title: Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11.
abstract: 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 microM glycine to growth medium containing all other nutrients in excess resulted in a linear increase in maximum cell density from 1.14 x 10(6) cells ml(-1) to 8.16 x 10(6) cells ml(-1) (R(2) = 0.992). Serine was capable of substituting for glycine at 1.5 microM. '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.
authors.affiliation: Department of Microbiology, Oregon State University, Corvallis, OR 97333, USA.
authors.forename: H James
authors.initials: HJ
authors.lastname: Tripp
authors.forename: Michael S
authors.initials: MS
authors.lastname: Schwalbach
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Meyer
authors.forename: Joshua B
authors.initials: JB
authors.lastname: Kitner
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Giovannoni
mesh_terms: D019342:Acetic Acid / Q000378:metabolism; D020561:Alphaproteobacteria / Q000254:growth & development / Q000378:metabolism*; D001483:Base Sequence; D005947:Glucose / Q000378:metabolism; D005998:Glycine / Q000378:metabolism*; D008292:Malate Synthase / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000235:genetics; D012623:Seawater / Q000382:microbiology; D012694:Serine / Q000378:metabolism*
chemical_list: D012329:RNA, Bacterial; D012694:Serine; D008292:Malate Synthase; D005947:Glucose; D019342:Acetic Acid; D005998:Glycine