suhB

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suhB
RF00519.jpg
Identifiers
Symbol suhB
Rfam RF00519
Other data
RNA type Gene; sRNA
Domain(s) Bacteria
GO 0006353 0003715
SO 0000655

suhB later renamed mmgR (makes more granules regulator) was a putative non-coding RNA found multiple times in the Agrobacterium tumefaciens genome and related alpha-proteobacteria. [1] Other non-coding RNAs uncovered in the same analysis include: speF, ybhL, metA, and serC.[1]

Several studies in Sinorhizobium meliloti showed that suhB element is indeed a non-coding RNA: firstly it was detected on Northern blot and called Sm8RNA[2], secondly in an RNAseq study referred to as SmelC689.[3]

The mutant phenotype's (strain lacking the small RNA) cytoplasm contains higher content of polyhydroxybutyrate (PBH) storage granules than wild type strain.[4] The sRNA is required to limit the PBH intracellular accumulation when the nitrogen-fixing Sinorhizobium meliloti is under condition of surplus carbon in relation to nitrogen. It has been renamed to mmgR. Further study confirmed that mmgR fine-tunes the regulation of PBH storage.[5]

Northern blot confirmed the expression of the sRNA in other rhizobia species. MmgR homologues were found in most alpha-proteobacteria. The Rho-independent terminator and a single stranded region 10-mer (UUUCCUCCCU) are completely conserved. Hence, it was proposed to define a new family of alpha-proteobacterial sRNA: alpha-r8 of which mmgR is a member.[6]

RNA binding protein Hfq is binding and stabilising mmgR.[7][8] Expression of the mmgR gene was shown to be controlled by nitrogen (N).[9] Further study[10] has shown that the regulatory proteins NtrC may be required for expression of mmgR gene upon N limitation. Under carbon (C) limitation, mmgR transcription is repressed by AntiA. [10]

References[edit]

  1. ^ a b Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR (2005). "Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria". Genome Biology. 6 (8): R70. doi:10.1186/gb-2005-6-8-r70. PMC 1273637Freely accessible. PMID 16086852. 
  2. ^ Valverde C, Livny J, Schlüter JP, Reinkensmeier J, Becker A, Parisi G (September 2008). "Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011". BMC Genomics. 9: 416. doi:10.1186/1471-2164-9-416. PMC 2573895Freely accessible. PMID 18793445. 
  3. ^ 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 2873474Freely accessible. PMID 20398411. 
  4. ^ Lagares, A (2015). The biological role of the small regulatory RNA Sm8 in free living and symbiotic Sinorhizobium meliloti. PhD Thesis; Universidad Nacional de La Planta, Argentina. 
  5. ^ Lagares A, Linne U, Becker A, Valverde C (April 2017). "Trans-Encoded Small RNA MmgR". Journal of Bacteriology. 199 (8). doi:10.1128/JB.00776-16. PMC 5370414Freely accessible. PMID 28167519. 
  6. ^ Lagares A, Roux I, Valverde C (June 2016). "Phylogenetic distribution and evolutionary pattern of an α-proteobacterial small RNA gene that controls polyhydroxybutyrate accumulation in Sinorhizobium meliloti". Molecular Phylogenetics and Evolution. 99: 182–193. doi:10.1016/j.ympev.2016.03.026. PMID 27033949. 
  7. ^ Torres-Quesada O, Reinkensmeier J, Schlüter JP, Robledo M, Peregrina A, Giegerich R, Toro N, Becker A, Jiménez-Zurdo JI (2014). "Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti". RNA Biology. 11 (5): 563–79. doi:10.4161/rna.28239. PMC 4152363Freely accessible. PMID 24786641. 
  8. ^ Sobrero P, Valverde C (September 2011). "Evidences of autoregulation of hfq expression in Sinorhizobium meliloti strain 2011". Archives of Microbiology. 193 (9): 629–39. doi:10.1007/s00203-011-0701-1. PMID 21484295. 
  9. ^ Ceizel Borella G, Lagares A, Valverde C (May 2016). "Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled by the nitrogen source". FEMS Microbiology Letters. 363 (9). doi:10.1093/femsle/fnw069. PMID 27010014. 
  10. ^ a b Ceizel Borella G, Lagares A, Valverde C (January 2018). "Expression of the small regulatory RNA gene mmgR is regulated negatively by AniA and positively by NtrC in Sinorhizobium meliloti 2011". Microbiology. 164 (1): 88–98. doi:10.1099/mic.0.000586. PMID 29214973. 

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