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PubMed2006

VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.

Comparative analysis of DNA sequences is becoming one of the major methods for discovery of functionally important genomic intervals. Presented here the VISTA family of computational tools was built to help researchers in this undertaking. These tools allow the researcher to align DNA sequences, quickly visualize conservation levels between them, identify highly conserved regions, and analyze sequences of interest through one of the following approaches: . Browse precomputed whole-genome alignments of vertebrates and other groups of organisms. . Submit sequences to Genome VISTA to align them to whole genomes. . Submit two or more sequences to mVISTA to align them with each other (a variety of alignment programs with several distinct capabilities are made available).. Submit sequences to Regulatory VISTA (rVISTA) to perform transcription factor binding site predictions based on conservation within sequence alignments.Use stand-alone alignment and visualization programs to run comparative sequence analysis locally All VISTA tools use standard algorithms for visualization and conservation analysis to make comparison of results from different programs more straightforward. The web page http://genome.lbl.gov/vista/ serves as a portal for access to all VISTA tools. Our support group can be reached by email at vista@lbl.gov.

Algorithms↗
PubMedDate not supplied

A novel human type I hair keratin gene: evidence for two keratin hHa3 isoforms.

We present the nucleotide and amino acid sequence for a novel human type I hair keratin, which could be identified through its high sequence homology and strict carboxyterminal length identity as a human ortholog of the murine hair keratin mHa3. Our hHa3 sequence differs, however, from that of a previously described hHa3 hair keratin (published only as an amino acid sequence; [13]) in 24 amino acid position, 8 of which occur in the middle of the carboxyterminal domain. PCR of genomic DNA from 25 normal human subjects using a primer pair derived from sequence segments located in the 3'-region of our hHa3 clone that encode conserved amino acid sequences in both keratins, resulted in the amplification of two distinct products of 0.38 kbp and 1.0 kbp. DNA sequence analysis of the cloned PCR products allowed identification of the 0.38 kb sequence as that originating from Yu et al. [13] and the 1.0 kb sequence as that being derived from our data. The difference in fragment length was due to unique intron 6 sequences, indicating that these two keratin species are encoded by genes of their own. Moreover, extensive Southern blot analyses with DNA from 25 unrelated individuals of different races using a 3'-noncoding sequence from our keratin and the intron 6 sequence of the keratin of Yu et al. [13], as hybridization probes showed that both keratin genes are present as single copy sequences occurring ubiquitously and without gross alterations in the human genome. Collectively, these data demonstrate that the human type I hair keratin described in this paper represents an isoform of the previously described hHa3 keratin.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1998

Allozyme and DNA sequence data support speciation of northern and southern populations of silver catfish, Schilbe intermedius (Rüppel, 1832).

Patterns of genetic variation in Schilbe intermedius were investigated due to morphological differences and taxonomic uncertainties regarding the Southern African schilbeids. A total of three populations, two Southern populations representing the former Eutropius depressirostris and a Northern population representing S. mystus, were electrophoretically analysed to determine the extent of genetic differentiation among these populations. The Northern and Southern populations were fixed for different alleles at the G3PDH-2 protein coding locus and allozyme differentiation between populations, using the 0.95 criterion, were also encountered at the PGDH-2 locus. Genetic distance values indicate greater genetic differentiation between the Northern and Southern populations compared to the two Southern populations. DNA sequence analysis of 900-1000 nucleotides of the cytochrome b gene revealed distances of 3.2-3.5% between the Schilbe/Eutropius complex. This finding, together with ingroup and outgroup analysis of evolutionary relationships, is congruent with the results from the electrophoretic analysis of the taxa. Sufficient differentiation exist between the Northern and Southern populations to regard them as distinct species.

Animals↗
PubMed2001

Unravelling the phylogenetic relationships of African trypanosomes of suids.

