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PubMed2005

SecY gene sequence analysis for finer differentiation of diverse strains in the aster yellows phytoplasma group.

Aster yellows (AY) group (16SrI) phytoplasmas are associated with more than 100 economically important diseases worldwide and represent the most diverse and widespread phytoplasma group. Phylogenetic analysis of secY gene sequences resolved 10 genetically distinct lineages. The 10 lineages coincide with those delineated by phylogenetic analysis based on ribosomal protein (rp) gene sequences. However, greater genetic variability among the 10 lineages was revealed based on secY gene sequences. The distinct phylogenetic lineages can be readily identified through restriction fragment length polymorphism (RFLP) analysis of secY gene sequences. Ten subgroups were differentiated among the AY group phytoplasmas based on RFLP analysis of secY gene sequences. Phylogenetic analysis based on secY gene sequences in this study, and previous studies on the 16S rRNA gene, tuf gene, and rp gene sequences reinforced the notion that most subgroups identified by RFLP analysis of secY and rp gene sequences represent distinct phylogenetic lineages.

DNA, Bacterial↗

PubMed2003

Sequence analysis of the fragment of the phosphoprotein gene of Polish distemper virus isolates.

The nucleotide sequence analysis of the 429 bp fragment of the P gene of 11 Polish field isolates of Canine distemper virus (CDV), reference strains and other virus isolates available in the GenBank was the aim of the studies. High homology between all dog strains from east-southern region of Poland and reference strains of CDV was demonstrated. It was estimated as 97-100 % for CDV-OND; 96.7-99.8 % for CDV-Rock; 96.7-99.8 % for CDV-LED and 96.3-97.9 % for A75-17. The 100 % homology of the nucleotide sequence was observed between CDV Pulawy 92, CDV Pulawy 97 and the reference CDV-OND. The homology between CDV-OND and viruses isolated from the mink and ferret was estimated as 97.7 % and 98.4 %, respectively. Virus strains isolated from blue foxes demonstrated the highest homology to CDV-OND - equal to 97.7 % for DV 79 and 99.5 % for DV 92. The fox isolate from 1992 had higher level of homology to dog isolates (96.5-99.5 %) than the strain isolated from the fox in 1979 (97.2-98.8 %). The phylogenetic tree has two main lineages representing two separated genetic groups: I containing PDV and II containing all distemper virus strains isolated from terrestrial carnivores. CDV strains isolated from dogs from Pulawy region between 1992-1998 and from the fox (DV 92) formed the separate lineage containing also reference strains. They differed from the native isolates from the mink and ferret as well as from Japanese strains of CDV.

Amino Acid Sequence↗

PubMed1997

Rat MDC family of proteins: sequence analysis, tissue distribution, and expression in prepubertal and adult rat testis.

Increasing number of sequence-related cysteine-rich membrane proteins containing metalloproteinase-like and disintegrin-like domains (the MDC protein family) have been identified in mammalian tissues. Here, we report the cloning and sequence analysis of cDNAs encoding several rat orthologues of this protein family, some of which are found to be expressed exclusively in the male reproductive tract, others exhibiting a broader tissue distribution. We also examine their expression in prepubertal an adult rat testis, which, in conjunction with the data on tissue distribution, form a necessary prelude to further studies aimed at establishing their individual functions.

ADAM Proteins↗

PubMed2006

Nucleotide sequence analysis of the ORF0 region of Potato leafroll virus isolates from Tunisia.

Potato leafroll virus (PLRV) isolates from potato plants from different regions of Tunisia were investigated for the ORF0 variable region of genomic RNA using PCR, nucleotide sequencing and sequence analysis. Based on the ORF0 variable region nucleotide sequence, individual Tunisian isolates were more homologous as a group compared to the isolates originating from other parts of the world. There was no correlation between bioclimatic origin of the isolates and their ORF0 sequence. Alignment of the deduced amino acid sequences showed that the P0 protein was not much conserved. Unexpectedly, Tunisian isolates were found to be most homologous to Peruvian ones both at nucleotide and amino acid level. A phylogenetic tree, based on the P0 amino acid sequence, showed that all the PLRV isolates were located in two major clusters regardless of their geographic origin. In the second cluster, three sub-clusters could be distinguished. These results provide valuable information for molecular characterization of the PLRV isolates occurring in Tunisia.

Base Sequence↗

PubMed2000

Characterization of Borrelia burgdorferi strains isolated from Korea by 16S rDNA sequence analysis and PCR-RFLP analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons.

