Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11 - PubMed (original) (raw)
Unique glycine-activated riboswitch linked to glycine-serine auxotrophy in SAR11
H James Tripp et al. Environ Microbiol. 2009 Jan.
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.
Figures
Figure 1
Molar growth yield curve for glycine. The maximum cell density achieved for batch cultures grown in the dark at 16° C is plotted against addition of glycine in the presence of excess nutrients (avg., N=2 for each data point, R2=0.992, error bars show complete range). Carbon was supplied as 10 μM glucose and 50 μM acetate. Other nutrients were 10 μM NH4Cl, 1 μM KH2PO4, 53.6 μM FeCl3 and a mix of vitamins (Davis and Guillard, 1958).
Figure 2
Secondary structure of SAR11 riboswitches and alignment to environmental data. Aptamers are labeled with Roman Numerals I and II, and base pairing stems are labeled P1, P2, and P3 with subsections labeled “a” and “b.” Base pairs with an asterisk were shown to be accessible to spontaneous cleavage, as would be expected if they are not part of a base pair. Base pairs shaded in grey show 100% conservation in upstream regions of metagenomic data. gcvT, glycine cleavage protein T; glcB, malate synthase.
Figure 3
Structural probing and KD measurements for gcvT and glcB riboswitches. A. Spontaneous cleavage products of the glcB associated riboswitch in the presence of 1 mM of ligand candidates and the absence of ligand. Selected RNase T1 cleavage products (cleaves 3′ of G residues) are identified on the left. Arrows on the right indicate bands used to quantify extent of RNA cleavage. B. Plot of percentage RNA cleaved (normalized between no ligand and saturating ligand conditions) versus the logarithm of the molar concentration of glycine used to determine KD and h constants for the glcB associated riboswitch. C. Identical to B for the gcvT associated riboswitch.
Fig 4
Maximum cell yields for glycine substitutes (avg., N=2 for each data point, error bars show complete range). Response to 1.5 μM additions of compounds. Gly, glycine; Bet, betaine; Ser, serine; Glc, glycolate; Glx, glyoxylate; Thr, threonine; No Gly, no glycine; No Glu, no glucose; No ace, no acetate. Excess nutrients were supplied as in Fig. 1.
Similar articles
- Nutrient requirements for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium.
Carini P, Steindler L, Beszteri S, Giovannoni SJ. Carini P, et al. ISME J. 2013 Mar;7(3):592-602. doi: 10.1038/ismej.2012.122. Epub 2012 Oct 25. ISME J. 2013. PMID: 23096402 Free PMC article. - A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome.
Gilbert JA, Mühling M, Joint I. Gilbert JA, et al. ISME J. 2008 Jul;2(7):790-3. doi: 10.1038/ismej.2008.49. Epub 2008 May 22. ISME J. 2008. PMID: 18496576 - SAR11 marine bacteria require exogenous reduced sulphur for growth.
Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ. Tripp HJ, et al. Nature. 2008 Apr 10;452(7188):741-4. doi: 10.1038/nature06776. Epub 2008 Mar 12. Nature. 2008. PMID: 18337719 - The unique metabolism of SAR11 aquatic bacteria.
Tripp HJ. Tripp HJ. J Microbiol. 2013 Apr;51(2):147-53. doi: 10.1007/s12275-013-2671-2. Epub 2013 Apr 27. J Microbiol. 2013. PMID: 23625213 Review. - Serine and glycine metabolism in cancer.
Amelio I, Cutruzzolá F, Antonov A, Agostini M, Melino G. Amelio I, et al. Trends Biochem Sci. 2014 Apr;39(4):191-8. doi: 10.1016/j.tibs.2014.02.004. Epub 2014 Mar 20. Trends Biochem Sci. 2014. PMID: 24657017 Free PMC article. Review.
Cited by
- The ultra-high affinity transport proteins of ubiquitous marine bacteria.
Clifton BE, Alcolombri U, Uechi GI, Jackson CJ, Laurino P. Clifton BE, et al. Nature. 2024 Oct;634(8034):721-728. doi: 10.1038/s41586-024-07924-w. Epub 2024 Sep 11. Nature. 2024. PMID: 39261732 Free PMC article. - Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum.
Aldeguer-Riquelme B, Antón J, Santos F. Aldeguer-Riquelme B, et al. mSystems. 2023 Aug 31;8(4):e0021523. doi: 10.1128/msystems.00215-23. Epub 2023 Jun 22. mSystems. 2023. PMID: 37345931 Free PMC article. - A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments.
Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. Noell SE, et al. Microbiol Mol Biol Rev. 2023 Jun 28;87(2):e0012422. doi: 10.1128/mmbr.00124-22. Epub 2023 Mar 30. Microbiol Mol Biol Rev. 2023. PMID: 36995249 Free PMC article. Review. - Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa.
Lanclos VC, Rasmussen AN, Kojima CY, Cheng C, Henson MW, Faircloth BC, Francis CA, Thrash JC. Lanclos VC, et al. ISME J. 2023 Apr;17(4):620-629. doi: 10.1038/s41396-023-01376-2. Epub 2023 Feb 4. ISME J. 2023. PMID: 36739346 Free PMC article. - Role of Bacterial Community Composition as a Driver of the Small-Sized Phytoplankton Community Structure in a Productive Coastal System.
Costas-Selas C, Martínez-García S, Logares R, Hernández-Ruiz M, Teira E. Costas-Selas C, et al. Microb Ecol. 2023 Aug;86(2):777-794. doi: 10.1007/s00248-022-02125-2. Epub 2022 Oct 28. Microb Ecol. 2023. PMID: 36305941 Free PMC article.
References
- Benner R. Chemical composition and reactivity. In: Hansell D, Carlson C, editors. Biogeochemistry of marine dissolved organic matter. New York: Academic Press; 2002. pp. 59–90.
Publication types
MeSH terms
Substances
Grants and funding
- F32 GM079974/GM/NIGMS NIH HHS/United States
- F32 GM079974-02/GM/NIGMS NIH HHS/United States
- F32GM079974/GM/NIGMS NIH HHS/United States
- HHMI/Howard Hughes Medical Institute/United States
LinkOut - more resources
Full Text Sources