ychO:Gene
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| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| Nomenclature | Location(s) and DNA Sequence | Sequence Features | Alleles and Phenotypes | Genetic Interactions | Genetic Resources | Accessions | Links | References | Suggestions |
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
ychO |
|---|---|
| Mnemonic |
Systematic nomenclature |
| Synonyms | |
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Notes
Location(s) and DNA Sequence
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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
| Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
|---|---|---|---|---|
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MG1655 |
27.44 minutes |
MG1655: 1273148..1274401 |
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NC_012967: 1274075..1275328 |
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NC_012759: 1161728..1163122 |
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W3110 |
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W3110: 1275502..1276755 |
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DH10B: 1313248..1314642 |
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Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
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Notes
Alleles and Phenotypes
See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.
| Allele | Nt change(s) | AA change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|---|
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ΔychO731::kan |
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Notes
Phenotypes of Escherichia coli APEC SEPT362 (NCBI Taxonomy ID:1196033) ychO(del) described in Pilatti, L. et al. (2016).[4]
- reduced adhesion to chicken embryo fibroblast cells in both the presence and absence of methyl-alpha-D[mannopyranoside (Fig. 2a)
- Expression of genes important for adhesion (aatA, aatB, fimH, eco, csgA, and lpfA) was analyzed by qRT-PCR analysis (Fig 2b) No statistically significant differences in expression level were seen in the 3 strains analyzed: SEPT362, SEPT362 ychO(del), and SEPT36s ychO(del)-complemented with plasmid borne ychO+.
- reduced invasion of cells from the chick embryo fibroblast cell line CEC-32 (Fig 3)
- reduced biofilm formation (assayed in 24-well polystyrene plates and quantified by crystal violet staining) (Fig.4)
- the authors conclude that ychO is important for virulence of APEC SEPT362 (Fig. 5)
- at day 7 post-inoculation, no statistically significant difference was seen in survival of chicks inoculated with SEPT362, SEPT362 ychO(del), or SEPT362 ychO(del) p(ychO))
- survival of chicks inoculated with SEPT362 ychO(del) was higher at day 4 and day 6 of the assay
- transcriptome sequencing (RNAseq) of SEPT362 and SEPT362 ychO(del) identified 426 genes whose transcript levels were altered
- among the altered genes, 94% were down regulated in the mutant (Fig. 6b)
- affected genes were grouped by functional category (Fig. 6a) but the paper did not include a list of the 426 genes whose transcript levels were altered
- RNAseq results were validated by comparison of the expression levels of 9 genes (csgA, lpfA, fimH, clic, flhD, motA, flgE, eco, and ychO) by qRT-PCR and the results were similar for both methods (data not shown)
Genetic Interactions
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| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
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Plasmid clone |
Status: Primer 1: Primer 2: | ||
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Kohara Phage |
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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References
See Help:References for how to manage references in EcoliWiki.
- ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
- ↑ Pilatti, L et al. (2016) The virulence factor ychO has a pleiotropic action in an Avian Pathogenic Escherichia coli (APEC) strain. BMC Microbiol. 16 35 PubMed
- ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
- ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
