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PubMed2003

A putative mitochondrial fission gene from the ectomycorrhizal ascomycete Tuber borchii Vittad.: cloning, characterisation and phylogeny.

Mitochondrial binary division is a complex process occurring in multiple steps, mediated by several proteins. In Saccharomyces cerevisiae, a mitochondrial membrane protein, Fis1p, is required for the proper assembly of the mitochondrial division apparatus. In this study, we report the cloning, characterisation and phylogenetic analysis of Tbfis1, a gene from the ectomycorrhizal ascomycetous truffle Tuber borchii, encoding for an orthologue of S. cerevisiae Fis1p. The Tbfis1 coding region consists of a 468-nucleotide open reading frame interrupted by four introns, which encodes for a polypeptide of 155 amino acids, having a predicted transmembrane domain structure typical of the Fis1p Family. Southern blot analysis revealed that Tbfis1 is a single-copy gene in the T. borchii genome. Tbfis1 is highly expressed during the first stages of T. borchii fruit body ripening, while its expression decreases during T. borchii mycelium ageing. Also, Virtual Northern blot analysis revealed Tbfis1 expression in the symbiotic phase of the fungus life cycle. Phylogenetic analysis allowed the identification of Tbfis1 orthologues in filamentous fungi, yeasts, plants, worms, flies and mammals, indicating that the function of the protein coded by this gene has been conserved during evolution.

Amino Acid Sequence↗

PubMed2004

A domain for editing by an archaebacterial tRNA synthetase.

The rules of the genetic code are established by aminoacylations of transfer RNAs by aminoacyl tRNA synthetases. New codon assignments, and the introduction of new kinds of amino acids, are blocked by vigorous tRNA-dependent editing reactions occurring at hydrolytic sites embedded within specialized domains in the synthetases. For some synthetases, these domains were present at the time of the last common ancestor and were fixed in evolution through all three of the kingdoms of life. Significantly, a well characterized domain for editing found in bacterial and eukaryotic threonyl- and all alanyl-tRNA synthetases is missing from archaebacterial threonine enzymes. Here we show that the archaebacterial Methanosarcina mazei ThrRS efficiently misactivates serine, but does not fuse serine to tRNA. Consistent with this observation, the enzyme cleared serine that was linked to threonine-specific tRNAs. M. mazei and most other archaebacterial ThrRSs have a domain, N2(A), fused to the N terminus and not found in bacterial or eukaryotic orthologs. Mutations at conserved residues in this domain led to an inability to clear threonine-specific tRNA mischarged with serine. Thus, these results demonstrate a domain for editing that is distinct from all others, is restricted to just one branch of the tree of life, and was most likely added to archaebacterial ThrRSs after the eukaryote/archaebacteria split.

Alanine-tRNA Ligase↗

PubMed2005

Intragenic Hill-Robertson interference influences selection intensity on synonymous mutations in Drosophila.

Natural selection influences synonymous mutations and synonymous codon usage in many eukaryotes to improve the efficiency of translation in highly expressed genes. Recent studies of gene composition in eukaryotes have shown that codon usage also varies independently of expression levels, both among genes and at the intragenic level. Here, we investigate rates of evolution (Ks) and intensity of selection (gamma(s)) on synonymous mutations in two groups of genes that differ greatly in the length of their exons, but with equivalent levels of gene expression and rates of crossing-over in Drosophila melanogaster. We estimate gamma(s) using patterns of divergence and polymorphism in 50 Drosophila genes (100 kb of coding sequence) to take into account possible variation in mutation trends across the genome, among genes or among codons. We show that genes with long exons exhibit higher Ks and reduced gamma(s) compared to genes with short exons. We also show that Ks and gamma(s) vary significantly across long exons, with higher Ks and reduced gamma(s) in the central region compared to flanking regions of the same exons, hence indicating that the difference between genes with short and long exons can be mostly attributed to the central region of these long exons. Although amino acid composition can also play a significant role when estimating Ks and gamma(s), our analyses show that the differences in Ks and gamma(s) between genes with short and long exons and across long exons cannot be explained by differences in protein composition. All these results are consistent with the Interference Selection (IS) model that proposes that the Hill-Robertson (HR) effect caused by many weakly selected mutations has detectable evolutionary consequences at the intragenic level in genomes with recombination. Under the IS model, exon size and exon-intron structure influence the effectiveness of selection, with long exons showing reduced effectiveness of selection when compared to small exons and the central region of long exons showing reduced intensity of selection compared to flanking coding regions. Finally, our results further stress the need to consider selection on synonymous mutations and its variation--among and across genes and exons--in studies of protein evolution.

Animals↗

PubMed2006

Deleterious epistatic interactions between electron transport system protein-coding loci in the copepod Tigriopus californicus.

