Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction

Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2) is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understood however, as the means for signal transduction appears varied among species, while AI-2 synthesis processes appear conserved. Approaches to reveal the recognition pathways of AI-2 will shed light on pathogenicity as we believe recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool) uses a local similarity search heuristic to study gene order, generating homology hits for the genomic arrangement of a query gene sequence. We develop and apply this tool for the E. coli lac and LuxS regulated (Lsr) systems. Lsr is of great interest as it mediates AI-2 uptake and processing. Both test searches generated results that were subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogenetic representation down to trackback plots that preserve genomic organizational information. Through a survey of these results, we demonstrate the identification of orthologs, paralogs, hitchhiking genes, gene loss, gene rearrangement within an operon context, and also horizontal gene transfer (HGT). We found a variety of operon structures that are consistent with our hypothesis that the signal can be perceived and transduced by homologous protein complexes, while their regulation may be key to defining subsequent phenotypic behavior.     

Necessary conditions for the method of inferring phylogeny by linear invariants.

It is known that if all the Markov transition matrices that govern the substitution of one nucleotide for another satisfy six linear constraints, then equations can be derived that permit one to infer evolutionary trees from nucleic acid sequences by the method of linear invariants. These sufficient conditions are also necessary. Any relaxation of them results in the loss of all linear invariants. Necessary conditions for any given set of linear invariants can be derived by examining conditions a matrix must satisfy to map a certain set of matrices into itself. To the extent that necessary conditions are incorrect, a method is not reliable. In a world where different parts of molecules evolve at different rates, the two-parameter model of Kimura may not be empirically distinguishable from the more general one treated here.     

Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms

Sequences from 14 slowly evolving chloroplast genes (including three highly conserved introns) were obtained for representative basal angiosperm and seed-plant taxa, using novel primers described here. These data were combined with published sequences from atpB, rbcL, and newly obtained sequences from ndhF. Combined data from these 17 genes permit sturdy, well-resolved inference of major aspects of basal angiosperm relationships, demonstrating that the new primers are valuable tools for sorting out the deepest events in flowering plant phylogeny. Sequences from the inverted repeat (IR) proved to be particularly reliable (low homoplasy, high retention index). Representatives of Cabomba and Illicium were the first two successive branches of the angiosperms in an initial sampling of 19 exemplar taxa. This result was strongly supported by bootstrap analysis and by two small insertion/deletion events in the slowly evolving introns. Several paleoherb groups (representatives of Piperales) formed a strongly supported clade with taxa representing core woody magnoliids (Laurales, Magnoliales, and Winteraceae). The monophyly of the sampled eudicots and monocots was also well supported. Analyses of three major partitions of the data showed many of the same clades and supported the rooting seen with all the data combined. While Amborella trichopoda was supported as the sister group of the remaining angiosperms when we added Amborella and Nymphaea odorata to the analysis, a strongly conflicting rooting was observed when Amborella alone was added.     

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

The rapid increase in published genomic sequences for bacteria presents the first opportunity to reconstruct evolutionary events on the scale of entire genomes. However, extensive lateral gene transfer (LGT) may thwart this goal by preventing the establishment of organismal relationships based on individual gene phylogenies. The group for which cases of LGT are most frequently documented and for which the greatest density of complete genome sequences is available is the gamma-Proteobacteria, an ecologically diverse and ancient group including free-living species as well as pathogens and intracellular symbionts of plants and animals. We propose an approach to multigene phylogeny using complete genomes and apply it to the case of the gamma-Proteobacteria. We first applied stringent criteria to identify a set of likely gene orthologs and then tested the compatibilities of the resulting protein alignments with several phylogenetic hypotheses. Our results demonstrate phylogenetic concordance among virtually all (203 of 205) of the selected gene families, with each of the exceptions consistent with a single LGT event. The concatenated sequences of the concordant families yield a fully resolved phylogeny. This topology also received strong support in analyses aimed at excluding effects of heterogeneity in nucleotide base composition across lineages. Our analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT. This gene set can be identified and used to yield robust hypotheses for organismal phylogenies, thus establishing a foundation for reconstructing the evolutionary transitions, such as gene transfer, that underlie diversity in genome content and organization.     

