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[Divergence of repetitive DNA sequences in Echinodermata. I. Comparison of sequences with a high degree of intragenomic divergence].

The molecular DNA-DNA hybridization method was used for comparison of repetitive sequences with a high degree of intragenomic divergence in seven species of echinodermata, representatives of three classes of this type, and also for a representative of the type Annelida. The value of intragenomic divergence was estimated with respect to a thermolabile fraction of repetitive [3H]DNA of Strongylocentrotus intermedius isolated by thermoelution at 70 degrees after reassociation up to C0t=140. The data obtained indicate a significant conservatism of the given fraction: its homologues are present in DNA of all the species studied. Hybridization of the thermolabile fraction of [3H]DNA S. intermedius at C0t=10 and 1000 allowed one to estimate the divergence of sequences in DNA of all the species studied. Hybridization of the thermolabile fraction of [3H]DNA highly repetitive sequences of the given DNA fraction is more appreciable than that of moderately repetitive ones. Intragenomic divergence of moderately repetitive thermolabile sequences is higher than that of highly repetitive sequences both in phylogenetically close and distant species of sea urchins.

Animals↗
PubMed2002

Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequences.

The compact genome of the pufferfish, Fugu rubripes, has been proposed as a 'reference' genome to aid in annotating and analysing the human genome. We have annotated and compared 85 kb of Fugu sequence containing 17 genes with its homologous loci in the human draft genome and identified three 'novel' human genes that were missed or incompletely predicted by the previous gene prediction methods. Two of the novel genes contain zinc finger domains and are designated ZNF366 and ZNF367. They map to human chromosomes 5q13.2 and 9q22.32, respectively. The third novel gene, designated C9orf21, maps to chromosome 9q22.32. This gene is unique to vertebrates, and the protein encoded by it does not contain any known domains. We could not find human homologs for two Fugu genes, a novel chemokine gene and a kinase gene. These genes are either specific to teleosts or lost in the human lineage. The Fugu-human comparison identified several conserved non-coding sequences in the promoter and intronic regions. These sequences, conserved during 450 million years of vertebrate evolution, are likely to be involved in gene regulation. The 85 kb Fugu locus is dispersed over four human loci, occupying about 1.5 Mb. Contiguity is conserved in the human genome between six out of 16 Fugu gene pairs. These contiguous chromosomal segments should share a common evolutionary history dating back to the common ancestor of mammals and teleosts. We propose contiguity as strong evidence to identify orthologous genes in distant organisms. This study confirms the utility of the Fugu as a supplementary tool to uncover and confirm novel genes and putative gene regulatory regions in the human genome.

Amino Acid Sequence↗
PubMed1997

Sequence analysis of a 33.2 kb segment from the left arm of yeast chromosome XV reveals eight known genes and ten new open reading frames including homologues of ABC transporters, inositol phosphatases and human expressed sequence tags.

The complete nucleotide sequence of a 33221 bp segment, contained in cosmid pEOA1044, derived from the left arm of chromosome XV of Saccharomyces cerevisiae, appears in public databases between coordinates 177013 and 210234 (http://speedy.mips.biochem.mpg.de/). Computer analysis of that sequence revealed the presence of the previously known genes IRA2, DEC1, NUF2, HST1, RTG1, RIB2 and HAL2, one previously partially sequenced open reading frame (ORF) of unknown function (SCORFAC) and ten newly identified ORFs. One of the new ORFs is similar to the Drosophila melanogaster white gene and other transmembrane ABC transporters, another one has similarities to inositol phosphatases and others are similar to ORFs of unknown function from various organisms, including human Expressed Sequence Tags (ESTs). Potential transmembrane regions, ATP/GTP-binding and WD motifs have also been identified. The existence of yeast ESTs for two of the newly identified ORFs indicates that they are transcribed.

ATP-Binding Cassette Transporters↗
PubMed1993

Multiple sequence analysis: pool sequencing of synthetic and natural peptide libraries.

