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Title: Quantitative tracking of isotope flows in proteomes of microbial communities

Abstract

Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic stable isotope probing (SIP) method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, {approx}50%, and {approx}98%. The method was then used to monitor incorporation of 15N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established into regrowing communities and provides insight into metabolism during biofilm formation. The SIP-proteomics method can be extended to many systems to track fluxes of 13C or 15N in microbial communities.

Authors:
 [1];  [2];  [3];  [1]
  1. University of California, Berkeley
  2. ORNL
  3. {Bob} L [ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1004958
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Molecular and Cellular Proteomics; Journal Volume: 10; Journal Issue: 4
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ATOMS; COMMUNITIES; METABOLISM; MONITORS; NUTRIENTS; PEPTIDES; PROTEINS; STABLE ISOTOPES

Citation Formats

Fisher, Curt, Hyatt, Philip Douglas, Hettich, Robert, and Banfield, Jillian F. Quantitative tracking of isotope flows in proteomes of microbial communities. United States: N. p., 2011. Web.
Fisher, Curt, Hyatt, Philip Douglas, Hettich, Robert, & Banfield, Jillian F. Quantitative tracking of isotope flows in proteomes of microbial communities. United States.
Fisher, Curt, Hyatt, Philip Douglas, Hettich, Robert, and Banfield, Jillian F. 2011. "Quantitative tracking of isotope flows in proteomes of microbial communities". United States. doi:.
@article{osti_1004958,
title = {Quantitative tracking of isotope flows in proteomes of microbial communities},
author = {Fisher, Curt and Hyatt, Philip Douglas and Hettich, Robert and Banfield, Jillian F.},
abstractNote = {Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic stable isotope probing (SIP) method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, {approx}50%, and {approx}98%. The method was then used to monitor incorporation of 15N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established into regrowing communities and provides insight into metabolism during biofilm formation. The SIP-proteomics method can be extended to many systems to track fluxes of 13C or 15N in microbial communities.},
doi = {},
journal = {Molecular and Cellular Proteomics},
number = 4,
volume = 10,
place = {United States},
year = 2011,
month = 1
}
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