Strengths and limitations of molecular sequence comparisons for inferring the phylogeny of the major groups of fishes

Although the phylogenetic relationships of the major groups of fishes have been extensively studied with morphological characters, not all have been convincingly resolved. Analyses of molecular sequences from these groups may provide additional insights into problematical relationships, but are only just beginning to appear. We compare our own results from analyses of 18s ribosomal RNA sequences with those of other studies using globins, parvalbumins, insulin, 28s ribosomal RNA, and portions of two mitochondria1 genes (12S ribosomal RNA and cytochrome b ). Our evaluation of these studies reveals some of the difficulties encountered in reconstructing ancient divergences within the fishes, including unequal rates of evolution (among regions of a molecule as well as among lineages), gene duplication, extinction of lineages, and a possible rapid radiation of gnathostome higher taxa. The importance of evaluating the robustness of particular phylogenetic hypotheses is stressed. Some molecules appear to be inappropriate for investigating higher level divergences within the fishes; others are more promising, but must be examined in more taxa to allow an adequate evaluation of their utility. Convincing support for particular hypotheses of relationship will ultimately require congruence of trees generated from independent molecular data sets.     

The CLC 'chloride channel' family: revelations from prokaryotes

Members of the CLC 'chloride channel' family play vital roles in a wide variety of physiological settings. Research on prokaryotic CLC homologues provided long-anticipated high-resolution structures as well as the unexpected discovery that some CLCs are not chloride channels, but rather are proton-chloride antiporters. Hence, CLCs encompass two functional classes of transport proteins once thought to be fundamentally different from one another. In this review, we discuss the structural features and molecular mechanisms of CLC channels and antiporters. We focus on ClC-0, the most thoroughly studied CLC channel, and ClC-ec1, the prokaryotic antiporter of known structure. We highlight some striking similarities between these CLCs and discuss compelling questions that remain to be addressed. Prokaryotic CLCs will undoubtedly continue to shed light upon this understudied family of proteins.     

A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny

Protein Domain Co-occurrence Network (DCN) is a biological network that has not been fully-studied. We analyzed the properties of the DCNs of H. sapiens, S. cerevisiae, C. elegans, D. melanogaster, and 15 plant genomes. These DCNs have the hallmark features of scale-free networks. We investigated the possibility of using DCNs to predict protein and domain functions. Based on our experiment conducted on 66 randomly selected proteins, the best of top 3 predictions made by our DCN-based aggregated neighbor-counting method achieved a semantic similarity score of 0.81 to the actual Gene Ontology terms of the proteins. Moreover, the top 3 predictions using neighbor-counting, χ(2), and a SVM-based method achieved an accuracy of 66%, 59%, and 61%, respectively, when used to predict specific Gene Ontology terms of human target domains. These predictions on average had a semantic similarity score of 0.82, 0.80, and 0.79 to the actual Gene Ontology terms, respectively. We also used DCNs to predict whether a domain is an enzyme domain, and our SVM-based and neighbor-inference method correctly classified 79% and 77% of the target domains, respectively. When using DCNs to classify a target domain into one of the six enzyme classes, we found that, as long as there is one EC number available in the neighboring domains, our SVM-based and neighboring-counting method correctly classified 92.4% and 91.9% of the target domains, respectively. Furthermore, we benchmarked the performance of using DCNs to infer species phylogenies on six different combinations of 398 single-chromosome prokaryotic genomes. The phylogenetic tree of 54 prokaryotic taxa generated by our DCNs-alignment-based method achieved a 93.45% similarity score compared to the Bergey's taxonomy. In summary, our studies show that genome-wide DCNs contain rich information that can be effectively used to decipher protein function and reveal the evolutionary relationship among species.     

A whole-genome phylogeny of the family Pasteurellaceae

A phylogenomic approach was used to generate an amino acid phylogeny for 12 whole genomes representing 10 species in the family Pasteurellaceae. Orthology of genes was determined using an approach similar to OrthologID (http://nypg.bio.nyu.edu/orthologid/about.html) and resulted in the generation of a matrix with 3130 genes with 1,194,615 aligned amino acid characters of which 239,504 characters are phylogenetically informative. Phylogenetic analysis of the concatenated matrix using all standard approaches (maximum parsimony, maximum likelihood, and Bayesian analysis) results in a single extremely robust phylogenetic hypothesis for the species examined in this study. Remarkably, no single gene partition gives the same tree as the concatenated analysis. By analyzing partitioned support in the data matrix, we show that there is very little negative support emanating from individual gene partitions to suggest that the concatenated hypothesis is not tenable. The large number of characters in the matrix allows us to test hypotheses concerning missing data and character number in phylogenomic studies, and we conclude that matrices constructed using genome level information are very robust to missing data. We show that a very large number of concatenated gene sequences (>160) are needed to reliably obtain the same topology as the overall analysis.     

