Molecular evolution of the Chlamydiaceae.
01 Jan 2001-International Journal of Systematic and Evolutionary Microbiology (Int J Syst Evol Microbiol)-Vol. 51, Iss: 1, pp 203-220
TL;DR: Trees for all five coding genes supported the current organization of the family Chlamydiaceae, and the distribution of virulence traits could not be explained by lateral transfer of the genes the authors studied, since they found no evidence for lateral gene transfer above the species level.
Abstract: Phylogenetic analyses of surface antigens and other chlamydial proteins were used to reconstruct the evolution of the Chlamydiaceae. Trees for all five coding genes [the major outer-membrane protein (MOMP), GroEL chaperonin, KDO-transferase, small cysteine-rich lipoprotein and 60 kDa cysteine-rich protein] supported the current organization of the family Chlamydiaceae, which is based on ribosomal, biochemical, serological, ecological and DNA-DNA hybridization data. Genetic distances between some species were quite large, so phylogenies were evaluated for robustness by comparing analyses of both nucleotide and protein sequences using a variety of algorithms (neighbour-joining, maximum-likelihood, maximum-parsimony with bootstrapping, and quartet puzzling). Saturation plots identified areas of the trees in which factors other than relatedness may have determined branch attachments. All nine species were clearly differentiated by distinctness ratios calculated for each gene. The distribution of virulence traits such as host and tissue tropism were mapped onto the consensus phylogeny. Closely related species were no more likely to share virulence characters than were more distantly related species. This phylogenetically disjunct distribution of virulence traits could not be explained by lateral transfer of the genes we studied, since we found no evidence for lateral gene transfer above the species level. One interpretation of this observation is that when chlamydiae gain access to a new niche, such as a new host or tissue, significant adaptation ensues and the virulence phenotype of the new species reflects adaptation to its environment more strongly than it reflects its ancestry.
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459 citations
TL;DR: The emergence of lymphogranuloma venereum proctitis in men who have sex with men, in Europe, and of a variant with a deletion in the cryptic plasmid, in Sweden, are new features of C. trachomatis infections in the last years.
270 citations
TL;DR: As the largest curated collection of sequences available for a protein-encoding gene, cpnDB provides a resource for researchers interested in exploiting the power of cpn60 as a diagnostic or as a target for phylogenetic or microbial ecology studies, as well as those interested in broader subjects such as lateral gene transfer and codon usage.
Abstract: The advent of genome-scale sequencing projects has led to the availability of full-genome sequences for a variety of organisms including eukaryotes, bacteria, and archaea. This data is an invaluable resource for studies of genome-scale evolutionary processes such as lateral gene transfer and organelle evolution, as well as providing fuel for debates surrounding topics such as the definition of “species,” particularly in the microbial world (Perna et al. 2001). NCBI currently lists 155 complete microbial genomes from 138 bacteria and 17 archaeal species. Obviously, this limited selection inadequately represents the vast microbial diversity present in the environment. As a result of this limitation, large collections of gene-specific sequence data, particularly from universal genes, are an important resource. Historically, small subunit ribosomal RNA (16S rRNA) sequences have been the primary resource for phylogenetic studies and for sequence-based taxonomy (Olsen et al. 1986; Woese et al. 1990; Cole et al. 2003). Given our current understanding of the dynamic nature of genomes and the impact of lateral gene transfer on genome evolution (Boucher et al. 2003), it is important that our view of taxonomy and phylogenetics be informed by more than one target.