Sequence analysis by automated Edman degradation has been one of the most powerful tools for the characterization of peptides for many years. Its sensitivity allows experiments in the low picomole range, and its results provide complete information about the primary structure of proteins and peptides. A new method in protein and peptide sequencing has been developed which allows for the direct application of automated Edman degradation to the analysis of peptide mixtures. With the aid of multiple sequence analysis, first, sequence motifs of isolated, naturally processed peptides binding to MHC molecules have been defined. Second, the method proved to be a valuable and reliable tool for the characterization of synthetic peptide libraries, and third, the specificity of proteases has been determined in a fast and efficient way.

Amino Acid Sequence↗
PubMed1997

Binding sequence of STAT4: STAT4 complex recognizes the IFN-gamma activation site (GAS)-like sequence (T/A)TTCC(C/G)GGAA(T/A).

Studies of transcriptional activation by interferons and various cytokines have led to the identification of a family of proteins that serve as signal transducers and activators of transcription (STAT). STAT4 is phosphorylated following interleukin (IL)-12 stimulation and is required for IL-12 signal transduction. By immunoprecipitation and PCR amplification, a specific consensus sequence for DNA binding of the STAT4 complex was determined. The binding sequence of the STAT4 complex, (T/A)TTCC(C/G)GGAA(T/A), proved to be palindromic and similar to the IFN-gamma activated site (GAS)-like sequence. The first (T/A) and last (T/A) sites of the consensus sequence were critical for the binding affinity of the STAT4 complex.

Amino Acid Sequence↗
PubMed1999

Mycoplasma orale has a sequence similar to the insertion-like sequence of M. fermentans.

Polymerase chain reaction (PCR) using the Mycoplasma fermentans insertion sequence-like element (ISLE) RW primer set amplifies DNA from Mycoplasma orale when more than 1 ng is present in the reaction tube. In this study, amplified products from 11 different clinical isolates and the ATCC prototype of M. orale were sequenced and compared to 206 bp amplicons from eight isolates and the ATCC strain of M. fermentans. The nucleotide sequences of the amplified M. orale products had high sequence homology (88-92%) to those from M. fermentans, but differed at several key positions. The M. orale products contained a DraI restriction enzyme site not found in any of the M. fermentans amplified products. Consistent with this finding, the PCR products from M. orale were digested by DraI while the PCR products from M. fermentans were resistant to DraI digestion. The results suggest that M. orale may carry a similar IS-like element that complicates but does not negate using the ISLE PCR assay designed to detect M. fermentans. It appears possible for the RW primers to amplify M. orale if the mycoplasmas are present at higher concentrations. The amplified products can be differentiated from those from M. fermentans by a rapid DraI restriction endonuclease digestion or by Southern blot analysis using the RW006 internal probe under highly stringent conditions.

Base Sequence↗
PubMed1991

Average values of a dissimilarity measure not requiring sequence alignment are twice the averages of conventional mismatch counts requiring sequence alignment for a variety of computer-generated model systems.

A measure of sequence similarity, dt, not requiring prior sequence alignment gave correct results for a variety of computer-generated model sequences without and with gaps for all degrees of substitution, s. Measure d was the squared Euclidean distance between vectors of counts of t-tuplets of characters in the two sequences. In models without gaps and without Needleman-Wunsch alignment, average d was very closely equal to twice average conventional mismatch counts, m. In these models one of each of the conditions on the Jukes-Cantor model was violated in turn: (1) both descendant lineages receive the same number of substitutions, (2) all sites are equally likely to be substituted, (3) all different replacement characters are equally likely to be chosen, and (4) all original characters are equally likely to be substituted. In Jukes-Cantor models with gaps Needleman-Wunsch alignment was necessarily performed, a procedure that generally produced incorrect values of m. For these models average d was found to be very closely equal to twice the average m estimated from the known value of s using the inverted Jukes-Cantor formula.

Algorithms↗
PubMed1993

Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism.

In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

Animals↗
PubMed1998

Phylogenetic position of an obligately chemoautotrophic, marine hydrogen-oxidizing bacterium, Hydrogenovibrio marinus, on the basis of 16S rRNA gene sequences and two form I RuBisCO gene sequences.

