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*  Antisense RNA
For example, in bacterial or eukaryotic cells where complex RNA polymerases are present, bidirectional transcription at the ... RNA I and RNA II forms a duplex which introduces a conformational change of RNA II. Consequently, RNA II cannot hybridize with ... RNA-RNA interactions either in nucleus or cytoplasm and RNA-protein interactions (epigenetic). Antisense RNAs can be ... The replication of ColE1 relies on the transcription of a primer RNA named RNA II. Once RNA II is transcribed, it hybridizes to ...
*  5S ribosomal RNA
Translation machineries of mitochondria and plastids (organelles of endosymbiotic bacterial origin), and their bacterial ... Binding between 5S rRNA and TFIIIA serves to both repress further transcription of the 5S RNA gene and stabilize the 5S RNA ... La protein is found in the nucleus in all eukaryotic organisms and associates with several types of RNAs transcribed by RNA pol ... Pelham, HRB; Brown DD (1980). "A specific transcription factor that can bind either the 5S RNA gene or 5S RNA". Proc. Natl. ...
*  Transfer-messenger RNA
... (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule ... November 2007). "Semiautomated improvement of RNA alignments". RNA. 13 (11): 1850-9. doi:10.1261/rna.215407. PMC 2040093 . PMID ... In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base ... Wower IK, Zwieb C, Wower J (May 2005). "Transfer-messenger RNA unfolds as it transits the ribosome". RNA. 11 (5): 668-73. doi: ...
*  Bacterial small RNA
Bacterial small RNAs (sRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, ... How ribonucleases dictate the rules in the control of small non-coding RNAs". RNA Biol. 5 (4): 230-43. doi:10.4161/rna.6915. ... a Staphylococcus regulatory RNA database". RNA. 21 (5): 1005-1017. doi:10.1261/rna.049346.114. ISSN 1469-9001. PMC 4408781 . ... Vogel J, Papenfort K (December 2006). "Small non-coding RNAs and the bacterial outer membrane". Curr. Opin. Microbiol. 9 (6): ...
*  Cis-regulatory element
Kortmann J, Narberhaus F (March 2012). "Bacterial RNA thermometers: molecular zippers and switches". Nature Reviews. ... Upstream activation sequence RNA List of cis-regulatory RNA elements Polyadenylation signals, mRNA AU-rich element, mRNA Other ... Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and ... Walczak R, Westhof E, Carbon P, Krol A (April 1996). "A novel RNA structural motif in the selenocysteine insertion element of ...
*  Richard H. Ebright
"Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex". Cell. 108 (5): ... "Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation ... and the identification of novel antibacterial drug targets in bacterial RNA polymerase. In 1994 Ebright was awarded the ... "Opening and closing of the bacterial RNA polymerase clamp". Science. 337 (6094): 591-595. doi:10.1126/science.1218716. PMC ...
*  Rifamycin
The antibacterial activity of rifamycins relies on the inhibition of bacterial DNA-dependent RNA synthesis. This is due to the ... The rifamycins have a unique mechanism of action, selectively inhibiting bacterial DNA-dependent RNA polymerase, and show no ... "Structural mechanism for rifampicin inhibition of bacterial RNA polymerase". Cell. 104 (6): 901-12. doi:10.1016/S0092-8674(01) ... high level resistance to the rifamycins occurs as the result of a single amino acid change in the bacterial DNA dependent RNA ...
*  RpoB
The rpoB gene encodes the β subunit of bacterial RNA polymerase. It codes for 1342 amino acids, making it the second-largest ... "Structural mechanism for rifampicin inhibition of bacterial RNA polymerase". Cell. 104 (6): 901-12. doi:10.1016/S0092-8674(01) ... Mutations in rpoB that confer resistance to rifamycins do so by altering residues of the rifamycin binding site on RNA ... "Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center". Proc Natl Acad Sci ...
*  Streptolydigin
... thus inhibiting RNA synthesis inside a cell. Streptolydigin inhibits bacterial RNA polymerase, but not eukaryotic RNA ... "Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation ... "Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation ... "Structural basis for substrate loading in bacterial RNA polymerase". Nature. 448 (7150): 163-8. doi:10.1038/nature05931. PMID ...