African trypanosomes of the subgenera Nannomonas and Pycnomonas have been recorded from both wild and domestic suids. However, complete descriptions of some of these trypanosomes with regard to host range, pathogenicity, transmission and distribution are still lacking. Neither the recently described Trypanosoma (Nannomonas) godfreyi nor Trypanosoma (Nannomonas) congolense Tsavo have been isolated from mammalian hosts, while Trypanosoma (Pycnomonas) suis remains the rarest of the Salivarian trypanosomes. The only isolate presumed to be of the latter species is maintained at the Kenya Trypanosomiasis Research Institute, Nairobi. We present here the results of characterization of this isolate by morphology, tsetse transmission, the use of species-specific DNA probes and DNA sequence analysis. Morphology in stained blood smears revealed a small trypanosome with a free flagellum. Experimental transmission through Glossina morsitans morsitans showed a developmental cycle typical of subgenus Nannomonas A positive identification was obtained with species-specific PCR primers for T. congolense Tsavo; moreover, the sequence of the SSU rRNA gene was almost identical to that of T. congolense Tsavo on database. In phylogenetic analysis of the SSU rRNA genes of Salivarian trypanosomes, T. congolense Tsavo grouped with T. simiae rather than T. congolense, suggesting that the name T. simiae Tsavo is more appropriate.

Animals↗
PubMed1999

Molecular cloning and expression in Escherichia coli of an aquaporin-like gene from adult buffalo fly (Haematobia irritans exigua).

A gene fragment encoding a putative member of the aquaporin gene family was amplified using cDNA prepared from unfed adult buffalo fly poly(A)+ RNA and degenerate PCR primers designed from highly conserved regions of amino acids found in all members of the aquaporin gene family. This PCR product was labelled with digoxigenin-dUTP and used as a probe to screen a lambdagt-11 cDNA library constructed from unfed adult buffalo fly. One positively hybridizing clone (AqpBF1), contained an insert of 1878 bp, and DNA sequence analysis revealed an open reading frame of 753 bp encoding a polypeptide of predicted Mr = 26 163 Da. Comparison of the AqpBF1 deduced protein sequence with the GenBank database revealed significant homology to many aquaporin genes, including 72% identity with a partial DNA sequence encoding a member (DRIP) of the MIP protein family isolated from Drosophila melanogaster. The most closely related, full-length, GenBank sequence was an aquaporin gene isolated from the digestive tract of the sap-sucking insect Cicadella viridis, which was 53% identical to the buffalo fly AqpBF1 protein sequence. The full-length coding sequence of AqpBF1 was cloned into the (His)6-fusion vector, pQE10, and the recombinant protein was expressed in Escherichia coli following induction by IPTG. The recombinant (His)6-fusion protein was localized predominantly in the membrane fraction of E. coli. The protein was solubilized from E. coli membranes with n-octyl beta-D-glucopyranoside and purified by affinity chromatography on a Ni++-sepharose column in the presence of detergent.

Amino Acid Sequence↗
PubMed2005

Isolation of the retinoblastoma cDNA from the marine flatfish dab (Limanda limanda) and evidence of mutational alterations in liver tumors.

We have isolated a dab (Limanda limanda) homologue of the human retinoblastoma (Rb) tumor suppressor gene. The L. limanda partial Rb cDNA encodes a partial predicted protein of 753 amino acids. DNA sequence analysis with other vertebrate Rb sequences demonstrates that the L. limanda Rb cDNA is highly conserved in regions of functional importance. The sequence reported herein, combined with the high degree of conservation observed in critical domains, has also facilitated an investigation of the molecular etiology of environmentally induced liver tumor samples in a feral fish species. Mutational alterations were detected in liver adenoma samples, also in apparently "normal" regions of liver samples dissected from fish displaying adenoma, but not in normal liver samples from otherwise healthy feral fish. These results are the first reporting the appearance of Rb mutations in wild-caught fish and suggest that the molecular etiology of fish cancer appears to involve Rb-implicated tumorigenesis. The ecotoxicological relevance of the Rb mutations in feral fish liver tumors, in terms of future genome instability and possible development of a genotoxicity biomarker, is discussed.

Animals↗
PubMed1994

Sequence analysis of a 3.5 Kb EcoRI fragment from the left arm of Saccharomyces cerevisiae chromosome XI reveals the location of the MBR1 gene and a sequence related to a GTPase-activating protein.

