MassIVE MSV000087298

Complete Public PXD025603

The acyl-proteome of Syntrophus aciditrophicus reveals metabolic relationship with benzoate degradation

Description

Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate and H2 that are utilized by methanogens and other hydrogen-consuming microbes. The degradation of benzoate by S. aciditrophicus proceeds by a multi-step pathway that involves many reactive acyl-Coenzyme A species (RACS) as intermediates which can potentially result in acylation of lysine residues in proteins. Herein, we investigate post-translational modifications in the S. aciditrophicus proteome to identify and characterize a variety of acyl-lysine modifications that correspond to RACS present in the benzoate degradation pathway. Modification levels are sufficient to support post-translational modification analyses without antibody enrichment, enabling the study of a range of acylations located, presumably, on the most extensively acylated proteins. Seven types of acyl modifications were identified throughout the proteome, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway. Benzoate-degrading proteins are heavily represented among acylated proteins. The presence of functional deacylase enzymes in S. aciditrophicus indicates a potential regulatory system/mechanism by which these bacteria modulate acylation. Uniquely, acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility of enzyme modulation during benzoate degradation in this, and potentially, other syntrophic bacteria. Our results outline candidates to further study the impact of acylations within syntrophic systems. [doi:10.25345/C5P526] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Shotgun proteomics ; Lysine acylation ; Syntrophs ; Syntrophus aciditrophicus

Contact

Principal Investigators:
(in alphabetical order)
Joseph Loo, University of California Los Angeles, United States
Submitting User: janinefu

Publications

John M. Muroski, Janine Y. Fu, Hong Hanh Nguyen, Neil Q. Wofford, Housna Mouttaki, Kimberly L. James, Michael J. McInerney, Robert P. Gunsalus, Joseph A. Loo, Rachel R. Ogorzalek Loo.
The acyl-proteome of Syntrophus aciditrophicus reveals metabolic relationships in benzoate degradation.
Molecular & Cellular Proteomics (2022), doi: https://doi.org/10.1016/j.mcpro.2022.100215.

Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files Browse Results
 
FTP Download Link (click to copy):

- Dataset Reanalyses


+ Dataset History


Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.