Synthesis of the viral glycoprotein of Rous-associated virus-2.

The synthesis of the viral glycoprotein of Rous-associated virus-2 was studied in vitro in a cell-free system programmed with viral RNA and supplemented with dog pancreas membranes. The protein synthesized was related structurally and immunologically to those found in Rous-associated virus-2-infected chicken embryo fibroblasts. This work confirms and extends earlier work on the nature and synthesis of viral glycoproteins.     

Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome

Summary Segments of the Japanese quail mito-chondrial genome encompassing many tRNA and protein genes, the small and part of the large rRNA genes, and the control region have been cloned and sequenced. Analysis of the relative position of these genes confirmed that the tRNA^Glu and ND6 genes in galliform mitochondrial DNA are located immediately adjacent to the control region of the molecule instead of between the cytochrome b and ND5 genes as in other vertebrates. Japanese quail and chicken display another distinctive characteristic, that is, they both lack an equivalent to the light-strand replication origin found between the tRNA^Cys and tRNA^Asn genes in all vertebrate mitochondrial genomes sequenced thus far. Comparison of the protein-encoding genes revealed that a great proportion of the substitutions are silent and involve mainly transitions. This bias toward transitions also occurs in the tRNA and rRNA genes but is not observed in the control region where transversions account for many of the substitutions. Sequence alignment indicated that the two avian control regions evolve mainly through base substitutions but are also characterized by the occurrence of a 57-bp deletion/addition event at their 5′ end. The overall sequence divergence between the two gallinaceous birds suggests that avian mitochondrial genomes evolve at a similar rate to other vertebrate mitochondrial DNAs.     

Nucleotide and amino acid sequence comparisons of preprosomatostatins

The amino acid and nucleotide sequences have been aligned for five preprosomatostatins: two from catfish, two from anglerfish, and one from rat. The physical characteristics of the aligned residues as well as substitutions in the nucleotide sequences suggest considerable mutability in one of the catfish and anglerfish precursors while three of the preprohormones which give rise to somatostatins-14 are closely related. Although there is a considerable number of amino acid substitutions within the aligned somatostatin-14 precursors, there is a high degree of structural relatedness among them. These results suggest that additional physiological roles for the amino acid sequences outside of the hormone region are likely. The predicted secondary structures of the three somatostatin-14 precursors are dominated by helical and turn configurations which are correlated with observed co- and post-translational processing of the preprohormones.     

Nucleotide sequence of the Escherichia coli replication gene dnaZX.

The Escherichia coli 2.2 kilobase dnaZX region contains one 1929 nucleotide reading frame which directs the synthesis of two protein products involved in DNA polymerization. The larger consists of 643 amino acids in a deduced 71,114 dalton chain which could be the tau subunit of DNA polymerase III. The smaller, the DNA polymerase III gamma subunit, is encoded by the same reading frame as the larger. The dnaZX sequence contains a region homologous to ATP binding sites, suggesting that these replication factors are adenine nucleotide binding proteins.     

Nucleotide sequence homologies in control regions of prokaryotic genomes

Functional recognition sites for several regulatory factors, including RNA polymerase, cyclic adenosine monophosphate receptor protein and ribosomes, do not always have strong consensus nucleotide sequence homology, yet they are capable of biological activity. Using the computer, other nucleotide sequences can be found that have equal or significantly greater consensus homology, but whose biological function has not been characterized. This analysis shows that no arbitrary 'cutoff score' can successfully distinguish active recognition sites from uncharacterized homologies, due to the great natural diversity in the strength and conservation of functional sites. It also predicts that the strong 'cryptic' homologies presented here are of two types: some might already have a biological function which has so far not been detected, whereas certain single-point mutations might be able to confer activity upon the others by correcting a key structural defect.     

Occurrence of protein structure elements in conserved sequence regions

Background  

Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified.     