Two form ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes from the obligately autotrophic, marine hydrogen oxidizer Hydrogenovibrio marinus were sequenced. The deduced amino acid sequences of both RuBisCOs revealed that they are similar to those of sulfur oxidizers (Thiobacillus) and a purple sulfur bacterium (Chromatium vinosum). According to the 16S rRNA gene sequences, H. marinus is also affiliated with these microorganisms, members of Thiomicrospira being the closest relatives. Sequence similarities of the 16S rRNA genes and of the RuBisCO genes among these gamma-Proteobacteria suggest a common autotrophic ancestry. An ancestor of purple sulfur bacteria might be a common root of H. marinus and related sulfur oxidizers.

Bacterial Proteins↗
PubMed1990

The amino terminal sequence of the developmentally regulated Ch21 protein shows homology with amino terminal sequences of low molecular weight proteins binding hydrophobic molecules.

Ch21 protein, a developmentally regulated chick embryo protein of 21,000 apparent molecular weight, was purified from culture medium of hypertrophic chondrocytes. The purification method included a DEAE cellulose chromatography column, a CM cellulose chromatography column and a HPLC molecular sieve column. The amino acid sequence of the amino terminal end of the protein was determined. Computer assisted analysis showed significant homology between this sequence and the amino terminal sequences of proteins that belong to the superfamily of the low molecular weight binding proteins sharing a basic framework for the binding and transport of small hydrophobic molecules. Determination of the amino terminal sequence of the chicken retinol binding protein excluded identity between this protein and the Ch21.

Amino Acid Sequence↗
PubMed1988

Nucleotide sequence of pig plasma gelsolin. Comparison of protein sequence with human gelsolin and other actin-severing proteins shows strong homologies and evidence for large internal repeats.

Pig plasma gelsolin (Mr = 81595; 739 residues) contains 704 identical residues out of a maximum 730 when compared to the cytoplasmic form of human gelsolin. The cDNA sequence also codes for a peptide of 33 residues N-terminal to the nine-residue plasma extension sequence previously reported: these 33 residues are highly homologous to the human signal peptide and plasma extension. Comparison of the gelsolin sequences with chicken brush border villin, severin from Dictyostelium discoideum and fragmin from Physarum polycephalum shows a strong evolutionary relationship between all these proteins. There are six large repeating segments in gelsolin and villin, and three similar segments in severin and fragmin. Although these multiple repeats cannot be related to any known function of these actin-severing proteins, this superfamily of proteins appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues.

Animals↗
PubMed1992

Molecular cloning and sequence analysis of the mumps virus gene encoding the L protein and the trailer sequence.

We have cloned and determined the nucleotide sequences of the seventh gene of the Miyahara strain of mumps virus (MuV) encoding the L protein. The L gene is 6925 nucleotides in length and contains a single long open reading frame which is capable of coding for a protein of 2261 amino acids with a calculated molecular weight of 256,571 Da. The deduced amino acid sequence of the L protein of MuV showed significant homology with those of six other paramyxoviruses, human parainfluenza type 2 virus, Newcastle disease virus, Sendai virus, measles virus, human parainfluenza type 3 virus, and human respiratory syncytial virus. The predicted MuV L protein contained distinct elements thought to be essential for RNA polymerase activity. A noncoding sequence of 24 nucleotides downstream of the presumed polyadenylation site of the L gene showed significant complementarity with the leader sequence composed of 55 nucleotide at the 3' end of the genomic RNA.

Amino Acid Sequence↗
PubMed1994

Nucleotide sequence between recA and alaSp in E. coli K12 and the sequence change in four recA mutations.

The sequence of 366 nucleotides between the C-terminal trailer region of recA and the N-terminal leader region of alaS is presented. This sequence reveals an open reading frame of 166 codons we have named oraA. An NdeI restriction nuclease cleavage site also revealed by the sequence was used to clone, map and sequence three recA mutations: recA11, recA12 and recA52. A mutation in recA (recA946), was discovered in strains originally reported to contain recH166. The relation between recA946 and recH166 is unclear.

