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Title: The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation

Journal Article · · Molecular and Cellular Proteomics

Syntrophus aciditrophicus is a syntrophic bacterium degrading fatty and aromatic acids into acetate, CO2, formate, and H2, consumed by methanogenic archaea. The syntroph’s acyllysine modifications were analyzed with a workflow avoiding antibody enrichment, enabling unbiased global acylation profiling. Seven acyl modification types were identified, six corresponding to reactive acyl-CoA species intermediates in benzoate degradation. Benzoatedegrading enzymes were also prominent among the 60 acylated proteins. The abundant acylations and active deacylases suggest that post-translational modifications directly regulate syntrophic benzoate degradation

Research Organization:
Univ. of California, Los Angeles, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)
Grant/Contract Number:
FC02-02ER63421; 447147-EL-21341; GM007185; 1911781; DGE-1650604; GM104610; GM085402
OSTI ID:
1904723
Journal Information:
Molecular and Cellular Proteomics, Vol. 21, Issue 4; ISSN 1535-9476
Publisher:
American Society for Biochemistry and Molecular BiologyCopyright Statement
Country of Publication:
United States
Language:
English

References (86)

Acetylation dynamics and stoichiometry in S accharomyces cerevisiae journal January 2014
Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data journal November 2018
SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion journal April 2017
Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus , a New Twist on ATP Formation journal August 2016
Use of benzoate as an electron acceptor by Syntrophus aciditrophicus grown in pure culture with crotonate journal December 2008
Reversible Nε-lysine acetylation regulates the activity of acyl-CoA synthetases involved in anaerobic benzoate catabolism in Rhodopseudomonas palustris: Acetylation control of benzoate catabolism journal March 2010
MoMo: discovery of statistically significant post-translational modification motifs journal December 2018
Anaerobic microbial metabolism can proceed close to thermodynamic limits journal January 2002
MS/MS of Synthetic Peptide Is Not Sufficient to Confirm New Types of Protein Modifications journal January 2013
The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth journal April 2007
Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes journal April 2019
Role of syntrophic microbial communities in high-rate methanogenic bioreactors journal July 2012
Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens: Benzoate metabolism in G. metallireducens journal October 2005
Crotonylation of key metabolic enzymes regulates carbon catabolite repression in Streptomyces roseosporus journal April 2020
The pimFABCDE operon from Rhodopseudomonas palustris mediates dicarboxylic acid degradation and participates in anaerobic benzoate degradation journal March 2005
Biochemical and Structural Characterization of the Paralogous Benzoate CoA Ligases from Burkholderia xenovorans LB400: Defining the Entry Point into the Novel Benzoate Oxidation (box) Pathway journal November 2007
Heterologous Expression of Mycobacterial Esx Complexes in Escherichia coli for Structural Studies Is Facilitated by the Use of Maltose Binding Protein Fusions journal November 2013
Isoaspartate in peptides and proteins: formation, significance, and analysis journal January 2000
Energetics and biochemistry of fermentative benzoate degradation by Syntrophus gentianae journal April 1999
Anaerobic metabolism of aromatic compounds via the benzoyl-CoA pathway journal December 1998
p53 β-hydroxybutyrylation attenuates p53 activity journal March 2019
Simultaneous Quantification of the Acetylome and Succinylome by ‘One-Pot’ Affinity Enrichment journal August 2018
Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms: Syntrophic butyrate and propionate oxidation processes journal March 2010
Anaerobic degradation of pimelate by newly isolated denitrifying bacteria journal February 1994
Probability-based protein identification by searching sequence databases using mass spectrometry data journal December 1999
Biologically Active Isoforms of CobB Sirtuin Deacetylase in Salmonella enterica and Erwinia amylovora journal October 2010
Enhanced FASP (eFASP) to Increase Proteome Coverage and Sample Recovery for Quantitative Proteomic Experiments journal March 2014
Nucleotide-binding sites can enhance N-acylation of nearby protein lysine residues journal November 2020
Lysine Glutarylation Is a Protein Posttranslational Modification Regulated by SIRT5 journal April 2014
Thioredoxins are required for protection against a reductive stress in the yeast Saccharomyces cerevisiae journal October 2002
Site-Specific Reactivity of Nonenzymatic Lysine Acetylation journal November 2014
Benzoate Fermentation by the Anaerobic Bacterium Syntrophus aciditrophicus in the Absence of Hydrogen-Using Microorganisms journal December 2001
Structure and Substrate Binding Properties of cobB, a Sir2 Homolog Protein Deacetylase from Escherichia coli journal March 2004
Identification of Lysine Succinylation Substrates and the Succinylation Regulatory Enzyme CobB in Escherichia coli journal October 2013
