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PubMed2001

Group I intron lateral transfer between red and brown algal ribosomal RNA.

How group I introns originate in nuclear ribosomal (r)RNA genes is an important question in evolutionary biology. Central to this issue is the multitude of group I introns present in evolutionarily distantly related plant, fungal, and protist lineages, together with an understanding of their origin and lateral transfer from one exon to another, between cell organelles, and between cells. These introns vary considerably in primary and secondary structure; and their provenance from a few or perhaps many mobile elements that have spread in rRNAs is unknown. Here we show that a novel lineage of group IC1 introns inserted at position 516 (Escherichia coli gene numbering) in the small subunit rRNA in bangiophyte red algae and a brown alga (Aureoumbra lagunensis) are specifically related, although their host cells are not. These bangiophyte and Aureoumbra introns are the only known cases that have a helical insertion in the P5b helix. The highly conserved primary and secondary structure of the extra P5b helix suggests that it is important, although its specific function is unknown. Our study attempts to understand the origin and movement of these IC1 introns.

Base Sequence↗
PubMed2002

The KLHL1-antisense transcript ( KLHL1AS) is evolutionarily conserved.

Spinocerebellar ataxia type 8 (SCA8) is caused by a CTG expansion in an untranslated, endogenous antisense RNA that overlaps the Kelch-like 1 ( KLHL1) gene. The normal function of this transcript is currently unknown. We have now identified the promoter region for the KLHL1-antisense ( KLHL1AS) RNA and report that a Klhl1as transcript is present in the mouse as well. Human and mouse KLHL1AS are transcribed from homologous promoter regions in the first intron of KLHL1 and extend through the transcription and translation start sites as well as the first splice donor sequence of KLHL1. We found that the mouse Klhl1as RNA is not spliced and terminates in a polyadenylation site in the Klhl1 promoter region, whereas both the present and previous work show that human KLHL1AS is highly variably spliced into processed transcripts that contain up to six exons. Mouse Klhl1as transcript was detected in RNA isolated from the cerebellum and from total adult brain and total fetal tissue, and at a low level in testis and ovary. Similarly, human KLHL1AS is expressed in various brain tissues, including the cerebellum, the tissue most affected by SCA8, and was detected at low levels in testis and kidney. The evolutionary conservation of this antisense/sense transcriptional organization strongly indicates that KLHL1AS transcripts play a significant biological role in both human and mouse, presumably as a regulator of KLHL1 expression.

Animals↗
PubMed2005

Survey of resistance gene analogs in Solanum caripense, a relative of potato and tomato, and update on R gene genealogy.

The resistance (R) proteins of the TIR- and non-TIR (or CC-) superfamilies possess a nucleotide binding site (NBS) domain. Within an R gene, the NBS is the region of highest conservation, suggesting an essential role in triggering R protein activity. We compared the NBS domain of functional R genes and resistance gene analogs (RGA) amplified from S. caripense genomic DNA via PCR using specific and degenerate primers with its counterpart from other plants. An overall high degree of sequence conservation was apparent throughout the P-loop, kinase-2 and kinase-3a motifs of NBS fragments from all plants. Within the non-TIR class of R genes a prominent sub-class similar to the potato R1 gene conferring resistance to late blight, was detected. All non-TIR-R1-like R gene fragments that were sequenced possessed an intact open reading frame, whereas 22% of all non-TIR-non-R1-like fragments and 59% of all TIR-NBS RGA fragments had an interrupted reading frame or contained transposon-specific sequence. The non-TIR-R1-like fragments had high similarity to Solanaceae R genes and low similarity to RGAs of other plant species including A. thaliana and the cereals. It is concluded that appearance of the non-TIR-R1-like NBS domain represents a relatively recent evolutionary development.

Amino Acid Motifs↗
PubMed2000

Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum.