Haenam strains of Borrelia burgdorferi, which had been isolated from Ixodes granulatus and Apodemus agrarius in Haenam, Korea, were characterized by PCR-RFLP analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons and by sequence analysis of the 16S rRNA gene (rDNA). The Msel and Dral restriction patterns of the 5S-23S intergenic spacer amplicons of Haenam strains differed from those of other B. burgdorferi sensu lato strains. Furthermore, in the phylogenetic tree based on the 16S rDNA sequences, Haenam strains formed a distinctive cluster, clearly separated from the other members of B. burgdorferi sensu lato. These results suggest that, apart from Borrelia garinii and Borrelia afzelii, other genotypes of B. burgdorferi sensu lato exist in Korea and the Haenam strain is a newly identified one.

Animals↗

PubMed2005

The major Aeromonas veronii outer membrane protein: gene cloning and sequence analysis.

The gene encoding the major outer membrane protein (OMP) from Aeromonas veronii, Omp38, was cloned and characterized. Sequence analysis revealed an open reading frame of 1,047 nucleotides coding for a primary protein of 349 amino acids with a 20-amino-acid signal peptide at the N-terminal and the consensus sequence Ala-X-Ala (Ala-Asn-Ala) as the signal peptidase I recognition site. The mature protein is composed of 329 amino acids with a calculated molecular mass of 36,327 Da. The degree of identity of the deduced Omp38 amino acid sequence to porins from enteric bacteria (OmpF, PhoE, and OmpC) was only 30%. Nevertheless, Omp38 possesses typical features of Gram-negative porins, including acidic pI, high glycine and low proline content, no cysteine residues, and a carboxy-terminal Phe. On the basis of PhoE-OmpF three-dimensional structure and the Kyte-Doolittle hydrophobicity analysis, it seems likely that Omp38 secondary structure consists of 16 antiparallel beta-strands and 8 loops. Phylogenetic analyses among Omp38 and related porins from Gram-negative bacteria originate well-defined clusters that agree with the taxonomy of the corresponding organisms.

Aeromonas↗

PubMed1984

Sequence analysis of a split gene involved in fruiting from the fungus Schizophyllum commune.

The sequence of a gene and its mRNA, which is abundantly expressed during fruiting body initiation in the Basidiomycete Schizophyllum commune, is described. This gene (1G2), the first to be analyzed in this group of fungi, contains an open reading frame coding for a polypeptide of 94 amino acids and a mol. wt. of 9842. A possible signal peptide of 20 residues and one glycosylation site were found. The sequence analysis was hampered by a sequence rearrangement in one of the cDNA clones, probably due to base pairing between short complementary sequences present at the 5' and 3' ends of the mRNA. The 5' untranslated leader sequence is 57 bp long and harbors a possible ribosome binding site close to the AUG start codon. A TATA box is found at position -31 upstream of transcription initiation. The 3' untranslated sequence is 200 bp long and contains the sequence -TATATAAT-, which most likely represents the polyadenylation signal. Some heterogeneity as to the site of addition of the poly(A) tail was observed. The coding region of the gene is interrupted by three very small introns of 53, 49 and 49 bp, respectively. The 5' and 3' splice junctions are conserved: GTGAGT- and -AG-, respectively. Each intron contains a sequence complementary to the 5' end of the intron. These sequences are compared with internal conserved sequences in yeast and filamentous fungi with regard to their possible role in splicing.

Journal Article↗

PubMed1993

A hypertext-like approach to navigating through the GCG sequence analysis package.

Programs of the recently released Unix version of the Genetics Computing Group (GCG) sequence analysis package can now be accessed via a user-friendly hypertext-like navigation system, HYGCG. The resultant system organizes the diverse suite of programs into logical groups, and provides a guide and explanation of commands. In addition, for users unfamiliar with the Unix operating system, the program also provides a similar interface to commonly used Unix commands. Options for personal customization and expansion to accommodate GCG extensions and other software are also provided. This system should be useful especially to the inexperienced or infrequent user as context-sensitive on-line help is provided within this simple and consistent approach. Written in the C language and using the curses and termcap libraries, the system is easily portable to most Unix environments and has been made freely available via anonymous file transfer protocol (FTP) through the Internet global computer network. No modification of the GCG package is needed.

Sequence Analysis↗

PubMed1997

Comparative sequence analysis and expression of the M6 gene, encoding the outer capsid protein VP5, of African horsesickness virus serotype nine.

The entire nucleotide and deduced amino acid sequence of the M6 gene of African horsesickness virus (AHSV) serotype nine has been determined from four overlapping cDNA clones. The gene was found to be 1566 bp long, encoding a protein of 505 amino acids with a molecular weight of 56 737 Da and a nett charge of - 1 at neutral pH Comparative sequence analysis of the deduced amino acid sequence with the VP5 protein of AHSV-4, showed that only 81% of amino acids were conserved in type and position, although alternating regions of lower and higher conservation was identified by alignment of the primary sequences of different orbiviral VP5 proteins. Antigenically authentic AHSV-9 VP5 was also expressed in a baculovirus expression system and the expressed protein was shown to react specifically with anti-AHSV-9 as well as AHSV-3 serum in Western blot analysis.

