Needles in the blue sea: Sub-species specificity in targeted protein biomarker analyses within the vast oceanic microbial metaproteome

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 i...

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Veröffentlicht in:Proteomics (Weinheim) Jg. 15; H. 20; S. 3521 - 3531
Hauptverfasser: Saito, Mak A., Dorsk, Alexander, Post, Anton F., McIlvin, Matthew R., Rappé, Michael S., DiTullio, Giacomo R., Moran, Dawn M.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Germany Blackwell Publishing Ltd 01.10.2015
Wiley Subscription Services, Inc
Schlagworte:
Biogeochemistry
Biomarkers
Cyanobacteria
Gene mapping
Genetic Variation
Genomes
Humans
Metagenome
Metatryp
Microbiology
Microorganisms
MRM
Needles
Nitrogen
Oceans and Seas
Peptide mapping
Peptides
Phylogeny
Prochlorococcus
Prochlorococcus - genetics
Proteins
Proteome - genetics
Proteomics
Python
Regulatory proteins
Species
Species Specificity
Synechococcus
Synechococcus - genetics
Targeted metaproteomics
Tryptic peptides
Workflow
Pacific Ocean
Biomarkers
MRM
Microbiology
Metatryp
Targeted metaproteomics
Cyanobacteria
ISSN:1615-9853, 1615-9861
Online-Zugang:Volltext
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Zusammenfassung: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 × 107, 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.
Bibliographie:Gordon and Betty Moore Foundation
ArticleID:PMIC12070
US National Science Foundation - No. 3782; No. 3934; No. OCE-1260233; No. OCE-1233261; No. OCE-1220484; No. OCE-1333212; No. OCE-1155566
istex:FF11CBEE1C92FAD71E1302BEB21407B140EF3A2A
ark:/67375/WNG-LJ0DJBW6-C
Center for Microbial Oceanography Research and Education
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ISSN:1615-9853
1615-9861
DOI:10.1002/pmic.201400630