*  RydC RNA
RyfA RNA RydB RNA RybB RNA Antal, M; Bordeau V; Douchin V; Felden B (2005). "A small bacterial RNA regulates a putative ABC ... RydC is a bacterial non-coding RNA. RydC is thought to regulate a mRNA, yejABEF, which encodes an ABC transporter protein. RydC ... biofilm formation in enteric bacteria are controlled by a dynamic small RNA module made up of a pseudoknot assisted by an RNA ... is known to bind the Hfq protein, which causes a conformational change in the RNA molecule. The Hfq/RydC complex is then ...
*  Salmonella enterica
enterica, serovar Typhi". 1984 Rajneeshee bioterror attack AsrC small RNA Bacterial small RNA HilD 3'UTR PinT small RNA Typhoid ... 97 bacterial sRNAs from Salmonella Typhi were discovered by Chinni et al. AsdA (antisense RNA of dnaA) is a cis-encoded ... Small non-protein coding RNAs (sRNA) are able to perform specific functions without being translated into proteins. ... Hensel M (2009). "Secreted Proteins and Virulence in Salmonella enterica". Bacterial Secreted Proteins: Secretory Mechanisms ...
*  Fidaxomicin
... of bacterial RNA polymerase. Switch motion is important for opening and closing of the DNA:RNA clamp, a process that occurs ... "New target for inhibition of bacterial RNA polymerase: 'switch region'". Current Opinion in Microbiology. 14 (5): 532-43. doi: ... throughout RNA transcription but especially during opening of double stranded DNA during transcription initiation. It has ...
*  Sib RNA
Papenfort K, Vogel J (July 2010). "Regulatory RNA in bacterial pathogens". Cell Host Microbe. 8 (1): 116-27. doi:10.1016/j.chom ... Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four ... Sib RNA regulates the expression of a toxic protein in a type I toxin-antitoxin system similar to that of hok/sok andldr-rdl ... These small RNA were identified computationally by searching the genome of E. coli for intergenic regions of high sequence ...
*  Bacteriophage
For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it ... RNA phage such as MS2 have the smallest genomes of only a few kilobases. However, some DNA phages such as T4 may have large ... Phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. One of the ... Of these, only two families have RNA genomes, and only five families are enveloped. Of the viral families with DNA genomes, ...
*  5' flanking region
Bacterial RNA polymerase binds to these regions to align itself and begin transcription. Promoter sequences that differ from ... It is the region of DNA that is not transcribed into RNA. Not to be confused with the 5' untranslated region, this region is ... This leads to RNA polymerase recruitment and interaction with transcription factors and the promoter, and an overall higher ... The TATA box is present in all genes that are transcribed by RNA polymerase II, which is most eukaryotic genes. The binding of ...
*  Cell-free system
Mehta, Preeti; Woo, Perry; Venkataraman, Krithika; Karzai, A. Wali (2012). Bacterial Regulatory RNA. Methods in Molecular ...
*  Rifampicin
... inhibits bacterial DNA-dependent RNA synthesis by inhibiting bacterial DNA-dependent RNA polymerase. Crystal ... Rifampicin inhibits bacterial RNA polymerase, thus it is commonly used to inhibit the synthesis of host bacterial proteins ... The inhibitor prevents RNA synthesis by physically blocking elongation, and thus preventing synthesis of host bacterial ... RNA encoding for the recombinant gene is usually transcribed from DNA by a viral T7 RNA polymerase, which is not affected by ...
*  Nucleoid
Qian, Z; Macvanin, M; Dimitriadis, EK; He, X; Zhurkin, V; Adhya, S (2015). "A New Noncoding RNA Arranges Bacterial Chromosome ... As in all cellular organisms, length of the DNA molecules of bacterial and archaeal chromosomes is very large compared to the ... The secondary structure but not the sequence of the RNA is important in nucleoid condensation. Changes in the structure of the ... Experimental evidence suggests that the nucleoid is largely composed of DNA, about 60%, with a small amount of RNA and protein ...
