chromosome are normally repressed by the binding of a LexA dimer (barbell structure) to their operators. (coursehero.com)
- The heat shock response in E. coli is regulated by the sigma factor σ32 (RpoH), whose regulon has been characterized as containing at least 89 open reading frames. (wikipedia.org)
- The Ada regulon in E. coli is a well-characterized example of a group of genes involved in the adaptive response form of DNA repair. (wikipedia.org)
- Na segunda estratégia recuperamos informações regulatórias experimentalmente validadas em E. coli e complementamos o conhecimento de dez regulons de X. fastidiosa, através de uma metodologia de scanning (varredura), dos quais algumas interações regulatórias já haviam sido previamente descritas por outros trabalhos. (usp.br)
- In addition, the common feature of the gene groups also provides information about the effect of the experimental condition, for example, which transcription factor or which functional group is active. (uva.nl)
- Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. (wikibooks.org)
- Our results provide basic information on CBF genes functional redundancy and differentiation and demonstrate that the CBF-DAM signaling pathway is involved in the pear bud endodormancy process. (springer.com)
Required for virulence1
- S. sanguinis virulence for IE has been examined in a number of studies  -  but very few genes or functions required for virulence have been identified. (plos.org)
- Transcription factors ( TF s) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. (plantphysiol.org)
- This specific response is regulated by the transcription factor Rlm1 that is known to mainly regulate cell wall related genes. (uva.nl)
- We have cloned the soxR locus, which is positioned near the uvrA gene at 92.2 min on the genetic map, by monitoring complementation of a delta soxR mutation. (nih.gov)
- To characterize in genetic terms how cells respond to zinc deprivation, zinc-regulated genes ( ZRG 's) were identified in yeast. (genetics.org)
- The genetic code stored in DNA in form of nucleotide sequence is "interpreted" by gene expression, and the properties of the expression products give rise to the organism's phenotype. (wikibooks.org)
- Genetic analysis of uxuR and exuR genes: evidence for ExuR and UxuR monomer repressors interactions. (bireme.br)
- A gene fusion library of Vibrio cholerae classical strain O395 was generated by using a broad host range vector for delivery of the transposon TnphoA. (asm.org)
- Several of these insertions were localized to a cluster of four genes, the disruption of any of which by TnphoA reduced the ability of strain O395 to colonize the intestines of suckling mice. (asm.org)
- Recently, the ability to analyze flagellar gene expression by transcriptome analysis using wild-type L. pneumophila strain Paris and the isogenic fliA mutant strain was developed. (asmscience.org)
- thermocellumLacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain. (osti.gov)
- The introduction of a uxuR negative dominant allele into a wild-type strain resulted in a significant increase in exu gene expression. (bireme.br)
- We also conclude that, by uncoupling mRNA synthesis from decay, cells control the mRNA abundance of those gene regulons that characterize fast and slow growth. (uv.es)
Transcription of the genes1
- The RR is often responsible for activating or repressing transcription of the genes involved in responding to the individual environmental signal in order to facilitate survival of the cell. (wiley.com)
- Also, most interesting for my neuro-tastes is the recent report from the Moore lab showing that the immediate-early gene implicated in neuronal homeostasis, Arc, may be part of a regulon defined by introns in the 3'UTR. (gnxp.com)
- This study compares the functions of Aft1 and Aft2 in regulating the transcription of genes involved in iron homeostasis, with reference to the presence/absence of the paralog. (asm.org)
- Northern blot analyses, combined with chromatin immunoprecipitation experiments on selected genes from each class, demonstrated that Aft2 directly activates the genes SMF3 and MRS4 involved in mitochondrial and vacuolar iron homeostasis, while Aft1 does not. (asm.org)
- Perturbations in these processes will have a great impact on ribosome homeostasis and thus on broad aspects of gene expression. (sciencemag.org)
- In 1996, the complete DNA sequence of the yeast genome has been deciphered, revealing that the whole genome contains 12 million basepairs and that the estimated amount of genes is around 6000. (uva.nl)
- These findings illustrate the utility of transposon tagging as an approach for studying regulated gene expression in yeast. (genetics.org)
- DNA microarray hybridisations revealed 49 genes with significantly increased and 48 with decreased transcript levels in presence of the native CysR compared to a cysR deletion mutant. (sigmaaldrich.com)
- Here, cold-activated CBF transcription factors (CBF1 to CBF3) are inducing cold response genes, which are for example responsible for the biosynthesis of protectants, and COLD-REGULATED ( COR ) genes 15 . (nature.com)
Groups of genes3
- The idea of T-profiler is not to focus on the transcription of individual genes but instead to look at groups of genes with a common feature. (uva.nl)
- This might be genes that are bound by the same transcription factor, or groups of genes with a similar biological function. (uva.nl)
- A major advantage of measuring transcription of groups of genes is reduction of the influence of noise. (uva.nl)
- ComE also activates expression of the comX gene, which is present in two copies. (plos.org)
- We show that expression of TetD activates transcription of a subset of the SoxS/MarA/Rob regulon genes and confers resistance to redox-cycling compounds and antibiotics. (umass.edu)
- Our results suggest that cAMP stimulates CREB-dependent gene transcription via a two-step process by inducing release of an excitatory amino acid, identified here as l -aspartate, which then activates NMDARs, leading to Ca 2+ entry and gene transcription. (jneurosci.org)
- Aft2 activates the transcription of genes involved in intracellular iron use in the absence of Aft1. (asm.org)