Australia's national genomic information system

Reisner, A. H.; Bucholtz, C.A.; Smelt, J.H.; McNeil, Sara

doi:10.1109/hicss.1993.270681

Cited by 15 publications

(14 citation statements)

References 6 publications

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“…Sequences were aligned using the  program (Feng & Doolittle, 1986), and phylogenetic analysis was carried out using the  (Felsenstein, 1993) and  programs. These programs were accessed using the Australian National Genomic Information Service (Reisner et al, 1993).…”

Section: Methodsmentioning

confidence: 99%

Molecular evolution of the GDP-mannose pathway genes (manB and manC) in Salmonella enterica The GenBank accession numbers for the sequences reported in this paper are AY012160–AY012201.

Jensen

Reeves

2001

Microbiology

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The evolutionary history of the GDP-mannose pathway in Salmonella enterica was studied via sequencing manB and manC genes from 13 representative strains for O antigens containing mannose and/or sugar derivatives of GDP-Dmannose. In addition, colanic acid (CA) manB and manC genes were sequenced from selected strains, as the basis for a detailed comparison. Interestingly, including the eight previously characterized O antigen gene clusters, 12 of the 21 S. enterica strains studied in total (each representing a different O antigen structure) possess a manB gene which displays DNA identity, ranging from 93 to 99 %, to the CA manB gene of S. enterica LT2. Furthermore, the CA-like manB genes (as well as the CA manB and manC genes) display subspecies specificity, and the CA and CA-like manB genes (for individual strains) appear to be evolving in concert via gene conversion events. In comparison, the manC genes were generally not CA-like, a situation also apparent in Escherichia coli, and therefore most strongly reflected the evolutionary history of the S. enterica O antigen GDP-mannose pathway. It appears that, in relatively recent times, gene capture from a distant source has occurred infrequently, and that groups of manB and manC genes have been maintained and are continuing to evolve within S. enterica and more closely related species.

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Section: Methodsmentioning

confidence: 99%

Molecular evolution of the GDP-mannose pathway genes (manB and manC) in Salmonella enterica The GenBank accession numbers for the sequences reported in this paper are AY012160–AY012201.

Jensen

Reeves

2001

Microbiology

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“…Computer programs were accessed through the Australian Genomic Information Service (54). Sequence data were assembled into contiguous sequences with the XDAP program (25).…”

Section: Materuils and Methodsmentioning

confidence: 99%

Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster

et al. 1994

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Escherichia coli K-12 has long been known not to produce an 0 antigen. We recently identified two independent mutations in different lineages of K-12 which had led to loss of 0 antigen synthesis (D. Liu and P. R. Reeves, Microbiology 140:49-57, 1994) and constructed a strain with all rjb (0 antigen) genes intact which synthesized a variant of 0 antigen 016, giving cross-reaction with anti-017 antibody. We determined the structure of this 0 antigen to be -with an 0-acetyl group on C-2 of the rhamnose and a side chain c-D-Glcp on C-6 of GlcNAc. 0 antigen synthesis is rfe dependent, and D-GlcpNAc is the first sugar of the biological repeat unit. We sequenced the rjb (0 antigen) gene cluster and found 11 open reading frames. Four rhamnose pathway genes are identified by similarity to those of other strains, the rhamnose transferase gene is identified by assay of its product, and the identities of other genes are predicted with various degrees of confidence. We interpret earlier observations on interaction between the rjb region ofEscherichia coli K-12 and those ofE. colh 04 and E. coi Flexneri. All K-12 rjb genes were of low G+C content for E. coil. The rhamnose pathway genes were similar in sequence to those of (Shigella) Dysenteriae 1 and Flexneri, but the other genes showed distant or no similarity. We suggest that the K-12 gene cluster is a member of a family of rjb gene clusters, including those of Dysenteriae 1 and Flexneri, which evolved outside E. coli and was acquired by lateral gene transfer.Escherichia coli K-12 was isolated in 1922 and used as a standard E. coli strain at Stanford University for many years; the strains which survive all derive from cultures given to E. Tatum and others in the 1940s and early 1950s, when E. coli K-12 was first used for the genetic studies which led to its adoption as the major strain for laboratory study. After 50 years of intensive study, E. coli K-12 is arguably the best understood of all organisms, having been used for studies of many facets of living organisms, outlined in a two-volume book on E. coli and Salmonella enterica (45). Currently, 50% of its genome has been sequenced (56), and completion of this task will increase the focus of attention on E. coli K-12 for studies which integrate genomic information and biochemical processes.There are, however, significant gaps in our knowledge of E. coli K-12. During its first 25 to 30 years in the laboratory, it probably accumulated a range of mutations which improved adaptation to a laboratory environment but destroyed its ability to survive in its natural environment. Among them were mutations in the rjb gene cluster which led to loss of 0 antigen synthesis. The 0 antigen, a repeat unit polysaccharide which is a component of lipopolysaccharide (LPS), is the major surface antigen of many gram-negative bacteria (see reference 53 for a review) and, for E. coli, was present in by far the majority of strains when first isolated. However, it is often lost during culture, presumably because it offers no advantage under suc...

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“…Sequencing was done with nested sets of deletions made by using exonuclease III, DNA from the derived plasmids being sequenced by the dideoxy method using fluorescent dye-labeled primers and running the reaction products on an ABI 373A sequencer. Sequence analysis was carried out by using the ANGIS system, which incorporates several sets of programs (30), at the University of Sydney. PEPPLOT and PLOTSTRUCTURE in the Genetics Computer Group package (6) were used to identify transmembrane segments and predict protein secondary structure.…”

Section: Methodsmentioning

confidence: 99%

C-terminal half of Salmonella enterica WbaP (RfbP) is the galactosyl-1-phosphate transferase domain catalyzing the first step of O-antigen synthesis

1996

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We previously showed that the product of the wbaP gene of Salmonella enterica serovar Typhimurium has two functions: it is involved in the first step of O-antigen synthesis (the galactosyltransferase [GT] function) and in a later step (the T function), first thought to be the flipping of the O-antigen subunit on undecaprenyl pyrophosphate from the cytoplasmic face to the periplasmic face of the cytoplasmic membrane. We now locate two wbaP(T) mutations within the first half of the wbaP gene by sequencing. Both mutants retain GT activity, although one was a frameshift mutation resulting in a stop codon 10 codons after the frameshift to give an open reading frame containing only 138 of the 476 codons in WbaP. We also show that there is a secondary translation starting within the wbaP gene resulting in the synthesis of a polypeptide with GT activity. These results indicate that the N-and C-terminal halves of WbaP are the T and GT functional domains, respectively. We now propose that the T block operates prior to the flippase function, probably at the release of undecaprenyl pyrophosphate-linked galactose from WbaP.

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Australia's national genomic information system

Cited by 15 publications

References 6 publications

Molecular evolution of the GDP-mannose pathway genes (manB and manC) in Salmonella enterica The GenBank accession numbers for the sequences reported in this paper are AY012160–AY012201.

Molecular evolution of the GDP-mannose pathway genes (manB and manC) in Salmonella enterica The GenBank accession numbers for the sequences reported in this paper are AY012160–AY012201.

Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster

C-terminal half of Salmonella enterica WbaP (RfbP) is the galactosyl-1-phosphate transferase domain catalyzing the first step of O-antigen synthesis

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