*  Rifaximin
... interferes with transcription by binding to the β-subunit of bacterial RNA polymerase. This results in the blockage ...
*  RpoN
2008). "Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor". Mol Microbiol. 38: ... The gene rpoN (RNA polymerase, nitrogen-limitation N) encodes the sigma factor sigma-54 (σ54, sigma N, or RpoN), a protein in ... link) Gruber, T; Gross, CA (2003). "Multiple Sigma subunits and the partitioning of bacterial transcription space". Annu Rev ... Hunt, TP; Magasanik, B (1985). "Transcription of glnA by purified Escherichia colicomponents: core RNA polymerase and the ...
*  Pribnow box
Feklistov, Andrey; Darst, Seth (2011). "Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ ... TATA box Pribnow, David (March 1975). "Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter". PNAS. 72 ... Schaller, Heinz; Gray, Christopher; Herrman, Karin (February 1975). "Nucleotide sequence of an RNA polymerase binding site from ... it is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also ...
*  CrfA RNA
Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit. Rev. Biochem. Mol. Biol. 40 (2): 93-113 ... CrfA RNA (Caulobacter response to famine RNA) is a family of non-coding RNAs found in Caulobacter crescentus. CrfA is expressed ... CrfA RNA is one of only 8 putative ncRNAs conserved in the closely related Caulobacter sp. K31. CrfA was found to be ... Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L (May 2008). "Small non-coding RNAs in Caulobacter crescentus ...
*  Small non-coding RNAs in the endosymbiotic diazotroph α-proteobacterium Sinorhizobium meliloti
Post-genomic research has rendered bacterial small non-coding RNAs (sRNAs) as major players in post-transcriptional regulation ... Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit Rev Biochem Mol Biol. 40 (2): 93-113. ... These new genomic loci were referred to as smr, for S. meliloti RNA. Seven of the Smr transcripts, which conservation is ... "Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by ...
*  5 prime ureB sRNA
Bacterial small RNA Wen, Y; Feng, J; Scott, DR; Marcus, EA; Sachs, G (January 2011). "A cis-encoded antisense small RNA ... In molecular biology, 5' ureB sRNA is a small RNA. It is located at the 5' end of the ureB gene in the urease gene cluster, and ... Wen, Y; Feng, J; Sachs, G (February 2013). "Helicobacter pylori 5'ureB-sRNA, a cis-encoded antisense small RNA, negatively ...
*  Aar small RNA
Bacterial small RNA Schilling, D; Findeiss, S; Richter, AS; Taylor, JA; Gerischer, U (September 2010). "The small RNA Aar in ... In molecular biology, the Aar small RNA is a small RNA (sRNA) produced by species of Acinetobacter. It was first discovered in ... Schilling, D; Findeiss, S; Richter, AS; Taylor, JA; Gerischer, U (September 2010). "The small RNA Aar in Acinetobacter baylyi: ... Schimmel, PR; Söll, D (1979). "Aminoacyl-tRNA synthetases: general features and recognition of transfer RNAs". Annual Review of ...
*  Phage display
Phage eluted in the final step can be used to infect a suitable bacterial host, from which the phagemids can be collected and ... Danner S, Belasco JG (November 2001). "T7 phage display: a novel genetic selection system for cloning RNA-binding proteins from ... Those that remain can be eluted, used to produce more phage (by bacterial infection with helper phage) and so produce a phage ... Following further bacterial-based amplification, the DNA within in the interacting phage is sequenced to identify the ...
*  Streptococcus sRNA
"An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in ... Bacterial small RNA Tsui, HC; Mukherjee, D; Ray, VA; Sham, LT; Feig, AL; Winkler, ME (Jan 2010). "Identification and ... "The small regulatory RNA FasX controls pilus expression and adherence in the human bacterial pathogen group A Streptococcus". ... RNA. 18 (3): 530-546. doi:10.1261/rna.027359.111. PMC 3285940 . PMID 22274957. Perez, N; Treviño, J; Liu, Z; Ho, SC; Babitzke, ...