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PubMed2005

ProbCons: Probabilistic consistency-based multiple sequence alignment.

To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consistency, a novel scoring function for multiple sequence comparisons. We present ProbCons, a practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment benchmark data sets. On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource.

Algorithms↗
PubMed2005

Compositional properties of random Boolean networks.

Random Boolean networks (RBNs) are used in a number of applications, including cell differentiation, immune response, evolution, gene regulatory networks, and neural networks. This paper addresses the problem of computing attractors in RBNs. An RBN with n vertices has up to 2(n) states. Therefore, for large n , computing attractors by full enumeration of states is not feasible. The state space can be reduced by removing irrelevant vertices, which have no influence on the network's dynamics. In this paper, we show that attractors of an RBN can be computed compositionally from the attractors of the independent components of the subgraph induced by the relevant vertices of the network. The presented approach reduces the complexity of the problem from O (2(n)) to O (2(l)), where l is the number of relevant vertices in the largest component.

Journal Article↗
PubMed1983

Soybean Mutants Lacking Constitutive Nitrate Reductase Activity : II. Nitrogen Assimilation, Chlorate Resistance, and Inheritance.

Nitrogen assimilation in three nitrate reductase (NR) mutants of soybean (Glycine max L. Merr. cv Williams) was studied in the growth chamber and in the field. These mutants, LNR-2, LNR-3, and LNR-4, lack the non-NO(3) (-)-inducible or constitutive fraction of leaf NR activity found in wild-type plants, but this had no effect on the concentration of nitrogen accumulated when grown on NO(3) (-) in the growth chamber. Dry weight accumulation of two of the mutants (LNR-3 and LNR-4) was decreased relative to LNR-2 and wild type. In the field, LNR-2 had dry weights and nitrogen concentrations similar to the wild type at 34 and 61 days after planting, and at maturity. Acetylene reduction activities were also similar at 61 days.Urea-grown LNR-2 seedlings lack both inducible and constitutive NR activity, and were resistant to four days of treatment with 0.5 mm ClO(3) (-). Urea-grown wild-type seedlings, having only constitutive NR activity, developed ClO(3) (-) toxicity symptoms and suffered decreases in unifoliolate leaf NR activity and chlorophyll concentration. This suggests that (a) the reduction of ClO(3) (-) to ClO(2) (-) by NR is the major cause of ClO(3) (-) toxicity in soybeans and (b) the constitutive NR is active in situ.Segregation of the F(2) of reciprocal crosses between the wild type and the mutants indicated that absence of constitutive NR activity was controlled by a single recessive nuclear gene. Evolution of NO((x)) gas was also absent in these mutants, and this was found to be inherited jointly with constitutive NR activity: in 346 segregants, no recombinants were found. Allelism tests between LNR-2 and LNR-3, and LNR-2 and LNR-4, indicated that the constitutive NR mutation was at the same locus in each mutant.

Journal Article↗
PubMed1997

The testis: the witness of the mating system, the site of mutation and the engine of desire.

There is now abundant evidence in a wide range of mammalian and non-mammalian species to show that the relative size of the testis and the morphology of the spermatozoa are infallible predictors of the mating system. Species with the largest testis/body weight ratios and the best spermatozoa have a multi-male or promiscuous mating system in which sperm competition operates. Judged by these criteria, men were not designed to be promiscuous. There is increasing evidence in humans to show that most spontaneous mutations of the germ line occur in the testis. Because these provide the variability on which natural selection can operate, the testis holds the key to evolution. Genes on the Y chromosome that control male fertility are particularly prone to mutations, perhaps because of the mutagenic metabolites produced by the metabolically active testis. Testicular descent into a scrotum, and cooling by countercurrent heat exchange between the spermatic artery and vein may have evolved as a way of holding the mutation rate in check. The hormones secreted by the testis, which control libido and aggression, ensure that these male mutations are disseminated as widely as possible throughout the population.

Animals↗
PubMed2006

Different levels of transcriptional regulation due to trophic constraints in the reduced genome of Buchnera aphidicola APS.