Electron transfer in syntrophic communities of anaerobic bacteria and archaea journal August 2009
An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets journal November 2005
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets journal November 2018
HDAC6 Modulates Cell Motility by Altering the Acetylation Level of Cortactin journal July 2007
Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms journal January 1999
Metabolism of Benzoate, Cyclohex-1-ene Carboxylate, and Cyclohexane Carboxylate by "Syntrophus aciditrophicus" Strain SB in Syntrophic Association with H2-Using Microorganisms journal April 2001
Intracellular Crotonyl-CoA Stimulates Transcription through p300-Catalyzed Histone Crotonylation journal April 2015
The Substrate Specificity of Sirtuins journal June 2016
Protein Acetylation in Bacteria journal September 2019
Syntrophy in anaerobic global carbon cycles journal December 2009
Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features journal November 2017
Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation journal April 2016
Sirtuin 4 Is a Lipoamidase Regulating Pyruvate Dehydrogenase Complex Activity journal December 2014
Lysine benzoylation is a histone mark regulated by SIRT2 journal August 2018
Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions journal July 2019
SIRT5 Regulates both Cytosolic and Mitochondrial Protein Malonylation with Glycolysis as a Major Target journal July 2015
Age-dependent deamidation of asparagine residues in proteins journal September 2001
Cyclohexane Carboxylate and Benzoate Formation from Crotonate in Syntrophus aciditrophicus journal December 2006
Determination of Deamidation Artifacts Introduced by Sample Preparation Using 18O-Labeling and Tandem Mass Spectrometry Analysis journal July 2012
MEME SUITE: tools for motif discovery and searching journal May 2009
Human αB-Crystallin Mutation Causes Oxido-Reductive Stress and Protein Aggregation Cardiomyopathy in Mice journal August 2007
Microbial degradation of phthalates: biochemistry and environmental implications journal August 2019
Alternate deacylating specificities of the archaeal sirtuins Sir2Af1 and Sir2Af2: Deacylating Specificities of the Archaeal Sirtuins journal October 2014
The Biochemistry of Sirtuins journal June 2006
Reactive Acyl-CoA Species Modify Proteins and Induce Carbon Stress journal May 2018
Accurate Quantification of Site-specific Acetylation Stoichiometry Reveals the Impact of Sirtuin Deacetylase CobB on the E. coli Acetylome journal March 2017
Protein Acetylation and Butyrylation Regulate the Phenotype and Metabolic Shifts of the Endospore-forming Clostridium acetobutylicum journal March 2018
Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function journal April 2016
KEGG Mapper for inferring cellular functions from protein sequences journal August 2019
Cyclohexa-1,5-Diene-1-Carbonyl-Coenzyme A (CoA) Hydratases of Geobacter metallireducens and Syntrophus aciditrophicus: Evidence for a Common Benzoyl-CoA Degradation Pathway in Facultative and Strict Anaerobes journal November 2006
Leveraging Immonium Ions for Targeting Acyl‐Lysine Modifications in Proteomic Datasets journal September 2020
High resolution two-dimensional electrophoresis of proteins. journal May 1975
Effect of glycosylation on the protein pattern in 2-D-gel electrophoresis journal January 2007
Reductive Stress: New Insights in Physiology and Drug Tolerance ofMycobacterium journal June 2020
Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option journal January 2020
Formaldehyde Derivatization: An Unexpected Side Reaction During Filter-Aided Sample Preparation journal August 2020
Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus journal June 2019
6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes: Gene probe for ring-opening hydrolases journal February 2008
Virtual 2-D Gel Electrophoresis:  Visualization and Analysis of the E. coli Proteome by Mass Spectrometry journal July 2001
Lysine 68 acetylation directs MnSOD as a tetrameric detoxification complex versus a monomeric tumor promoter journal June 2019
Protein acetylation dynamics in response to carbon overflow in E scherichia coli : Acetylation dynamics and overflow metabolism journal September 2015
Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry journal August 2015
Protein carbonylation, cellular dysfunction, and disease progression journal April 2006
Common errors in mass spectrometry-based analysis of post-translational modifications journal March 2016
Anaerobic bacterium that degrades fatty acids in syntrophic association with methanogens journal August 1979
Acetylation Is Indispensable for p53 Activation journal May 2008
Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation journal March 2019
Metabolic regulation of gene expression by histone lactylation journal October 2019
Bayesian false discovery rates for post-translational modification proteomics journal January 2012
The importance of hydrogen and formate transfer for syntrophic fatty, aromatic and alicyclic metabolism: Importance of interspecies hydrogen and formate transfer journal October 2013
Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids journal March 2019
Anaerobic Catabolism of Aromatic Compounds: a Genetic and Genomic View journal March 2009