A comparison of the sequences of the Escherichia coli groEL gene, which encodes a protein identified as being essential for the posttranslational assembly of bacteriophage particles and the Rubisco subunit-binding protein of higher plant chloroplasts, led to the discovery that these two proteins represent a ubiquitous protein family now known as the type I chaperonins (CPN60; Hemmingsen et al. 1988). “CPN60” is our preferred term for the type I chaperonins that are variously referred to in the literature as “GroEL,” “MopA,” and “Hsp60.” Among the bacterial and eukaryal organisms for which complete genome sequences are available, only the intracellular organisms Mycoplasma pulmonis and Ureaplasma urealyticum have been found to lack cpn60 genes. These organisms also lack other genes previously considered essential for prokaryotic life (Glass et al. 2000; Chambaud et al. 2001). Originally thought to be confined to the bacteria and eukaryotes, cpn60 genes have recently been identified in two members of the archaeal genus, Methanosarcina (Klunker et al. 2003).
Multiple functions have been ascribed to CPN60. Whereas the primary intracellular role of CPN60 is thought to be as a molecular chaperone in the processes of posttranslational protein folding and assembly of protein complexes (for review, see Saibil and Ranson 2002), CPN60 also appears to function as an intercellular signaling molecule (for review, see Maguire et al. 2002). Bacterial and mitochondrial CPN60 complexes consist of homo-14mers, whereas plastid CPN60 complexes contain two subunit types. Multiple cpn60 genes are rare in bacteria but commonplace in eukaryotes, particularly in plants where the genomes contain genes for the mitochondrial cpn60, as well as the two chloroplast cpn60 subunits. For example, the model plant Arabidopsis thaliana contains a total of nine cpn60 genes, three mitochondrial, two chloroplast cpn60-α, and four chloroplast cpn60-β subunit genes (Hill and Hemmingsen 2001).
The universal nature of cpn60 genes makes them attractive targets for phylogenetic studies (Viale and Arakaki 1994; Viale et al. 1994; Viale 1995; Bush and Everett 2001; Jian et al. 2001), as well as clinical tools for detection and identification of organisms (Goh et al. 1997, 1998, 2000; Dale et al. 1998; Kwok et al. 2002; Kwok and Chow 2003; Lew et al. 2003). An analysis of the cpn60 sequences from a variety of bacterial and eukaryotic species led to the design of universal, degenerate PCR primers, which can be applied for the amplification of a 549- to 567-bp region of cpn60 corresponding to nucleotides 274–828 of the E. coli cpn60 sequence from virtually any genome (Goh et al. 1996). The utility of this cpn60 “universal target” (UT) for discriminating closely related bacterial species has been established, and it has been demonstrated that the cpn60 UT region generally provides more discriminating and phylogenetically informative data than the 16S rDNA target (Marston et al. 1999; Brousseau et al. 2001).
The ability to amplify the cpn60 UT from any genomic template has also facilitated the study of complex microbial communities, in which the UT region is amplified from a complex template and libraries of cloned UT sequences are created and sequenced (Hill et al. 2002). A number of the characteristics of the cpn60 gene and of the UT region offer significant advantages over 16S rDNA for studies of complex microbial populations and for quantitative assays. As protein-coding genes, cpn60 sequences are less constrained from sequence variation than are structural RNA-encoding genes. Furthermore, sequence variation extends quite uniformly throughout the cpn60 coding region, whereas variable regions of 16S rRNA genes are dispersed between regions of highly conserved sequence. Highly stable secondary structure that is associated with 16S rRNA is not present in cpn60 genes or transcripts. Generally, cpn60 genes are single copy in prokaryotic genomes, and the relatively small size of the UT facilitates high-throughput sequencing approaches.
Our ongoing efforts to exploit cpn60 as a target for phylogenetic studies, microbial detection and identification, and microbial ecology have led us to gather and curate a large collection of cpn60 (Type I chaperonin) sequence data, as well as sequence from the archaeal thermosome (Type II chaperonin), a homolog of cpn60. To share this resource with the scientific community, we have designed and implemented a Web interface for cpnDB, a curated collection of cpn60 sequence data that is available at http://cpndb.cbr.nrc.ca.
229 citations
TL;DR: These genomic islands, identified in seven tetracycline-resistant C. suis strains, represent the first examples of horizontally acquired DNA integrated into a natural isolate of chlamydiae or within any other obligate intracellular bacterium.
