The evolution of the tape measure protein: units, duplications and losses

<p>Abstract</p> <p>Background</p> <p>A large family of viruses that infect bacteria, called <it>phages</it>, is characterized by long tails used to inject DNA into their victims' cells. The <it>tape measure protein</it> got its name because the length of the corresponding gene is proportional to the length of the phage's tail: a fact shown by actually copying or splicing out parts of DNA in exemplar species. A natural question is whether there exist <it>units</it> for these tape measures, and if different tape measures have different units and lengths. Such units would allow us to retrace the evolution of tape measure proteins using their duplication/loss history. The vast number of sequenced phages genomes allows us to attack this problem with a comparative genomics approach.</p> <p>Results</p> <p>Here we describe a subset of phages whose tape measure proteins contain variable numbers of an 11 amino acids sequence repeat, aligned with sequence similarity, structural properties, and simple arithmetics. This subset provides a unique opportunity for the combinatorial study of phage evolution, without the added uncertainties of multiple alignments, which are trivial in this case, or of protein functions, that are well established. We give a heuristic that reconstructs the duplication history of these sequences, using divergent strains to discriminate between mutations that occurred before and after speciation, or lineage divergence. The heuristic is based on an efficient algorithm that gives an exhaustive enumeration of all possible parsimonious reconstructions of the duplication/speciation history of a single nucleotide. Finally, we present a method that allows, when possible, to discriminate between duplication and loss events.</p> <p>Conclusions</p> <p>Establishing the evolutionary history of viruses is difficult, in part due to extensive recombinations and gene transfers, and high mutation rates that often erase detectable similarity between homologous genes. In this paper, we introduce new tools to address this problem.</p

Parsimony and likelihood reconstruction of human segmental duplications

Motivation: Segmental duplications > 1 kb in length with ≥ 90% sequence identity between copies comprise nearly 5% of the human genome. They are frequently found in large, contiguous regions known as duplication blocks that can contain mosaic patterns of thousands of segmental duplications. Reconstructing the evolutionary history of these complex genomic regions is a non-trivial, but important task

Tandemly Arrayed Genes in Vertebrate Genomes

Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Background: Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences. Results: We describe a polynomial-time exact algorithm to compute duplication distance, a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string. This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions. Finally, we provide an description of a sequence of duplication events as a context-free grammar (CFG). Conclusion: These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes.

Deep conservation of human protein tandem repeats within the eukaryotes

Tandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture for proteins TRs, we performed a proteome-wide analysis of the mode of evolution for human TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs we reconstructed bi-species TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Mya ago. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from http://www.atgc-montpellier.fr/TRE

Duplication and inversion history of a tandemly repeated genes family

International audienceGiven a phylogenetic tree for a family of tandemly repeated genes and their signed order on the chromosome, we aim to find the minimum number of inversions compatible with an evolutionary history of this family. This is the first attempt to account for inversions in an evolutionary model of tandemly repeated genes. We present a branch-and-bound algorithm that finds the exact solution, and a polynomial-time heuristic based on the breakpoint distance. We show, on simulated data, that those algorithms can be used to improve phylogenetic inference of tandemly repeated gene families. An application on a published phylogeny of KRAB zinc finger genes is presented

Applications of AI planning in genome rearrangement and in multi-robot systems

In AI planning the aim is to plan the actions of an agent to achieve the given goals from a given initial state. We use AI planning to solve two challenging problems: the genome rearrangement problem in computational biology and the decoupled planning problem in multi-robot systems. Motivated by the reconstruction of phylogenies, the genome rearrangement problem seeks to find the minimum number of rearrangement events (i.e., genome-wide mutations) between two given genomes. We introduce a novel method (called GENOMEPLAN) to solve this problem for single chromosome circular genomes with unequal gene content and/or duplicate genes, by formulating the pairwise comparison of entire genomes as an AI planning problem and using the AI planner TLPlan to compute solutions. The idea is to plan genome rearrangement events to transform one genome to the other. To improve computational efficiency, GENOMEPLAN embeds several heuristics in the descriptions of these events. To better understand the evolutionary history of species and to find more plausible solutions, GENOMEPLAN allows assigning costs and priorities to rearrangement events. The applicability of GENOMEPLAN is shown by some experiments on real data sets as well as randomly generated instances. In multi-robot systems, multiple teams of heterogeneous robots work in separate workspaces towards different goals. The teams are allowed to lend robots to one another. The goal is to find an overall plan of minimum length where each team completes its assigned task. We introduce an intelligent algorithm to solve this problem. The idea is, on the one hand, to allow each team to autonomously find its own plan and, on the other hand, to allow a central agent to communicate with the representatives of the teams to find an optimal decoupled plan. We prove the soundness and completeness of our decoupled planning algorithm, and analyze its computational complexity. We show the applicability of our approach on an intelligent factory scenario, using the action description language C+ for representing the domain and the causal reasoner CCALC for reasoning about the domain