Symbiotic associations involving intracellular microorganisms and animals are widespread, especially for species feeding on poor or unbalanced diets. Buchnera aphidicola, the obligate intracellular bacterium associated with most aphid species, provides its hosts with essential amino acids (EAAs), nutrients in short supply in the plant phloem sap. The Buchnera genome has undergone severe reductions during intracellular evolution. Genes for EAA biosynthesis are conserved, but most of the transcriptional regulatory elements are lost. This work addresses two main questions: is transcription in Buchnera (i) regulated and (ii) scaled to aphid EAA demand? Two microarray experiments were designed for profiling the gene expression in Buchnera. The first one was characterized by a specific depletion of tyrosine and phenylalanine in the aphid diet, and the second experiment combined a global diminution of EAAs in the aphid diet with a sucrose concentration increase to manipulate the aphid growth rate. Aphid biological performance and budget analysis (the balance between EAAs provided by the diet and those synthesized by Buchnera) were performed to quantify the nutritional demand from the aphids toward their symbiotic bacteria. Despite the absence of known regulatory elements, a significant transcriptional regulation was observed at different levels of organization in the Buchnera genome: between genes, within putative transcription units, and within specific metabolic pathways. However, unambiguous evidence for transcriptional changes underpinning the scaling of EAA biosynthesis to aphid demand was not obtained. The phenotypic relevance of the transcriptional response from the reduced genome of Buchnera is addressed.

Amino Acids, Essential↗
PubMed2004

Diverse tetracycline resistance genotypes of Megasphaera elsdenii strains selectively cultured from swine feces.

A total of 30 Megasphaera elsdenii strains, selectively isolated from the feces of organically raised swine by using Me109 M medium, and one bovine strain were analyzed for tetracycline resistance genotypic and phenotypic traits. Tetracycline-resistant strains carried tet(O), tet(W), or a tet gene mosaic of tet(O) and tet(W). M. elsdenii strains carrying tet(OWO) genes exhibited the highest tetracycline MICs (128 to >256 microg/ml), suggesting that tet(O)-tet(W) mosaic genes provide the selective advantage of greater tetracycline resistance for this species. Seven tet genotypes are now known for M. elsdenii, an archetype commensal anaerobe and model for tet gene evolution in the mammalian intestinal tract.

Animals↗
PubMed2005

cse, a Chimeric and variable gene, encodes an extracellular protein involved in cellular segregation in Streptococcus thermophilus.

The isolation of a Streptococcus thermophilus CNRZ368 mutant displaying a long-chain phenotype allowed us to identify the cse gene (for cellular segregation). The N terminus of Cse exhibits high similarity to Streptococcus agalactiae surface immunogenic protein (SIP), while its C terminus exhibits high similarity to S. thermophilus PcsB. In CNRZ368, deletion of the entire cse open reading frame leads to drastic lengthening of cell chains and altered colony morphology. Complementation of the Deltacse mutation with a wild-type allele restored both wild-type phenotypes. The central part of Cse is a repeat-rich region with low sequence complexity. Comparison of cse from CNRZ368 and LMG18311 strains reveals high variability of this repeat-rich region. To assess the impact of this central region variability, the central region of LMG18311 cse was exchanged with that of CNRZ368 cse. This replacement did not affect chain length, showing that divergence of the central part does not modify cell segregation activity of Cse. The structure of the cse locus suggests that the chimeric organization of cse results from insertion of a duplicated sequence deriving from the pcsB 3' end into an ancestral sip gene. Thus, the cse locus illustrates the module-shuffling mechanism of bacterial gene evolution.

Cell Compartmentation↗
PubMed1982

Isolation and characterization of a variant of mouse plasmacytoma J558 synthesizing a 110,000-dalton immunoglobulin heavy chain and of secondary variants synthesizing either a 55,000-dalton or an 80,000-dalton immunoglobulin heavy chain: possible implications.