Gene therapy of T helper cells in HIV infection: Mathematical model of the criteria for clinical effect

The paper presents a mathematical analysis of the criteria for gene therapy of T helper cells to have a clinical effect on HIV infection. The analysis indicates that for such a therapy to be successful, it must protect the transduced cells against HIV-induced death. The transduced cells will not survive as a population if the gene therapy only blocks the spread of virus from transduced cells that become infected. The analysis also suggests that the degree of protection against disease-related cell death provided by the gene therapy is more important than the fraction of cells that is initially transduced. If only a small fraction of the cells can be transduced, transduction of T helper cells and transduction of haematopoietic progenitor cells will result in the same steady-state level of transduced T helper cells. For gene therapy to be efficient against HIV infection, our analysis suggests that a 100% protection against viral escape must be obtained. The study also suggests that a gene therapy against HIV infection should be designed to give the transduced cells a partial but not necessarily total protection against HIV-induced cell death, and to avoid the production of viral mutants insensitive to the gene therapy.     

Reinterpretation of thecal plate homology and phylogeny in the Class Crinoidea

Since the Class Crinoidea was erected in 1821 there has been a consistent failure to resolve the phylogeny of this major group on even the coarsest scale. Reinterpretation of crinoid thecal plate homology, using the orientation of the stem rather than the position of the arms as a reference point for the theca, indicates that two-circlet (monocyclic) crinoids may be derived from three-circlet (dicyclic) taxa by the loss of any one of the three plate circlets in the theca rather than just the lowest circlet as has been assumed previously. Cladistic analysis utilizing this new homology, which is supported by evidence from ontogeny and from the position of other plates in the theca, suggests that Aethocrinus is sister group to all other crinoids and that the Cladida are primitive sister group to both the Disparida and Camerata. The Disparida, Hybocrinida and Perittocrinidae together represent a monophyletic clade. The Camerata also are monophyletic, but the orders Monobathrida and Diplobathrida can no longer be considered to represent natural taxa, with two-circlet camerates probably having evolved more than once. This reinterpretation of thecal plate homology sheds new light on the relationships between the major crinoid groups and the pattern of early crinoid evolution. □ Echinodermata, Crinoidea, homology, phylogeny.     

Molecular evolution of the equilibrative nucleoside transporter family: identification of novel family members in prokaryotes and eukaryotes

Equilibrative nucleoside transporters (ENTs) are integral membrane proteins which enable the movement of hydrophilic nucleosides and nucleoside analogs down their concentration gradients across cell membranes. ENTs were only recently characterized at the molecular level, and little is known about the tertiary structure or distribution of these proteins in nonmammalian organisms. To identify conserved regions, residues, and motifs of ENTs that may indicate functionally important parts of the protein and to better understand the evolutionary history of this protein family, we conducted an exhaustive analysis to characterize and compare ENTs in taxonomically diverse organisms. We have identified novel ENT family members in humans, mice, fish, tunicates, slime molds, and bacteria. This greatly extends our knowledge on the distribution of the ENTs in eukaryotes, and we have identified, for the first time, family members in bacteria. The prokaryote ENTs are attractive models for future studies on transporter tertiary structure and mechanism of substrate translocation. Using sequence similarities, we have identified regions, residues, and motifs that are conserved across all family members. These areas are presumably correlated with function and therefore are important targets for future analysis. Finally, we propose an evolutionary history for the ENT family which clarifies the origin(s) of multiple isoforms in different taxa.     

The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny

We used RT-PCR to sequence approximately 3 kb of the gene coding for the largest subunit of RNA polymerase II (rpb1) from nine land plants. Our results show that plant rpb1 genes all have a similar GC-content and that their amino acid sequences evolve at a similar rate in most species we examined, except for the Arabidopsis thaliana and rice sequences which evolve faster. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve the evolutionary relationships among seed plants. Protein maximum parsimony, as well as neighbor-joining and maximum likelihood analyses of DNA and protein sequences, all generated identical tree topologies with similar strong support values at each node. The angiosperms are a clade comprising Amborella as a sister group to all other angiosperms, followed by Nymphaea, Magnolia, Arabidopsis, and a monocot clade containing maize and rice. The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycas and Zamia clade. These findings concur with recent studies that refute the Anthophyte Hypothesis and place Amborella at the base of the angiosperm tree. These rpb1 sequences also give a more consistent picture of seed plant relationships than similar analyses performed on data sets made of 18S rDNA, atpB, and rbcL sequences from the same species. These sequences therefore show great promise to help further resolve the phylogenetic relationships of seed plants.     

