suhB

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]

suhB
Predicted secondary structure and sequence conservation of suhB
Identifiers
Symbol	suhB
Rfam	RF00519
Other data
RNA type	Gene; sRNA
Domain(s)	Bacteria
GO	0006353 0003715
SO	0000655
PDB structures	PDBe

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]

suhB is also present in Sphingopyxis granuli strain TFA [11], an alpha-proteobacterium that uses the solven tetralin as carbon and energy source ([12] and references therein). SuhB has been detected as a 61 nt long sRNA by Northern blot in TFA cells growing at high rates. β-galactosidase activity of a PsuhB::lacZ fusion confirmed the lower expression of suhB in TFA cells growing at low rates. A mutant lacking suhB express the thn genes (tetralin degradation) even in the presence of a preferential carbon source (catabolite repression conditions). This phenotype is due to the release of the negative effect of SuhB on ThnR translation (positive regulator of thn genes). Hfq is also involved in the interaction between SuhB and the 5′ UTR thnR mRNA, which results in thn genes repression in catabolite repression conditions.[11]