The variation in transposition history of different Ty1-copia group LTR retrotransposons in the species lineages of the Pisum genus has been investigated. A heterogeneous population of Ty1-copia elements was isolated by degenerate PCR and two of these (Tps12 and Tps19) were selected on the basis of their copy number and sequence conservation between closely related species for further in-depth study of their transpositional history in Pisum species. The insertional polymorphism of these elements and the previously characterised PDR1 element was studied by sequence-specific amplification polymorphism (SSAP). Each of these elements reveals a unique transpositional history within 55 diverse Pisum accessions. Phylogenetic trees based on the SSAP data show that SSAP markers for individual elements are able to resolve different species lineages within the Pisum genus. Finally, the SSAP data from all of these retrotransposon markers were combined to reveal a detailed picture of the intra and interspecies relationships within Pisum.

Amino Acid Sequence↗
PubMed2005

Molecular characterization of a virus from the family Luteoviridae associated with cotton blue disease.

Cotton blue disease is an aphid-transmitted cotton disease described in Brazil in 1962 as Vein Mosaic "var. Ribeirão Bonito". At present it causes economically important losses in cotton crops if control measures are not implemented. The observed symptoms and mode of transmission have prompted researchers to speculate that cotton blue disease could be attributed to a member of the family Luteoviridae, but there was no molecular evidence supporting this hypothesis. We have amplified part of the genome of a virus associated with this disease using degenerate primers for members of the family Luteoviridae. Sequence analysis of the entire capsid and a partial RdRp revealed a virus probably belonging to the genus Polerovirus. Based on our results we propose that cotton blue disease is associated with a virus with the putative name Cotton leafroll dwarf virus (CLRDV).

Amino Acid Sequence↗
PubMed2002

Evolutionary and taxonomic implications of conserved structural motifs between picornaviruses and insect picorna-like viruses.

A comparison of the recently determined structure of an insect picorna-like virus, Cricket paralysis virus (CrPV), with that of the mammalian picornaviruses shows that several structural features are highly conserved between these viruses. These conserved features include the topology of the coat proteins, the conformation of most loops, and the general arrangement of the internally located N-terminal arms of the coat proteins. The conformational conservation of the N-termini of the three major coat proteins between CrPV and the picornaviruses suggests a putative ancestral T = 3 virus. Comparisons of the genome structure and amino-acid sequence of the coat proteins of CrPV with a number of other insect picorna-like viruses show that most of them belong to a novel group, recently given the interim name Cricket paralysis-like viruses. Two other insect picorna-like viruses, Infectious flacherie virus (IFV) and Sacbrood virus (SBV), for which the genome sequences have recently been determined, have very different coat protein sequences and a genome organization more like the picornaviruses. However, the position of the small VP4 protein in the structural protein polyprotein as well as the mechanism for its cleavage from VP3 upon assembly strongly suggests an evolutionary link to the "Cricket paralysis-like viruses". We propose that the picornaviruses, Cricket paralysis-like viruses and IFV/SBV group are a natural assemblage. The ancestor for this assemblage had a structure based upon the CrPV/picornavirus paradigm and a genome encoding a single major coat protein; gene duplication and rearrangements have subsequently produced the viruses that we observe today. We also discuss the possible relatives of the proposed assemblage and the likely implications of future structural studies that may be carried out on the putative relatives.

Amino Acid Motifs↗
PubMed1996

BTF3 is evolutionarily conserved in fission yeast.

BTF3 is a protein initially identified in HeLa cells that may be involved in the initiation of transcription. Although its specific role in transcription is unclear, BTF3 can form a stable complex with RNA polymerase II. Recently, BTF3 has also been shown to bind to nascent polypeptide chains. We have cloned a homolog of BTF3 from the fission yeast, Schizosaccharomyces pombe. This homolog, spBTF3, encodes a putative 151 amino acid protein that shares 72% similarity with human BTF3, 73% similarity with the Caenorhabditis elegans homolog and between 52 and 53% similarity with the Saccharomyces cerevisiae homologs, EGD1 and BTT1.

