Control of <i>exuT</i> Activity for Galacturonate Transport by the Negative Regulator ExuR in <i>Erwinia chrysanthemi</i> EC16

Valmeekam, Venugopal; Loh, Yen-Lin; Francisco, M.

doi:10.1094/mpmi.2001.14.6.816

Cited by 7 publications

(6 citation statements)

References 18 publications

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“…This sequence is referred to as the ‘target’ for the probes. These targets are available from Affymetrix through their NetAffx web site (20). We used these targets for the initial survey of possible transcripts that each probeset might detect.…”

Section: Methodsmentioning

confidence: 99%

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

Harbig

Sprinkle

Enkemann

2005

Nucleic Acids Research

115

102

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One of the biggest problems facing microarray experiments is the difficulty of translating results into other microarray formats or comparing microarray results to other biochemical methods. We believe that this is largely the result of poor gene identification. We re-identified the probesets on the Affymetrix U133 plus 2.0 GeneChip array. This identification was based on the sequence of the probes and the sequence of the human genome. Using the BLAST program, we matched probes with documented and postulated human transcripts. This resulted in the redefinition of approximately 37% of the probes on the U133 plus 2.0 array. This updated identification specifically points out where the identification is complicated by cross-hybridization from splice variants or closely related genes. More than 5000 probesets detect multiple transcripts and therefore the exact protein affected cannot be readily concluded from the performance of one probeset alone. This makes naming difficult and impacts any downstream analysis such as associating gene ontologies, mapping affected pathways or simply validating expression changes. We have now automated the sequence-based identification and can more appropriately annotate any array where the sequence on each spot is known.

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Section: Methodsmentioning

confidence: 99%

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

Harbig

Sprinkle

Enkemann

2005

Nucleic Acids Research

115

102

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“…The aec-36 product shares similarity (62% similar amino acids) with ExuT of E. coli K-12 MG1655, a major facilitator superfamily transporter of the anion:cation symporter family 14 (48). ExuT is involved in galacturonate uptake in E. coli and in other bacteria such as Erwinia chrysanthemi and Ralstonia solanacearum (26,45,63). Aec-36, like ExuT, is predicted to be an integral membrane protein.…”

Section: Vol 188 2006mentioning

confidence: 99%

A selC -Associated Genomic Island of the Extraintestinal Avian Pathogenic Escherichia coli Strain BEN2908 Is Involved in Carbohydrate Uptake and Virulence

Chouikha¹,

Germon²,

Brée³

et al. 2006

J Bacteriol

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The complete nucleotide sequence and genetic organization of a new genomic island (AGI-3) isolated from the extraintestinal avian pathogenic Escherichia coli strain BEN2908 is reported. This 49,600-bp island is inserted at the selC locus and contains putative mobile genetic elements such as a phage-related integrase gene, transposase genes, and direct repeats. AGI-3 shows a mosaic structure of five modules. Some of these modules are present in other E. coli strains and in other pathogenic bacterial species. The gene cluster aec-35 to aec-37 of module 1 encodes proteins associated with carbohydrates assimilation such as a major facilitator superfamily transporter (Aec-36), a glycosidase (Aec-37), and a putative transcriptional regulator of the LacI family (Aec-35). The aec-35 to aec-37 cluster was found in 11.6% of the tested pathogenic and nonpathogenic E. coli strains. When present, the aec-35 to aec-37 cluster is strongly associated with the selC locus (97%). Deletion of the aec-35-aec-37 region affects the assimilation of seven carbohydrates, decreases the growth rate of the strain in minimal medium containing galacturonate or trehalose, and attenuates the virulence of E. coli BEN2908 for chickens.Escherichia coli, a commensal inhabitant of the gastrointestinal tract of mammals and birds, is also the causative agent of several diseases in animals and human worldwide. Pathogenic E. coli strains have been divided into intestinal pathogenic E. coli and extraintestinal pathogenic E. coli (ExPEC) depending on the location of the infection they are causing. ExPEC strains are responsible for a variety of infections, including bacteremia, urinary tract infections, neonatal meningitis, pneumonia, deep surgical wound infections, endovascular infections, vertebral osteomyelitis, and septicemia (35, 54).Avian pathogenic Escherichia coli (APEC) strains belong to the ExPEC group. They are mainly responsible for a respiratory disease in poultry usually followed by a systemic infection and a fatal septicemia. Characteristic fibrinopurulent lesions are aerosacculitis, pericarditis, and perihepatitis. APEC strains can also be involved in localized infections such as omphalitis, salpingitis, swollen head syndrome, and cellulitis (2, 17). APEC isolates commonly belong to serogroups O1, O2, O5, O8, O18, O35, and O78 (4, 17). Various virulence factors of APEC strains, such as adhesins (F1 and P fimbriae and curli), anti-host defense factors (OmpA, Iss, lipopolysaccharide, and K1), iron acquisition systems (aerobactin, Iro proteins, yersiniabactin, and the Sit iron acquisition locus), autotransporters (Tsh and Vat), and the IbeA protein have been identified (20, 21, 25, 36-38, 42, 46, 50). Using various genomic approaches, several putative virulence factors of APEC strains have been identified (9,20,38,58). However, the above components cannot explain all the disease process, suggesting the existence of other, unidentified components.It is well described that pathogenicity factors can be encoded by mobile genetic elements (transpos...

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“…(13) They found that about 10.5% nonspecific probes could cross-hybridize to multiple genes and 9.3% probes miss target transcript sequences on the Affymetrix U95A/Av2 array; proportions of nonspecific and mis-targeted probes on the U133A array are 12.1% and 8.0%, respectively. (13) Harbig et al got the target sequence information of each probe from the NetAffx web site, (16) and they re-identified about 37% of the genes detected by the U133 Plus 2.0 array based on results of target sequence alignment. (14) In the most recent work, Dai et al aligned the probes to different sources of genome information (UniGene, Refseq, etc.)…”

Section: Introductionmentioning

confidence: 99%

The effect of GeneChip gene definitions on the microarray study of cancers

Zhang

2006

BioEssays

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The Affymetrix GeneChip is a popular microarray platform for genome-wide expression profiling and has been widely used in functional genomics especially in the classification of cancers. Due to the updating of genome data, much of the genome information with which the chips were designed is out-of-date and it has been reported that many of the genes/transcripts on the chips differ from their original definition when mapping the probes to the new genome information. Dai et al. have reported that the updated definition can cause as much as 30-50% discrepancy in the genes selected as differentially expressed on a heart tissue expression profiling dataset. Understanding the nature of this difference is therefore very important for the utilization of the data. In this work, with a large cancer dataset as an example, we compared two major definitions and investigated their effects on classification, clustering, discovery of differentially expressed genes and gene-set-based analysis. Results show that the two definitions agree well on clustering and classification results but genes and gene sets discovered as differentially expressed or enriched can be very different. Discoveries based on the Affymetrix definition can cover most of those based on the new definition, but tend to have more false positives.

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Control of exuT Activity for Galacturonate Transport by the Negative Regulator ExuR in Erwinia chrysanthemi EC16

Cited by 7 publications

References 18 publications

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

A selC -Associated Genomic Island of the Extraintestinal Avian Pathogenic Escherichia coli Strain BEN2908 Is Involved in Carbohydrate Uptake and Virulence

The effect of GeneChip gene definitions on the microarray study of cancers

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