• genome
  • The completion of the Human Genome Project has not only yielded an extraordinary amount of primary sequence data but also generated a huge selection of well-mapped constructs containing large genomic DNA inserts in the forms of bacterial artificial chromosomes (BACs), P1 artificial chromosomes (PACs), and yeast artificial chromosomes (YACs). (pubmedcentralcanada.ca)
  • The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, mitigating possible gene annotation errors. (pubmedcentralcanada.ca)
  • These alignments, available for download, can be used as search profiles to improve genome annotation of r-proteins and for further comparative genomics studies. (pubmedcentralcanada.ca)
  • A comparison of gene order in the mtDNAs of J. libera…" show "clusters that are otherwise not found in bacteria but that evidently appeared during evolution of the mitochondrial genome after the divergence of the proto-mitochondrion from the bacterial lineage. (wikipedia.org)
  • Here we demonstrate that the alignment-free analysis method feature frequency profiling (FFP) can be used to rapidly construct phylogenetic trees of draft bacterial genome sequences on a standard desktop computer and that coupling with in silico genotyping methods gives useful information for comparative and clinical genomic and molecular epidemiology applications. (surrey.ac.uk)
  • FFP-based phylogenetic trees of seven gastric Helicobacter species matched those obtained by analysis of 16S rRNA genes and ribosomal proteins, and FFP- and core genome single nucleotide polymorphism-based analysis of 63 H. pylori genomes again showed comparable phylogenetic clustering, consistent with genomotypes assigned by using multilocus sequence typing (MLST). (surrey.ac.uk)
  • The mimivirus genome also possesses 21 genes encoding homologs to proteins which are seen to be highly conserved in the majority of NCLDVs, and further work suggests that mimivirus is an early divergent of the general NCLDV group. (wikipedia.org)
  • In addition to the large size of the genome, mimivirus possesses an estimated 979 protein-coding genes, far exceeding the minimum 4 genes required for viruses to exist (c.f. (wikipedia.org)
  • Analysis of its genome revealed the presence of genes not seen in any other viruses, including aminoacyl tRNA synthetases, and other genes previously thought only to be encoded by cellular organisms. (wikipedia.org)
  • Taken together with previous results, 22 of the 54 E. coli ribosomal protein genes can be individually deleted from the genome. (wikipedia.org)
  • Human MALSU1 genome location and MALSU1 gene details page in the UCSC Genome Browser. (wikipedia.org)
  • ChIP-exo is a chromatin immunoprecipitation based method for mapping the locations at which a protein of interest (transcription factor) binds to the genome. (wikipedia.org)
  • These sequences are then mapped to the genome to identify the locations on the genome at which the protein binds. (wikipedia.org)
  • Briefly, a protein of interest (engineering one with an epitope tag can be useful for immunoprecipitation) is crosslinked in vivo to its natural binding locations across a genome using formaldehyde. (wikipedia.org)
  • This method allows for resolution of up to a single base pair for any protein binding site within any genome, which is a much higher resolution than either ChIP-chip or ChIP-seq. (wikipedia.org)
  • The regulation of this gene is more complex than most other genes in the E. coli genome, as FIS is an important protein which regulates expression of other genes. (wikipedia.org)
  • tRNA
  • DUF143 has also been shown to interact with UFD1, tRNA synthetases class II, and Cytidylyltransferase in various architectures. (wikipedia.org)
  • The crystal structure of a bacterial RNase P holoenzyme with tRNA has been recently resolved, showing how the large, coaxially stacked helical domains of the RNase P RNA engage in shape selective recognition of the pre-tRNA target. (wikipedia.org)
  • As revealed by in vitro reconstitution experiments these protein subunits are individually dispensable for tRNA processing that is essentially mediated by the RNA component. (wikipedia.org)
  • Based on a study of ribosomal protein genes, it had been concluded that UGA does not code for tryptophan in plant-pathogenic mycoplasma-like organisms (MLO) and the Acholeplasmataceae (Lim and Sears, 1992) and there seems to be only a single tRNA-CCA for tryptophan in Acholeplasma laidlawii (Tanaka et al. (wikipedia.org)
  • The fis gene is cotranscribed with the upstream dusB gene encoding a tRNA-modifying enzyme. (wikipedia.org)
  • vitro
  • Experiments show that triclocarban activates constitutive androstane receptor and estrogen receptor alpha both in vivo and in vitro and might have the potential to alter normal physiological homeostasis. (wikipedia.org)
  • T6SSs have been shown to contribute to spatial organization of bacterial communities in vitro ( 5 , 6 ). (asm.org)