Amino Acid Sequence↗
PubMed2005

Two Plasmodium falciparum ribonucleotide reductase small subunits, PfR2 and PfR4, interact with each other and are components of the in vivo enzyme complex.

Ribonucleotide reductase (RNR) is a tetrameric enzyme, composed of two large (R1) and two small (R2) subunits, which regulates the nucleotide balance in cells by controlling the rate-limiting step for deoxyribonucleotide synthesis. We have identified a second copy of the small subunit gene, termed PfR4, encoding a 324 amino acid residue polypeptide that shares only 25% identity with the previously identified PfR2 small subunit of Plasmodium falciparum. PfR4 expression is cell-cycle-regulated, and the profile of transcript and protein expression corresponds to that of PfR2. A 1.3 kb PfR4 5'-flanking fragment contained a functional promoter activity. We have detected interaction between PfR2 and PfR4 by co-immunoprecipitation experiments. Indirect immunofluorescence analysis showed distinct localization of two small RNR subunits with some colocalization. The association of PfR1 large subunit with PfR4 was detected by GST pull-down assay. This interaction is reduced significantly when using a PfR4 truncated at the COOH terminus, suggesting the involvement of COOH-terminal residues in PfR4-PfR1 interaction. All three RNR subunits co-eluted on a Superose 12 size-exclusion column corresponding to fractions with a molecular mass of around 250 kDa. This suggests the existence of all three RNR subunits in Plasmodium in a native complex of alpha2betabeta' configuration.

Amino Acid Sequence↗
PubMed2005

An evolutionary scenario for one of the largest yeast gene families.

The DUP gene family of Saccharomyces cerevisiae comprises 23 members that can be divided into two subfamilies--DUP240 and DUP380. The location of the DUP loci suggests that at least three mechanisms were responsible for their genomic dispersion: nonreciprocal translocation at chromosomal ends, tandem duplication and Ty-associated duplication. The data we present here suggest that these nonessential genes encode proteins that facilitate membrane trafficking processes. Dup240 proteins have three conserved domains (C1, C2 and C3) and two predicted transmembrane segments (H1 and H2). A direct repetition of the C1-H1-H2-C2 module is observed in Dup380p sequences. In this article, we propose an evolutionary model to account for the emergence of the two gene subfamilies.

Amino Acid Sequence↗
PubMed2005

Molecular characterization of two soybean-infecting begomoviruses from India and evidence for recombination among legume-infecting begomoviruses from South [corrected] South-East Asia.

The complete nucleotide sequences of two soybean-infecting begomoviruses have been determined from central and southern parts of India. Sequence analyses show that the isolate from central India is a strain of Mungbean yellow mosaic India virus (MYMIV) and the southern Indian isolate is a strain of Mungbean yellow mosaic virus (MYMV). Multiple DNA B components could be detected with the soybean strain of Mungbean yellow mosaic virus species. The nucleotide sequence similarity between the DNA A components of the two isolates is higher (82%) than that between the corresponding DNA B components (71%). Analyses of the common region of the genomic components of these two virus isolates indicate considerable divergence in the origin of replication (ori), which did not impair their infectivity as demonstrated for the central Indian isolate by agroinfection with partial tandem repeats (PTRs) of the genomic components. Detailed sequence and phylogenetic analyses reveal the distribution and possible recombination events among legume-infecting begomoviruses from South-East Asia.

Base Sequence↗
PubMed2006

Sperm protein "DE" mediates gamete fusion through an evolutionarily conserved site of the CRISP family.

