{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	ychO
Gene Synonym(s)	ychP, ECK1214, b1220, JW1211^[1]^[2], JW1211
Product Desc.	predicted invasin^[2]^[3] Intimin/invasin homolog, function unknown^[4]
Product Synonyms(s)	predicted invasin^[1], B1220^[2]^[1], YchO^[2]^[1], YchP^[2]^[1] , ECK1214, JW1211, ychP, b1220
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ychO^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

Extension based on homology to S. typhimurium SinH. YchO has a 24 aa signal peptide predicted.^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ychO
Mnemonic	Systematic nomenclature
Synonyms	ychP, ECK1214, b1220, JW1211^[1]^[2], JW1211
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<protect> 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
MG1655	27.44 minutes	MG1655: 1273148..1274401 <gbrowseImage> name=NC_000913:1273148..1274401 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1274075..1275328 <gbrowseImage> name=NC_012967:1274075..1275328 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1161728..1163122 <gbrowseImage> name=NC_012759:1161728..1163122 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1275502..1276755 <gbrowseImage> name=NC_007779:1275502..1276755 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1313248..1314642 <gbrowseImage> name=NC_010473:1313248..1314642 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

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
ΔychO731::kan					PMID:16738554	CGSC:106384
edit table

Notes

Phenotypes of Escherichia coli APEC SEPT362 (NCBI Taxonomy ID:1196033) ychO(del) described in Pilatti, L. et al. (2016).^[5]

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

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource

Resource Type

Source

Notes/Reference

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

13H6

Kohara Phage

Genobase

PMID:3038334

edit table

Notes

Accessions in Other Databases

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12405	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12405	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002267	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945801	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2305	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004095	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	YchP
Synonyms	predicted invasin^[1], B1220^[2]^[1], YchO^[2]^[1], YchP^[2]^[1] , ECK1214, JW1211, ychP, b1220
Product description	predicted invasin^[2]^[3] Intimin/invasin homolog, function unknown^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	Seeded from EcoCyc (v14.0)	complete
edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	rhsA	PMID:16606699	Experiment(s):EBI-1139210
Protein	groL	PMID:16606699	Experiment(s):EBI-1139210
Protein	rhsC	PMID:16606699	Experiment(s):EBI-1139210
Protein	nadE	PMID:16606699	Experiment(s):EBI-1139210
Protein	mreB	PMID:16606699	Experiment(s):EBI-1139210
Protein	rsuA	PMID:16606699	Experiment(s):EBI-1139210
Protein	aspS	PMID:16606699	Experiment(s):EBI-1139210
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MAPENHDGEK HFAEIVKDFG ETSMNDNGLD TGEQAKAFAL GKVRDALSQQ VNQHVESWLS PWGNASVDVK VDNEGHFTGS RGSWFVPLQD NDRYLTWSQL GLTQQDNGLV SNVGVGQRWA RGNWLVGYNT FYDNLLDENL QRAGFGAEAW GEYLRLSANF YQPFAAWHEQ TATQEQRMAR GYDLTARMRM PFYQHLNTSV SLEQYFGDRV DLFNSGTGYH NPVALSLGLN YTPVPLVTVT AQHKQGESGE NQNNLGLNLN YRFGVPLKKQ LSAGEVAESQ SLRGSRYDNP QRNNLPTLEY RQRKTLTVFL ATPPWDLKPG ETVPLKLQIR SRYGIRQLIW QGDTQILSLT PGAQANSAEG WTLIMPDWQN GEGASNHWRL SVVVEDNQGQ RVSSNEITLT LVEPFDALSN DELRWEP
Length	417
Mol. Wt	47.022 kDa
pI	5.1 (calculated)
Extinction coefficient	97,860 (calc based on 14 Y, 14 W, and 0 C residues)
edit table

Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
motif	1-24	UniProt Manual:Signal Peptides	UniProt:P39165
Domain	57..341	PF11924 Protein of unknown function (DUF3442)		PMID:19920124
edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ychO taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:145698248	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945801	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004095	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39165	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12405	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12405	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945801	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002267	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2305	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	26	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	21	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	12^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
ychO
edit table

Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

ychO in APEC strain SEPT362 (NCBI Taxonomy ID:1196033) is expressed in culture in LB medium and is also expressed in the spleen and lungs of chicks 24 and 48 h post-inoculation.^[5]

Translation and Regulation of Translation

[back to top]

<protect><gbrowseImage> name=NC_000913:1273128..1273168 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b1220 (EcoliWiki Page)	NCBI GEO profiles for ychO
microarray	GenExpDB:b1220 (EcoliWiki Page)	Summary of data for ychO from multiple microarray studies
edit table

Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to ychO Expression

[back to top]

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG12405	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2305	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1220
EcoGene	EcoGene:EG12405	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002267	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004095	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Shigella flexneri	YCHP	From SHIGELLACYC
E. coli O157	YCHP	From ECOO157CYC
edit table

Notes

Families

[back to top]

<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF11924 Protein of unknown function (DUF3442)
edit table

</protect> <protect></protect>

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 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

ychO:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ychO Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search