TY - JOUR T1 - Stoichiometry of site-specific lysine acetylation in an entire proteome. JF - J Biol Chem Y1 - 2014 A1 - Baeza, Josue A1 - Dowell, James A A1 - Smallegan, Michael J A1 - Fan, Jing A1 - Amador-Noguez, Daniel A1 - Khan, Zia A1 - Denu, John M KW - Acetylation KW - Amino Acid Sequence KW - Bacterial Proteins KW - Chromatography, High Pressure Liquid KW - Computational Biology KW - Escherichia coli KW - Lysine KW - Molecular Sequence Data KW - Proteome KW - Tandem Mass Spectrometry AB -

Acetylation of lysine ϵ-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here, we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of Escherichia coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD(+)-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins involved in transcriptional and translational processes displayed the highest degree of acetylation. Loss of CobB led to increased global acetylation at low stoichiometry sites and induced site-specific changes at high stoichiometry sites, and biochemical analysis revealed altered acetyl-CoA metabolism. Thus, this study demonstrates that sirtuin deacetylase deficiency leads to both site-specific and global changes in protein acetylation stoichiometry, affecting central metabolism.

VL - 289 CP - 31 M3 - 10.1074/jbc.M114.581843 ER - TY - JOUR T1 - Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. JF - J Bacteriol Y1 - 2012 A1 - Haft, Daniel H A1 - Payne, Samuel H A1 - Selengut, Jeremy D KW - Amino Acid Sequence KW - Aminoacyltransferases KW - Archaeal Proteins KW - Bacterial Proteins KW - Cell Membrane KW - Cysteine Endopeptidases KW - Gene Expression Regulation, Archaeal KW - Gene Expression Regulation, Bacterial KW - Gene Expression Regulation, Enzymologic KW - Molecular Sequence Data KW - Protein Processing, Post-Translational AB -

Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster. Defining hidden Markov models were constructed for all. PGF-CTERM occurs in 29 archaeal species, some of which have more than 50 proteins that share the domain. PGF-CTERM proteins include the major cell surface protein in Halobacterium, a glycoprotein with a partially characterized diphytanylglyceryl phosphate linkage near its C terminus. Comparative genomics identifies a distant exosortase homolog, designated archaeosortase A (ArtA), as the likely protein-processing enzyme for PGF-CTERM. Proteomics suggests that the PGF-CTERM region is removed. Additional systems include VPXXXP-CTERM/archeaosortase B in two of the same archaea and PEF-CTERM/archaeosortase C in four others. Bacterial exosortases often fall into subfamilies that partner with very different cohorts of extracellular polymeric substance biosynthesis proteins; several species have multiple systems. Variant systems include the VPDSG-CTERM/exosortase C system unique to certain members of the phylum Verrucomicrobia, VPLPA-CTERM/exosortase D in several alpha- and deltaproteobacterial species, and a dedicated (single-target) VPEID-CTERM/exosortase E system in alphaproteobacteria. Exosortase-related families XrtF in the class Flavobacteria and XrtG in Gram-positive bacteria mark distinctive conserved gene neighborhoods. A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes. Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation.