African Horse Sickness Virus↗

PubMed1997

Sequence analysis of a 10.5 kb DNA fragment from the yeast chromosome VII reveals the presence of three new open reading frames and of a tRNAThr gene.

We report the sequence analysis of a 10,531 bp DNA of Saccharomyces cerevisiae chromosome VII. This sequence contains five complete open reading frames (ORFs) potentially encoding proteins longer than 100 amino acids and incomplete ORF encoding for the 3' part of the GCN5 gene (Georgakopoulos and Thireos, 1992). ORFs G9160 and G9155 correspond to the genes ENO1 (Holland et al. 1981) and PUP2 (Gergatsou et al., 1992) respectively. ORF G9165 codes for a protein which shares significant homology with known proteins present in databases (see below). The translated sequence of ORF G9170 shows 88% identity to the 6-phosphogluconate dehydrogenase encoded by the gene 6PGD from S. cerevisiae present in the SwissProt data library (P38720). This indicates that G9170 might code for a second 6-phosphogluconate dehydrogenase. ORF G9175 codes for a putative new member of the mitochondrial carrier family. A hypothetical tRNAThr (TGT) is also present in position 6842-6913.

Chromosomes, Fungal↗

PubMed2003

[Complete sequence analysis on potato virus M infecting Solanum muricatum].

The complete sequence of Potato virus M from Solanum muricatum was determined. The liner, single-strand and positive sense genomic RNA was 8526 nucleotides long and six open reading frames were identified. The genome organization was typical feature of genus Carlavirus. Sequence analysis showed that PVM isolates shared 62.5% - 97.2% nucleotide and 60.9% - 97.4% amino acid identities. The coat protein gene was most conserved and TGB3 gene was greatly variable. Phylogenetic tree analysis suggested that the Idaho potato isolate (PVM-Id) was a distant strain, and other 4 isolates were grouped discriminatively based on CP and NABP amino acid sequences respectively. This is the first report of PVM from Solanum muricatum.

Capsid Proteins↗

PubMed1992

Chance and statistical significance in protein and DNA sequence analysis.

Statistical approaches help in the determination of significant configurations in protein and nucleic acid sequence data. Three recent statistical methods are discussed: (i) score-based sequence analysis that provides a means for characterizing anomalies in local sequence text and for evaluating sequence comparisons; (ii) quantile distributions of amino acid usage that reveal general compositional biases in proteins and evolutionary relations; and (iii) r-scan statistics that can be applied to the analysis of spacings of sequence markers.

Amino Acid Sequence↗

PubMed1993

Sequence analysis and functional studies of interleukin-3 receptor alpha subunit-encoding cDNAs amplified from KG-1 leukemic cells and normal human marrow.

Two partial cDNAs encoding the human interleukin-3 receptor alpha subunit (IL-3R alpha) were cloned from KG-1 leukemic cells using the polymerase chain reaction. Sequence analysis of these cDNAs predicted two single-amino-acid (aa) changes as compared with the published TF-1 leukemic cell IL-3R alpha sequence [Kitamura et al., Cell 66 (1991) 1165-1174]. These changes were confirmed by sequence analysis of a second set of independently derived cDNAs. Identical aa changes were found in the IL-3R alpha encoded by cDNAs cloned from normal CD34+ human marrow cells. Ligation of the partial cDNAs derived from KG-1 cells resulted in a full-length functional IL-3R alpha cDNA clone. Deletion of the extracellular 'LSXWS' consensus sequence resulted in complete loss of detectable [125I]IL-3 binding when this mutant receptor was co-expressed in COS-7 cells with the beta subunit of the IL-3 receptor.

Base Sequence↗

PubMed1996

Cloning and sequence analysis of a Marek's disease virus origin binding protein (OBP) reveals strict conservation of structural motifs among OBPs of divergent alphaherpesviruses.

