SAM-II riboswitch explained

The SAM-II riboswitch is an RNA element found predominantly in Alphaproteobacteria that binds S-adenosyl methionine (SAM).^[1] Its structure and sequence appear to be unrelated to the SAM riboswitch found in Gram-positive bacteria. This SAM riboswitch is located upstream of the metA and metC genes in Agrobacterium tumefaciens, and other methionine and SAM biosynthesis genes in other alpha-proteobacteria. Like the other SAM riboswitch, it probably functions to turn off expression of these genes in response to elevated SAM levels. A significant variant of SAM-II riboswitches was found in Pelagibacter ubique and related marine bacteria and called SAM-V.^[2] Also, like many structured RNAs, SAM-II riboswitches can tolerate long loops between their stems.^[3]

Structure

The SAM-II riboswitch is short with less than 70 nucleotides and is structurally relatively simple being composed of a single hairpin and a pseudoknot.

See also

• SAM-I riboswitch
• SAM-III riboswitch
• SAM-IV riboswitch
• SAM-V riboswitch
• SAM-VI riboswitch

Notes and References

1. Corbino KA, Barrick JE, Lim J, etal . Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria . Genome Biol. . 6 . 8 . R70 . 2005 . 16086852 . 10.1186/gb-2005-6-8-r70 . 1273637 . free .
2. Poiata E, Meyer MM, Ames TD, Breaker RR . A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria . RNA . 15 . 11 . 2046–2056 . November 2009 . 19776155 . 2764483 . 10.1261/rna.1824209 .
3. Weinberg Z, Wang JX, Bogue J, etal . Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes . Genome Biol . 11 . 3 . R31 . March 2010 . 20230605 . 10.1186/gb-2010-11-3-r31 . 2864571 . free .