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Ding Y, Shiota T, Le Brun AP, Dunstan RA, Wang B, Hsu HY, Lithgow T, Shen HH. Characterization of BamA reconstituted into a solid-supported lipid bilayer as a platform for measuring dynamics during substrate protein assembly into the membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183317. [DOI: 10.1016/j.bbamem.2020.183317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
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2
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Genome-wide evidence of positive selection in Bacteroides fragilis. Comput Biol Chem 2014; 52:43-50. [DOI: 10.1016/j.compbiolchem.2014.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/02/2014] [Accepted: 09/02/2014] [Indexed: 11/20/2022]
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3
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Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Holmes EC, Birren B, Galagan J, Feldman MW. The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog 2013; 9:e1003543. [PMID: 23966858 PMCID: PMC3744410 DOI: 10.1371/journal.ppat.1003543] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 06/24/2013] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new host every second. While analyses of genetic data from natural populations of M.tb have emphasized the role of genetic drift in shaping patterns of diversity, the influence of natural selection on this successful pathogen is less well understood. We investigated the effects of natural selection on patterns of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence of strong purifying selection, with an estimated genome-wide selection coefficient equal to -9.5 × 10(-4) (95% CI -1.1 × 10(-3) to -6.8 × 10(-4)); this is several orders of magnitude higher than recent estimates for eukaryotic and prokaryotic organisms. We also identified different patterns of variation across categories of gene function. Genes involved in transport and metabolism of inorganic ions exhibited very low levels of non-synonymous polymorphism, equivalent to categories under strong purifying selection (essential and translation-associated genes). The highest levels of non-synonymous variation were seen in a group of transporter genes, likely due to either diversifying selection or local selective sweeps. In addition to selection, we identified other important influences on M.tb genetic diversity, such as a 25-fold expansion of global M.tb populations coincident with explosive growth in human populations (estimated timing 1684 C.E., 95% CI 1620-1713 C.E.). These results emphasize the parallel demographic histories of this obligate pathogen and its human host, and suggest that the dominant effect of selection on M.tb is removal of novel variants, with exceptions in an interesting group of genes involved in transportation and defense. We speculate that the hostile environment within a host imposes strict demands on M.tb physiology, and thus a substantial fitness cost for most new mutations. In this respect, obligate bacterial pathogens may differ from other host-associated microbes such as symbionts.
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Affiliation(s)
- Caitlin S Pepperell
- Departments of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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4
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Omp85 genosensor for detection of human brain bacterial meningitis. Biotechnol Lett 2013; 35:929-35. [DOI: 10.1007/s10529-013-1161-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
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5
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Quick diagnosis of human brain meningitis using omp85 gene amplicon as a genetic marker. Indian J Microbiol 2013; 53:238-40. [PMID: 24426115 DOI: 10.1007/s12088-013-0371-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 02/01/2013] [Indexed: 10/27/2022] Open
Abstract
The usual diagnosis of life-threatening human brain bacterial meningitis are expensive, time consuming or non-confirmatory. A quick PCR based diagnosis of meningitis in cerebrospinal fluids (CSF) using specific primers of virulent Omp85 gene of Neisseria meningitidis can detect as low as 1.0 ng of genomic DNA (G-DNA) in 80 min for confirmation of bacterial meningitis caused by N. meningitidis infection. The 257 bp amplicon of Omp85 gene does not show homology with other suspected pathogens in CSF and can be used as a specific genetic marker for diagnosis of the disease.
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6
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Parker JK, Havird JC, De La Fuente L. Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E). Appl Environ Microbiol 2012; 78:1385-96. [PMID: 22194287 PMCID: PMC3294468 DOI: 10.1128/aem.06679-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/13/2011] [Indexed: 11/20/2022] Open
Abstract
Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though <1 due to high sequence similarity, are significantly greater than housekeeping gene dN/dS ratios and correlate with increased sequence variability. MLSA-E can more precisely resolve relationships between closely related bacterial strains with low genetic variability, such as X. fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.
