GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library

Harr, Robert; Fällman, Per; Häggström, Mikael; Wahlström, Leif; Gustafsson, Petter

doi:10.1093/nar/14.1.273

Cited by 63 publications

(27 citation statements)

References 14 publications

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“…(1989a). Sequences were assembled using GENEUS (Harr et al, 1986) software for VAX computers (DEC). Further nucleotide sequence and protein sequence analyses were performed using the University of Wisconsin GCG sequence analysis software for VAX computers.…”

Section: Methodsmentioning

confidence: 99%

Expression of the flagellin gene in Borrelia is controlled by an alternative factor

Noppa

Burman²,

Sadziene³

et al. 1995

Microbiology

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Section: Methodsmentioning

confidence: 99%

Expression of the flagellin gene in Borrelia is controlled by an alternative factor

Noppa

Burman²,

Sadziene³

et al. 1995

Microbiology

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“…Labeled fragments were separated on 0.2-mm-thick 6% sequencing gels (36). The DNA sequence was analyzed with the Geneus computer program (20).…”

Section: Methodsmentioning

confidence: 99%

Genetic analysis of the yopE region of Yersinia spp.: identification of a novel conserved locus, yerA, regulating yopE expression

Försberg

Wolf‐Watz

1990

J Bacteriol

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The yopE gene of Yersinia pseudotuberculosis was recently sequenced, and YopE was identified as an indispensable virulence determinant when tested in a mouse model (A. Forsberg and H. Wolf-Watz, Mol. Microbiol. 2:121-133, 1988). In the study described here, the DNA sequences of the yopE genes of Yersinia pestis EV76 and Yersinia enterocolitica 8081 were determined and compared with that of the Y. pseudotuberculosis gene. Only two codons were found to differ, both leading to amino acid replacements, when the gene from Y. pestis was compared. These two replacements were also present in the gene from Y. enterocolitica; in addition, 18 other codons were found to differ. Thirteen of these substitutions led to amino acid replacements. Downstream of the yopE gene, the plasmid partition locus par was found to be conserved in all three species. In Y. enterocolitica 8081, the sequence homology was interrupted by a putative insertion sequence element inserted between the yopE gene and the par region at a position only 5 base pairs downstream of the yopE stop codon. Upstream of the yopE gene, 620 base pairs were conserved in the three species. This region contained a 130-amino-acid-long open reading frame reading in the opposite direction to the yopE gene and expressed a 14-kilodalton protein in minicells. An insertion mutation in this region constructed in Y. pseudotuberculosis expressed significantly lower amounts of YopE protein in vitro than did the corresponding wild type. The expression level could be restored by transcomplementation. This new locus was designated yerA, for yopE-regulating gene A. The yerA mutant was avirulent when mice were challenged by oral infection.

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“…Dideoxy sequencing of DNA (32) was performed as described by Amersham Corp. (Arlington Heights, Ill.). The DNA sequences obtained were analyzed with the GENEUS computer system (13).…”

Section: Methodsmentioning

confidence: 99%

Transcriptional organization of the phycocyanin subunit gene clusters of the cyanobacterium Anacystis nidulans UTEX 625

Kalla¹,

Lind²,

Lidholm³

et al. 1988

J Bacteriol

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The phycocyanin subunit gene cluster is duplicated on the chromosome of the cyanobacterium Anacystis nidulans UTEX 625. The two gene clusters cpcBIAl (left) and cpcB2A2 (right) are separated by about 2,500 base pairs, and in each cluster the (-subunit gene is located upstream from the at-subunit gene. Filter hybridizations with phycocyanin-specific probes to total RNA detected at least two major transcripts that were 1,300 to 1,400 nucleotides long. Besides these major mRNA species, two minor transcripts of 3,400 and 3,700 nucleotides covering one of the gene clusters and the region between the clusters were found. No additional minor transcripts were found in the intergenic region between the two phycocyanin gene clusters. The lengths of the major mRNAs indicated that the (-and a-subunit genes were cotranscribed. No apparent homologies were found when the DNA sequences located upstream from the proposed ribosome-binding site of the two phycocyanin ,B-subunit genes were compared. Northern hybridizations with gene cluster-specific probes from the regions 5' of the (-subunit genes, as well as S1 nuclease mapping and mRNA primer extension experiments, showed that both gene clusters were transcribed. The minor transcripts were found to initiate upstream from the left gene cluster. Two mRNA 5' ends were mapped upstream from the cpcBIAl gene cluster, while only one 5' end was mapped in front of the cpcB2A2 gene cluster. All transcripts were present in RNA preparations from cultures grown under high levels of white light as well as under low levels of red light. The level of phycocyanin-specific mRNA, measured as part of the total RNA, was lower under low levels of red light compared with that under high levels of white light. Conserved sequence motifs were found when the promoter region of the cpcBlAl gene cluster and promoter regions from other cyanobacterial photosynthesis genes were compared. The DNA sequences covering the proposed transcriptional attenuators and transcriptional stop signals contained several potential hairpin structures. One potential hairpin structure was located immediately downstream of the left phycocyanin gene cluster and was concluded to limit the level of transcription for the minor transcripts initiating upstream of the cpcBlAl gene cluster.Cyanobacteria are procaryotic organisms equipped with the capability to perform oxygenic photosynthesis (35). Their photosynthetic apparatus consists of two photosystems, PSI and PSII, and one major light-harvesting antenna, the phycobilisome, which is connected to PSII (8,9,35). The phycobilisome of Anacystis nidulans UTEX 625 (hereafter designated A. nidulans 625) is a large, multiprotein aggregate that is mainly composed of phycobiliproteins such as allophycocyanin and phycocyanin; these are directly involved in the harvesting and transport of light energy. Each phycobiliprotein is a multimeric form of two nonidentical polypeptide chains, a and P. Open-chain tetrapyrroles are covalently attached to the subunit polypeptides and serve as chromophores ...

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GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library

Cited by 63 publications

References 14 publications

Expression of the flagellin gene in Borrelia is controlled by an alternative factor

Expression of the flagellin gene in Borrelia is controlled by an alternative factor

Genetic analysis of the yopE region of Yersinia spp.: identification of a novel conserved locus, yerA, regulating yopE expression

Transcriptional organization of the phycocyanin subunit gene clusters of the cyanobacterium Anacystis nidulans UTEX 625

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