VL - 194 CP - 1 M3 - 10.1128/JB.06026-11 ER - TY - JOUR T1 - Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification JF - Journal of bacteriologyJournal of bacteriology Y1 - 2012 A1 - Haft, Daniel H. A1 - Payne, Samuel H. A1 - J. Selengut KW - Amino Acid Sequence KW - Aminoacyltransferases KW - Archaeal Proteins KW - Bacterial Proteins KW - Cell Membrane KW - Cysteine Endopeptidases KW - Gene Expression Regulation, Archaeal KW - Gene Expression Regulation, Bacterial KW - Gene Expression Regulation, Enzymologic KW - Molecular Sequence Data KW - Protein Processing, Post-Translational AB - Multiple new prokaryotic C-terminal protein-sorting signals were found that reprise the tripartite architecture shared by LPXTG and PEP-CTERM: motif, TM helix, basic cluster. Defining hidden Markov models were constructed for all. PGF-CTERM occurs in 29 archaeal species, some of which have more than 50 proteins that share the domain. PGF-CTERM proteins include the major cell surface protein in Halobacterium, a glycoprotein with a partially characterized diphytanylglyceryl phosphate linkage near its C terminus. Comparative genomics identifies a distant exosortase homolog, designated archaeosortase A (ArtA), as the likely protein-processing enzyme for PGF-CTERM. Proteomics suggests that the PGF-CTERM region is removed. Additional systems include VPXXXP-CTERM/archeaosortase B in two of the same archaea and PEF-CTERM/archaeosortase C in four others. Bacterial exosortases often fall into subfamilies that partner with very different cohorts of extracellular polymeric substance biosynthesis proteins; several species have multiple systems. Variant systems include the VPDSG-CTERM/exosortase C system unique to certain members of the phylum Verrucomicrobia, VPLPA-CTERM/exosortase D in several alpha- and deltaproteobacterial species, and a dedicated (single-target) VPEID-CTERM/exosortase E system in alphaproteobacteria. Exosortase-related families XrtF in the class Flavobacteria and XrtG in Gram-positive bacteria mark distinctive conserved gene neighborhoods. A picture emerges of an ancient and now well-differentiated superfamily of deeply membrane-embedded protein-processing enzymes. Their target proteins are destined to transit cellular membranes during their biosynthesis, during which most undergo additional posttranslational modifications such as glycosylation. VL - 194 N1 - http://www.ncbi.nlm.nih.gov/pubmed/22037399?dopt=Abstract ER - TY - JOUR T1 - Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. JF - Genome Biol Y1 - 2011 A1 - Khan, Zia A1 - Amini, Sasan A1 - Bloom, Joshua S A1 - Ruse, Cristian A1 - Caudy, Amy A A1 - Kruglyak, Leonid A1 - Singh, Mona A1 - Perlman, David H A1 - Tavazoie, Saeed KW - algorithms KW - Amino Acid Sequence KW - Bacterial Proteins KW - Escherichia coli KW - Isotope Labeling KW - Mass Spectrometry KW - Molecular Sequence Data KW - Nitrogen Isotopes KW - Proteome KW - proteomics KW - Sensitivity and Specificity KW - software AB -

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.

VL - 12 CP - 12 M3 - 10.1186/gb-2011-12-12-r122 ER - TY - JOUR T1 - TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes JF - Nucleic acids researchNucleic Acids Research Y1 - 2007 A1 - J. Selengut A1 - Haft, Daniel H. A1 - Davidsen, Tanja A1 - Ganapathy, Anurhada A1 - Gwinn-Giglio, Michelle A1 - Nelson, William C. A1 - Richter, R. Alexander A1 - White, Owen KW - Archaeal Proteins KW - Bacterial Proteins KW - Databases, Protein KW - Genome, Bacterial KW - Genomics KW - Internet KW - Phylogeny KW - software KW - User-Computer Interface AB - TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe 