Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

Zhou Li; Yingfeng Wang; Qiuming Yao; Nicholas B. Justice; Tae Hyuk Ahn; Dong Xu; Robert L. Hettich; Jillian F. Banfield; Chongle Pan

doi:10.1038/ncomms5405

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

Zhou Li, Yingfeng Wang, Qiuming Yao, Nicholas B. Justice, Tae Hyuk Ahn, Dong Xu, Robert L. Hettich, Jillian F. Banfield, Chongle Pan

Bioanalytical Mass Spectrometry

Research output: Contribution to journal › Article › peer-review

47 Scopus citations

Abstract

Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.

Original language	English
Article number	4405
Journal	Nature Communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms5405
State	Published - Jul 25 2014

Funding

We thank Dr. Annika Mosier for providing a GS2 sample; Dr. Ritin Sharma for providing an E. coli sample; and Dr. Jennifer Doudna and Dr. Rodolphe Barrangou for discussion about the CRISPR-Cas system. This work was funded by the US Department of Energy Office of Science, Biological and Environmental Research, Carbon Cycling program for Z.L., N.B.J., R.L.H., J.F.B. and C.P., Knowledgebase program for Y.W. and T.-H.A., and National Institutes of Health grant (R01-GM100701) for Q.Y. and D.X. This research used resources of the Oak Ridge Leadership Computing Facility. Oak Ridge National Laboratory is supported by the Office of Science of the US Department of Energy.

Funders	Funder number
US Department of Energy
US Department of Energy Office of Science
National Institutes of Health
National Institute of General Medical Sciences	R01GM100701
Office of Science
Biological and Environmental Research

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title = "Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community",

abstract = "Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.",

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AU - Ahn, Tae Hyuk

AU - Xu, Dong

AU - Hettich, Robert L.

AU - Banfield, Jillian F.

AU - Pan, Chongle

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Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

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