| MicX Vibrio cholerae sRNA | |
|---|---|
Secondary structure of MicX sRNA. | |
| Identifiers | |
| Symbol | MicX |
| Rfam | RF01808 |
| Other data | |
| RNA type | sRNA |
| Domain(s) | Vibrio cholerae |
| PDB structures | PDBe |
MicX sRNA (formerly known as A10) [1] is a small non-coding RNA found in Vibrio cholerae. [2] It was given the name MicX as it has a similar function to MicA, MicC and MicF in E. coli. [3] MicX sRNA negatively regulates an outer membrane protein (coded for by VC0972) and also a component of an ABC transporter (gene VC0620). [4] These interactions were predicted and then confirmed using a DNA microarray. [2]
MicX was identified through a bioinformatics screen of V. cholerae having been previously predicted. [1] Levels of transcription of this sRNA were compared under several conditions: it was found to be expressed on all tested mediums; richer mediums slightly reduced transcription; repression of certain sigma factors (δS and δE) did not change transcription but it was dramatically reduced in the absence of Hfq protein. [2] This observation is in accordance with other sRNA expression patterns. [5] [6]
The MicX RNA gene overlaps with VCA0943 - a gene coding for a maltose transporter permease - but the ribonuclease RNAase E processes the MicX transcript to create an active and stable form containing only the VCA0943 3′ UTR. [2]
See also
References
- ^ a b Livny J, Fogel MA, Davis BM, Waldor MK (2005). "sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes". Nucleic Acids Research. 33 (13): 4096–4105. doi: 10.1093/nar/gki715. PMC 1180744. PMID 16049021.
- ^ a b c d Davis BM, Waldor MK (July 2007). "RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA". Molecular Microbiology. 65 (2): 373–385. doi: 10.1111/j.1365-2958.2007.05796.x. PMC 1976385. PMID 17590231.
- ^ Mizuno T, Chou MY, Inouye M (April 1984). "A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA)". Proceedings of the National Academy of Sciences of the United States of America. 81 (7): 1966–1970. Bibcode: 1984PNAS...81.1966M. doi: 10.1073/pnas.81.7.1966. PMC 345417. PMID 6201848.
- ^ Song T, Mika F, Lindmark B, Liu Z, Schild S, Bishop A, Zhu J, Camilli A, Johansson J, Vogel J, Wai SN (October 2008). "A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles". Molecular Microbiology. 70 (1): 100–111. doi: 10.1111/j.1365-2958.2008.06392.x. PMC 2628432. PMID 18681937.
- ^ Sledjeski DD, Whitman C, Zhang A (March 2001). "Hfq is necessary for regulation by the untranslated RNA DsrA". Journal of Bacteriology. 183 (6): 1997–2005. doi: 10.1128/JB.183.6.1997-2005.2001. PMC 95095. PMID 11222598.
- ^ Massé E, Escorcia FE, Gottesman S (October 2003). "Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli". Genes & Development. 17 (19): 2374–2383. doi: 10.1101/gad.1127103. PMC 218075. PMID 12975324.
Further reading
- Gottesman S (2004). "The small RNA regulators of Escherichia coli: roles and mechanisms*". Annual Review of Microbiology. 58: 303–328. doi: 10.1146/annurev.micro.58.030603.123841. PMID 15487940.
- Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A (April 2010). "A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti". BMC Genomics. 11: 245. doi: 10.1186/1471-2164-11-245. PMC 2873474. PMID 20398411.
- Sittka A, Sharma CM, Rolle K, Vogel J (July 2009). "Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes". RNA Biology. 6 (3): 266–275. doi: 10.4161/rna.6.3.8332. PMID 19333007.
External links
| MicX Vibrio cholerae sRNA | |
|---|---|
|
Secondary structure of MicX sRNA. | |
| Identifiers | |
| Symbol | MicX |
| Rfam | RF01808 |
| Other data | |
| RNA type | sRNA |
| Domain(s) | Vibrio cholerae |
| PDB structures | PDBe |
MicX sRNA (formerly known as A10) [1] is a small non-coding RNA found in Vibrio cholerae. [2] It was given the name MicX as it has a similar function to MicA, MicC and MicF in E. coli. [3] MicX sRNA negatively regulates an outer membrane protein (coded for by VC0972) and also a component of an ABC transporter (gene VC0620). [4] These interactions were predicted and then confirmed using a DNA microarray. [2]
MicX was identified through a bioinformatics screen of V. cholerae having been previously predicted. [1] Levels of transcription of this sRNA were compared under several conditions: it was found to be expressed on all tested mediums; richer mediums slightly reduced transcription; repression of certain sigma factors (δS and δE) did not change transcription but it was dramatically reduced in the absence of Hfq protein. [2] This observation is in accordance with other sRNA expression patterns. [5] [6]
The MicX RNA gene overlaps with VCA0943 - a gene coding for a maltose transporter permease - but the ribonuclease RNAase E processes the MicX transcript to create an active and stable form containing only the VCA0943 3′ UTR. [2]
See also
References
- ^ a b Livny J, Fogel MA, Davis BM, Waldor MK (2005). "sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes". Nucleic Acids Research. 33 (13): 4096–4105. doi: 10.1093/nar/gki715. PMC 1180744. PMID 16049021.
- ^ a b c d Davis BM, Waldor MK (July 2007). "RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA". Molecular Microbiology. 65 (2): 373–385. doi: 10.1111/j.1365-2958.2007.05796.x. PMC 1976385. PMID 17590231.
- ^ Mizuno T, Chou MY, Inouye M (April 1984). "A unique mechanism regulating gene expression: translational inhibition by a complementary RNA transcript (micRNA)". Proceedings of the National Academy of Sciences of the United States of America. 81 (7): 1966–1970. Bibcode: 1984PNAS...81.1966M. doi: 10.1073/pnas.81.7.1966. PMC 345417. PMID 6201848.
- ^ Song T, Mika F, Lindmark B, Liu Z, Schild S, Bishop A, Zhu J, Camilli A, Johansson J, Vogel J, Wai SN (October 2008). "A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles". Molecular Microbiology. 70 (1): 100–111. doi: 10.1111/j.1365-2958.2008.06392.x. PMC 2628432. PMID 18681937.
- ^ Sledjeski DD, Whitman C, Zhang A (March 2001). "Hfq is necessary for regulation by the untranslated RNA DsrA". Journal of Bacteriology. 183 (6): 1997–2005. doi: 10.1128/JB.183.6.1997-2005.2001. PMC 95095. PMID 11222598.
- ^ Massé E, Escorcia FE, Gottesman S (October 2003). "Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli". Genes & Development. 17 (19): 2374–2383. doi: 10.1101/gad.1127103. PMC 218075. PMID 12975324.
Further reading
- Gottesman S (2004). "The small RNA regulators of Escherichia coli: roles and mechanisms*". Annual Review of Microbiology. 58: 303–328. doi: 10.1146/annurev.micro.58.030603.123841. PMID 15487940.
- Schlüter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen S, Jänicke S, Becker JD, Giegerich R, Becker A (April 2010). "A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti". BMC Genomics. 11: 245. doi: 10.1186/1471-2164-11-245. PMC 2873474. PMID 20398411.
- Sittka A, Sharma CM, Rolle K, Vogel J (July 2009). "Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes". RNA Biology. 6 (3): 266–275. doi: 10.4161/rna.6.3.8332. PMID 19333007.