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Affiliation(s)
- Jennifer K. Parker
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Justin C. Havird
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
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7
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Kim KH, Aulakh S, Tan W, Paetzel M. Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1350-8. [PMID: 22102230 DOI: 10.1107/s174430911103363x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 08/18/2011] [Indexed: 11/10/2022]
Abstract
In Gram-negative bacteria, the BAM complex catalyzes the essential process of assembling outer membrane proteins. The BAM complex in Escherichia coli consists of five proteins: one β-barrel membrane protein, BamA, and four lipoproteins, BamB, BamC, BamD and BamE. Here, the crystal structure of the C-terminal domain of E. coli BamC (BamC(C): Ala224-Ser343) refined to 1.5 Å resolution in space group H3 is reported. BamC(C) consists of a six-stranded antiparallel β-sheet, three α-helices and one 3(10)-helix. Sequence and surface analysis reveals that most of the conserved residues within BamC(C) are localized to form a continuous negatively charged groove that is involved in a major crystalline lattice contact in which a helix from a neighbouring BamC(C) binds against this surface. This interaction is topologically and architecturally similar to those seen in the substrate-binding grooves of other proteins with BamC-like folds. Taken together, these results suggest that an identified surface on the C-terminal domain of BamC may serve as an important protein-binding surface for interaction with other BAM-complex components or substrates.
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Affiliation(s)
- Kelly H Kim
- Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
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8
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Chen D, Li P, Guo W, Ye F, Wu J, Wei D, Guo Z, Ye C. Molecular evolution of candidate sour taste receptor gene PKD1L3 in mammals. Genome 2011; 54:890-7. [PMID: 22011139 DOI: 10.1139/g11-057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The PKD1L3 gene encodes an ion channel protein that can interact with the PKD2L1 protein to form a candidate sour taste receptor. In the present study, we have analyzed the evolutionary patterns of PKD1L3 genes from 10 mammalian species. The results showed that PKD1L3 genes have evolved under a dominant purifying selection force. However, for some branches and sites, PKD1L3 genes were detected to have been operated by positive selection. Moreover, some of these positive evolutionary sites are likely to participate in acid stimulus recognition. In rodents, PKD1L3 genes evolved more rapidly than other mammalian lineages. Combined with other functional research reports, our results suggest that rodents may not be the most appropriate model for functional research on the PKD1L3 gene.
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Affiliation(s)
- Dazhi Chen
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, Sichuan 610031, PR China
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9
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Kim KH, Paetzel M. Crystal structure of Escherichia coli BamB, a lipoprotein component of the β-barrel assembly machinery complex. J Mol Biol 2010; 406:667-78. [PMID: 21168416 DOI: 10.1016/j.jmb.2010.12.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/07/2010] [Accepted: 12/09/2010] [Indexed: 01/20/2023]
Abstract
In Gram-negative bacteria, the BAM (β-barrel assembly machinery) complex catalyzes the essential process of assembling outer membrane proteins. The BAM complex in Escherichia coli consists of five proteins: one β-barrel membrane protein, BamA, and four lipoproteins, BamB, BamC, BamD, and BamE. Despite their role in outer membrane protein biogenesis, there is currently a lack of functional and structural information on the lipoprotein components of the BAM complex. Here, we report the first crystal structure of BamB, the largest and most functionally characterized lipoprotein component of the BAM complex. The crystal structure shows that BamB has an eight-bladed β-propeller structure, with four β-strands making up each blade. Mapping onto the structure the residues previously shown to be important for BamA interaction reveals that these residues, despite being far apart in the amino acid sequence, are localized to form a continuous solvent-exposed surface on one side of the β-propeller. Found on the same side of the β-propeller is a cluster of residues conserved among BamB homologs. Interestingly, our structural comparison study suggests that other proteins with a BamB-like fold often participate in protein or ligand binding, and that the binding interface on these proteins is located on the surface that is topologically equivalent to where the conserved residues and the residues that are important for BamA interaction are found on BamB. Our structural and bioinformatic analyses, together with previous biochemical data, provide clues to where the BamA and possibly a substrate interaction interface may be located on BamB.