'equivalog' families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at http://www.tigr.org/TIGRFAMs and http://www.tigr.org/Genome_Properties. VL - 35 N1 - http://www.ncbi.nlm.nih.gov/pubmed/17151080?dopt=Abstract ER - TY - JOUR T1 - Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic JF - BMC biologyBMC biology Y1 - 2006 A1 - Haft, Daniel H. A1 - Paulsen, Ian T. A1 - Ward, Naomi A1 - J. Selengut KW - Amino Acid Motifs KW - Amino Acid Sequence KW - bacteria KW - Bacterial Proteins KW - Biofilms KW - Genome, Bacterial KW - Markov chains KW - Molecular Sequence Data KW - Phylogeny KW - Polysaccharides, Bacterial KW - Protein Sorting Signals KW - Protein Transport KW - Seawater KW - sequence alignment KW - Soil Microbiology AB - BACKGROUND: Protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. Detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families. RESULTS: We describe a short C-terminal homology domain, sporadically distributed in bacteria, with several key characteristics of protein sorting signals. The domain includes a near-invariant motif Pro-Glu-Pro (PEP). This possible recognition or processing site is followed by a predicted transmembrane helix and a cluster rich in basic amino acids. We designate this domain PEP-CTERM. It tends to occur multiple times in a genome if it occurs at all, with a median count of eight instances; Verrucomicrobium spinosum has sixty-five. PEP-CTERM-containing proteins generally contain an N-terminal signal peptide and exhibit high diversity and little homology to known proteins. All bacteria with PEP-CTERM have both an outer membrane and exopolysaccharide (EPS) production genes. By a simple heuristic for screening phylogenetic profiles in the absence of pre-formed protein families, we discovered that a homolog of the membrane protein EpsH (exopolysaccharide locus protein H) occurs in a species when PEP-CTERM domains are found. The EpsH family contains invariant residues consistent with a transpeptidase function. Most PEP-CTERM proteins are encoded by single-gene operons preceded by large intergenic regions. In the Proteobacteria, most of these upstream regions share a DNA sequence, a probable cis-regulatory site that contains a sigma-54 binding motif. The phylogenetic profile for this DNA sequence exactly matches that of three proteins: a sigma-54-interacting response regulator (PrsR), a transmembrane histidine kinase (PrsK), and a TPR protein (PrsT). CONCLUSION: These findings are consistent with the hypothesis that PEP-CTERM and EpsH form a protein export sorting system, analogous to the LPXTG/sortase system of Gram-positive bacteria, and correlated to EPS expression. It occurs preferentially in bacteria from sediments, soils, and biofilms. The novel method that led to these findings, partial phylogenetic profiling, requires neither global sequence clustering nor arbitrary similarity cutoffs and appears to be a rapid, effective alternative to other profiling methods. VL - 4 N1 - http://www.ncbi.nlm.nih.gov/pubmed/16930487?dopt=Abstract ER - TY - JOUR T1 - Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition JF - Journal of bacteriologyJournal of bacteriology Y1 - 2005 A1 - Joardar, Vinita A1 - Lindeberg, Magdalen A1 - Jackson, Robert W. A1 - J. Selengut A1 - Dodson, Robert A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Deboy, Robert A1 - Durkin, A. Scott A1 - Giglio, Michelle Gwinn A1 - Madupu, Ramana A1 - Nelson, William C. A1 - Rosovitz, M. J. A1 - Sullivan, Steven A1 - Crabtree, Jonathan A1 - Creasy, Todd A1 - Davidsen, Tanja A1 - Haft, Dan H. A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Halpin, Rebecca