Unique glycine‐activated riboswitch linked to glycine–serine auxotrophy in SAR11
Open Access
- 2 January 2009
- journal article
- Published by Wiley in Environmental Microbiology
- Vol. 11 (1), 230-238
- https://doi.org/10.1111/j.1462-2920.2008.01758.x
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 μM glycine to growth medium containing all other nutrients in excess resulted in a linear increase in maximum cell density from 1.14 × 106 cells ml−1 to 8.16 × 106 cells ml−1 (R2 = 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.Keywords
This publication has 39 references indexed in Scilit:
- SAR11 marine bacteria require exogenous reduced sulphur for growthNature, 2008
- Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteriaRNA, 2008
- The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome DatabasesNucleic Acids Research, 2007
- Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic dataBiology Direct, 2007
- Abundance and functional diversity of riboswitches in microbial communitiesBMC Genomics, 2007
- The Speed of RNA Transcription and Metabolite Binding Kinetics Operate an FMN RiboswitchMolecular Cell, 2005
- Responses of coastal phytoplankton populations to nitrogen additions: dynamics of cell-associated dimethylsulfoniopropionate (DMSP), glycine betaine (GBT), and homarineCanadian Journal of Fisheries and Aquatic Sciences, 2004
- Glycine betaine uptake, retention, and degradation by microorganisms in seawaterLimnology and Oceanography, 1998
- PHOTORESPIRATION IN CONTINUOUS CULTURE OF DUNALIELLA TERTIOLECTA (CHLOROPHYTA): RELATIONSHIPS BETWEEN SERINE, GLYCINE, AND EXTRACELLULAR GLYCOLATEJournal of Phycology, 1998
- HPLC determination of glycolic acid in seawater. An estimation of phytoplankton photorespiration in the Gulf of Lions, western Mediterranean SeaJournal of Plankton Research, 1994