The nature of epistatic interactions between genes encoding interacting proteins in hybrid organisms can have important implications for the evolution of postzygotic reproductive isolation and speciation. At this point very little is known about the fitness differences caused by specific closely interacting but evolutionarily divergent proteins in hybrids between populations or species. The intertidal copepod Tigriopus californicus provides an excellent model in which to study such interactions because the species range includes numerous genetically divergent populations that are still capable of being crossed in the laboratory. Here, the effect on fitness due to the interactions of three complex III proteins of the electron transport system in F2 hybrid copepods resulting from crosses of a pair of divergent populations is examined. Significant deviations from Mendelian inheritance are observed for each of the three genes in F2 hybrid adults but not in nauplii (larvae). The two-way interactions between these genes also have a significant impact upon the viability of these hybrid copepods. Dominance appears to play an important role in mediating the interactions between these loci as deviations are caused by heterozygote/homozygote deleterious interactions. These results suggest that the fitness consequences of the interactions of these three complex III-associated genes could influence reproductive isolation in this system.

Animals↗

PubMed1984

Tetrahymena H4 genes: structure, evolution and organization in macro- and micronuclei.

The ciliated protozoan Tetrahymena thermophila contains two types of H4 histone genes (H4-I and H4-II). Southern blotting and analysis of DNA from nullisomic strains indicate that H4-I and H4-II are on different chromosomes and that only H4-II is closely linked to an H3 gene. No DNA sequence rearrangements are observed for either of the H4 genes when the transcriptionally inert, germ line, micronucleus is compared to the transcriptionally active, somatic macronucleus. Comparison of the H4-I gene and its flanking sequences to H4 gene sequences of other organisms indicates that there are evolutionary constraints on coding nucleotides that are unrelated to their protein coding function and that these evolutionary pressures operate at the level of translation.

Amino Acid Sequence↗

PubMed1998

Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution.

Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition, and distribution of short repetitive sequences we observed among green algal mitochondrial genomes on the other. It is conceivable that the accumulation of GC-rich short repeated sequences in the Chlamydomonas-like but not Prototheca-like mitochondrial genomes might have triggered evolutionary events responsible for the distinct series of evolutionary changes undergone by the two green algal mitochondrial lineages. The similarity in base composition, nucleotide sequence, abundance, and mode of organization we observed between the short repetitive sequences present in Chlamydomonas-like mitochondrial genomes on one hand and fungal and vertebrate homologs on the other might extend to some of the roles that the short repetitive sequences have been shown to have in the latter. Potential involvements we propose for the short repetitive sequences in the evolution of Chlamydomonas-like mitochondrial genomes include fragmentation and scrambling of the ribosomal-RNA-coding regions, extensive gene rearrangements, coding-region deletions, surrogate origins of replication, and chromosomal linearization.

Animals↗

PubMed2026

Toward life with a 19-amino acid alphabet through generative artificial intelligence design.

Because all known living organisms are made from at least 20 canonical amino acids, the feasibility of life using a more simplified alphabet remains unclear. In this work, we leveraged computational design and synthetic biology to explore building a cell from a 19-amino acid alphabet. Initial analyses suggested that isoleucine (Ile) may be dispensable, which we confirmed by directly replacing Ile residues in essential proteins in Escherichia coli. Critically, protein language models and structure-based models were necessary to redesign functional Ile-less proteins in most cases. We systematically replaced all 382 Ile residues from the ribosome and combined 21 redesigned subunits at a native genomic locus to produce a viable, evolutionarily stable cell. This work provides a roadmap to create the first 19-amino acid organism since early evolution.

Escherichia coli↗

PubMed1987

Evolutionary changes of sequences and factors that direct transcription termination of human and mouse ribsomal genes.

We have analyzed the sequences required for termination of human rDNA transcription. The human ribosomal transcription unit is shown to extend about 350 nucleotides into the 3'-terminal spacer and ends immediately upstream of a region with a distinct sequence heterogeneity. This heterogeneous region contains a cluster of conserved 10-base pair sequence elements which exert a striking homology to the proximal part of the 18-base pair murine rDNA transcription termination signal sequence, termed SalI box. Exonuclease III protection assays and in vitro transcription experiments with both homologous and heterologous human-mouse minigene constructs, and extracts from HeLa or Ehrlich ascites cells, reveal a functional analogy of the human sequence to the mouse SalI box. It mediates binding of a nuclear protein which functions as a transcription termination factor. The murine signal sequence is recognized by the human factor but not vice versa. The different sequence specificities and electrophoretic properties of the functionally equivalent protein factors suggest that a molecular coevolution has taken place between the termination signal sequences and the genes coding for the termination factors.