The first member of the cysteine-rich secretory protein (CRISP) family was described by our laboratory in the rat epididymis, and it is known as DE or CRISP-1. Since then, numerous CRISPs exhibiting a high amino acid sequence similarity have been identified in animals, plants and fungi, although their functions remain largely unknown. CRISP-1 proteins are candidates to mediate gamete fusion in the rat, mouse and human through their binding to complementary sites on the egg surface. To elucidate the molecular mechanisms underlying CRISP-1 function, in the present work, deletion mutants of protein DE were generated and examined for their ability to bind to the rat egg and interfere with gamete fusion. Results revealed that the egg-binding ability of DE resides within a 45-amino acid N-terminal region containing the two motifs of the CRISP family named Signature 1 and Signature 2. Subsequent assays using synthetic peptides and other CRISPs support that the egg-binding site of DE falls in the 12-amino-acid region corresponding to Signature 2. The interesting finding that the binding site of DE resides in an evolutionarily conserved region of the molecule provides novel information on the molecular mechanisms underlying CRISP-1 function in gamete fusion with important implications on the structure-function relationship of other members of the widely distributed CRISP family.

Amino Acid Sequence↗
PubMed1999

Evolutionary relationship between K(+) channels and symporters.

The hypothesis is presented that at least four families of putative K(+) symporter proteins, Trk and KtrAB from prokaryotes, Trk1,2 from fungi, and HKT1 from wheat, evolved from bacterial K(+) channel proteins. Details of this hypothesis are organized around the recently determined crystal structure of a bacterial K(+) channel: i. e., KcsA from Streptomyces lividans. Each of the four identical subunits of this channel has two fully transmembrane helices (designated M1 and M2), plus an intervening hairpin segment that determines the ion selectivity (designated P). The symporter sequences appear to contain four sequential M1-P-M2 motifs (MPM), which are likely to have arisen from gene duplication and fusion of the single MPM motif of a bacterial K(+) channel subunit. The homology of MPM motifs is supported by a statistical comparison of the numerical profiles derived from multiple sequence alignments formed for each protein family. Furthermore, these quantitative results indicate that the KtrAB family of symporters has remained closest to the single-MPM ancestor protein. Strong sequence evidence is also found for homology between the cytoplasmic C-terminus of numerous bacterial K(+) channels and the cytoplasm-resident TrkA and KtrA subunits of the Trk and KtrAB symporters, which in turn are homologous to known dinucleotide-binding domains of other proteins. The case for homology between bacterial K(+) channels and the four families of K(+) symporters is further supported by the accompanying manuscript, in which the patterns of residue conservation are demonstrated to be similar to each other and consistent with the known 3D structure of the KcsA K(+) channel.

Amino Acid Sequence↗
PubMed2002

Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3.

We report the complete genome sequence (38,208 bp) of bacteriophage T3 and provide a bioinformatic comparative analysis with other completely sequenced members of the T7 group of phages. This comparison suggests that T3 has evolved from a recombinant between a T7-like coliphage and a yersiniophage. To assess this, recombination between T7 and the Yersinia enterocolitica serotype O:3 phage phiYeO3-12 was accomplished in vivo; coliphage progeny from this cross were selected that had many biological properties of T3. This represents the first experimentally observed recombination between lytic phages whose normal hosts are different bacterial genera.

Amino Acid Sequence↗
PubMed1998

Modeling the covarion hypothesis of nucleotide substitution.

A "covarion" model for nucleotide substitution that allows sites to turn "on" and "off" with time was proposed in 1970 by Fitch and Markowitz. It has been argued recently that evidence supports such models over later, alternative models that postulate a static distribution of rates across sites. However, in contrast with these latter well-studied models, little is known about the analytic properties of the former model. Here we analyze a covarion-style model and show (i) how to obtain the evolutionary distance between two species from the expected proportion of sites where two species differ, (ii) that the covarion model gives identical results to a suitably chosen rates-across-sites model if several sequences are compared in pairs by using only the expected proportion of sites at which they differ, (iii) conditions under which the two models will give identical results if the full joint probability matrix is examined, and (iv) that the two models can, in principle, be distinguished when there are at least four monophyletic groups of species. This last result is based on a distance measure that is tree additive under certain versions of the covarion model but, in general, will not be additive under a rates-across-sites model. The measure constructed does not require knowledge of the parameters of the model and so shows that sequences generated by the covarion model do in fact contain information about the underlying tree.

Analysis of Variance↗