A mutant has been isolated from the J558 (immunoglobulin A, lambda, anti-alpha 1 leads to 3 dextran) cell line which synthesizes a heavy-chain immunoglobulin twice the size of normal heavy chain. Secondary variants that synthesized heavy chains either 1.5 times as large as wild type or the same size as wild type were identified. All mutants were serologically immunoglobulin continued to bind antigen, and retained the individual idiotype of the parent. Northern blot analysis and in vitro synthesis studies showed that the large heavy chains were primary synthetic products and not the consequence of abnormal covalent bonds. Cleavage of genomic DNA with restriction endonucleases and molecular hybridization studies showed new fragments in the 2 X and 1.5 X mutants which disappeared in the 1 X revertant. These data cannot easily be reconciled with the mutants arising either by unequal recombination or gene conversion. Further molecular characterization of these mutants should give additional insight into immunoglobulin gene evolution.

Animals↗
PubMed1989

A moveable 5' splice site in adenine phosphoribosyltransferase genes of Drosophila species.

In two distantly related Drosophila species, the use of alternate 5' splice sites to process an intron in pre-mRNA from homologous adenine phosphoribosyltransferase (APRT)-encoding genes led to RNAs encoding nonfunctional peptides in addition to APRT. The production of aberrantly spliced transcripts as a normal feature of gene expression supports a general model of eucaryotic gene evolution through alternative splicing and moveable splice junctions.

Adenine Phosphoribosyltransferase↗
PubMedDate not supplied

Conserved and non-conserved loci of the glucagon gene in old world ruminating ungulates.

The homology and diversification of genomic sequence encoding glucagon gene among native Egyptian buffalos, camel and sheep were tested using cattle as model. Oligodeoxynucleotide primers designed from the available GenBank data were used for PCR probing of the glucagon gene encoding sequence at different loci. The DNA oligomer probes were constructed to flank either the whole gene encoding sequence or different intra-gene encoding sequences. The PCR products were visualized using agarose gel electrophoresis. All species showed a same size band of prepro-glucagon when PCR was used to amplify the whole gene encoding sequence. In contrary, amplifications of different intra-gene loci failed to give the same results. The results indicated variable degrees of diversity among old world ruminating ungulates in the glucagon gene encoding sequence. Compared with other ruminants, the variation appears predominantly in camel. Surprisingly, the similarity in size between both amplification products of whole gene encoding sequence and the proposed size of glucagon cDNA definitely excludes the possibility of large intervening introns spanning the genomic sequence of the glucagon gene in these species. This indicates that, in contrast to other tested mammals, the glucagon gene includes an essentially full-length copy of glucagon mRNA. The study revealed a possible new aspect of glucagon gene evolution in order to correlate its corresponding protein function among different ruminant species.

Amino Acid Sequence↗
PubMed1997

MIRs are present in coding regions of human genes.

By using a weighted function and the method of enlarged similarity a search has been performed to identify mammalian interspersed repeats (MIRs) in DNA sequences from the EMBL data bank. The existence of MIRs is shown in coding regions of human genes and also in chicken and duck genomes. It is possible to conclude from the results obtained that MIRs were established in the coding regions of some genes and may have taken part in gene evolution. Furthermore, MIRs may have been amplified in vertebrate genomes before the origin of mammals.

Algorithms↗
PubMed2003

[Fundamental and applied aspects of comparative genomics of vertebrates].

The Human Genome Project stimulated the development of efficient strategies and relevant hardware for complete genome sequencing. The comparative genomic approach extends the possibilities of using the sequencing data to identify new genes or conserved regulatory regions by means of nucleotide sequence alignment of the particular regions of the mouse and human genomes, or to trace the evolutionary events resulting in the genome structure of modern mammals. The review focuses on the use of new molecular cytogenetic methods along with computer-aided analysis of the genomes in vertebrates. Several factors hindering data analysis are considered. The currently available information on gene evolution rate inferred from comparative genomic data is presented. The origin and evolution of the genomes of several species are discussed.

Animals↗
PubMed2005

An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus.

