Location of repeat elements in glucansucrases of Leuconostoc and Streptococcus species

Janeček, Štefan; Svensson, Birte; Russell, R. R. B.

doi:10.1111/j.1574-6968.2000.tb09358.x

Cited by 44 publications

(15 citation statements)

References 33 publications

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“…It is possible that the copy number of the coding tandem repeat influences the rate or substrate preference of this enzymatic reaction. Tandem repeats in glucansucrases have been previously identified near the active site of these enzymes in Leuconostoc and Streptococcus species where they may contribute to their function through substrate binding [48]. …”

Section: Resultsmentioning

confidence: 99%

Diversity in coding tandem repeats in related Neisseria spp.

2003

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Background: Tandem repeats contained within coding regions can mediate phase variation when the repeated units change the reading frame of the coding sequence in a copy number dependent manner. Coding tandem repeats are those which do not alter the reading frame with copy number, and the changes in copy number of these repeats may then potentially alter the function or antigenicity of the protein encoded. Three complete neisserial genomes were analyzed and compared to identify coding tandem repeats where the number of copies of the repeat will have some structural consequence for the protein. This is the first study to address coding tandem repeats that may affect protein structures using comparative genomics, combined with a population survey to investigate which show interstrain variability.

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Section: Resultsmentioning

confidence: 99%

Diversity in coding tandem repeats in related Neisseria spp.

2003

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“…Its C -terminal domain (also referred to as glucan-binding domain or GBD) exhibits short repeats specific for ASR, which could contribute to its distinct features (Janeček et al. 2000). The resulting polymer has a unique structure with alternating α-(1→3)/α-(1→6)-linked glucose residues, present for 46% and 54%, respectively.…”

Section: Introductionmentioning

confidence: 99%

Expression of alternansucrase in potato plants

et al. 2007

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Alternan, which consists of alternating a-(1 fi 3)/a-(1 fi 6)-linked glucosyl residues, was produced in potato tubers by expressing a mature alternansucrase (Asr) gene from Leuconostoc mesenteroides NRRL B-1355 in potato. Detection of alternan was performed by enzyme-linked immunosorbent assay in tuber juices, revealing a concentration between 0.3 and 1.2 mg g -1 fresh wt. The Asr transcript levels correlated well with alternan accumulation in tuber juices. It appeared that the expression of sucrose-regulated starchsynthesizing genes (ADP-glucose pyrophosphorylase subunit S and granule-bound starch synthase I) was down-regulated. Despite this, the physicochemical properties of the transgenic starches were unaltered. These results are compared to those obtained with other transgenic potato plants producing mutan [a-(1 fi 3)-linked glucosyl residues] and dextran [a-(1 fi 6)-linked glucosyl residues].

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“…HMMER 3.0 [9] searches using hidden Markov models (HMM) derived from Pfam and Superfam are used to detect known Gram-positive surface sequence motifs. These include LPxTG [10] [PF00746 and the HMM used by SurfG+ [5], GW repeat domains [11] [Superfam models 0040855, 0040856, 0040857], peptidoglycan (PG) binding domain (Type 1) [12] [PF01471, PF08823, PF09374]], Choline binding repeats [13], [PF01473] LysM domain [14] PF01476, Cell-wall binding domain (Type 2) [15], [PF04122], S-layer homology domain [16] [PF04122] motifs and the NLPC_P60 cell wall associated domain [17] [PF00877]. PFAM HMMs are from most recent version of at the time of writing, release 26.0.…”

Section: Methods and Implementationmentioning

confidence: 99%

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes

Perry

2013

Source Code Biol Med

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BackgroundThe annotation of surface exposed bacterial membrane proteins is an important step in interpretation and validation of proteomic experiments. In particular, proteins detected by cell surface protease shaving experiments can indicate exposed regions of membrane proteins that may contain antigenic determinants or constitute vaccine targets in pathogenic bacteria.ResultsInmembrane is a tool to predict the membrane proteins with surface-exposed regions of polypeptide in sets of bacterial protein sequences. We have re-implemented a protocol for Gram-positive bacterial proteomes, and developed a new protocol for Gram-negative bacteria, which interface with multiple predictors of subcellular localization and membrane protein topology. Through the use of a modern scripting language, inmembrane provides an accessible code-base and extensible architecture that is amenable to modification for related sequence annotation tasks.ConclusionsInmembrane easily integrates predictions from both local binaries and web-based queries to help gain an overview of likely surface exposed protein in a bacterial proteome. The program is hosted on the Github repository http://github.com/boscoh/inmembrane.

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Location of repeat elements in glucansucrases of Leuconostoc and Streptococcus species

Cited by 44 publications

References 33 publications

Diversity in coding tandem repeats in related Neisseria spp.

Diversity in coding tandem repeats in related Neisseria spp.

Expression of alternansucrase in potato plants

Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes

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