Amino Acid Sequence↗
PubMed1988

Purification methods for the sequence-specific DNA-binding protein nuclear factor I (NFI)--generation of protein sequence information.

The paper describes a potent purification method, preparative gel retention, for the purification of sequence-specific DNA-binding proteins. This procedure exploits the sequence-specific DNA-binding affinity of such proteins for their enrichment, comparable to recognition site DNA affinity chromatography. The method was employed to obtain a pure preparation of nuclear factor I (NFI) from porcine liver from which sequences of partial peptides could be obtained. Oligonucleotide probes derived from these amino-acid sequences were used to identify genomic and cDNA clones of NFI.

Amino Acid Sequence↗
PubMed1990

The primary structure of rat ribosomal proteins: the amino acid sequences of L27a and L28 and corrections in the sequences of S4 and S12.

The amino acid sequences of rat ribosomal proteins L27a and L28 were deduced from the sequences of nucleotides in recombinant cDNAs and confirmed from the NH2-terminal amino acid sequences of the proteins. L27a contains 147 amino acids (the NH2-terminal methionine is removed after translation of the mRNA) and has a molecular weight of 16 476. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 18-22 copies of the L27a gene. The mRNA for the protein is about 600 nucleotides in length. L27a is homologous to mouse L27a (there are 3 amino acid changes) and to yeast L29. Rat ribosomal protein L28 has 136 amino acids (its NH2-terminal methionine is also processed after translation) and has a molecular weight of 15 707. Hybridization of the cDNA to digests of nuclear DNA suggests that there are 9 or 10 copies of the L28 gene. The mRNA for the protein is about 640 nucleotides in length. L28 contains a possible internal duplication of 9 residues. Corrections are recorded in the sequences reported before for rat ribosomal proteins S4 and S12.

Amino Acid Sequence↗
PubMed1993

A highly conserved repetitive sequence from Physarum polycephalum contains nucleotide arrangements similar to replicator sequences.

An interspersed repetitive sequence from Physarum polycephalum has been cloned and analysed. The 394 bp sequence is highly conserved and contains several homopolymeric (dA)-(dT) tracts capable of forming bent DNA structures and a 10/11 match to the yeast-ARS-consensus sequence. The repetition frequency of the described sequence is about 3000 to 7000, a number that would fit with the distribution of replicator segments in Physarum.

Animals↗
PubMed1991

The complete amino acid sequence of feline beta-lactoglobulin II and a partial revision of the equine beta-lactoglobulin II sequence.

The amino acid sequence of feline beta-lactoglobulin (designated II) has been determined. The protein chain is 163 amino acids long with a relative molecular mass of 18,558. The primary structure was determined by sequencing of native protein (residues 1-25), BPNS-skatole cleavage fragments and the peptides obtained by proteolytic cleavage with V8 proteinase and TPCK-trypsin. Feline beta-lactoglobulin II has 53 and 57% positional identities with bovine beta-lactoglobulin A and equine beta-lactoglobulin I, respectively, and approx. 68% with a revised sequence of equine beta-lactoglobulin II. The equine beta-lactoglobulin II sequence was re-examined between positions 78 and 122 resulting in a major revision in this area with only a single insertion to give a total of 163 residues.

Amino Acid Sequence↗
PubMed1992

Comparative analysis of 23S ribosomal RNA gene sequences of Bacillus anthracis and emetic Bacillus cereus determined by PCR-direct sequencing.

The primary structures of the 23S ribosomal RNA genes of Bacillus anthracis and an emetic strain of Bacillus cereus were determined by direct sequencing of enzymatically amplified chromosomal DNA. The 23S rRNA gene sequences of B. anthracis and B. cereus were found to be almost identical and showed only two differences (a single nucleotide change, and a single base insertion in B. cereus). The feasibility of using PCR-direct sequencing for the rapid sequence determination of large-subunit rRNA genes is demonstrated.

Bacillus anthracis↗