Teleost fish genome projects involving model species are resulting in a rapid accumulation of genomic and expressed DNA sequences in public databases. The expressed sequence tags (ESTs) collected in the databases can be mined for the analysis of both structural and functional genomics. In this study, we in silico analyzed 49,430 unigenes representing a total of 692,654 ESTs from four model fish for their potential use in developing simple sequence repeats (SSRs), or microsatellites. After bioinformatical mining, a total of 3,018 EST derived SSRs (EST-SSRs) were identified for 2,335 SSR containing ESTs (SSR-ESTs). The frequency of identified SSR-ESTs ranged from 1.5% for Xiphophorus to 7.3% for zebrafish. The dinucleotide repeat motif is the most abundant SSR, accounting for 47%, 52%, 64%, and 78% for medaka, Fundulus, zebrafish, and Xiphophorus, respectively. Simulation analysis suggests that a majority of these EST-SSRs have sufficient flanking sequences for polymerase chain reaction (PCR) primer design. Comparative DNA sequence analyses of SSR-ESTs identified several cross-species SSRs and sequences that may be used as cross-reference genes in comparative studies. For example, the flanking sequences of one SSR (CTG)n within the pituitary tumor-transforming gene (PTTG) 1 interacting protein (PTTGIP), showed conservation spanning the medaka, Fundulus, human, and mouse genomes. This study provides a large body of information on EST-SSRs that can be useful for the development of polymorphic markers, gene mapping, and comparative genome analysis. Functional analysis of these SSR-ESTs may reveal their role in metabolism and gene evolution of these model species.

Amino Acid Sequence↗
PubMedDate not supplied

Cloning and characterization of the gene encoding M.FauI DNA methyltransferase.

The enzymes of the FauI restriction-modification system from the Flavobacterium aquatile strain recognize the non-palindromic sequence 5'-CCCGC-3'/3'-GG-GCG-5'. We have cloned the gene encoding the DNA modifying component of this system and determined its nucleotide sequence. The deduced amino acid sequence contains ten conserved motifs characteristic for [cytosine-5] DNA methyltransferases. Part of the gene sequence that encodes the putative target recognizing domain of the M.FauI shows some homology with the downstream region, thus indicating that duplication of the DNA segment was probably involved in the gene evolution.

Amino Acid Sequence↗
PubMed1991

Independent gene duplications, not concerted evolution, explain relationships among class I MHC genes of murine rodents.

It has been claimed that class I MHC loci are homogenized within species by frequent events of interlocus genetic exchange ("concerted evolution"). Evidence for this process includes the fact that certain rat class I loci (including RT1.A) located centromeric to class II and class III are more similar to each other than to the mouse K locus (also centromeric to class II/class III). However, a phylogenetic analysis showed that the rat RT1.A locus is in fact orthologous to the mouse K1 pseudogene (also centromeric to class II/class III). Thus, two independent events of translocation of genes centromeric to class II/class III have occurred in the history of the murine rodents, at least one of which (involving the ancestor of RT1.A and K1) occurred prior to the divergence of rat and mouse. It was also found that the rat nonclassical class I gene RT.BM1 is orthologous to the mouse nonclassical gene 37d. These results argue that interlocus genetic exchange does not occur at a rate sufficient to cause within-species homogenization of class I MHC loci.

Animals↗
PubMed2001

Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution.

Unlike in animals, the functional transfer of mitochondrial genes to the nucleus is an ongoing process in plants. All but one of the previously reported transfers in angiosperms involve ribosomal protein genes. Here we report frequent transfer of two respiratory genes, sdh3 and sdh4 (encoding subunits 3 and 4 of succinate dehydrogenase), and we also show that these genes are present and expressed in the mitochondria of diverse angiosperms. Southern hybridization surveys reveal that sdh3 and sdh4 have been lost from the mitochondrion about 40 and 19 times, respectively, among the 280 angiosperm genera examined. Transferred, functional copies of sdh3 and sdh4 were characterized from the nucleus in four and three angiosperm families, respectively. The mitochondrial targeting presequences of two sdh3 genes are derived from preexisting genes for anciently transferred mitochondrial proteins. On the basis of the unique presequences of the nuclear genes and the recent mitochondrial gene losses, we infer that each of the seven nuclear sdh3 and sdh4 genes was derived from a separate transfer to the nucleus. These results strengthen the hypothesis that angiosperms are experiencing a recent evolutionary surge of mitochondrial gene transfer to the nucleus and reveal that this surge includes certain respiratory genes in addition to ribosomal protein genes.

Amino Acid Sequence↗