An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins

Annotations of the genes and their products are largely guided by inferring homology. Sequence similarity is the primary measure used for annotation purpose however, the domain content and order were given less importance albeit the fact that domain insertion, deletion, positional changes can bring in functional varieties. Of late, several methods developed quantify domain architecture similarity depending on alignments of their sequences and are focused on only homologous proteins. We present an alignment-free domain architecture-similarity search (ADASS) algorithm that identifies proteins that share very poor sequence similarity yet having similar domain architectures. We introduce a “singlet matching-triplet comparison” method in ADASS, wherein triplet of domains is compared with other triplets in a pair-wise comparison of two domain architectures. Different events in the triplet comparison are scored as per a scoring scheme and an average pairwise distance score (Domain Architecture Distance score - DAD Score) is calculated between protein domains architectures. We use domain architectures of a selected domain termed as centric domain and cluster them based on DAD score. The algorithm has high Positive Prediction Value (PPV) with respect to the clustering of the sequences of selected domain architectures. A comparison of domain architecture based dendrograms using ADASS method and an existing method revealed that ADASS can classify proteins depending on the extent of domain architecture level similarity. ADASS is more relevant in cases of proteins with tiny domains having little contribution to the overall sequence similarity but contributing significantly to the overall function.     

An application of dynamic homology to morphological characters: direct optimization of setae sequences and phylogeny of the family Odontellidae (Poduromorpha, Collembola)

The concept of character and the definition of the attribute are two major theoretical issues of phylogenetics. Lately, great progress has been made in the conceptual development of attributes as historical individuals undergoing series of transformations. While operational application of this ideographic concept of character has been possible since the publication of the direct optimization algorithm and POY software, it has been restricted to molecular characters only. The present paper proposes the first application of direct optimization to morphological characters, in the case study of the phylogeny of Odontellidae. This new homology regime is compared to the traditional homology scheme. The theoretical and operational limitations of the application of direct optimization to morphological characters are discussed. Some thoughts on the basics of its generalization to all morphological characters analyzed in a dynamic homology phylogenetic framework are given.
© The Willi Hennig Society 2009;.     

Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms [corrected

Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships. Traditionally a gene or a set of gene sequences was used for generating phylogenetic trees. Incomplete evolutionary information in few selected genes causes problems in phylogenetic tree construction. Whole genomes are used as remedy. Now, the task is to identify the suitable parameters to extract the hidden information from whole genome sequences that truly represent evolutionary information. In this study we explored a random anchor (a stretch of 100 nucleotides) based approach (ABWGP) for finding distance between any two genomes, and used the distance estimates to compute evolutionary trees. A number of strains and species of Mycobacteria were used for this study. Anchor-derived parameters, such as cumulative normalized score, anchor order and indels were computed in a pair-wise manner, and the scores were used to compute distance/phylogenetic trees. The strength of branching was determined by bootstrap analysis. The terminal branches are clearly discernable using the distance estimates described here. In general, different measures gave similar trees except the trees based on indels. Overall the tree topology reflected the known biology of the organisms. This was also true for different strains of Escherichia coli. A new whole genome-based approach has been described here for studying evolutionary relationships among bacterial strains and species.     

A cladistic phylogeny of the family Patellidae (Mollusca: Gastropoda)

A phylogenetic hypothesis for the patellid limpets is reconstructed by cladistic analysis of morphological characters from 37 species, representing all but one of the living members of the family. Characters included in the analysis are derived from shell shape and microstructure, headfoot and pallial complex, radula and sperm. The species fall into four clades, providing the basis for a new phylogenetic classification into four monophyletic genera: Helcion (four species; southern Africa), Cymbula (eight species; southern Africa, eastern Atlantic, southern Indian Ocean), Scutellastra (17 species; southern and southwestern Africa, Australia, Indo-West Pacific, Eastern Pacific) and Patella (nine species; northeastern Atlantic and Mediterranean). The analysis suggests sister-group relationships between Helcion and Cymbula, and between Scutellastra and Patella. In combination with present-day patterns of geographical distribution, this phylogenetic hypothesis is used to discuss the historical biogeography of the Patellidae. Scutellastra may have originated in southern Africa and dispersed across the Pacific, or alternatively may be a primitively Tethyan group. Both Helcion and Cymbula appear to have originated in southern Africa, but three Cymbula species have dispersed respectively to northwest Africa, St Helena and the southern Indian Ocean. The patellids of the northeastern Atlantic form a single clade, Patella (including P. pellucida), which may have arrived by northward dispersal of an ancestor from southern Africa, or possibly by vicariance of a widespread ancestral Tethyan distribution. The known fossil record of patellids is too fragmentary to permit choice between these alternatives.