6S / SsrS RNA

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6S / SsrS RNA
RF00013-rscape.svg
Predicted secondary structure and sequence conservation of 6S
Identifiers
Symbol6S
Rfam RF00013
Other data
RNA type Gene
Domain(s) Bacteria
SO SO:0000376
PDB structures PDBe

In the field of molecular biology the 6S RNA is a non-coding RNA that was one of the first to be identified and sequenced. [1] What it does in the bacterial cell was unknown until recently. In the early 2000s scientists found out the function of 6S RNA to be as a regulator of sigma 70-dependent gene transcription. All bacterial RNA polymerases have a subunit called a sigma factor. The sigma factors are important because they control how DNA promoter binding and RNA transcription start sites. Sigma 70 was the first one to be discovered in Escherichia coli. [2] [3]

Contents

Structure

The structure of 6S RNA was defined in 1971. [2] It is a small RNA strand consisting of 184 nucleotides. 6S RNA is a long double-stranded structure and has a single strand loop. The structure is similar to an open promoter complex of DNA structure. Various analyses discovered that 6S RNAs are capable of forming a secondary structure. [4] The secondary structure consists of two irregular helical stem regions, making a large core loop which is called a central knot.

Function and Regulation

The function of 6S RNA is to regulate transcription for E. coli cell survival because it is essential in the process. [5] 6S RNA specifically associates with RNA polymerase holoenzyme containing the sigma70 specificity factor. This interaction represses expression from sigma70-dependent promoters during stationary phase. [6] Which will lead to activate the transcription from sigma 70 dependent promoters. Therefore, during the change in E. coli from logarithmic growth to stationary phase, the 6S RNA performs as a regulator of transcription. 6S RNA homologs have recently been identified in most bacterial genomes. [3] [7] Polymerase holoenzyme, which contains the housekeeping sigma factor and it can be expressed during different stages of growth. In many Pseudomonadota, 6S RNA may be processed from a transcript encoding homologs of the E. coli YgfA protein, which is a putative methenyltetrahydrofolate synthetase. Diverged 6S RNAs have been identified in additional bacterial lineages. [8] [9] The purD RNA motif has been experimentally shown to overlap with 6S RNA. [8] One way to examine if the activity of 6S RNA by doing a knockout of 6S RNA. Strains with mutations in 6S RNA have a reduction of lifespan in contrast to the wild-type cells after more than 20 days of nonstop culture. When mutant 6S cells cultured with wild-type cells, it will be at a modest disadvantage in the following days of growth. [10]

Summary

The recently discovered homologs of 6S are two Bacillus subtilis RNAs and cyanobacterial RNAs. Two 6S RNA, 6S-1 and 2 along with their encoding genes bsrA and B present at various positions of a genome. In stationary phase deletion of 6S-1 in B. subtilis results in inhibition of its growth. The absence of 6S-2 RNA, on the other hand, does not appear to influence growth and sporulation in the stationary phase. [11] 6S RNA conserved feature shows that it binds to the RNA polymerase by replicating the structure of DNA template. [12] Promoter-dependent transcriptional regulation is mediated by 6S RNA as some of the promoters may be down-regulated and some are insensitive in the presence of 6S RNA. Gene expression studies revealed that 6S RNA is integrated in different global pathways e.g., it regulates various factors that influence transcription like Crp, FNR etc. and translation mechanism. [13]

Scientist discovered that 6S RNA binds with the active site of RNA polymerase and can serve as a template for RNA synthesis required for the RNA synthesis. [14] It down-regulates transcription from 3´-5´fold at various promoters but doesn't inhibit transcription during late stationary phase. In a nutrient-deficient environment, 6S RNA control transcription leads to altered cell survival, possibly through redirecting resource consumption. [13]

Through SDS-PAGE analysis 6S RNA was identified present in E. coli and cover almost 25% of the total ribosomal number. 1000-1500 molecules were estimated to be present in E. coli genome. Although 6S RNA does not appear to be associated with ribosomes, it does appear to be complexed with several proteins and migrates at around 11S. [15]

