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Standard Name	rsmF
Gene Synonym(s)	yebU, ECK1834, b1835, JW5301^[1]^[2], JW5301
Product Desc.	16S rRNA m⁵C1407 specific methyltransferase^[3]^[2]^[4]. Inactivation of the yebU gene leads to loss of methylation at C1407 in 16 S rRNA, but does not interfere with methylation at C1962 in 23 S rRNA. Purified recombinant YebU protein retains its specificity for C1407 in vitro, and methylates 30 S subunits (but not naked 16 S rRNA or 70 S ribosomes) isolated from yebU knockout strains.^[3]. Andersen and Douthwaite suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF. 16S rRNA m(5)C1407 methyltransferase, SAM-dependent^[5]
Product Synonyms(s)	predicted methyltransferase^[1], B1835^[2]^[1], YebU^[2]^[1], RsmF^[2]^[1] , ECK1834, JW5301, yebU, b1835
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yebU^[2]
Regulation/Activity
Quick Links
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Notes

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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	rsmF
Mnemonic	Ribosomal Small subunit Methyltransferase
Synonyms	yebU, ECK1834, b1835, JW5301^[1]^[2], JW5301
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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	41.34 minutes, 41.34 minutes	MG1655: 1918247..1919686 <gbrowseImage> name=NC_000913:1918247..1919686 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1898800..1900239 <gbrowseImage> name=NC_012967:1898800..1900239 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1810306..1811745 <gbrowseImage> name=NC_012759:1810306..1811745 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1921937..1923376 <gbrowseImage> name=NC_007779:1921937..1923376 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
ΔrsmF760::kan					PMID:16738554	CGSC:106330
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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:

19H3

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:G7008	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003595	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946348	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3777	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006106	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	YebU, m⁵C methyltransferase
Synonyms	predicted methyltransferase^[1], B1835^[2]^[1], YebU^[2]^[1], RsmF^[2]^[1] , ECK1834, JW5301, yebU, b1835
Product description	16S rRNA m⁵C1407 specific methyltransferase^[3]^[2]^[4]. Inactivation of the yebU gene leads to loss of methylation at C1407 in 16 S rRNA, but does not interfere with methylation at C1962 in 23 S rRNA. Purified recombinant YebU protein retains its specificity for C1407 in vitro, and methylates 30 S subunits (but not naked 16 S rRNA or 70 S ribosomes) isolated from yebU knockout strains.^[3]. Andersen and Douthwaite suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF. 16S rRNA m(5)C1407 methyltransferase, SAM-dependent^[5]
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
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011023	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018314	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01579	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0070475	rRNA base methylation	PMID:16678201	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
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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	Notes	References	Evidence
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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
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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 MLVAQHTVYF PDAFLTQMRE AMPSTLSFDD FLAACQRPLR RSIRVNTLKI SVADFLQLTA PYGWTLTPIP WCEEGFWIER DNEDALPLGS TAEHLSGLFY IQEASSMLPV AALFADGNAP QRVMDVAAAP GSKTTQISAR MNNEGAILAN EFSASRVKVL HANISRCGIS NVALTHFDGR VFGAAVPEMF DAILLDAPCS GEGVVRKDPD ALKNWSPESN QEIAATQREL IDSAFHALRP GGTLVYSTCT LNQEENEAVC LWLKETYPDA VEFLPLGDLF PGANKALTEE GFLHVFPQIY DCEGFFVARL RKTQAIPALP APKYKVGNFP FSPVKDREAG QIRQAATGVG LNWDENLRLW QRDKELWLFP VGIEALIGKV RFSRLGIKLA ETHNKGYRWQ HEAVIALASP DNMNAFELTP QEAEEWYRGR DVYPQAAPVA DDVLVTFQHQ PIGLAKRIGS RLKNSYPREL VRDGKLFTGN A
Length	481
Mol. Wt	53.44 kDa
pI	5.4 (calculated)
Extinction coefficient	71,390 - 72,265 (calc based on 11 Y, 10 W, and 7 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	29..209	PF01189 NOL1/NOP2/sun family	PMID:19920124
Domain	199..479	PF01189 NOL1/NOP2/sun family	PMID:19920124
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<motif_map/>

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

Structures

<beststructure> gene=rsmF 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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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:90111341	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946348	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006106	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76273	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7008	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14023	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946348	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003595	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3777	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	Reference(s)
Protein	E. coli K-12 MG1655	447	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	85	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	144	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)
yebU
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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_000913:1918227..1918267 source=MG1655 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:b1835 (EcoliWiki Page)	NCBI GEO profiles for rsmF
microarray	GenExpDB:b1835 (EcoliWiki Page)	Summary of data for rsmF 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 (1918085..1918262) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:A4^[6]
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Notes

Accessions Related to rsmF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7008	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3777	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1835
EcoGene	EcoGene:EG14023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003595	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006106	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
Arabidopsis thaliana	AT4G26600 (score: 1.000; bootstrap: 93%) AT5G55920 (score: 0.585)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000019607 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00029233 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00021073 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000022151 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000017430 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050309-7 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0204605 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0033741 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21153-PA (score: 1.000; bootstrap: 91%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000023281 (score: 1.000; bootstrap: 92%)	From Inparanoid:20070104
Homo sapiens	ENSP00000313272 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000024589 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000022546 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Mus musculus	MGI:107891 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Oryza gramene	Q69MP1 (score: 1.000; bootstrap: 88%) Q6Z5K9 (score: 1.000; bootstrap: 88%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000007827 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000024938 (score: 1.000; bootstrap: 100%) ENSRNOP00000041755 (score: 0.096)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL061W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBP8B70c (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000156109 (score: 1.000; bootstrap: 93%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00013399001 (score: 1.000; bootstrap: 53%)	From Inparanoid:20070104
E. coli O157	YEBU	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)	PF01189 NOL1/NOP2/sun family
Pfam (EcoliWiki Page)	PF01189 NOL1/NOP2/sun family
Superfamily (EcoliWiki Page)	SUPERFAMILY:53335
Panther (EcoliWiki Page)	PTHR22807:SF20
EcoCyc	EcoCyc:G7008	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003595	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3777	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006106	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 ^3.2 ^3.3 Andersen, NM & Douthwaite, S (2006) YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 777-86 PubMed
↑ ^4.0 ^4.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^5.0 ^5.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rsmF: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 rsmF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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