We present the DNA sequence analysis of a region covering a 3.5 kb EcoRI fragment from the left arm of chromosome XI from Saccharomyces cerevisiae. This region contains five open reading frames (ORFs) which code for proteins of greater than 100 amino acids. ORF YKL425 codes for the previously sequenced Mbr1 (Valens et al., 1991; Daignan-Fornier et al., 1993) which participates in mitochondrial biogenesis. YKL424 has identity with a GTPase-activating protein of higher eukaryotes. The three remaining ORFs have no identity to known proteins within the databases screened and are not assigned ORF numbers as they are completely contained with ORFs YKL424 and YKL425.

Amino Acid Sequence↗
PubMed2004

Speciation in the large-spored Metschnikowia clade and establishment of a new species, Metschnikowia borealis comb. nov.

The reproductive boundaries among species in the large-spored Metschnikowia clade were studied by prototrophic recombinant selection, electrophoretic karyotyping, mitochondrial DNA restriction analysis, and DNA sequence analysis. Inviable ascospores arose from crosses between the two varieties of Metschnikowia continentalis, indicating that they should be recognized as separate species. Prototrophic recombinants were recovered from crosses between auxotrophic mutants of Metschnikowia borealis, M. continentalis, Metschnikowia lochheadii, Metschnikowia sp. UWO(PS)00-154.1, and Candida ipomoeae, showing that some genetic exchange is possible in spite of the sterility of the asci formed in interspecific crosses. Metschnikowia hawaiiensis, although capable of ascus formation when its h(-) mating type is crossed with the h(+) mating type of the other species, did not give rise to recombinants. In the other species, some recombinants acquired the ability to form asci directly from single cells. These often contained the chromosomes of both parents, suggesting formation of allodiploid hybrids. Other recombinants behaved as haploids and were similar to one parent except for having inherited the selectable wild-type allele from the other parent. In most, but not all cases, inheritance of the mitochondrial genome was uniparental and correlated with the inheritance of the nuclear chromosome complement. In some cases, what appeared to be a recombinant mitochondrial genome was observed. Phylogenies derived from the sequences of various DNA regions were not congruent, indicating that hybridization may have taken place in nature as the large-spored species diverged from their common ancestor. Further evidence that C. ipomoeae arose from a natural recombination event was obtained, but a pair of Metschnikowia species that might represent derived forms of the parents could not be identified conclusively. C. ipomoeae and most of its closely related Metschnikowia species contained a group-II intron in the mitochondrial small-subunit ribosomal gene. The intron was absent in M. borealis, M. hawaiiensis, and other species in the genus Metschnikowia.

Candida↗
PubMed1999

Genetic similarity among pheromone and voltinism races of Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae).

The genetic variability of seven European corn borer populations, Ostrinia nubilalis, from North America and Europe was assessed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and DNA sequencing. The nuclear ribosomal internal transcribed spacer 1 (ITS-1) region (approximately 500 base pair [bp]) and four mitochondrial (mtDNA) regions (1550 bp total) were examined. The smartweed borer, Ostrinia obumbratalis, and south-Western corn borer, Diatraea grandiosella, were used for comparisons. Of 106 restriction sites identified (80 in mtDNA and 26 in ITS-1), none differentiated geographical populations, pheromone races, or voltine ecotypes of the European corn borer. The lack of variation in the ITS-1 of European corn borer was confirmed by DNA sequence analysis. The genetic similarity of European corn borer populations, despite their wide geographical range and physiological differences, may be explained by a relatively recent origin for the voltinism and pheromone races, gene flow among races, and/or expansion from genetic bottlenecks.

Animals↗
PubMed1997

Cloning of an outer membrane protein gene from Campylobacter jejuni.

