Giovannoni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242-1245

Department of Microbiology, Oregon State University, Corvallis, OR 97331, USA.
Science (Impact Factor: 33.61). 09/2005; 309(5738):1242-5. DOI: 10.1126/science.1114057
Source: PubMed


The SAR11 clade consists of very small, heterotrophic marine alpha-proteobacteria that are found throughout the oceans, where they account for about 25% of all microbial cells. Pelagibacter ubique, the first cultured member of this clade, has the smallest genome and encodes the smallest number of predicted open reading frames known for a free-living microorganism. In contrast to parasitic bacteria and archaea with small genomes, P. ubique has complete biosynthetic pathways for all 20 amino acids and all but a few cofactors. P. ubique has no pseudogenes, introns, transposons, extrachromosomal elements, or inteins; few paralogs; and the shortest intergenic spacers yet observed for any cell.

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    • "As the N content of a proteome is strongly and positively correlated with that of the genome in various bacterial lineages (Bragg and Hyder 2004), depletion in genomic G/C may reduce the N requirement of both genome and proteome of a cell and thus can be an important way that bacteria adapt to surface oceans. Freeliving marine bacterioplankton with G+C-poor genomes are found in multiple lineages (Swan et al. 2013), including the alphaproteobacterial SAR11 clade (Giovannoni et al. 2005) and the uncultivated marine Roseobacter lineages (Luo et al. 2014a, 2014b), the gammaproteobacterial SAR86 clade (Dupont et al. 2012), and the cyanobacterial Prochlorococcus (Dufresne et al. 2003). These are among the most abundant lineages in global oceans, and thus studying the ecological and evolutionary mechanisms shaping their low genomic G+C content has important implications for oceanic N cycles. "
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    ABSTRACT: The genomic G+C content of ocean bacteria varies from below 30% to over 60%. This broad range of base composition is likely shaped by distinct mutational processes, recombination, effective population size, and selection driven by environmental factors. A number of studies have hypothesized that depletion of G/C in genomes of marine bacterioplankton cells is an adaptation to the nitrogen-poor pelagic oceans, but they failed to disentangle environmental factors from mutational biases and population history. Here, we reconstructed the evolutionary changes of bases at synonymous sites in genomes of two marine SAR11 populations and a freshwater counterpart with its evolutionary origin rooted in the marine lineage. Although they all have similar genome sizes, DNA repair gene repertoire, and base compositions, there is a stronger bias toward A/T changes, a reduced frequency of nitrogenous amino acids, and an exclusive occurrence of polyamine, opine, and taurine transport systems in the ocean populations, consistent with a greater nitrogen stress in surface oceans compared to freshwater lakes. Furthermore, the ratio of nonsynoymous to synonymous nucleotide diversity is not statistically distinguishable among these populations, suggesting that population history has a limited effect. Taken together, the ecological transition of SAR11 from ocean to freshwater habitats makes nitrogen more available to these organisms, and thus relaxation of purifying selection drove a genome-wide reduction in the frequency of G/C to A/T changes in the freshwater population. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail:
    Full-text · Article · Jun 2015 · Molecular Biology and Evolution
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    • "respectively (Fig. 4). As strains of SAR11 most likely do not produce extracellular hydrolytic enzymes (Malmstrom et al., 2005) but possess the Entner-Doudoroff pathway required for assimilation of alginate monomers (Giovannoni et al., 2005; Schwalbach et al., 2010), the stimulation of SAR11 may have been attributed to crossfeeding on alginate monomers and other metabolic products released by alginolytic Alteromonadaceae. Interestingly , only a single alginate monomer, guluronate, significantly decreased in concentration (Fig. 4). "
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    ABSTRACT: The bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm experiments at four contrasting locations in the Southern and Atlantic Oceans. At the Southern polar front, chitin-supplemented microcosms were characterized by higher fractions of actively growing cells and a community shift from Alphaproteobacteria to Gammaproteobacteria and Bacteroidetes. At the Antarctic ice shelf, chitin degradation was associated with growth of Bacteroidetes, with 24% higher cell numbers compared with the control. At the Patagonian continental shelf, alginate and agarose degradation covaried with growth of different Alteromonadaceae populations, each with specific temporal growth patterns. At the Mauritanian upwelling, only the alginate hydrolysis product guluronate was consumed, coincident with increasing abundances of Alteromonadaceae and possibly cross-feeding SAR11. 16S rRNA gene amplicon libraries indicated that growth of the Bacteroidetes-affiliated genus Reichenbachiella was stimulated by chitin at all cold and temperate water stations, suggesting comparable ecological roles over wide geographical scales. Overall, the predominance of location-specific patterns showed that bacterial communities from contrasting oceanic biomes have members with different potentials to hydrolyse polysaccharides.
    Full-text · Article · Mar 2015 · Environmental Microbiology
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    • "C. pelagibacter ubique grows in a low nutrient medium and is one of the most abundant organisms in the ocean. It is a Gram negative proteobacteria originally isolated from the Oregon coast and has an optimum growth temperature of 16 °C [13], while S. nassauensis is an aerobic, Gram positive, mesophilic actinomycete originally isolated from roadside soil sample in Nassau, Bahamas [14]. The putative EHs, cpeh and sneh were then cloned and overexpressed in the heterologous host, Escherichia coli. "
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    ABSTRACT: Epoxide hydrolases (EHs), are enantioselective enzymes as they catalyze the kinetic resolution of racemic epoxides into the corresponding enantiopure vicinal diols, which are useful precursors in the synthesis of chiral pharmaceutical compounds. Here, we have identified and cloned two putative epoxide hydrolase genes (cpeh and sneh) from marine bacteria, Candidatus pelagibacter ubique and terrestrial bacteria, Stackebrandtia nassauensis, respectively and overexpressed them in pET28a vector in Escherichia coli BL21(DE3). The CPEH protein (42 kDa) was found to be overexpressed as inactive inclusion bodies while SNEH protein (40 kDa) was found to form soluble aggregates. In this study, the recombinant CPEH protein was successfully transformed from insoluble aggregates to the soluble and functionally active form, using pCold TF vector, though with low EH activity. To prevent the soluble aggregate formation of SNEH, it was co-expressed with GroEL/ES chaperone and was also fused with trigger factor (TF) chaperone at its N-terminus. The TF chaperone-assisted correct folding of SNEH led to a purified active EH with a specific activity of 3.85 μmol/min/mg. The pure enzyme was further used to biocatalyze the hydrolysis of 10 mM benzyl glycidyl ether (BGE) and α-methyl styrene oxide (MSO) with an enantiomeric excess of the product (eep) of 86% and 73% within 30 and 15 min, respectively. In conclusion, this is the first report about the heterologous expression of epoxide hydrolases using TF as a molecular chaperone in pCold TF expression vector, resulting in remarkable increase in the solubility and activity of the otherwise improperly folded recombinant epoxide hydrolases.
    Full-text · Article · Dec 2014 · Protein Expression and Purification
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