6S RNA is a regulator of RNA polymerase and abundantly present in bacteria. Studies has shown that the 6S RNA forms a complex with RNA polymerase to initiate transcription. Lack of 6S RNA in cells result in altered phenotypes. [13]

A unique feature of 6S RNA is that it acts like a template for RNA synthesis and the length and abundance of RNAs vary according to cell physiology. pRNA synthesis is critical as it releases RNA polymerase that allows the inhibition to be reversed. [16]

Structural and functional analyses showed the interactions between RNA polymerase and E. coli 6S RNA. The functional variety of 6S RNAs was discovered by genome-wide transcriptome studies. Numerous recent investigations have suggested that 6S RNA serves as a guardian, regulating the efficient utilisation of cellular resources under restricted conditions and stress. [17] By interacting with the sigma 70-dependent RNA polymerase holoenzyme in the stationary phase, high abundant 6S RNA is discovered to influence gene transcription, resulting in bacterial response regulation to challenges such as hunger. [11]

6S RNA in E. coli abundantly increases throughout in log and early stationary phase. So, the increase level of 6S RNA regulate alterations in gene expression are expected to aid adaptation to environmental challenges such as nutritional scarcity and high cell density.

6S RNA role in bacterial virulence has been identified that includes  L. pneumophila and Salmonella enterica serovar Typhimurium specifically where pathogenesis is linked to replication and stress resistance. [18]

Related Research Articles

<span class="mw-page-title-main">Promoter (genetics)</span> Region of DNA encouraging transcription

In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA . Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism.

<span class="mw-page-title-main">Transcription (biology)</span> Process of copying a segment of DNA into RNA

Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). mRNA comprises only 1–3% of total RNA samples. Less than 2% of the human genome can be transcribed into mRNA, while at least 80% of mammalian genomic DNA can be actively transcribed, with the majority of this 80% considered to be ncRNA.

<span class="mw-page-title-main">RNA polymerase</span> Enzyme that synthesizes RNA from DNA

In molecular biology, RNA polymerase, or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.

In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in multicellular eukaryotes, as studied in evolutionary developmental biology.

A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).

<span class="mw-page-title-main">General transcription factor</span> Class of protein transcription factors

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator constitute the basic transcriptional apparatus that first bind to the promoter, then start transcription. GTFs are also intimately involved in the process of gene regulation, and most are required for life.

<i>trp</i> operon Operon that codes for the components for production of tryptophan

The trp operon is a group of genes that are transcribed together, encoding the enzymes that produce the amino acid tryptophan in bacteria. The trp operon was first characterized in Escherichia coli, and it has since been discovered in many other bacteria. The operon is regulated so that, when tryptophan is present in the environment, the genes for tryptophan synthesis are repressed.

The gene rpoS encodes the sigma factor sigma-38, a 37.8 kD protein in Escherichia coli. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. rpoS is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The rpoS gene most likely originated in the gammaproteobacteria.

<span class="mw-page-title-main">Bacterial transcription</span>

Bacterial transcription is the process in which a segment of bacterial DNA is copied into a newly synthesized strand of messenger RNA (mRNA) with use of the enzyme RNA polymerase.

<span class="mw-page-title-main">Anti-sigma factors</span>

In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and inhibit transcriptional activity. Anti-sigma factors have been found in a number of bacteria, including Escherichia coli and Salmonella, and in the T4 bacteriophage. Anti-sigma factors are antagonists to the sigma factors, which regulate numerous cell processes, including flagellar production, stress response, transport, and cellular growth. For example, anti-sigma factor 70 Rsd in E. coli is present in the stationary phase and blocks the activity of sigma factor 70, which, in essence, initiates gene transcription. This allows the sigma S factor to associate with RNA polymerase (RNAP) and direct the expression of the stationary genes. Although the binding of Rsd to σ70 has been shown and numerous structural studies on Rsd have been performed, the detailed mechanism of action is still unknown.

fis E. coli gene

fis is an E. coli gene encoding the Fis protein. 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. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.