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Affiliation(s)
- Kelly H Kim
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada
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10
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Weynants VE, Feron CM, Goraj KK, Bos MP, Denoël PA, Verlant VG, Tommassen J, Peak IRA, Judd RC, Jennings MP, Poolman JT. Additive and synergistic bactericidal activity of antibodies directed against minor outer membrane proteins of Neisseria meningitidis. Infect Immun 2007; 75:5434-42. [PMID: 17664268 PMCID: PMC2168297 DOI: 10.1128/iai.00411-07] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Neisseria meningitidis serogroup B is a major cause of bacterial meningitis in younger populations. The available vaccines are based on outer membrane vesicles obtained from wild-type strains. In children less than 2 years old they confer protection only against strains expressing homologous PorA, a major, variable outer membrane protein (OMP). We genetically modified a strain in order to eliminate PorA and to overproduce one or several minor and conserved OMPs. Using a mouse model mimicking children's PorA-specific bactericidal activity, it was demonstrated that overproduction of more than one minor OMP is required to elicit antibodies able to induce complement-mediated killing of strains expressing heterologous PorA. It is concluded that a critical density of bactericidal antibodies needs to be reached at the surface of meningococci to induce complement-mediated killing. With minor OMPs, this threshold is reached when more than one antigen is targeted, and this allows cross-protection.
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Affiliation(s)
- Vincent E Weynants
- GlaxoSmithKline Biologicals, Rue de l'Institut 89, B-1330 Rixensart, Belgium
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11
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Padhi A, Verghese B, Otta SK. Detecting the form of selection in the outer membrane protein C of Enterobacter aerogenes strains and Salmonella species. Microbiol Res 2007; 164:282-9. [PMID: 17418551 DOI: 10.1016/j.micres.2006.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 12/13/2006] [Indexed: 11/22/2022]
Abstract
The types of selective pressure operating on the outer membrane protein C (ompC) of Enterobacter aerogenes strains, the causative agent for nosocomial infections, and Salmonella sp., the hazardous pathogen are investigated using the maximum likelihood-based codon substitution models. Although the rate of amino acid replacement to the silent substitution (omega) across the entire codon sites of ompC of E. aerogenes (omega=0.3194) and Salmonella sp. (omega=0.2047) indicate that the gene is subjected to purifying selection (i.e. omega<1), approximately 3.7% of ompC codon sites in E. aerogenes (omega=21.52) are under the influence of positive Darwinian selection (i.e. omega>1). Such contrast in the intensity of selective pressures in both pathogens could be associated with the differential response to the adverse environmental changes. In E. aerogenes, majority of the positively selected sites are located in the hypervariable cell-surface-exposed domains whereas the trans-membrane domains are functionally highly constrained.
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Affiliation(s)
- Abinash Padhi
- Department of Biological Science, University of Tulsa, Tulsa, OK-74104, USA.
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12
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Mes THM, van Putten JPM. Positively selected codons in immune-exposed loops of the vaccine candidate OMP-P1 of Haemophilus influenzae. J Mol Evol 2007; 64:411-22. [PMID: 17479342 PMCID: PMC1915622 DOI: 10.1007/s00239-006-0021-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 01/11/2007] [Indexed: 11/28/2022]
Abstract
The high levels of variation in surface epitopes can be considered as an evolutionary hallmark of immune selection. New computational tools enable analysis of this variation by identifying codons that exhibit high rates of amino acid changes relative to the synonymous substitution rate. In the outer membrane protein P1 of Haemophilus influenzae, a vaccine candidate for nontypeable strains, we identified four codons with this attribute in domains that did not correspond to known or assumed B- and T-cell epitopes of OMP-P1. These codons flank hypervariable domains and do not appear to be false positives as judged from parsimony and maximum likelihood analyses. Some closely spaced positively selected codons have been previously considered part of a transmembrane domain, which would render this region unsuited for inclusion in a vaccine. Secondary structure analysis, three-dimensional structural database searches, and homology modeling using FadL of E. coli as a structural homologue, however, revealed that all positively selected codons are located in or near extracellular looping domains. The spacing and level of diversity of these positively selected and exposed codons in OMP-P1 suggest that vaccine targets based on these and conserved flanking residues may provide broad coverage in H. influenzae.
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Affiliation(s)
- Ted H M Mes
- Netherlands Institute of Ecology NIOO-KNAW, Centre for Estuarine and Marine Ecology, AC, Yerseke, The Netherlands.