Abstract: Many strains of Chlamydia suis, a pathogen of pigs, express a stable tetracycline resistance phenotype. We demonstrate that this resistance pattern is associated with a resistance gene, tet(C), in the chlamydial chromosome. Four related genomic islands were identified in seven tetracycline-resistant C. suis strains. All resistant isolates carry the structural gene tet(C) and the tetracycline repressor gene tetR(C). The islands share significant nucleotide sequence identity with resistance plasmids carried by a variety of different bacterial species. Three of the four tet(C) islands also carry a novel insertion sequence that is homologous to the IS605 family of insertion sequences. In each strain, the resistance gene and associated sequences are recombined into an identical position in a gene homologous to the inv gene of the yersiniae. These genomic islands represent the first examples of horizontally acquired DNA integrated into a natural isolate of chlamydiae or within any other obligate intracellular bacterium.
163 citations
Cites background from "Molecular evolution of the Chlamydi..."
...It is not likely that this was a single integration event that has been expanded and altered through pig populations, as the major outer membrane protein sequences of each resistant strain are different (5)....
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TL;DR: An overview on methodologies and technologies used currently in diagnosis of chlamydial infections with emphasis on recently developed tests is given, and a combination of a specific real-time PCR assay and a microarray test for chlamydiae is proposed as an alternative reference standard to isolation by cell culture.
150 citations
Cites background from "Molecular evolution of the Chlamydi..."
...Later, additional sequence data, based on the genes 83 of GroEL chaperonin, KDO-transferase, small cysteine-rich lipoprotein and 60 kDa cysteine84 rich protein (ompB), confirmed the new taxonomy (Bush and Everett, 2001)....
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...Later, additional sequence data, based on the genes 83 of GroEL chaperonin, KDO-transferase, small cysteine-rich lipoprotein and 60 kDa cysteine-84 rich protein (ompB), confirmed the new taxonomy (Bush and Everett, 2001)....
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References
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TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
63,427 citations
"Molecular evolution of the Chlamydi..." refers methods in this paper
...Sequences were aligned using (Thompson et al., 1994) and corrected by eye....
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...Sequences were aligned using (Thompson et al., 1994) and corrected by eye....
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TL;DR: Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965), and a number of other parsimony methods have since appeared in the systematic literature and found widespread use in studies of molecular evolution.
Abstract: Felsenstein, J. (Department of Genetics, University of Washington, Seattle, WA 98195) 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.-For some simple threeand four-species cases involving a character with two states, it is determined under what conditions several methods of phylogenetic inference will fail to converge to the true phylogeny as mo,re and more data are accumulated. The methods are the Camin-Sokal parsimony method, the compatibility method, and Farris's unrooted Wagner tree parsimony method. In all cases the conditions for this failure (which is the failure to be statistically consistent) are essentially that parallel changes exceed informative, nonparallel changes. It is possible for these methods to be inconsistent even when change is improbable a priori, provided that evolutionary rates in different lineages are sufficiently unequal. It is by extension of this approach that we may provide a sound methodology for evaluating methods of phylogenetic inference. [Numerical cladistics; phylogenetic inference; maximum likelihood estimation; parsimony; compatibility.] Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965). This class of methods for inferring an evolutionary tree from discrete-character data involves making a reconstruction of the changes in a given set of characters on a given tree, counting the smallest number of times that a given kind of event need have happened, and using this as the measure of the adequacy of the evolutionary tree. (Alternatively, one can compute the weighted sum of the numbers of times several different kinds of events have occurred.) One attempts to find that evolutionary tree which requires the fewest of these evolutionary events to explain the observed data. Camin and Sokal treated the case of irreversible changes along a character state tree, minimizing the number of changes I This report was prepared as an account of work sponsored by the United States Government. Neither the United States nor the