Anti small RNA

Antisense small RNA are short RNA sequences (about 50-500 nucleotides long) that are complementary to other small RNA (sRNA) in the cell. [2]

Proposed mechanism for anti-sRNA relief of sRNA mediated translation inhibition. [1]
Anti GcvB sRNA
Predicted secondary structure and sequence conservation Anti GcvB sRNA
Identifiers
RfamRF02702
Other data
Domain(s)Bacteria
GO0045975
SO0000370
PDB structuresPDBe
Anti stx2 sRNA
Predicted secondary structure and sequence conservation Anti stx2 sRNA
Identifiers
RfamRF02703
Other data
Domain(s)Bacteria
GO0045975
SO0000370
PDB structuresPDBe

sRNAs can repress translation via complementary base-pairing with their target mRNA sequence.[3] Anti-sRNAs function by complementary pairing with sRNAs before the mRNA can be bound, thus freeing the mRNA and relieving translation inhibition.[1]

Function

Antisense small RNA are found in all of life including Eukaryotes, Bacteria and Archaea.[4][5] They are non-coding RNA sequences involved in regulatory processes, metabolism, and aiding transcription.[4]

Antisense RNA can also be engineered and utilized by scientists to perform experimental functions.[6]

Identification Methods

Numerous studies have been performed to identify potential antisense sRNA candidates. Recent experiments have used Northern blot analysis and 5'-end mapping to correctly identify potential antisense sRNA candidates.[7] In 2019, a new algorithm called APERO was established which allows the detection of small transcripts from paired-end bacterial RNA-seq data. [8]  RNA-seq is a popular method used for the identification of small RNA. [8] However, while reliable for eukaryotic sRNA, it remains inaccurate for bacterial sRNA. [8]

Examples

AsxR

AsxR, previously known as EcOnc02, is an anti-sRNA encoded within the 3' region of the stx2B gene of E.Coli bacteria.[1] It acts to increase expression of the ChuS heme oxygenase via destabilisation of FnrS sRNA[1]. This aids bacterial infection of the animal host gut. [1]

AgvB

AgvB, previously known as EcOnc01, inhibits GcvB sRNA repression.[1] Pathogenicity island associated AgvB aids enterohemorrhagic E. coli growth at the colonized site within the host animal.[1]

References
  1. Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL (July 2014). "Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli". Molecular Cell. 55 (2): 199–213. doi:10.1016/j.molcel.2014.05.006. PMC 4104026. PMID 24910100.
  2. Bhatt S, Egan M, Jenkins V, Muche S, El-Fenej J (2016). "Escherichia coli". Frontiers in Cellular and Infection Microbiology. 6: 105. doi:10.3389/fcimb.2016.00105. PMC 5030294. PMID 27709103.
  3. Grosshans H, Filipowicz W (January 2008). "Molecular biology: the expanding world of small RNAs". Nature. 451 (7177): 414–6. Bibcode:2008Natur.451..414G. doi:10.1038/451414a. PMID 18216846.
  4. Bernick DL, Dennis PP, Lui LM, Lowe TM (2012). "Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species". Frontiers in Microbiology. 3: 231. doi:10.3389/fmicb.2012.00231. PMC 3388794. PMID 22783241.
  5. Figueroa-Bossi N, Valentini M, Malleret L, Fiorini F, Bossi L (September 2009). "Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target". Genes & Development. 23 (17): 2004–15. doi:10.1101/gad.541609. PMC 2751969. PMID 19638370.
  6. Rodrigo G, Prakash S, Cordero T, Kushwaha M, Jaramillo A (February 2016). "Functionalization of an Antisense Small RNA". Journal of Molecular Biology. Engineering Tools and Prospects in Synthetic Biology. 428 (5 Pt B): 889–92. doi:10.1016/j.jmb.2015.12.022. PMC 4819895. PMID 26756967.
  7. Thomason MK, Storz G (2010). "Bacterial antisense RNAs: how many are there, and what are they doing?". Annual Review of Genetics. 44 (1): 167–88. doi:10.1146/annurev-genet-102209-163523. PMC 3030471. PMID 20707673.
  8. Leonard S, Meyer S, Lacour S, Nasser W, Hommais F, Reverchon S (September 2019). "APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data". Nucleic Acids Research. 47 (15): e88. doi:10.1093/nar/gkz485. PMC 6735904. PMID 31147705.
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