Bacteriophage P4 DNA replication. Nucleotide sequence of the P4 replication gene and the cis replication region

A 3100 base piece of DNA from the 11,500 base genome of bacteriophage P4 was analyzed for its nucleotide sequence. This segment of DNA contains two open reading frames of 106 and 777 amino acid residues; the latter of which is the coding sequence for the Mr 84,841 alpha protein, which is necessary for P4 DNA replication and is thought to act as a P4-specific DNA primase. A region of about 300 base-pairs localized just beyond the alpha gene and about 4500 bases from the origin of replication (ori), was defined as the locus for P4's cis replication region (crr). This region is required for replication both in vivo and in vitro, and consists of two directly repeated sequences of 120 base-pairs that match one another at 98 positions. These directly repeated sequences are separated by 60 base-pairs, which are not necessary for replication. Each repeat in crr contains three copies of the octamer TGTTCACC that is found six times in ori. Either of the 120 base-pair repeat sequences in crr is sufficient for replication, and the entire crr can function in an inverted orientation. crr is also active at a distance of 1800 bases from the P4 origin of replication.     

Searching databases of conserved sequence regions by aligning protein multiple-alignments.

A general searching method for comparing multiple sequence alignments was developed to detect sequence relationships between conserved protein regions. Multiple alignments are treated as sequences of amino acid distributions and aligned by comparing pairs of such distributions. Four different comparison measures were tested and the Pearson correlation coefficient chosen. The method is sensitive, detecting weak sequence relationships between protein families. Relationships are detected beyond the range of conventional sequence database searches, illustrating the potential usefulness of the method. The previously undetected relation between flavoprotein subunits of two oxidoreductase families points to the potential active site in one of the families. The similarity between the bacterial RecA, DnaA and Rad51 protein families reveals a region in DnaA and Rad51 proteins likely to bind and unstack single-stranded DNA. Helix--turn--helix DNA binding domains from diverse proteins are readily detected and shown to be similar to each other. Glycosylasparaginase and gamma-glutamyltransferase enzymes are found to be similar in their proteolytic cleavage sites. The method has been fully implemented on the World Wide Web at URL: http://blocks.fhcrc.org/blocks-bin/LAMAvsearch.     

Nucleotide sequence of small ColE1 derivatives: Structure of the regions essential for autonomous replication and colicin E1 immunity

Summary A small ColE1 derivative, pAO2, which replicates like the original ColE1 and confers immunity to colicin E1 on its host cell has been constructed from a quarter region of ColE1 DNA (Oka, 1978). The entire nucleotide sequence of pAO2 (1,613 base pairs) was determined based on its fine cleavage map. The sequence of a similar plasmid, pAO3, carrying additional 70 base pairs was also deduced.The sequence in the region covering the replication initiation site on these plasmids was consistent with those reported for ColE1 by Tomizawa et al. (1977) and by Bastia (1977). DNA sequences indispensable for autonomous replication were examined by constructing plasmids from various restriction fragments of pAO2 DNA. As a result, a region of 436 base pairs was found to contain sufficient information to permit replication. The occurrence of initiation and termination codons and of the ribosome-binding sequence on pAO2 DNA suggests that a polypeptide chain consisting of 113 amino acid residues may be encoded by the region in which the colicin E1 immunity gene has been mapped.Abbreviations ColE1 colicin E1 plasmid - Tris tris-(hydroxymethyl)aminomethane - EDTA ethylenediaminetetraacetate - dNTP deoxyribonucleoside triphosphates - ATP adenosine 5-triphosphate     

Evolutionarily conserved regions in Caenorhabditis transposable elements deduced by sequence comparison.