United States Department of Energy, nor any of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use would not infringe privatelyowned rights. of character states required. A number of other parsimony methods have since appeared in the systematic literature (Kluge and Farris, 1969; Farris, 1969, 1970, 1972, 1977; Farris, Kluge, and Eckhardt, 1970) and parsimony methods have also found widespread use in studies of molecular evolution (Fitch and Margoliash, 1967, 1970; Dayhoff and Eck, 1968; see also Fitch, 1973). Cavalli-Sforza and Edwards (1967; Edwards and Cavalli-Sforza, 1964) earlier formulated a minimum evolution method for continuous-character data. An alternative methodology for phylogenetic inference is the compatibility method, introduced by Le Quesne (1969, 1972). He suggested that phylogenetic inference be based on finding the largest possible set of characters -which could simultaneously have all states be uniquely derived -on the same ftree. The estimate of the phylogeny is then takento be that tree.-While Le Quesne's specific suggestions as to how this might be done have been criticized by Farris (1969), his general approach, which is based on Camin and Sokal's (1965) concept of the compatibility of two characters, has been made rigorous and extended in a series of papers by G. F. Estabrook, C. S. Johnson, Jr., and F. R. McMorris (Estabrook,
3,220 citations
"Molecular evolution of the Chlamydi..." refers background in this paper
...When no correlation remains (as the slope approaches zero), mutational saturation is said to have occurred, and processes such as longbranch attraction (Felsenstein, 1978) rather than relatedness might be determining the attachment of branches between distantly related clades....
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TL;DR: A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data and outperforms neighbor joining in some cases with high transition/transversion bias.
Abstract: A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximum-likelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet trees serve as starting points to reconstruct a set of optimal n-taxon trees. The majority rule consensus of these trees defines the quartet puzzling tree and shows groupings that are well supported. Computer simulations show that the performance of quartet puzzling to reconstruct the true tree is always equal to or better than that of neighbor joining. For some cases with high transition/transversion bias quartet puzzling outperforms neighbor joining by a factor of 10. The application of quartet puzzling to mitochondrial RNA and tRNAVd’ sequences from amniotes demonstrates the power of the approach. A PHYLIP-compatible ANSI C program, PUZZLE, for analyzing nucleotide or amino acid sequence data is available.
2,620 citations
TL;DR: The phylogenetic mosaic of chlamydial genes, including a large number of genes with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to obligate intracellular parasitism.
Abstract: Analysis of the 1,042,519-base pair Chlamydia trachomatis genome revealed unexpected features related to the complex biology of chlamydiae. Although chlamydiae lack many biosynthetic capabilities, they retain functions for performing key steps and interconversions of metabolites obtained from their mammalian host cells. Numerous potential virulence-associated proteins also were characterized. Several eukaryotic chromatin-associated domain proteins were identified, suggesting a eukaryotic-like mechanism for chlamydial nucleoid condensation and decondensation. The phylogenetic mosaic of chlamydial genes, including a large number of genes with phylogenetic origins from eukaryotes, implies a complex evolution for adaptation to obligate intracellular parasitism.
1,627 citations
"Molecular evolution of the Chlamydi..." refers background in this paper
...Recent studies showing that a large number of sequences in the genomes of both Chlamydia trachomatis and Chlamydophila pneumoniae appear to be distantly related to genes in plants and other organisms has encouraged such hypotheses (Stephens et al., 1998; Wolf et al., 1999)....
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...Recent studies showing that a large number of sequences in the genomes of both Chlamydia trachomatis and Chlamydophila pneumoniae appear to be distantly related to genes in plants and other organisms has encouraged such hypotheses (Stephens et al., 1998; Wolf et al., 1999)....
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TL;DR: Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.
Abstract: From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a "universal tree of life," taking it as the basis for a "natural" hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties. More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If "chimerism" or "lateral gene transfer" cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the "true tree," not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.
1,585 citations