  • In this paper, the association between polymorphism of the small sub-unit ribosomal RNA apicoplastic gene pfssrRNA (PFC10_API0057) and in vitro susceptibilities of P. falciparum isolates to doxycycline were investigated. (biomedcentral.com)
  • The pfssrRNA gene is not associated with in vitro decreased susceptibility of P. falciparum to doxycycline. (biomedcentral.com)
  • In C. crescentus , a P168V mutant is not activating in vivo , although in vitro , the P168V protein showed a modest reduction in the affinity for GDP. (umich.edu)
  • bacteria
  • In bacteria and archaea, genes encoding r-proteins are organized in genomic clusters that include several partially conserved operons and are often called ribosomal superoperons , . (pubmedcentralcanada.ca)
  • Here we report a comprehensive reannotation of r-proteins in genomes of 995 bacteria and 87 archaea and discuss trends of their distribution across the different branches of life and patterns in their evolution. (pubmedcentralcanada.ca)
  • Triclocarban is only unquestionably bacteriostatic for gram-positive bacteria such as Staphylococcus aureus, which suggests that the mechanism of triclocarban's antibacterial activity is through its destabilization of bacterial cell walls. (wikipedia.org)
  • With the passage of time, the burden of bacterial infections is showing an ascending trend and this is largely due to the generation of resistance mechanisms by bacteria [ 2 , 3 ]. (hindawi.com)
  • There are three general mechanisms that may allow bacteria to become resistant to beta-lactam antibiotics: inability to access/target penicillin-binding protein (PBP) enzyme inhibition of binding to PBP via modification of the enzyme hydrolysis/inactivation of the antibiotic by beta-lactamases. (wikipedia.org)
  • Some Gram-negative bacteria employ type VI secretion systems (T6SSs) to inject protein toxins into neighboring cells. (asm.org)
  • Approximately 42.5 and 38.1% of the tested Streptococcus suis and Streptococcus agalactiae clinical isolates respectively contained ICE Sa 2603 family Type IV secretion system (T4SS) genes, and 80.5 and 62.5% of which also respectively carried int ICE Sa 2603 , indicating that ICE Sa 2603 family is widely distributed across these bacteria. (frontiersin.org)
  • species
  • Our results suggest that coevolution among bacterial species in the bee gut has favored toxin diversification and maintenance of T6SS machinery, and demonstrate the importance of antagonistic interactions within host-associated microbial communities. (asm.org)
  • these findings suggest roles for these complexes in the cocolonization and persistence of bacterial species in the human gut ( 7 - 10 ). (asm.org)
  • Despite their high conservation over billions of years of evolution, the absence of several ribosomal proteins in certain species shows that ribosomal subunits have been added and lost over the course of evolution. (wikipedia.org)
  • There are four predicted exons in the human gene with conservation occurring across most mammalian species. (wikipedia.org)
  • For this reason, genes that encode the rRNA (rDNA) are sequenced to identify an organism's taxonomic group, calculate related groups, and estimate rates of species divergence. (wikipedia.org)
  • strands
  • Transcribed genes are found on both DNA strands. (wikipedia.org)
  • In this review, we summarized the binding characteristics of the miRNA ∗ strands with ARGONAUTE proteins, their tissue-specific accumulations and their biological functions, illustrating the essential roles of miRNA ∗ s in biological processes and therefore providing directions for further exploration. (frontiersin.org)
  • It employs the use of exonucleases to degrade strands of the protein-bound DNA in the 5'-3' direction to within a small number of nucleotides of the protein binding site. (wikipedia.org)
  • Lambda exonuclease then digests double DNA strands from the 5′ end until digestion is blocked at the border of the protein-DNA covalent interaction. (wikipedia.org)
  • genomic
  • Di- to pentanucleotide usage and the list of the most abundant octa- to tetradecanucleotides are useful measures of the bacterial genomic signature. (wikipedia.org)
  • Secondly, contaminating DNA presents a grave problem since so few genetic loci are cross-linked to the protein of interest, making any non-specific genomic DNA a significant source of background noise. (wikipedia.org)
  • interactions
  • We propose that collectively the Taf4, Taf5, and Taf12 subunits of TFIID represent the physical and functional targets for Rap1 interaction and, furthermore, that these interactions drive ribosomal protein gene transcription. (pubmedcentralcanada.ca)
  • TFIID, a complex composed of TATA-binding protein (TBP) and 14 evolutionarily conserved Taf subunits ( 4 , - 6 ), is an attractive candidate target for transactivator regulatory interactions within the PIC, both because TFIID promoter binding appears to be rate-limiting in vivo ( 7 ) and because transactivators have been shown to bind directly to TFIID subunits ( 8 , 9 ). (pubmedcentralcanada.ca)