The gene rpoF encodes the sigma factor sigma-28, a protein in Escherichia coli and other species of bacteria. Depending on the bacterial species, this gene may be referred to as sigD or fliA. The protein encoded by this gene has been found to be necessary for flagellum formation.

<span class="mw-page-title-main">OmrA-B RNA</span>

The OmrA-B RNA gene family is a pair of homologous OmpR-regulated small non-coding RNA that was discovered in E. coli during two large-scale screens. OmrA-B is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well. RygB is adjacent to RygA a closely related RNA. These RNAs bind to the Hfq protein and regulate gene expression by antisense binding. They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ompT by binding in the vicinity of the Shine-Dalgarno sequence, suggesting the control of these targets is dependent on Hfq protein and RNase E. Taken together, these data suggest that OmrA-B participates in the regulation of outer membrane composition, responding to environmental conditions.

<span class="mw-page-title-main">ArcZ RNA</span>

In molecular biology the ArcZ RNA is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.

<span class="mw-page-title-main">Guanosine pentaphosphate</span> Chemical compound

(p)ppGpp, guanosine pentaphosphate and tetraphosphate, also known as the "magic spot" nucleotides, are alarmones involved in the stringent response in bacteria that cause the inhibition of RNA synthesis when there is a shortage of amino acids. This inhibition by (p)ppGpp decreases translation in the cell, conserving amino acids present. Furthermore, ppGpp and pppGpp cause the up-regulation of many other genes involved in stress response such as the genes for amino acid uptake and biosynthesis.

In a screen of the Bacillus subtilis genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions (IGRs) over 500 base pairs in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All the small RNAs except BsrD RNA were expressed in transformed Escherichia coli cells harboring a plasmid with PCR-amplified IGRs of B. subtilis, indicating that their own promoters independently express small RNAs. Under non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase, but undetectable during the stationary phase. Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a recognition site for RNA polymerase sigma factor σA.

Bacterial small RNAs (bsRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.

The gene rpoN encodes the sigma factor sigma-54, a protein in Escherichia coli and other species of bacteria. RpoN antagonizes RpoS sigma factors.

<span class="mw-page-title-main">Paul Babitzke</span>

Paul Babitzke is a professor of biochemistry and molecular biology and director of the Center for RNA Molecular Biology at Pennsylvania State University.

Transcription-translation coupling is a mechanism of gene expression regulation in which synthesis of an mRNA (transcription) is affected by its concurrent decoding (translation). In prokaryotes, mRNAs are translated while they are transcribed. This allows communication between RNA polymerase, the multisubunit enzyme that catalyzes transcription, and the ribosome, which catalyzes translation. Coupling involves both direct physical interactions between RNA polymerase and the ribosome, as well as ribosome-induced changes to the structure and accessibility of the intervening mRNA that affect transcription.

