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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 SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, 50%, and 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 communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13C or 15N in microbial communities. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.006049, 1–11, 2011.

Authors:
 [1];  [2];  [3];  [4];  [5];  [2]
+ Show Author Affiliations
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioScience Division; Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Sciences Dicision; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Sciences Division
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioScience Division
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division
OSTI Identifier:
1625095
Grant/Contract Number:  
AC05-00OR22725; SC0004665; SC0004918
Resource Type:
Accepted Manuscript
Journal Name:
Molecular and Cellular Proteomics
Additional Journal Information:
Journal Volume: 10; Journal Issue: 4; Journal ID: ISSN 1535-9476
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

Pan, Chongle, Fischer, Curt R., Hyatt, Doug, Bowen, Benjamin P., Hettich, Robert L., and Banfield, Jillian F. Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities. United States: N. p., 2011. Web. doi:10.1074/mcp.m110.006049.
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Pan, Chongle, Fischer, Curt R., Hyatt, Doug, Bowen, Benjamin P., Hettich, Robert L., & Banfield, Jillian F. Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities. United States. https://doi.org/10.1074/mcp.m110.006049
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Pan, Chongle, Fischer, Curt R., Hyatt, Doug, Bowen, Benjamin P., Hettich, Robert L., and Banfield, Jillian F. Tue . "Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities". United States. https://doi.org/10.1074/mcp.m110.006049. https://www.osti.gov/servlets/purl/1625095.
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@article{osti_1625095,
title = {Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities},
author = {Pan, Chongle and Fischer, Curt R. and Hyatt, Doug and Bowen, Benjamin P. and Hettich, Robert L. 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 SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, 50%, and 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 communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13C or 15N in microbial communities. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.006049, 1–11, 2011.},
doi = {10.1074/mcp.m110.006049},
journal = {Molecular and Cellular Proteomics},
number = 4,
volume = 10,
place = {United States},
year = {Tue Feb 01 00:00:00 EST 2011},
month = {Tue Feb 01 00:00:00 EST 2011}
}
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https://doi.org/10.1074/mcp.m110.006049
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Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP)
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  • DOI: 10.1002/rcm.3684

Synthesis/Degradation Ratio Mass Spectrometry for Measuring Relative Dynamic Protein Turnover
journal, January 2004

  • Cargile, Benjamin J.; Bundy, Jonathan L.; Grunden, Amy M.
  • Analytical Chemistry, Vol. 76, Issue 1
  • DOI: 10.1021/ac034841a

Performance Evaluation of a Hybrid Linear Ion Trap/Orbitrap Mass Spectrometer
journal, April 2006

  • Makarov, Alexander; Denisov, Eduard; Kholomeev, Alexander
  • Analytical Chemistry, Vol. 78, Issue 7
  • DOI: 10.1021/ac0518811

Method for Estimating the Isotopic Distributions of Metabolically Labeled Proteins by MALDI-TOFMS:  Application to NMR Samples
journal, August 2006

  • Choudhary, Kajal; Spicer, Victor L.; Donald, Lynda J.
  • Analytical Chemistry, Vol. 78, Issue 15
  • DOI: 10.1021/ac060507d

ProRata:  A Quantitative Proteomics Program for Accurate Protein Abundance Ratio Estimation with Confidence Interval Evaluation
journal, October 2006

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  • Analytical Chemistry, Vol. 78, Issue 20
  • DOI: 10.1021/ac060654b

Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis:  The Yeast Proteome
journal, February 2003

  • Peng, Junmin; Elias, Joshua E.; Thoreen, Carson C.
  • Journal of Proteome Research, Vol. 2, Issue 1
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Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers
journal, April 1998

  • Boschker, H. T. S.; Nold, S. C.; Wellsbury, P.
  • Nature, Vol. 392, Issue 6678
  • DOI: 10.1038/33900

Stable-isotope probing as a tool in microbial ecology
journal, February 2000

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  • DOI: 10.1038/35001054

Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001

  • Washburn, Michael P.; Wolters, Dirk; Yates, John R.
  • Nature Biotechnology, Vol. 19, Issue 3
  • DOI: 10.1038/85686

Protein-based stable isotope probing (Protein-SIP) reveals active species within anoxic mixed cultures
journal, June 2008

  • Jehmlich, Nico; Schmidt, Frank; von Bergen, Martin
  • The ISME Journal, Vol. 2, Issue 11
  • DOI: 10.1038/ismej.2008.64

Natural acidophilic biofilm communities reflect distinct organismal and functional organization
journal, October 2008

  • Wilmes, Paul; Remis, Jonathan P.; Hwang, Mona
  • The ISME Journal, Vol. 3, Issue 2
  • DOI: 10.1038/ismej.2008.90

Cultivation and quantitative proteomic analyses of acidophilic microbial communities
journal, December 2009

  • Belnap, Christopher P.; Pan, Chongle; VerBerkmoes, Nathan C.
  • The ISME Journal, Vol. 4, Issue 4
  • DOI: 10.1038/ismej.2009.139

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature
journal, February 2010

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  • The ISME Journal, Vol. 4, Issue 5
  • DOI: 10.1038/ismej.2009.158

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
journal, March 2007

  • Lo, Ian; Denef, Vincent J.; VerBerkmoes, Nathan C.
  • Nature, Vol. 446, Issue 7135
  • DOI: 10.1038/nature05624

Enigmatic, ultrasmall, uncultivated Archaea
journal, April 2010

  • Baker, B. J.; Comolli, L. R.; Dick, G. J.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 19
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A Dual Pressure Linear Ion Trap Orbitrap Instrument with Very High Sequencing Speed*
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Decimal Place Slope, A Fast and Precise Method for Quantifying 13 C Incorporation Levels for Detecting the Metabolic Activity of Microbial Species
journal, January 2010

Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis
journal, December 2006

Calculation of partial isotope incorporation into peptides measured by mass spectrometry
journal, June 2010

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    Works referencing / citing this record:

    Protein-based stable isotope probing (protein-SIP) in functional metaproteomics
    journal, March 2012

    • Seifert, Jana; Taubert, Martin; Jehmlich, Nico
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    Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
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    • Petzold, Christopher J.; Chan, Leanne Jade G.; Nhan, Melissa
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    Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
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    • Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R.
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    • DOI: 10.3389/fmicb.2016.00238

    Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
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    Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol
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    Microbial Competition in Polar Soils: A Review of an Understudied but Potentially Important Control on Productivity
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    Analytics for Metabolic Engineering
    journal, September 2015

    • Petzold, Christopher J.; Chan, Leanne Jade G.; Nhan, Melissa
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00135

    Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage
    journal, March 2016

    • Mosier, Annika C.; Miller, Christopher S.; Frischkorn, Kyle R.
    • Frontiers in Microbiology, Vol. 7
    • DOI: 10.3389/fmicb.2016.00238
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