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Gene |

Product(s) |

Expression|

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Standard Name	csrD
Gene Synonym(s)	yhdA, ECK3240, b3252, JW3221^[1]^[2], JW3221
Product Desc.	regulator of CsrB and CsrC decay^[2]^[3] Targets csrB/C sRNAs for degradation by RNase E; carbon flux regulator; mechanism unknown; indirectly affects CsrA function^[4]
Product Synonyms(s)	conserved inner membrane protein^[1], B3252^[2]^[1], YhdA^[2]^[1], CsrD^[2]^[1] , ECK3240, JW3221, yhdA, b3252
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhdA^[2]
Regulation/Activity
Quick Links
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Notes

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CsrD has a central GGDEF putative diguanylate cyclase, then a C-terminal putative cyclic-di-GMP phosphodiesterase EAL domain. CsrD's role in csrB/C destabilization does not involve cyclic-di-GMP metabolism; very low level of CsrD expression; CsrD may work at substoichiometric concentrations (Suzuki, 2006). False positive lipoprotein prediction, Cys not conserved.^[4]

Gene

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Nomenclature

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

Standard name	csrD
Mnemonic	Carbon storage regulator
Synonyms	yhdA, ECK3240, b3252, JW3221^[1]^[2], JW3221
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Notes

Location(s) and DNA Sequence

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<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	73.27 minutes	MG1655: 3401354..3399414 <gbrowseImage> name=NC_000913:3399414..3401354 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3286562..3288502 <gbrowseImage> name=NC_012759:3286562..3288502 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3403187..3401247 <gbrowseImage> name=NC_007779:3401247..3403187 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
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Notes

Sequence Features

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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

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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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Notes

Genetic Interactions

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

Genetic Resources

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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:
21D3	Kohara Phage	Genobase	PMID:3038334
6G3	Kohara Phage	Genobase	PMID:3038334
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Notes

Accessions in Other Databases

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10018	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10018	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000016	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947702	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0018	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010663	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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

Standard name	YhdA
Synonyms	conserved inner membrane protein^[1], B3252^[2]^[1], YhdA^[2]^[1], CsrD^[2]^[1] , ECK3240, JW3221, yhdA, b3252
Product description	regulator of CsrB and CsrC decay^[2]^[3] Targets csrB/C sRNAs for degradation by RNase E; carbon flux regulator; mechanism unknown; indirectly affects CsrA function^[4]
EC number (for enzymes)
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Notes

Function

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<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
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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	rpsT	PMID:19402753	LCMS(ID Probability):99.6
Protein	mreB	PMID:19402753	MALDI(Z-score):21.621922
Protein	rplI	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplW	PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane	C-terminus localized in the cytoplasm with 2 predicted transmembrane domains	Daley et al. (2005) ^[5]
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Notes

Structure and Physical Properties

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<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 MRLTTKFSAF VTLLTGLTIF VTLLGCSLSF YNAIQYKFSH RVQAVATAID THLVSNDFSV LRPQITELMM SADIVRVDLL HGDKQVYTLA RNGSYRPVGS SDLFRELSVP LIKHPGMSLR LVYQDPMGNY FHSLMTTAPL TGAIGFIIVM LFLAVRWLQR QLAGQELLET RATRILNGER GSNVLGTIYE WPPRTSSALD TLLREIQNAR EQHSRLDTLI RSYAAQDVKT GLNNRLFFDN QLATLLEDQE KVGTHGIVMM IRLPDFNMLS DTWGHSQVEE QFFTLTNLLS TFMMRYPGAL LARYHRSDFA ALLPHRTLKE AESIAGQLIK AVDTLPNNKM LDRDDMIHIG ICAWRSGQDT EQVMEHAESA TRNAGLQGGN SWAIYDDSLP EKGRGNVRWR TLIEQMLSRG GPRLYQKPAV TREGQVHHRE LMCRIFDGNE EVSSAEYMPM VLQFGLSEEY DRLQISRLIP LLRYWPEENL AIQVTVESLI RPRFQRWLRD TLMQCEKSQR KRIIIELAEA DVGQHISRLQ PVIRLVNALG VRVAVNQAGL TLVSTSWIKE LNVELLKLHP GLVRNIEKRT ENQLLVQSLV EACSGTSTQV YATGVRSRSE WQTLIQRGVT GGQGDFFASS QPLDTNVKKY SQRYSV
Length	646
Mol. Wt	73.34 kDa
pI	8.9 (calculated)
Extinction coefficient	81,820 - 82,445 (calc based on 18 Y, 10 W, and 5 C residues)
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Domains/Motifs/Modification Sites

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

Type	Residues	Description	References
Domain	224..381	PF00990 GGDEF domain	PMID:19920124
Domain	400..630	PF00563 EAL domain	PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131140	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947702	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010663	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P13518	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10018	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10018	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947702	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000016	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0018	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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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

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	Ecoli K-12	7.66+/-0.112	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.032731959	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	71	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	33	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	45	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
yhdA
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Figure courtesy of RegulonDB

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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.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3401334..3401374 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3252 (EcoliWiki Page)	NCBI GEO profiles for csrD
microarray	GenExpDB:b3252 (EcoliWiki Page)	Summary of data for csrD from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (3400889..3401142) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:E7^[6]
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Notes

Accessions Related to csrD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10018	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0018	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3252
EcoGene	EcoGene:EG10018	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010663	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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

Organism	Homologs (Statistics)	Comments
Shigella flexneri	YHDA	From SHIGELLACYC
E. coli O157	YHDA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00990 GGDEF domain
Pfam (EcoliWiki Page)	PF00563 EAL domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:55073
Superfamily (EcoliWiki Page)	SUPERFAMILY:141868
EcoCyc	EcoCyc:EG10018	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10018	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000016	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0018	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010663	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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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.
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

csrD:On One Page

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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 csrD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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