Animals↗

PubMed1981

Immunochemical evidence in two haplotypes for at least three D region-encoded molecules, D, L, and R.

Sequential immunoprecipitation analyses have defined a new transplantation antigen, designated R, which in addition to the 2 previously isolated D and L molecules is encoded in the D region. All 3 of these gene products are 45,000 m.w. glycoprotein, and each bears a unique combination of specificities as recognized by monoclonal and/or conventional anti-H-2 sera. Three D region products, D, L, and R, have now been isolated from soluble antigens of both the H-2d and H-2q haplotypes. The resulted reported here also indicate that the loss-mutant BALB/c-H-2dm2 fails to express both Ld and Rd antigens. Further chemical comparisons of the primary structure of R molecules with D and L molecules will now be necessary to determine whether R antigens are the products of a unique gene, as opposed to a glycosylation or conformational variant of D and/or L molecules. In either case, the discovery of 3 D region-encoded gene products in certain haplotypes raises new questions about the evolution and regulation of expression of H-2 loci.

Animals↗

PubMed2003

Phylogeography of the fungal pathogen Histoplasma capsulatum.

Until recently, Histoplasma capsulatum was believed to harbour three varieties, var. capsulatum (chiefly a New World human pathogen), var. duboisii (an African human pathogen) and var. farciminosum (an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein-coding genes. At least eight clades were idengified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny. Histoplasma capsulatum var. capsulatum individuals were found in all eight clades. The African clade included all of the H. capsulatum var. duboisii individuals as well as individuals of the other two varieties. The 13 individuals of var. farciminosum were distributed among three phylogenetic species. These findings suggest that the three varieties of Histoplasma are phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein-coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.

Cluster Analysis↗

PubMed1977

Genetic control of mitochondrial malate dehydrogenases: evidence for duplicated chromosome segments.

The genetic control of the major mitochondrial isoenzymes of malate dehydrogenase (L-malate:NAD+ oxidoreductase; EC 1.1.1.37) has been investigated in Zea mays. The mitochondrial isozymes are coded at four nuclear gene loci. Two of the loci (mdh1 and mdh2) are diallelic and tightly linked. The other two loci (mdh3 and mdh4) appear to have arisen by duplication of the chromosome segment carrying mdh1 and mdh2, but are not linked to them. The segregation of such a duplicate segment can explain anomalous backcross and F2 segregation ratios.

Alleles↗

PubMed1996

Molecular and genetic characterization of SLC1, a putative Saccharomyces cerevisiae homolog of the metazoan cytoplasmic dynein light chain 1.

Cytoplasmic dynein is a multisubunit, microtubule-dependent motor enzyme that has been proposed to function in a variety of intracellular movements. As part of an effort to understand the evolution and the biological roles of cytoplasmic dynein, we have identified the first non-metazoan dynein light chain 1, SLC1, in the yeast Saccharomyces cerevisiae. The amino acid sequence of the SLC1 protein is similar to those of the human, Drosophila and Caenorhabditis cytoplasmic dynein light chains 1. The SLC1 gene lies adjacent to the YAP2 (= CAD1) transcription unit. The SLC1 coding sequence is split by two introns and its mRNA is detectable throughout the cell cycle. Tetrad analysis of heterozygotes harboring a TRP insertion in the SLC1 coding region indicate that SLC1 function is not essential for cell viability. Furthermore, we demonstrate that double mutants, defective for SLC1 and the kinesin-related CIN8 genes are non-lethal. The redundancy of SLC1 function in yeast contrasts with the cell death caused by loss-of-function mutations in the dynein light chain 1 gene in Drosophila melanogaster.

Acyltransferases↗

PubMed2006

Haplotype block structure is conserved across mammals.

Genetic variation in genomes is organized in haplotype blocks, and species-specific block structure is defined by differential contribution of population history effects in combination with mutation and recombination events. Haplotype maps characterize the common patterns of linkage disequilibrium in populations and have important applications in the design and interpretation of genetic experiments. Although evolutionary processes are known to drive the selection of individual polymorphisms, their effect on haplotype block structure dynamics has not been shown. Here, we present a high-resolution haplotype map for a 5-megabase genomic region in the rat and compare it with the orthologous human and mouse segments. Although the size and fine structure of haplotype blocks are species dependent, there is a significant interspecies overlap in structure and a tendency for blocks to encompass complete genes. Extending these findings to the complete human genome using haplotype map phase I data reveals that linkage disequilibrium values are significantly higher for equally spaced positions in genic regions, including promoters, as compared to intergenic regions, indicating that a selective mechanism exists to maintain combinations of alleles within potentially interacting coding and regulatory regions. Although this characteristic may complicate the identification of causal polymorphisms underlying phenotypic traits, conservation of haplotype structure may be employed for the identification and characterization of functionally important genomic regions.