In this paper we present the sequence of an intact Caenorhabditis briggsae transposable element, Tcb2. Tcb2 is 1606 base pairs in length and contains 80 base pair imperfect terminal repeats and a single open reading frame. We have identified blocks of T-rich repeats in the regions 150-200 and 1421-1476 of this element which are conserved in the Caenorhabditis elegans element Tc1. The sequence conservation of these regions in elements from different Caenorhabditis species suggests that they are of functional importance. A single open reading frame corresponding to the major open reading frame of Tc1 is conserved among Tc1, Tcb1, and Tcb2. Comparison of the first 550 nucleotides of the sequence among the three elements has allowed the evaluation of a model proposing an extension of the major open reading frame. Our data support the suggestion that Tc1 is capable of producing a 335 amino acid protein. A comparison of the sequence coding for the amino and carboxy termini of the 273 amino acid transposase from Caenorhabditis Tc1-like elements and Drosophila HB1 showed different amounts of divergence for each of these regions, indicating that the two functional domains have undergone different amounts of selection. Our data are not compatible with the proposal that Tc1-related sequences have been acquired via horizontal transmission. The divergence of Tc1 from the two C. briggsae elements, Tcb1 and Tcb2, indicated that all three elements have been diverging from each other for approximately the same amount of time as the genomes of the two species.     

Highly conserved eight amino acid sequence in SH2 is important for recognition of phosphotyrosine site.

Src homology region 2(SH2) has been demonstrated to recognize phosphotyrosine site. To clarify the precise mechanism of the recognition, we developed in vitro binding assay system using EGF receptor and SH2/SH3 region of phospholipase C(PLC) gamma 1. Phosphorylated EGF receptor bound to immobilized SH2/SH3 of PLC gamma 1 in Sepharose beads, while nonphosphorylated EGF receptor did not bind. In SH2 domain of PLC gamma 1, there are several highly conserved amino acid sequences that are common in a variety of SH2-containing proteins. Especially the eight amino acid sequence, G(S/T)FLVR(E/D)S is highly conserved in these proteins. We synthesized several peptides related to these sequences and examined the effect of peptides on the binding of EGF receptor to SH2 of PLC gamma 1. P1, GSFLVRES was the most effective inhibitor to suppress the binding. P2, GSFLVAES in which one amino acid, arginine of P1 is substituted by alanine is still effective. But a peptide, P3, SFLVRE in which two amino acids are deleted from P1 did not inhibit markedly. Moreover, P1 peptide immobilized in Sepharose beads also bound phosphorylated EGF receptor. These data suggest that highly conserved amino acid sequence GSFLVRES is the minimum essential unit to recognize tyrosine phosphorylated site.     

CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences

SUMMARY: CREDO is a user-friendly, web-based tool that integrates the analysis and results of different algorithms widely used for the computational detection of conserved sequence motifs in noncoding sequences. It enables easy comparison of the individual results. CREDO offers intuitive interfaces for easy and rapid configuration of the applied algorithms and convenient views on the results in graphical and tabular formats. AVAILABILITY: http://mips.gsf.de/proj/regulomips/credo.htm.     

Nucleotide sequence of chicken myb proto-oncogene promoter region: detection of an evolutionarily conserved element.

The nucleotide sequence of the chicken myb proto-oncogene putative promoter region was determined and compared with the corresponding sequence of the mouse c-myb gene (1). 118 bp upstream from the initiation codon suggested by Gerondakis and Bishop (2) for the chicken c-myb protein, a 124-bp-long conserved element was found (92% identity in chicken and mouse sequences). Sequences homologous to this element were detected on Southern blots of restricted genomic DNAs from mouse, man, lizard, frog, and carp. No hybridization was observed with Drosophila, yeast, or Escherichia coli DNA. In human DNA, sequences homologous to this element were located at the 5' end of the c-myb gene, i.e. in the same position as in the chicken and mouse genes. Several lines of evidence suggest that the element is not a coding exon of a gene overlapping the c-myb gene. It may be of importance that one of the DNase I-sensitive sites and several c-myb mRNA cap sites localized recently in the mouse c-myb gene (3,4) lie within this region. It is suggested that this evolutionarily conserved element is involved in the regulation of myb proto-oncogene expression in vertebrates.