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13
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Mes THM, Doeleman M, Lodders N, Nübel U, Stal LJ. Selection on protein-coding genes of natural cyanobacterial populations. Environ Microbiol 2007; 8:1534-43. [PMID: 16913914 DOI: 10.1111/j.1462-2920.2006.01044.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the distribution of synonymous and non-synonymous changes in 12 protein-coding genes of natural populations of cyanobacteria to infer changes in gene functionality. By comparing mutation distributions within and across species using the McDonald-Kreitman test, we found data sets to contain evidence for purifying selection (hetR of Trichodesmium, nifH of Cylindrospermopsis raceborskii and rpoC1 of Anabaena lemmermannii) and positive selection (kaiC of Microcoleus chthonoplastes and rbcX of Anabaena and Aphanizomenon sp.). Other genes from the same set of clonal isolates (petB and rbcL in M. chthonoplastes and Anabaena/Aphanizomenon, respectively) did not harbour evidence for either form of selection. The results of branch models of codon evolution agreed fully with the results of the McDonald-Kreitman test in terms of significance and absolute value of the dN/dS estimates. The high frequency of gene-specific mutation patterns and their association with branches that separate closely related cyanobacterial genera suggest that evolutionary tests are suited to uncover gene-specific selective differentiation in cyanobacterial genomes. At the same time, given the lack of information about the history of cyanobacteria, analysis of larger numbers of protein-coding genes of clonal cyanobacterial isolates will produce more detailed pictures of the effects of natural selection.
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Affiliation(s)
- Ted H M Mes
- Netherlands Institute of Ecology (NIOO-KNAW), Centre for Estuarine and Marine Ecology, POB 140, 4400 AC, Yerseke, the Netherlands.
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14
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Bredemeier R, Schlegel T, Ertel F, Vojta A, Borissenko L, Bohnsack MT, Groll M, von Haeseler A, Schleiff E. Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family. J Biol Chem 2006; 282:1882-90. [PMID: 17088246 DOI: 10.1074/jbc.m609598200] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
beta-Barrel-shaped channels of the Omp85 family are involved in the translocation or assembly of proteins of bacterial, mitochondrial, and plastidic outer membranes. We have compared these proteins to understand the evolutionary development of the translocators. We have demonstrated that the proteins from proteobacteria and mitochondria have a pore diameter that is at least five times smaller than found for the Omp85 in cyanobacteria and plastids. This finding can explain why Omp85 from cyanobacteria (but not the homologous protein from proteobacteria) was remodeled to become the protein translocation pore after endosymbiosis. Further, the pore-forming region of the Omp85 proteins is restricted to the C terminus. Based on a phylogenetic analysis we have shown that the pore-forming domain displays a different evolutionary relationship than the N-terminal domain. In line with this, the affinity of the N-terminal domain to the C-terminal region of the Omp85 from plastids and cyanobacteria differs, even though the N-terminal domain is involved in gating of the pore in both groups. We have further shown that the N-terminal domain of nOmp85 takes part in homo-oligomerization. Thereby, the differences in the phylogeny of the two domains are explained by different functional constraints acting on the regions. The pore-forming domain, however, is further divided into two functional regions, where the distal C terminus itself forms a dimeric pore. Based on functional and phylogenetic analysis, we suggest an evolutionary scenario that explains the origin of the contemporary translocon.
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Affiliation(s)
- Rolf Bredemeier
- Ludwig Maximilians University (LMU), Department of Biology I, Menzinger Strasse 67, 80638 München, Germany
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Ichihara H, Kuma KI, Toh H. Positive selection in the ComC-ComD system of Streptococcal Species. J Bacteriol 2006; 188:6429-34. [PMID: 16923913 PMCID: PMC1595358 DOI: 10.1128/jb.00484-06] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Competence-stimulating peptide (CSP) and ComD of the streptococcal species are a pheromone and its receptor, respectively, involved in the regulation of competence for natural genetic transformation. We show here that these molecules have undergone positive selection. This study is the first report of positive selection due to competition among bacterial populations.
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Affiliation(s)
- Hisako Ichihara
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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