A1 - Holley, Tara A1 - Khouri, Hoda A1 - Feldblyum, Tamara A1 - White, Owen A1 - Fraser, Claire M. A1 - Chatterjee, Arun K. A1 - Cartinhour, Sam A1 - Schneider, David J. A1 - Mansfield, John A1 - Collmer, Alan A1 - Buell, C. Robin KW - Bacterial Proteins KW - DNA, Bacterial KW - Genes, Bacterial KW - Genome, Bacterial KW - Molecular Sequence Data KW - Pseudomonas syringae KW - Species Specificity KW - virulence AB - Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific. VL - 187 N1 - http://www.ncbi.nlm.nih.gov/pubmed/16159782?dopt=Abstract ER - TY - JOUR T1 - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2004 A1 - Seshadri, Rekha A1 - Myers, Garry S. A. A1 - Tettelin, Hervé A1 - Eisen, Jonathan A. A1 - Heidelberg, John F. A1 - Dodson, Robert J. A1 - Davidsen, Tanja M. A1 - DeBoy, Robert T. A1 - Fouts, Derrick E. A1 - Haft, Dan H. A1 - J. Selengut A1 - Ren, Qinghu A1 - Brinkac, Lauren M. A1 - Madupu, Ramana A1 - Kolonay, Jamie A1 - Durkin, A. Scott A1 - Daugherty, Sean C. A1 - Shetty, Jyoti A1 - Shvartsbeyn, Alla A1 - Gebregeorgis, Elizabeth A1 - Geer, Keita A1 - Tsegaye, Getahun A1 - Malek, Joel A1 - Ayodeji, Bola A1 - Shatsman, Sofiya A1 - McLeod, Michael P. A1 - Smajs, David A1 - Howell, Jerrilyn K. A1 - Pal, Sangita A1 - Amin, Anita A1 - Vashisth, Pankaj A1 - McNeill, Thomas Z. A1 - Xiang, Qin A1 - Sodergren, Erica A1 - Baca, Ernesto A1 - Weinstock, George M. A1 - Norris, Steven J. A1 - Fraser, Claire M. A1 - Paulsen, Ian T. KW - ATP-Binding Cassette Transporters KW - Bacterial Proteins KW - Base Sequence KW - Borrelia burgdorferi KW - Genes, Bacterial KW - Genome, Bacterial KW - Leptospira interrogans KW - Models, Genetic KW - Molecular Sequence Data KW - Mouth KW - Sequence Homology, Amino Acid KW - Treponema KW - Treponema pallidum AB - We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function. VL - 101 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15064399?dopt=Abstract ER - TY - JOUR T1 - Genome of Geobacter sulfurreducens: metal reduction in subsurface environments JF - Science (New York, N.Y.)Science (New York, N.Y.) Y1 - 2003 A1 - Methé, B. A. A1 - Nelson, K. E. A1 - Eisen, J. A. A1 - Paulsen, I. T. A1 - Nelson, W. A1 - Heidelberg, J. F. A1 - Wu, D. A1 - Wu, M. A1 - Ward, N. A1 - Beanan, M. J. A1 - Dodson, R. J. A1 - Madupu, R. A1 - Brinkac, L. M. A1 - Daugherty, S. C. A1 - DeBoy, R. T. A1 - Durkin, A. S. A1 - Gwinn, M. A1 - Kolonay, J. F. A1 - Sullivan, S. A. A1 - Haft, D. H. A1 - J. Selengut A1 - Davidsen, T. M. A1 - Zafar, N. A1 - White, O. A1 - Tran, B. A1 - Romero, C. A1 - Forberger, H. A. A1 - Weidman, J. A1 - Khouri, H. A1 - Feldblyum, T. V. A1 - Utterback, T. R. A1 - Van Aken, S. E. A1 - Lovley, D. R. A1 - Fraser, C. M. KW - Acetates KW - Acetyl Coenzyme A KW - Aerobiosis KW - Anaerobiosis KW - Bacterial Proteins KW - Carbon KW - Chemotaxis KW - Chromosomes, Bacterial KW - Cytochromes c KW - Electron Transport KW - Energy Metabolism KW - Genes, Bacterial KW - Genes, Regulator KW - Genome, Bacterial KW - Geobacter KW - Hydrogen KW - Metals KW - Movement KW - Open Reading Frames KW - Oxidation-Reduction KW - Phylogeny AB - The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity. VL - 302 N1 - http://www.ncbi.nlm.nih.gov/pubmed/14671304?dopt=Abstract ER - TY - JOUR T1 - Sequence similarity. JF - Nature Y1 - 1987 A1 - Mount, S M KW - Adenosine Triphosphate KW - Amino Acid Sequence KW - Animals KW - Bacterial Proteins KW - Biological Transport, Active KW - Carrier Proteins KW - Drosophila melanogaster KW - genes KW - HUMANS KW - Pigments, Biological KW - Sequence Homology, Nucleic Acid VL - 325 CP - 6104 M3 - 10.1038/325487c0 ER -