Predicted protein subcellular localization in dominant surface ocean bacterioplankton - PubMed (original) (raw)

Predicted protein subcellular localization in dominant surface ocean bacterioplankton

Haiwei Luo. Appl Environ Microbiol. 2012 Sep.

Abstract

Bacteria consume dissolved organic matter (DOM) through hydrolysis, transport and intracellular metabolism, and these activities occur in distinct subcellular localizations. Bacterial protein subcellular localizations for several major marine bacterial groups were predicted using genomic, metagenomic and metatranscriptomic data sets following modification of MetaP software for use with partial gene sequences. The most distinct pattern of subcellular localization was found for Bacteroidetes, whose genomes were substantially enriched with outer membrane and extracellular proteins but depleted of inner membrane proteins compared with five other taxa (SAR11, Roseobacter, Synechococcus, Prochlorococcus, oligotrophic marine Gammaproteobacteria). When subcellular localization patterns were compared between genes and transcripts, three taxa had expression biased toward proteins localized to cell locations outside of the cytosol (SAR11, Roseobacter, and Synechococcus), as expected based on the importance of carbon and nutrient acquisition in an oligotrophic ocean, but two taxa did not (oligotrophic marine Gammaproteobacteria and Bacteroidetes). Diel variations in the fraction and putative gene functions of transcripts encoding inner membrane and periplasmic proteins compared to cytoplasmic proteins suggest a close coupling of photosynthetic extracellular release and bacterial consumption, providing insights into interactions between phytoplankton, bacteria, and DOM.

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Figures

Fig 1

High-throughput multidimensional scaling (HiT-MDS) plot of MetaP using whole-genome-sequence-predicted protein subcellular localization among major marine bacterial lineages.

Fig 2

High-throughput multidimensional scaling (HiT-MDS) plot of MetaP using genome, metagenome, and metatranscriptome sequence-predicted protein subcellular localization of marine bacteria. (A) Roseobacter, (B) Bacteroidetes, (C) oligotrophic marine Gammaproteobacteria (OMG), (D) Synechococcus, and (E) SAR11.

Fig 3

Differential gene expression in protein subcellular localizations between day and night in surface waters of the North Pacific Subtropical Gyre. The letter above the bars indicates the significance level: a, P < 0.001; b, P < 0.05.

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Predicted protein subcellular localization in dominant surface ocean bacterioplankton - PubMed (original) (raw)