Post-Translational Modifications of Desulfovibrio vulgaris Hildenborough Sulfate Reduction Pathway Proteins

Journal Article · Sat Mar 01 04:00:00 EST 2008 · Journal of Proteome Research

DOI:https://doi.org/10.1021/pr700772s· OSTI ID:965767

Gaucher, S P; Redding, A M; Mukhopadhyay, A; Keasling, J D; Singh, A K

Recent developments in shotgun proteomics have enabled high-throughput studies of a variety of microorganisms at a proteome level and provide experimental validation for predicted open reading frames in the corresponding genome. More importantly, advances in mass spectrometric data analysis now allow mining of large proteomics data sets for the presence of post-translational modifications(PTMs). Although PTMs are a critical aspectof cellular activity, such information eludes cell-wide studies conducted at the transcript level. Here, we analyze several mass spectrometric data sets acquired using two-dimensional liquid chromatography tandem mass spectrometry, 2D-LC/MS/MS, for the sulfate reducing bacterium, Desulfovibrio vulgaris Hildenborough. Our searches of the raw spectra led us to discover several post-translationally modified peptides in D. vulgaris. Of these, several peptides containing a lysine with a +42 Da modification were found reproducibly across all data sets. Both acetylation and trimethylation have the same nominal +42 Da mass, and are therefore candidates for this modification. Several spectra were identified having markers for trimethylation, while one is consistent with an acetylation. Surprisingly, these modified peptides predominantly mapped to proteins involved in sulfate respiration. Other highly expressed proteins in D. vulgaris, such as enzymes involved in electron transport and other central metabolic processes, did not contain this modification. Decoy database searches were used to control for random spectrum/sequence matches. Additional validation for these modifications was provided by alternate workflows, for example, two-dimensional gel electrophoresis followed by mass spectrometry analysis of the dissimilatory sulfite reductase gamma-subunit(DsrC) protein. MS data for DsrC in this alternate workflow also contained the +42 Da modification at the same loci. Furthermore, the DsrC homologue in another sulfate reducing bacterium, Desulfovibrio desulfuricans G20, also showed similar +42 Da modifications in the same pathway. Here, we discuss our methods and implications of potential trimethylation in the D. vulgaris sulfate reduction pathway.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Physical Biosciences Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 965767
• Report Number(s): LBNL-2188E
• Journal Information: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 6 Vol. 7; ISSN 1535-3893
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
ACETYLATION
CHROMATOGRAPHY
DATA ANALYSIS
DESULFOVIBRIO
ELECTROPHORESIS
ENZYMES
LYSINE
MASS SPECTROSCOPY
MICROORGANISMS
MODIFICATIONS
OXIDOREDUCTASES
PEPTIDES
PROTEINS
SPECTRA
SULFATES
SULFITES
iTRAQ
SRB
DsrC
trimethyl-lysine
acetylation
PTMs