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 - ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process JF - BMC bioinformaticsBMC Bioinformatics Y1 - 2011 A1 - Basu, Malay K. A1 - J. Selengut A1 - Haft, Daniel H. KW - algorithms KW - Archaea KW - Archaeal Proteins KW - DNA KW - Methane KW - Phylogeny KW - software AB - BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies. RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries. CONCLUSION: ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/. VL - 12 N1 - http://www.ncbi.nlm.nih.gov/pubmed/22070167?dopt=Abstract ER - TY - JOUR T1 - ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. JF - BMC Bioinformatics Y1 - 2011 A1 - Basu, Malay K A1 - Selengut, Jeremy D A1 - Haft, Daniel H KW - algorithms KW - Archaea KW - Archaeal Proteins KW - DNA KW - Methane KW - Phylogeny KW - software AB -

BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies.

RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather than by relying on prebuilt protein families or fixed sequence similarity thresholds. Double Partial Phylogenetic Profiling (DPPP) is a related procedure that begins with a single sequence and searches for optimal granularities for its surrounding protein family in order to generate the best query profiles for PPP. We present ProPhylo, a high-performance software package for phylogenetic profiling studies through creating individually optimized protein family boundaries. ProPhylo provides precomputed databases for immediate use and tools for manipulating the taxonomic profiles used as queries.

CONCLUSION: ProPhylo results show universal markers of methanogenesis, a new DNA phosphorothioation-dependent restriction enzyme, and efficacy in guiding protein family construction. The software and the associated databases are freely available under the open source Perl Artistic License from ftp://ftp.jcvi.org/pub/data/ppp/.

VL - 12 M3 - 10.1186/1471-2105-12-434 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 - Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock. JF - Environ Microbiol Y1 - 2005 A1 - Boonyaratanakornkit, Boonchai B A1 - Simpson, Anjana J A1 - Whitehead, Timothy A A1 - Fraser, Claire M A1 - el-Sayed, Najib M A A1 - Clark, Douglas S KW - Adaptation, Physiological KW - Archaeal Proteins KW - Cold Temperature KW - Gene Expression Profiling KW - Gene Expression Regulation, Archaeal KW - Heat-Shock Proteins KW - Hot Temperature KW - Methanococcus KW - Temperature KW - Transcription, Genetic AB -

Temperature shock of the hyperthermophilic methanarchaeon Methanococcus jannaschii from its optimal growth temperature of 85 degrees C to 65 degrees C and 95 degrees C resulted in different transcriptional responses characteristic of both the direction of shock (heat or cold shock) and whether the shock was lethal. Specific outcomes of lethal heat shock to 95 degrees C included upregulation of genes encoding chaperones, and downregulation of genes encoding subunits of the H+ transporting ATP synthase. A gene encoding an alpha subunit of a putative prefoldin was also upregulated, which may comprise a novel element in the protein processing pathway in M. jannaschii. Very different responses were observed upon cold shock to 65 degrees C. These included upregulation of a gene encoding an RNA helicase and other genes involved in transcription and translation, and upregulation of genes coding for proteases and transport proteins. Also upregulated was a gene that codes for an 18 kDa FKBP-type PPIase, which may facilitate protein folding at low temperatures. Transcriptional profiling also revealed several hypothetical proteins that respond to temperature stress conditions.

VL - 7 CP - 6 M3 - 10.1111/j.1462-2920.2005.00751.x ER -