Biology:RyhB

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Short description: 90 nucleotide RNA
Secondary structure for the RyhB RNA. The Sm-like protein Hfq binds to the AU-rich unstructured region of RyhB as indicated. Below the secondary structure, the primary sequence of RyhB is shown along with its putative binding interaction to the target mRNA sodB. The start codon for sodB is underlined. RyhB nucleotides that participate in the interaction are in bold.[1]

RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur (Ferric uptake regulator).

Discovery

The gene was independently identified in two screens, named RyhB by Wassarman et al. and called SrI by Argaman et al. and was found to be expressed only in stationary phase.[2][3]

Function and regulation

RyhB RNA levels are inversely correlated with mRNA levels for the sdhCDAB operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle, acnA and fumA, two ferritin genes, ftnA and bfr, and a gene for superoxide dismutase, sodB.[4] A number of other genes have been predicted computationally and verified as targets by microarray analysis: napF, sodA, cysE, yciS, acpS, nagZ and dadA.[1] RyhB is bound by the Hfq protein, that increases its interaction with its target messages.

A comparative genomics target prediction approach suggests that the mRNAs of eleven additional iron containing proteins are controlled by RyhB in Escherichia coli. Two of those (erpA, nirB) and two additional targets that are not directly related to iron (nagZ, marA) were verified with a GFP reporter system.[5][6]

It has been shown that RyhB has a role in targeting the polycistronic transcript iscRSUA for differential degradation. RyhB binds to the second cistron of iscRSUA, which encodes machinery for biosynthesis of Fe-S clusters. This binding promotes cleavage of the downstream iscSUA transcript. This cleavage leaves the 5′ IscR transcript which is a transcriptional regulator responsible regulating several genes that depend on cellular Fe-S level.[7]

More recent data indicate a potential dual function role for RyhB. In this capacity it may act both as an RNA-RNA interaction based regulator and as a transcript encoding for a small protein.[8]

RyhB is analogous to PrrF RNA found in Pseudomonas aeruginosa,[9] to HrrF RNA in Haemophilus species [10] and to IsaR1 in cyanobacteria.[11][12]

First sRNA shown to mediate persistence to antibiotics in E.coli. The finding may lead to discovery of novel treatments for persistent infections.[13]

Naming

The RyhB gene name is an acronym composed of R for RNA, y for unknown function (after the protein naming convention), with the h representing the ten-minute-interval section of the E. coli map the gene is found in. The B comes from the fact that this was one of two RNA genes identified in this interval.[3] Other RNAs using this nomenclature include RydB RNA, RyeB RNA, RyeE RNA and RyfA RNA.

References

  1. ↑ 1.0 1.1 "Target prediction for small, noncoding RNAs in bacteria". Nucleic Acids Research 34 (9): 2791–2802. 2006. doi:10.1093/nar/gkl356. PMID 16717284. 
  2. ↑ "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli". Current Biology 11 (12): 941–950. June 2001. doi:10.1016/S0960-9822(01)00270-6. PMID 11448770. 
  3. ↑ 3.0 3.1 "Identification of novel small RNAs using comparative genomics and microarrays". Genes & Development 15 (13): 1637–1651. July 2001. doi:10.1101/gad.901001. PMID 11445539. 
  4. ↑ "A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli". Proceedings of the National Academy of Sciences of the United States of America 99 (7): 4620–4625. April 2002. doi:10.1073/pnas.032066599. PMID 11917098. Bibcode: 2002PNAS...99.4620M. 
  5. ↑ "Comparative genomics boosts target prediction for bacterial small RNAs". Proceedings of the National Academy of Sciences of the United States of America 110 (37): E3487–3496. September 2013. doi:10.1073/pnas.1303248110. PMID 23980183. Bibcode: 2013PNAS..110E3487W. 
  6. ↑ "Translational control and target recognition by Escherichia coli small RNAs in vivo". Nucleic Acids Research 35 (3): 1018–1037. 2007. doi:10.1093/nar/gkl1040. PMID 17264113. 
  7. ↑ "Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA". The EMBO Journal 28 (11): 1551–1561. June 2009. doi:10.1038/emboj.2009.116. PMID 19407815. 
  8. ↑ "Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP". BMC Genomics 18 (1): 216. February 2017. doi:10.1186/s12864-017-3586-9. PMID 28245801. 
  9. ↑ "Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis". Proceedings of the National Academy of Sciences of the United States of America 101 (26): 9792–9797. June 2004. doi:10.1073/pnas.0403423101. PMID 15210934. Bibcode: 2004PNAS..101.9792W. 
  10. ↑ "HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae". PLOS ONE 9 (8): e105644. 2014-01-01. doi:10.1371/journal.pone.0105644. PMID 25157846. Bibcode: 2014PLoSO...9j5644S. 
  11. ↑ "Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1". Current Biology 27 (10): 1425–1436.e7. May 2017. doi:10.1016/j.cub.2017.04.010. PMID 28479323. https://pearl.plymouth.ac.uk/bitstream/handle/10026.1/9292/UoP_Deposit_Agreement%20v1.1%2020160217.pdf?sequence=2&isAllowed=y. 
  12. ↑ "The iron-stress activated RNA 1 (IsaR1) coordinates osmotic acclimation and iron starvation responses in the cyanobacterium Synechocystis sp. PCC 6803". Environmental Microbiology 20 (8): 2757–2768. February 2018. doi:10.1111/1462-2920.14079. PMID 29468839. 
  13. ↑ "Escherichia coli by Reducing Cellular Metabolism". Frontiers in Microbiology 9: 136. 2018. doi:10.3389/fmicb.2018.00136. PMID 29467745. 

Further reading

External links



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