References

  1. ↑ Brownlee GG (February 1971). "Sequence of 6S RNA of E. coli". Nature. 229 (5): 147–149. doi:10.1038/229147a0. PMID   4929322. S2CID   27493698.
  2. 1 2 Lee JY, Park H, Bak G, Kim KS, Lee Y (September 2013). "Regulation of transcription from two ssrS promoters in 6S RNA biogenesis". Molecules and Cells. 36 (3): 227–234. doi:10.1007/s10059-013-0082-1. PMC   3887979 . PMID   23864284.
  3. 1 2 Trotochaud AE, Wassarman KM (April 2005). "A highly conserved 6S RNA structure is required for regulation of transcription". Nature Structural & Molecular Biology. 12 (4): 313–319. doi:10.1038/nsmb917. PMID   15793584. S2CID   20895035.
  4. ↑ Sun, Peter D.; Foster, Christine E.; Boyington, Jeffrey C. (February 2004). "Overview of Protein Structural and Functional Folds". Current Protocols in Protein Science. 35 (1): 1711–171189. doi:10.1002/0471140864.ps1701s35. ISSN   1934-3655. PMC   7162418 . PMID   18429251.
  5. ↑ Steuten B, Hoch PG, Damm K, Schneider S, Köhler K, Wagner R, Hartmann RK (2014-05-01). "Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems". RNA Biology. 11 (5): 508–521. doi:10.4161/rna.28827. PMC   4152359 . PMID   24786589.[ verification needed ]
  6. ↑ Wassarman KM, Storz G (June 2000). "6S RNA regulates E. coli RNA polymerase activity". Cell. 101 (6): 613–623. doi: 10.1016/S0092-8674(00)80873-9 . PMID   10892648. S2CID   493590.
  7. ↑ Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR (May 2005). "6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter". RNA. 11 (5): 774–784. doi:10.1261/rna.7286705. PMC   1370762 . PMID   15811922.
  8. 1 2 Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, et al. (March 2010). "The primary transcriptome of the major human pathogen Helicobacter pylori". Nature. 464 (7286): 250–255. Bibcode:2010Natur.464..250S. doi:10.1038/nature08756. PMID   20164839. S2CID   205219639.
  9. ↑ Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes". Genome Biology. 11 (3): R31. doi: 10.1186/gb-2010-11-3-r31 . PMC   2864571 . PMID   20230605.
  10. ↑ Steuten B, Hoch PG, Damm K, Schneider S, Köhler K, Wagner R, Hartmann RK (2014-05-01). "Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems". RNA Biology. 11 (5): 508–521. doi:10.4161/rna.28827. PMC   4152359 . PMID   24786589.
  11. 1 2 Li, Zhou; Zhu, Li; Yu, Zhaoqing; Liu, Lu; Chou, Shan-Ho; Wang, Jieping; He, Jin (2020). "6S-1 RNA Contributes to Sporulation and Parasporal Crystal Formation in Bacillus thuringiensis". Frontiers in Microbiology. 11: 2997. doi: 10.3389/fmicb.2020.604458 . ISSN   1664-302X. PMC   7726162 . PMID   33324388.
  12. ↑ Barrick, Jeffrey E.; Sudarsan, Narasimhan; Weinberg, Zasha; Ruzzo, Walter L.; Breaker, Ronald R. (May 2005). "6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter". RNA. 11 (5): 774–784. doi:10.1261/rna.7286705. PMC   1370762 . PMID   15811922.
  13. 1 2 3 Wassarman, Karen M. (May 2018). "6S RNA, a Global Regulator of Transcription". Microbiology Spectrum. 6 (3). doi:10.1128/microbiolspec.RWR-0019-2018. ISSN   2165-0497. PMC   6013841 . PMID   29916345.
  14. ↑ Gildehaus, Nina; Neusser, Thomas; Wurm, Reinhild; Wagner, Rolf (2007). "Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts". Nucleic Acids Research. 35 (6): 1885–1896. doi:10.1093/nar/gkm085. ISSN   1362-4962. PMC   1874619 . PMID   17332013.
  15. ↑ Kim, Kwang-sun; Lee, Younghoon (2004). "Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases". Nucleic Acids Research. 32 (20): 6057–6068. doi:10.1093/nar/gkh939. ISSN   0305-1048. PMC   534622 . PMID   15550566.
  16. ↑ Burenina, O. Y.; Elkina, D. A.; Hartmann, R. K.; Oretskaya, T. S.; Kubareva, E. A. (2015-11-01). "Small noncoding 6S RNAs of bacteria". Biochemistry (Moscow). 80 (11): 1429–1446. doi:10.1134/S0006297915110048. ISSN   1608-3040. PMID   26615434. S2CID   15550447.
  17. ↑ Steuten, Benedikt; Schneider, Sabine; Wagner, Rolf (2014). "6S RNA: recent answers – future questions". Molecular Microbiology. 91 (4): 641–648. doi: 10.1111/mmi.12484 . ISSN   1365-2958. PMID   24308327. S2CID   24702667.
  18. ↑ Drecktrah, Dan; Hall, Laura S.; Brinkworth, Amanda J.; Comstock, Jeanette R.; Wassarman, Karen M.; Samuels, D. Scott (2020). "Characterization of 6S RNA in the Lyme disease spirochete". Molecular Microbiology. 113 (2): 399–417. doi:10.1111/mmi.14427. ISSN   1365-2958. PMC   7047579 . PMID   31742773.
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