An antigen in the outer membrane protein (OMP) fraction of Campylobacter jejuni was identified and characterized. Western blot analysis demonstrated antigenic differences in this protein between two congenic C. jejuni strains. Strain A74/C, which colonizes chickens, expressed the antigen at 34 kDa, while strain A74/O, which poorly colonizes chickens, expressed the antigen at 32 and 34 kDa. A genomic library was constructed in lambdagt11 with DNA from A74/O and screened with antibody raised against C. jejuni OMPs. A clone that possessed a 1.3-kb insert and expressed an immunoreactive protein fused to beta-galactosidase was isolated and purified. DNA sequence analysis revealed the insert contained one open reading frame 864 bases long. The deduced amino acid sequence demonstrated 56.3% similarity with Bacillus steorothermophilus glnH, a glutamine-binding protein, and 54.0% similarity with C. jejuni PEB1, a putative colonization adhesin. Southern hybridization, Northern hybridization, and DNA sequence analyses of the congenic colonizing and noncolonizing strains of C. jejuni failed to distinguish the two strains and revealed only one copy of the gene. Post-translational modification may be an alternate explanation for the antigenic differences seen between the two strains.

Amino Acid Sequence↗
PubMed1999

A universal polymerase chain reaction for the detection of psittacine beak and feather disease virus.

A universal PCR assay was designed that consistently detected psittacine beak and feather disease virus (BFDV) in psittacine birds affected with psittacine beak and feather disease (PBFD) from different geographic regions across Australia. Primers within open reading frame 1 (ORF1) of the BFDV genome consistently amplified a 717 bp product from blood and/or feathers of 32 birds with PBFD lesions. The PCR did not amplify a product from the feathers or blood from 7 clinically normal psittacine birds. Primers based on regions outside of ORF1 did not consistently produce a PCR product, suggesting there was some genomic variation outside ORF1. The amplified ORF1 PCR products of 10 BFDV isolates, from different psittacine species and from various regions around Australia, were cloned and comparative DNA sequence analysis demonstrated 88-99% of the ORF1 fragments. The derived amino acid sequences of the amplified ORF1 fragments demonstrated similar identity between all 10 isolates. Within ORF1, there was complete conservation of the putative nucleotide binding site and marked conservation of 2 other motifs previously identified as essential components of the replication-associated proteins of other circoviruses and geminiviruses.

Amino Acid Sequence↗
PubMed1999

An operon that confers UV resistance by evoking the SOS mutagenic response in streptococcal conjugative transposon Tn5252.

Streptococcus pneumoniae Rx1 is capable of repairing lesions caused by DNA-damaging agents in an error-free manner but lacks a UV-inducible error-prone repair system due to the absence of chromosomally encoded UmuDC-like proteins. We have identified an operon-like structure 8 kb from the left end of the pneumococcal conjugative transposon Tn5252 that confers SOS function in the host cells. DNA sequence analysis of this region revealed the presence of four open reading frames (ORFs). The deduced amino acid sequence of one of them, ORF13, which is capable of encoding a protein of 49.7 kDa, showed significant homology to UmuC, MucB, and other proteins involved in the SOS response. The carboxy-terminal region of another, ORF14, which is predicted to encode a 26-kDa polypeptide, shared similarity with UmuD- and MucA-like proteins that carry the amino acid residues recognized by the activated RecA* protein for proteolytic cleavage. The presence of plasmids carrying subcloned DNA from this region was found to restore UV-inducible mutagenic repair of chromosomal DNA in Escherichia coli cells defective in error-prone repair as well as in pneumococcus and Enterococcus faecalis UV202. Mutations within ORF13 abolished UV-induced mutagenesis but did not affect the conjugal transposition of the element.

Amino Acid Sequence↗
PubMed1994

Sequence analysis of a 10 kb fragment of yeast chromosome XI identifies the SMY1 locus and reveals sequences related to a pre-mRNA splicing factor and vacuolar ATPase subunit C plus a number of unidentified open reading frames.

We report the DNA sequence analysis of a region on the left arm of chromosome XI of Saccharomyces cerevisiae extending over 10 kb. The region contains five open reading frames (ORFs) of greater than 100 amino acids which do not show significant overlap with other ORFs. YKL408 contains a sequence with strong similarity to the RNA helicase pre-mRNA splicing factors PRP2, PRP16 and PRP22 (Burgess et al., 1990; Company et al., 1991; Ruby et al., 1991). YKL409 corresponds to the gene SMY1, the sequence of which was previously reported by Lillie and Brown (1992). YKL410 is identical to ATPase subunit C (Beltran et al., 1992) except for an N-terminal extension. YKL406 and YKL407 show no significant identity with any sequences in the databases searched.