  • Protein-protein interactions. (wikipedia.org)
  • Protein-protein interactions also exist to hold structure together by electrostatic and hydrogen bonding interactions. (wikipedia.org)
  • Chromatin immunoprecipitation (ChIP) techniques have been in use since 1984 to detect protein-DNA interactions. (wikipedia.org)
  • vivo
  • We find that S. alvi Rhs loci have a conserved architecture, consistent with the C-terminal displacement model of toxin diversification, with Rhs toxins, toxin fragments, and cognate immunity genes that are expressed and confer strong fitness effects in vivo . (asm.org)
  • This technique has limited sensitivity and specificity, especially in vivo where microarrays are constrained by thousands of proteins present in the nuclear compartment, resulting in a high rate of false positives. (wikipedia.org)
  • clusters
  • Examples are the clusters sdh3 to nad5, (comprising 5 genes), atp8-[trn]-rps4-atp9 and nad11-nad1-cox11-cox3-tufA. (wikipedia.org)
  • transcription
  • Recombineering technology allows the modification of large DNA constructs without using restriction enzymes, enabling the use of bacterial artificial chromosomes (BACs) in genetic engineering of animals and plants as well as in the studies of structures and functions of chromosomal elements in DNA replication and transcription. (pubmedcentralcanada.ca)
  • Explicit in this model is the transcription and translation of the ribosomal components. (illinois.edu)
  • Transcription factor IID (TFIID) plays a key role in regulating eukaryotic gene expression by directly binding promoters and enhancer-bound transactivator proteins. (pubmedcentralcanada.ca)
  • Cells expressing altered Rap1 binding domains exhibit conditional growth, synthetic phenotypes when expressed in combination or with altered Rap1, and are selectively defective in ribosomal protein gene transcription. (pubmedcentralcanada.ca)
  • Classical studies have shown that ADs enhance transcription rates by directly stimulating the formation and/or function of the PIC, which is an assortment of over 40 distinct polypeptides often termed the general transcription factors TFIIA, -B, -D, -E, -F, -H, and RNA pol II ( 2 , 3 ). (pubmedcentralcanada.ca)
  • However, subsequent work has shown that the ADs of transactivators can also directly bind chromatin-directed coactivators to modulate transcription ( 1 ). (pubmedcentralcanada.ca)
  • Therefore, the organelles must feed back to the nucleus to induce or reduce transcription of organellar proteins depending on developmental cues and environmental conditions. (frontiersin.org)
  • Fis has been known to activate ribosomal RNA transcription, as well other genes. (wikipedia.org)
  • DusB protein levels are very low even under conditions when there is high transcription of the operon and high levels of Fis protein. (wikipedia.org)
  • expression
  • The two widely used recombineering systems are based on bacterial phage-encoded resombinases, one uses episomal plasmids to supply RecE/RecT of the Rac phage ( 5 , 7 ), and the other utilizes a temperature-sensitive λ repressor to control the expression of recombinases from a λ prophage ( 7 - 9 ). (pubmedcentralcanada.ca)
  • Activation of these receptors amplifies gene expression and, in doing so, may be the mechanistic base of triclocarban's health impact on humans. (wikipedia.org)
  • These pre-packaged transcripts can be translated without viral gene expression and are likely to be necessary to Mimivirus for replication. (wikipedia.org)
  • Its mechanism remains unknown, but it is tempting to speculate a regulatory involvement of the NusA protein, which expression has been shown to lower the operon expression, and which is already involved in the attenuation of the Trp, His and S10 operons. (wikipedia.org)
  • These overlapping gene expression changes appear to be common with general abiotic, biotic, and nutrient stresses. (frontiersin.org)
  • In the unlikely event that the protein cannot be expressed or purified we do not charge anything (other companies might charge you for any performed steps in the expression process for custom-made proteins, e.g. fees might apply for the expression plasmid, the first expression experiments or purification optimization). (antibodies-online.com)
  • Recombination
  • The plasmids containing TEM-1 could be passed from bacterium to bacterium via conjugation Quinolones are a class of synthetic antibiotics that inhibit DNA replication, recombination, and repair by interacting with the bacterial DNA gyrase and/or topoisomerase IV. (wikipedia.org)
  • Pathogens
  • Thiopeptides such as nosiheptide have potent activity against various bacterial pathogens, primarily gram positive, including methicillin-resistant Staphylococcus aureus, penicillin-resistant Streptococcus pneumoniae, and vancomycin-resistant enterococci. (wikipedia.org)
  • distinct
