Recurring cluster and operon assembly for Phenylacetate degradation genes

<p>Abstract</p> <p>Background</p> <p>A large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. Most of these theories have been dismissed because empirical data do not match the expectations of the models. In this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process.</p> <p>Results</p> <p>We have selected an exemplar well-characterised biochemical pathway, the phenylacetate degradation pathway, and we show that its complex history is only compatible with a model where a selective advantage accrues from moving genes closer together. This selective pressure is likely to be reasonably weak and only twice in our dataset of 102 genomes do we see independent formation of a complete cluster containing all the catabolic genes in the pathway. Additionally, <it>de novo </it>clustering of genes clearly occurs repeatedly, even though recombination should result in the random dispersal of such genes in their respective genomes. Interspecies gene transfer has frequently replaced <it>in situ </it>copies of genes resulting in clusters that have similar content but very different evolutionary histories.</p> <p>Conclusion</p> <p>Our model for cluster formation in prokaryotes, therefore, consists of a two-stage selection process. The first stage is selection to move genes closer together, either because of macromolecular crowding, chromatin relaxation or transcriptional regulation pressure. This proximity opportunity sets up a separate selection for co-transcription.</p

The causes of protein evolutionary rate variation

The rate of protein evolution varies more than 1000-fold and, for the past 30 years, it was thought that the rate was determined by protein function. Drummond and co-workers have now shown that a single factor underlying mRNA expression, protein abundance and synonymous codon usage is the chief causal agent of protein evolutionary rate in yeast. It will be interesting to see whether this is shown to be a universal rule for all biological systems

The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods

<p>Abstract</p> <p>Background</p> <p>In the past decade or more, the emphasis for reconstructing species phylogenies has moved from the analysis of a single gene to the analysis of multiple genes and even completed genomes. The simplest method of scaling up is to use familiar analysis methods on a larger scale and this is the most popular approach. However, duplications and losses of genes along with horizontal gene transfer (HGT) can lead to a situation where there is only an indirect relationship between gene and genome phylogenies. In this study we examine five widely-used approaches and their variants to see if indeed they are more-or-less saying the same thing. In particular, we focus on Conditioned Reconstruction as it is a method that is designed to work well even if HGT is present.</p> <p>Results</p> <p>We confirm a previous suggestion that this method has a systematic bias. We show that no two methods produce the same results and most current methods of inferring genome phylogenies produce results that are significantly different to other methods.</p> <p>Conclusion</p> <p>We conclude that genome phylogenies need to be interpreted differently, depending on the method used to construct them.</p

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing

With the number of fully sequenced genomes increasing steadily, there is greater interest in performing large-scale phylogenomic analyses from large numbers of individual gene families. Maximum likelihood (ML) has been shown repeatedly to be one of the most accurate methods for phylogenetic construction. Recently, there have been a number of algorithmic improvements in maximum-likelihood-based tree search methods. However, it can still take a long time to analyse the evolutionary history of many gene families using a single computer. Distributed computing refers to a method of combining the computing power of multiple computers in order to perform some larger overall calculation. In this article, we present the first high-throughput implementation of a distributed phylogenetics platform, MultiPhyl, capable of using the idle computational resources of many heterogeneous non-dedicated machines to form a phylogenetics supercomputer. MultiPhyl allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching and bootstrapping of each of the alignments using many desktop machines. The program implements a set of 88 amino acid models and 56 nucleotide maximum likelihood models and a variety of statistical methods for choosing between alternative models. A MultiPhyl webserver is available for public use at: http://www.cs.nuim.ie/distributed/multiphyl.php

New methods ring changes for the tree of life

Relationships among prokaryotes and the origin of eukaryotes have both proven controversial, with results depending upon the gene sequences and methods used. Extensive horizontal gene transfer is one possible reason why inferring such deep phylogenetic relationships is difficult. In two recent papers, Lake and Rivera introduce new methods that can be used to reconstruct the genomic tree in the presence of horizontal gene transfers, but which suggest that a ring rather than a tree is a better representation of some parts of the history of life on Earth

New methods ring changes for the tree of life

Relationships among prokaryotes and the origin of eukaryotes have both proven controversial, with results depending upon the gene sequences and methods used. Extensive horizontal gene transfer is one possible reason why inferring such deep phylogenetic relationships is difficult. In two recent papers, Lake and Rivera introduce new methods that can be used to reconstruct the genomic tree in the presence of horizontal gene transfers, but which suggest that a ring rather than a tree is a better representation of some parts of the history of life on Earth

Adaptive evolution of the human fatty acid synthase gene: Support for the cancer selection and fat utilization hypotheses?