Adenosine Triphosphatases↗
PubMed1998

Characterisation of the mob locus from Rhodobacter sphaeroides required for molybdenum cofactor biosynthesis.

A clone carrying the mob locus from Rb. sphaeroides WS8 has been isolated from a cosmid library by Southern blotting with a probe covering the mob genes of Escherichia coli. The mob DNA has been subcloned and partially restores molybdoenzyme activities when transformed into E. coli mob strains. DNA sequence analysis of the subclone carrying the mob genes predicted at least 2 open reading frames. The mobA gene encodes protein FA whilst mobB encodes a nucleotide binding protein which has at least one extra domain relative to its E. coli counterpart.

Amino Acid Sequence↗
PubMed2003

Cloning and sequencing a HemK-family gene in Porphyromonas gingivalis.

HemK, a universally conserved protein of unknown function, has high amino acid similarity with DNA-(adenine-N6) methyltransferases (MTases). In the present study, we sequenced a 5026 bp DNA fragment just downstream of the PgPepO gene reported previously. The DNA sequence analysis revealed three ORFs. The ORF2 gene encoded a protein of 294 amino acids with a calculated molecular weight of 32,160 Da. The deduced amino acid sequence of the ORF2 gene exhibited a significant similarity to sequence of HemK from E. coli (35% identical residues). The ORF2 gene complemented an E. coli hemK mutant. Thus, ORF2 was named PgHemK. From the point of veiw of our recent finding, that E. coli HemK catalyses the methylation of polypeptide chain release factors such as RF1 and RF2, we postulated that PgHemK might function as a protein MTase containing the DNA MTase motif.

Amino Acid Sequence↗
PubMed1997

Molecular cloning and biochemical characterization of carbonic anhydrase from Populus tremula x tremuloides.

A leaf cDNA library from hybrid aspen, Populus tremula x tremuloides, was constructed. From this two different cDNA clones, denoted CA1a and CA1b, encoding a chloroplastic carbonic anhydrase (CA) were isolated and DNA sequenced. Analysis of the deduced amino acid sequences showed that the isolated CAs belong to the beta-CA family, and have identities around 70% to other dicotyledonous plant CAs. The two hybrid aspen cDNA clones display a high nucleotide sequence identity, only 12 nucleotides differ. Since only one gene copy of this soluble chloroplastic CA is present in the nuclear genome, we postulate that the two isolated cDNA clones are alleles. Northern blot hybridization revealed a CA transcript of ca. 1300 bases, 140 bases shorter than in pea. Western and northern blot hybridizations on crude protein extracts and on total RNA, respectively, isolated from stem and leaves, showed that hybrid aspen CA is expressed specifically in the leaf under the growth conditions used. Based on the deduced amino acid sequence, the mature hybrid aspen CA enzyme subunit has a molecular mass of 24.8 kDa. The enzyme was over-expressed in Escherichia coli, and purified by affinity chromatography. Biochemical characterization showed that the protein structure and the CO2-hydration activity are similar to the pea enzyme. Molecular characterization of a CA from a perennial plant has not previously been performed, and it demonstrates that both the structure and activity of hybrid aspen CA resembles CAs from annual plants.

Amino Acid Sequence↗
PubMed1994

A cold-induced gene from Medicago sativa encodes a bimodular protein similar to developmentally regulated proteins.

A new cold-regulated (COR) gene, msa CIC, was isolated by differential screening of a cDNA library from cold-acclimated crowns of alfalfa (Medicago sativa L. cv. Apica). Transcripts of msa CIC were not detectable in unacclimated alfalfa and accumulated to higher levels in cold-acclimated plants of the cold-tolerant cv. Apica than in those of the cold-sensitive cv. CUF-101. The DNA sequence analysis of a full-length cDNA clone revealed that msa CIC encodes for a putative protein (MSACIC) of 166 amino acids with distinct proline-rich and hydrophobic domains. Protein sequence comparisons indicated that MSACIC is similar to a group of bimodular proteins that are developmentally regulated in other plant species.

Adaptation, Biological↗