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Unique glycine‐activated riboswitch linked to glycine–serine auxotrophy in SAR11
Author(s) -
Tripp H. James,
Schwalbach Michael S.,
Meyer Michelle M.,
Kitner Joshua B.,
Breaker Ronald R.,
Giovani Stephen J.
Publication year - 2009
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2008.01758.x
Subject(s) - glycine cleavage system , glycine , serine , glyoxylate cycle , biology , malate synthase , auxotrophy , biochemistry , alanine , betaine , amino acid , purine metabolism , serine hydroxymethyltransferase , metabolism , escherichia coli , isocitrate lyase , gene , enzyme
Summary The genome sequence of the marine bacterium ‘ Candidatus Pelagibacter ubique’ and subsequent analyses have shown that while it has a genome as small as many obligate parasites, it nonetheless possesses a metabolic repertoire that allows it to grow as one of the most successful free‐living cells in the ocean. An early report based on metabolic reconstruction indicated that SAR11 cells are prototrophs for all amino acids. However, here we report experimental evidence that ‘ Cand. P. ubique’ is effectively auxotrophic for glycine and serine. With glucose and acetate added to seawater to supply organic carbon, the addition of 125 nM to 1.5 μM glycine to growth medium containing all other nutrients in excess resulted in a linear increase in maximum cell density from 1.14 × 10 6 cells ml −1 to 8.16 × 10 6 cells ml −1 ( R 2 = 0.992). Serine was capable of substituting for glycine at 1.5 μM. ‘ Cand. P. ubique’ contains a glycine‐activated riboswitch preceding malate synthase, an unusual genomic context that is conserved in the SAR11 group. Malate synthase plays a critical role in central metabolism by enabling TCA intermediates to be regenerated through the glyoxylate cycle. In vitro analysis of this riboswitch indicated that it responds solely to glycine but not close structural analogues, such as glycine betaine, malate, glyoxylate, glycolate, alanine, serine or threonine. We conclude that ‘ Cand. P. ubique’ is therefore a glycine–serine auxotroph that appears to use intracellular glycine level to regulate its use of carbon for biosynthesis and energy. Comparative genomics and metagenomics indicate that these conclusions may hold throughout much of the SAR11 clade.