Marek's disease virus (MDV) is a highly cell-associated avian herpesvirus. In its natural host, MDV induces Marek's disease (MD), a lethal condition characterized by malignant lymphoma of T cells. Although symptoms of MD may be prevented by vaccination, no practical pharmacological method of control has been widely accepted. Viral replication represents a point at which pharmacological control of herpesvirus infection may be most successful. However, this requires detailed knowledge of viral replication proteins. Studies in HSV-1 DNA replication implicate the UL9 protein as a key initiator of replication. For example, binding of UL9 to HSV-1 origins is a prerequisite for assembly of additional replication proteins. In this study, a protein, whose apparent molecular size is similar to that of HSV-1 UL9, was identified in extracts of MDV infected cells by western blot analysis with anti-HSV-1 UL9 antibody. A putative MDV UL9 gene was subsequently identified through sequencing of MDV genome fragments (BamHI G and C). Extended DNA sequence analysis revealed an open reading frame (ORF) which could encode a protein homologous to HSV-1 UL9. The MDV UL9 ORF encodes 841 amino acids, producing a sequence 49% identical to HSV-1 UL9 and 46% identical to VZV gene 51 product (VZV UL9). MDV UL9 shares numerous structural motifs with HSV-1 and VZV UL9 proteins, including six conserved N-terminal helicase motifs, an N-terminal leucine zipper motif, a C-terminal pseudo-leucine zipper sequence, and a putative helix-turn-helix structure.

Alphaherpesvirinae↗

PubMed2007

Sequence handling by sequence analysis toolbox v1.0.

The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl inositol-anchored proteins.

Computational Biology↗

PubMed1997

Cloning and sequence analysis of the gene (eprA1) encoding an extracellular protease from Aeromonas hydrophila.

A gene (eprA1) encoding the extracellular protease of Aeromonas hydrophila AH1 has been cloned and sequenced. Nucleotide sequence analysis of eprA1 predicted a single open reading frame (ORF) of 1038 bp encoding a 346 amino acid (aa) polypeptide, with a potential 21-aa signal peptide. When the eprA1 gene was expressed in minicells, one major band of approx. 37 kDa was identified, while protease activity staining experiments identified a caseinolytic band of approx. 29 kDa determined by SDS-PAGE analysis of the minicells. The deduced C-terminal aa region (Arg-290 to Gly-313) showed sequence homology to partial C-terminal sequences of other zinc metalloproteases including Penicillium citrinum metalloprotease (PlnC), Aspergillus oryzae metalloprotease (NpII), Aspergillus flavus metalloprotease (MepA), and Aspergillus fumigatus metalloprotease (Mep20), particularly with respect to zinc-binding residues.

Aeromonas hydrophila↗

PubMed2006

Molecular cloning and sequence analysis of interferon-gamma and interleukin-6 from Tibetan macaque (Macaca thibetana).

The cloning and sequence analysis of Tibetan macaque IFN-(gamma) and the IL-6 cDNAs are described. The Tibetan macaque IFN-gamma and IL-6 cDNAs were found to be 498 and 639 bp in length, with open reading frames encoding 165 and 212 amino acids, respectively. Homology analyses indicated that the identity levels of nucleotide and deduced amino acid sequences of IFN-gamma among primates ranged from 93.4 to 99.2%, and 87.3 to 99.4%, respectively, and that of IL-6 ranged from 92.6 to 99.8%, and 85.4 to 99.5%, respectively. Phylogenetic analysis based on amino acid sequences showed that the Tibetan macaque is most closely related to Old World monkeys, as compared to Hominoidea and New World monkeys. These findings provide insights into the evolution of primate IFN-gamma and IL-6 and additional valuable information regarding amino acid residues essential for their biological activity.

Amino Acid Sequence↗

PubMed1995

Molecular cloning, sequencing and sequence analysis of the fox-2 gene of Neurospora crassa encoding the multifunctional beta-oxidation protein.

We present the molecular cloning and sequencing of genomic and cDNA clones of the fox-2 gene of Neurospora crassa, encoding the multifunctional beta-oxidation protein (MFP). The coding region of the fox-2 gene is interrupted by three introns, one of which appears to be inefficiently spliced out. The encoded protein comprises 894 amino acid residues and exhibits 45% and 47% sequence identity with the MFPs of Candida tropicalis and Saccharomyces cerevisiae, respectively. Sequence analysis identifies three regions of the fungal MFPs that are highly conserved. These regions are separated by two segments that resemble linkers between domains of other MFPs, suggesting a three-domain structure. The first and second conserved regions of each MFP are homologous to each other and to members of the short-chain alcohol dehydrogenase family. We discuss these homologies in view of recent findings that fungal MFPs contain enoyl-CoA hydratase 2 and D-3-hydroxyacyl-CoA dehydrogenase activities, converting trans-2-enoyl-CoA via D-3-hydroxyacyl-CoA to 3-ketoacyl-CoA. In contrast to its counterparts in yeasts, the Neurospora MFP does not have a C-terminal sequence resembling the SKL motif involved in protein targeting to microbodies.

3-Hydroxyacyl CoA Dehydrogenases↗