Article

Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF et al.. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J (in press)

Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA.
The ISME Journal (Impact Factor: 9.3). 10/2008; 3(1):93-105. DOI: 10.1038/ismej.2008.83
Source: PubMed

ABSTRACT

The northwestern Sargasso Sea undergoes annual cycles of productivity with increased production in spring corresponding to periods of upwelling, and oligotrophy in summer and autumn, when the water column becomes highly stratified. The biological productivity of this region is reduced during stratified periods as a result of low concentrations of phosphorus and nitrogen in the euphotic zone. To better understand the mechanisms of microbial survival in this oligotrophic environment, we used capillary liquid chromatography (LC)-tandem mass spectrometry to detect microbial proteins in surface samples collected in September 2005. A total of 2215 peptides that mapped to 236 SAR11 proteins, 1911 peptides that mapped to 402 Prochlorococcus proteins and 2407 peptides that mapped to 404 Synechococcus proteins were detected. Mass spectra from SAR11 periplasmic substrate-binding proteins accounted for a disproportionately large fraction of the peptides detected, consistent with observations that these extremely small cells devote a large proportion of their volume to periplasm. Abundances were highest for periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars and spermidine. Proteins implicated in the prevention of oxidative damage and protein refolding were also abundant. Our findings support the view that competition for multiple nutrients in oligotrophic systems is extreme, but nutrient flux is sufficient to sustain microbial community activity.

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    • "Only a ß10% divergence in the amino acid sequence (90% identity) of a protein can be tolerated before insufficient tryptic peptides remain for identification [7]. Metaproteomics, often defined as the analysis of a complex community of organisms [8], has unique challenges relative to " standard " proteomics of a single organism. By considering these challenges we can evaluate the limitations of existing algorithms and pipelines, as well as provide motivation for future software development. "

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    • "Only a ß10% divergence in the amino acid sequence (90% identity) of a protein can be tolerated before insufficient tryptic peptides remain for identification [7]. Metaproteomics, often defined as the analysis of a complex community of organisms [8], has unique challenges relative to " standard " proteomics of a single organism. By considering these challenges we can evaluate the limitations of existing algorithms and pipelines, as well as provide motivation for future software development. "
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    ABSTRACT: Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P-II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open-source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8±1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13±15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P-II peptide showed specificity to the high-light Prochlorococcus ecotype. Distributions of NtcA and P-II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ∼4×10(7) , 1000-fold larger than an individual microbial proteome and 27-fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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    • "There may be a difference between oligotrophic and coastal sites with regard to bacterial proteins, as our Washington margin samples contain proportionally more α-proteobacterial proteins than the oligotrophic sites, which are dominated by γ-proteobacterial proteins at depth (Fig. 4). Yin et al. (2013) and Van Mooy et al. (2004) showed that α-proteobacteria can be dominant in the oligotrophic Pacific, while γ-proteobacteria such as SAR11 and SAR83 are dominant in the oligotrophic Atlantic (Morris et al., 2002; Sowell et al., 2009). Previously, Moore et al. (2012a) stated that while functional information on proteins can be attained with confidence, taxonomic information cannot yet be gained when performing metaproteomics on ocean samples with no corresponding metagenome. "
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    ABSTRACT: Metaproteomic analyses were performed on suspended sediments collected in one coastal environment (Washington margin, Pacific Ocean, n = 5) and two oligotrophic environments (Atlantic Ocean near BATS, n = 5, and Pacific Ocean near HOTS, n = 5). Using a database of 2.3 million marine proteins developed using the NCBI database, 443 unique peptides were detected from which 363 unique proteins were identified. Samples from the euphotic zone contained on average 2-3x more identifiable proteins than deeper waters (150-1500 m) and these proteins were predominately from photosynthetic organisms. Diatom peptides dominate the spectra of the Washington margin while peptides from cyanobacteria, such as Synechococcus sp. dominated the spectra of both oligotrophic sites. Despite differences in the exact proteins identified at each location, there is good agreement for protein function and cellular location. Proteins in surface waters code for a variety of cellular functions including photosynthesis (24% of detected proteins), energy production (10%), membrane production (9%) and genetic coding and reading (9%), and are split 60-40 between membrane proteins and intracellular cytoplasmic proteins. Sargasso Sea surface waters contain a suite of peptides consistent with proteins involved in circadian rhythms that promote both C and N fixation at night. At depth in the Sargasso Sea, both muscle-derived myosin protein and the muscle-hydrolyzing proteases deseasin MCP-01 and metalloprotease Mcp02 from γ-proteobacteria were observed. Deeper waters contain peptides predominately sourced from γ-proteobacteria (37% of detected proteins) and α-proteobacteria (26%), although peptides from membrane and photosynthetic proteins attributable to phytoplankton were still observed (13%). Relative to surface values, detection frequencies for bacterial membrane proteins and extracellular enzymes rose from 9 to 16 and 2 to 4% respectively below the thermocline and the overall balance between membrane proteins and intracellular proteins grows to an approximate 75-25 split. Unlike the phytoplankton membrane proteins, which are detrital in nature, the bacterial protein suite at depth is consistent with living biomass.
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