Animals↗

PubMed2005

A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate.

Under prevailing theories, the nonsynonymous-to-synonymous substitution ratio (i.e. K(a)/K(s)), which measures the fixation probability of nonsynonymous mutations, is correlated with the strength of selection. In this article, we report that K(a)/K(s) is also strongly correlated with the mutation rate as measured by K(s), and that this correlation appears to have a similar magnitude as the correlation between K(a)/K(s) and selective strength. This finding cannot be reconciled with current theories. It suggests that we should re-evaluate the current paradigms of coding-sequence evolution, and that the wide use of K(a)/K(s) as a measure of selective strength needs reassessment.

Animals↗

PubMed2002

Mnd1p: an evolutionarily conserved protein required for meiotic recombination.

We used a functional genomics approach to identify a gene required for meiotic recombination, YGL183c or MND1. MND1 was spliced in meiotic cells, extending the annotated YGL183c ORF N terminus by 45 aa. Saccharomyces cerevisiae mnd1-1 mutants, in which the majority of the MND1 coding sequence was removed, arrested before the first meiotic division with a phenotype reminiscent of dmc1 mutants. Physical and genetic analysis showed that these cells initiated recombination, but did not form heteroduplex DNA or double Holliday junctions, suggesting that Mnd1p is involved in strand invasion. Orthologs of MND1 were identified in protists, several yeasts, plants, and mammals, suggesting that its function has been conserved throughout evolution.

Amino Acid Sequence↗

PubMed1981

The conservation of DNA sequences over very long periods of evolutionary time. Evidence against intergeneric chromosomal transfer as an explanation for the presence of Escherichia coli tuf gene sequences in taxonomically-unrelated prokaryotes.

In the present study we tried to determine whether the presence of DNA sequences homologous to the Escherichia coli tuf gene (encodes peptide chain elongation factor Tu) in many taxonomically-unrelated prokaryotes is due to selective pressure for these sequences or due to the transfer of chromosomal material subsequent to the divergence of the genera from their progenitors. We found that the degree of sequence homology to the DNA immediately adjacent to the E. coli tuf A gene is either nonexistent or much less than that found for the tuf gene. Furthermore, the tuf-homologous sequences present in one prokaryote were found to be in large part the same as or a subset of those present in others. That is, various prokaryotes share a common subset of tuf-homologous sequences. These findings suggest that strong selective pressure and not recent intergeneric chromosomal transfer is responsible for the ubiquitous presence of certain tuf-homologous sequences. Because the genetic code is degenerate, DNA sequence need not be conserved to conserve protein sequence. Therefore, if the only function of these sequences is to encode protein, their persistence must mean that in some instances codon sequence is selected for.

Bacteria↗

PubMedDate not supplied

[5S genes of the loach: determination of the primary structure of the transcription termination region and nontranscribed spacer].

The primary structure of a 5S gene spacer has been determined by sequencing three cloned 5S rDNA fragments of the loach genome. The region of the spacer adjacent to the 3'-termini of the gene structural part was shown to comprise an AT-rich sequence (24 bp long) including an oligo (T)6-9 block corresponding to the terminator of RNA polymerase III. The results supported our previous data about the 5S rRNA precursor synthesis during the transcription of cloned 5S rDNAs injected into oocyte nuclei. The comparative sequence analysis revealed a homology between the spacer region from -54 to -26 bp and the 5'-termini (1-18 bp) and the 3'-termini (108-117 bp) stretches of the gene coding region. In addition, both the coding part and nontranscribed spacer of 5S DNA include highly diversed repeats which are homologous to the 3'-termini sequence (111-+8 bp) of the gene. Apparently the nontranscribed spacer of loach 5S genes derived in evolution from numerous replicated 5S genes as a result of subsequent base elimination and substitution in the most of the 5S rRNA coding sequences.

Animals↗

PubMed2003

Is there an evolutionary relationship between WARP (von Willebrand factor A-domain-related protein) and the FACIT and FACIT-like collagens?

We suggest that there is an evolutionary relationship between von Willebrand factor A-domain-related protein (WARP), and the fibril-associated collagen with interrupted triple helix (FACIT) and FACIT-like subfamilies of collagens. Data from a comparison of amino acid sequences, domain organisation and chromosomal location are consistent with the hypothesis that WARP and these collagens share a common collagen ancestor. In support of this is the observation that the WARP 3' coding region is GC-rich suggesting that this may represent the remnant of a triple helix protein domain which WARP has 'lost' during evolution.

Animals↗