  • The Obg subfamily of bacterial GTP-binding proteins are biochemically distinct from Ras-like proteins raising the possibility that they are not controlled by conventional guanine nucleotide exchange factors (GEFs) and/or guanine nucleotide activating proteins (GAPs). (umich.edu)
  • If a protein-DNA complex has multiple locations of cross-linking within a single binding event, then it can appear as though there are multiple distinct binding events. (wikipedia.org)
  • resistance
  • Trends in antimicrobial resistance have shown a clear correlation between use of antibiotics in the veterinary medicine and animal production and resistant isolates of Campylobacter in humans. (hindawi.com)
  • Among the various patterns of resistance, reports across the globe continue to emerge on the resistance to aminoglycoside antibiotics which otherwise have been reported as highly potent drugs against life threatening Gram-negative bacterial infections [ 4 , 5 ]. (hindawi.com)
  • Resistance patterns and prevalence of the aminoglycoside modifying enzymes in clinical isolates showing multidrug-resistant patterns have also been reported from various parts of India and it has been shown that high level aminoglycoside resistance genes are widely disseminated among Indian populations [ 11 , 12 ]. (hindawi.com)
  • In addition, ICEs contain genes that confer specific phenotypes that are related to its existence in its hosts such as resistance to antibiotics and heavy metals. (frontiersin.org)
  • enzyme
  • RNase P is unique from other RNases in that it is a ribozyme - a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. (wikipedia.org)
  • The primary role of the C5 protein is to enhance the substrate binding affinity and the catalytic rate of the M1 RNA enzyme probably by increasing the metal ion affinity in the active site. (wikipedia.org)
  • Ribonuclease E (EC 3.1.26.12, endoribonuclease E, RNase E, Rne protein) is an enzyme. (wikipedia.org)
  • This enzyme catalyses the following chemical reaction Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions RNase E is a bacterial ribonuclease that participates in the processing of ribosomal RNA (9S to 5S rRNA) and the chemical degradation of bulk cellular RNA. (wikipedia.org)
  • Systematic
  • The results presented here suggest that gene trapping, using nptII as a reporter gene, can be as high as 80% and opens novel perspectives for systematic gene tagging in A. thaliana. (ugent.be)
  • small
  • Atomic coordinates (PDB files) and structure factors of the eukaryotic ribosome have been deposited in the Protein Data Bank (PDB) under the following accession codes: Some general architectural features of the ribosome are conserved across kingdoms: The shape of the small subunit can be subdivided into two large segments, the head and the body. (wikipedia.org)
  • The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography. (wikipedia.org)
  • genetic
  • The genetic determinants of these enzymes are often located on mobile elements facilitating the rapid dissemination of the genes in various bacterial populations [ 8 ]. (hindawi.com)
  • The genetic markers that contribute to detecting and monitoring the susceptibility of P. falciparum to doxycycline, the pfmdt and pftetQ genes, have recently been identified. (biomedcentral.com)
  • amino acids
  • Nosiheptide is constructed solely of proteinogenic amino acids and has ribosomal origin, making it a member of the ribosomally synthesized and posttranslationally modified peptide family of natural products. (wikipedia.org)
  • All moieties of the peptidyl backbone of nosiheptide were shown to originate exclusively from proteinogenic amino acids. (wikipedia.org)
  • regulatory
  • The translation and modification of the precursor peptide is undertaken by several enzymes encoded in a localized gene cluster containing 14 structural genes and 1 regulatory gene. (wikipedia.org)
  • combined A repressive effect of Fis and previously characterized negative regulatory factors could be responsible to keep the gene silenced most of the time. (wikipedia.org)
  • nucleotide
  • Proteins that are inefficiently bound to a nucleotide fragment are more likely to be detected by ChIP-exo. (wikipedia.org)
  • Binding motifs of Gal4 showed a strong preference for three of the four nucleotides, suggesting a negative interaction between Gal4 and the excluded nucleotide. (wikipedia.org)
  • horizontal gene tra
  • N. gonorrheoea has a high affinity for horizontal gene transfer, and as a result, the existence of any strain resistant to a given drug could spread easily across strains. (wikipedia.org)
  • Some toxins are shared with Gilliamella apicola , a coresident gut symbiont, implicating horizontal gene transfer as a source of toxin diversity in the bee gut. (asm.org)
  • large
  • Like other large DNA viruses, mimivirus contains several genes for sugar, lipid and amino acid metabolism, as well as some metabolic genes not found in any other virus. (wikipedia.org)