Cancer may act as the etiological agent for natural selection in some genes. This selective pressure would act to reduce the success of neoplastic lineages over normal cell lineages in individuals of reproductive age. In addition, humanâs relatively larger brain and longer lifespan may have also acted as a selective force requiring new genotypes. One of the most important proteins in both processes is the fatty acid synthase (FAS) gene involved in fatty acid biosynthesis. Avariety of other proteins, including PTEN, MAPK1, SREBP1, SREBP2 and PI are also involved in the regulation of fatty acid biosynthesis. We have specifically analysed variability in selective pressure across all these genes in human, mouse and other vertebrates.We have found that the FAS gene alone has signatures indicative of adaptive evolution.We did not find any signatures of adaptive evolution in any of the other proteins. In the FAS gene, we have detected an excess of non-synonymous over synonymous substitutions in approximately 6% of sites in the human lineage. Contrastingly, the substitution process at these sites in other available vertebrates and mammals indicates strong purifying selection. This is likely to reflect a functional shift in human FAS and correlates well with previously observed changes in FAS biochemical activities. We speculate that the role played by FAS either in cancer development or in human brain development has created this selective pressure, although we cannot rule out the various other functions of FAS

Characterization of endospore-forming bacteria associated with entomopathogenic nematodes, Heterorhabditis spp., and description of Paenibacillus nematophilus sp. nov.

Endospore-forming bacteria were isolated from insect-pathogenic nematodes, Heterorhabditis spp., from three diverse geographical locations. Spindle-shaped sporangia of these bacteria adhere to the free-living infective stage of the nematode, which carries them to new insect hosts, where the bacterium reproduces. These isolates were characterized based on phenotypic and chemotaxonomic properties and 16S rRNA gene sequences. Analysis of the 16S rRNA gene placed the isolates within the genus Paenibacillus. The isolates shared higher sequence similarities with each other (95.1-100%) than they did with any other named species within the genus (89.2-94%). Paenibacillus macquariensis, Paenibacillus azoreducens, Paenibacillus amylolyticus and Paenibacillus durus were among the species with highest sequence similarity to these isolates. The isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C15:0 and C16:0 were among the major fatty acid types and the DNA G + C content was approximately 44 mol% in all isolates. DNA-DNA similarity studies revealed genomic heterogeneity among the isolates, such that they are likely to represent more than one species. Two of the isolates (both from a Heterorhabditis megidis isolate from Estonia) are phenotypically distinguishable from the others and are proposed as a single species, Paenibacillus nematophilus sp. nov. The type strain for this novel species is NEM1aT (=DSM 13559T =NCIMB 13845T). The other isolates, although closely related to the proposed species, are likely to represent at least one, but most likely two, novel species

Genome Phylogenies Indicate a Meaningful a-Proteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales

Placement of the mitochondrial branch on the tree of life has been problematic. Sparse sampling, the uncertainty of how lateral gene transfer might overwrite phylogenetic signals, and the uncertainty of phylogenetic inference have all contributed to the issue. Here we address this issue using a supertree approach and completed genomic sequences. We first determine that a sensible a-proteobacterial phylogenetic tree exists and that it can confidently be inferred using orthologous genes. We show that congruence across these orthologous gene trees is significantly better than might be expected by random chance. There is some evidence of horizontal gene transfer within the a-proteobacteria, but it appears to be restricted to a minority of genes (;23%) most of whom (;74%) can be categorized as operational. This means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer. We then show that there is a consistently strong signal for placement of the mitochondrion on this tree and that this placement is relatively insensitive to methodological approach or data set. A concatenated alignment was created consisting of 15 mitochondrion-encoded proteins that are unlikely to have undergone any lateral gene transfer in the timeline under consideration. This alignment infers that the sister group of the mitochondria, for the taxa that have been sampled, is the order Rickettsiales