68 research outputs found
Sequence and phylogenetic analyses of the twin-arginine targeting (Tat) protein export system
Twin-arginine targeting (Tat) protein secretion systems consist of two protein types, members of the TatA and TatC families. Homologues of these proteins are found in many archaea, bacteria, chloroplasts and mitochondria. Every prokaryotic organism with a fully sequenced genome exhibits either neither family member, or between one and three paralogues of these two family members. The Arabidopsis thaliana genome encodes three of each. Although many mitochondrially encoded TatC homologues have been identified, corresponding TatA homologues have not been found in this organelle. Phylogenetic analyses reveal that most prokaryotic Tat systems consist of one TatC homologue and two sequence-divergent TatA homologues (TatA and TatB). When only one TatA homologue is present, TatB is missing, and when three TatA homologues are present, the third one arose by duplication of TatA, not TatB. Further, homologues most resembling TatB are more sequence-divergent than those more closely resembling TatA. In contrast to the TatA family, the TatC family shows phylogenetic clustering in strict accordance with organismal type. These results are discussed in terms of their probable structural, functional and evolutionary significance
Evolution of the bacterial phosphotransferase system: From carriers and enzymes to group translocators
Learning to Find Relevant Biological Articles Without Negative Training Examples
Abstract. Classifiers are traditionally learned using sets of positive and negative training examples. However, often a classifier is required, but for training only an incomplete set of positive examples and a set of unlabeled examples are available. This is the situation, for example, with the Transport Classification Database (TCDB, www.tcdb.org), a repository of information about proteins involved in transmembrane transport. This paper presents and evaluates a method for learning to rank the likely relevance to TCDB of newly published scientific articles, using the articles currently referenced in TCDB as positive training examples. The new method has succeeded in identifying 964 new articles relevant to TCDB in fewer than six months, which is a major practical success. From a general data mining perspective, the contributions of this paper are (i) devising and evaluating two novel approaches that solve the positive-only problem effectively, (ii) applying support vector machines in a state-ofthe-art way for recognizing and ranking relevance, and (iii) deploying a system to update a widely-used, real-world biomedical database. Supplementary information including all data sets are publicly available at www.cs.ucsd.edu/users/knoto/pub/ajcai08.
Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp70 superfamily
Supplementary Material for: Bioinformatic Analyses of Transmembrane Transport: Novel Software for Deducing Protein Phylogeny, Topology, and Evolution
<p>During the past decade, we have experienced a revolution in the
biological sciences resulting from the flux of information generated by
genome-sequencing efforts. Our understanding of living organisms, the
metabolic processes they catalyze, the genetic systems encoding cellular
protein and stable RNA constituents, and the pathological conditions
caused by some of these organisms has greatly benefited from the
availability of complete genomic sequences and the establishment of
comprehensive databases. Many research institutes around the world are
now devoting their efforts largely to genome sequencing, data collection
and data analysis. In this review, we summarize tools that are in
routine use in our laboratory for characterizing transmembrane transport
systems. Applications of these tools to specific transporter families
are presented. Many of the computational approaches described should be
applicable to virtually all classes of proteins and RNA molecules.</p
Electron cryotomography reveals novel structures of a recently cultured termite gut spirochete
Protein-translocating outer membrane porins of Gram-negative bacteria
Five families of outer membrane porins that function in protein secretion in Gram-negative bacteria are Currently recognized. In this report these five porin families are analyzed from structural and phylogenetic standpoints, They, are the fimbrial usher protein (FUP), outer membrane factor (OMF), autotransporter (AT). two-partner secretion (TPS) and outer membrane secretin (Secretin) families, All members of these families in the current databases were identified, and ill full-length homologues were multiply aligned for structural and phylogenetic analyses. The organismal distribution of homologgues in each family proved to be unique with some families being restricted to proteobacteria and others being widespread in other bacterial kingdoms as well as eukaryotes, The compositions of and size differences between subfamilies provide evidence for specific orthologous relationships, which agree with available functional information and intra-subfamily phylogeny. The results reveal that horizontal transfer of genes encoding these proteins between phylogenetically distant organisms has been exceptionally rare although transfer within select bacterial kingdoms may have occurred, The resultant in silico analyses are correlated with available experimental evidence to formulate models relevant to the structures and evolutionary origins of these proteins. (C) 2002 Elsevier Science B.V. All rights reserved
Export of l-isoleucine from Corynebacterium glutamicum: A two-gene-encoded member of a new translocator family
Bacteria possess amino acid export systems, and Corynebacterium glutamicum excretes L-isoleucine in a process dependent on the proton motive force. In order to identify the system responsible for L-isoleucine export, we have used transposon mutagenesis to isolate mutants of C. glutamicum sensitive to the peptide isoleucyl-isoleucine. In one such mutant, strong peptide sensitivity resulted from insertion into a gene designated brnF encoding a hydrophobic protein predicted to possess seven transmembrane spanning helices. brnE is located downstream of brnF and encodes a second hydrophobic protein with four putative membrane-spanning helices. A mutant deleted of both genes no longer exports L-isoleucine, whereas an overexpressing strain exports this amino acid at an increased rate. BrnF and BrnE together are also required for the export Of L-leucine and L-valine. BrnFE is thus a two-component export permease specific for aliphatic hydrophobic amino acids. Upstream of brnFE and transcribed divergently is an Lrp-like regulatory gene required for active export. Searches for homologues of BrnFE show that this type of exporter is widespread in prokaryotes but lacking in eukaryotes and that both gene products which together comprise the members of a novel family, the LIV-E family, generally map together within a single operon. Comparisons of the BrnF and BrnE phylogenetic trees show that gene duplication events in the early bacterial lineage gave rise to multiple paralogues that have been retained in alpha-proteobacteria but not in other prokaryotes analyzed
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