Subsystem Info

Name:mnm5U34 biosynthesis bacteria
Author:vcrecy
Version:119
Last Modified:/vol/public-pseed/FIGdisk/FIG/Data/Subsystems/mnm5U34 biosynthesis bacteria/Backup
Literature
Websites
Description
NotesNotes copied from tRNA_modification_Bacteria:
s4U like the other thiolated modification ms2i6A,s4U,s2C requires also a series of accessory proteins to transfer the sulfur atom
These are
CDS=Cysteine desulfurase (EC 2.8.1.7),IscU,IscA

TruD is a divergent family of pseudouridine synthase
It is not yet known in E.coli the specificity of the three Dus family of enzyme. Only for dusA that modifies position 20
RluA modifies both RNA and tRNA
.

Psi38-40=truA=hisT
Kammen, H. O., Marvel, C. C., Hardy, L. and Penhoet, E. E., Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J Biol Chem 1988, 263, 2255-63

Psi55=truB= b3166
Gutgsell, N., Englund, N., Niu, L., Kaya, Y., Lane, B. G. and Ofengand, J., Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA 2000, 6, 1870-81.
Nurse, K., Wrzesinski, J., Bakin, A., Lane, B. G. and Ofengand, J., Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. RNA 1995, 1, 102-12.

D16,17,20,20a dusA=yjbN;dusB=yhdG,dusC=yohI

I34= tadA=yfhC
Wolf, J., Gerber, A. P. and Keller, W., tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. Embo J 2002, 21, 3841-51.

m2A37 trmG=yfiF
Prediction from genome mapping Find from where test with mutant

Missing
m6A37 missing methylase
Cm32/Um32 G. Bjork has info not out yet

m5U54=trmA
Ny, T. and Björk, G. R., Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12. J Bacteriol 1980, 142, 371-9.
Persson, B. C., Gustafsson, C., Berg, D. E. and Björk, G. R., The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli. Proc Natl Acad Sci U S A 1992, 89, 3995-8.

Gm18 =trmH= spoU
Persson, B. C., Jager, G. and Gustafsson, C., The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity. Nucleic Acids Res 1997, 25, 4093-7.

What about lasT double checkb same family

Cm34 =trmX=yibK Glenn Bjork personnal info?)

m7G46=trmB=yggH
De Bie, L. G., Roovers, M., Oudjama, Y., Wattiez, R., Tricot, C., Stalon, V., Droogmans, L. and Bujnicki, J. M., The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J Bacteriol 2003, 185, 3238-43.

RluB ribosomal RNA Pseudouridine synathse

t6A37=YrdC V. de Crecy-lagard unpublished
paralog YciO in E. coli does not seem to be t6A enzyme Function unknown
missing MtaA se with Ken Ridd prediction

Q34 The fact that FolE is also involved in Q biosynthesis (de crecy-lagard unpublished)
See queuosine subsytem
tgt and queA ref
Reuter, K., Slany, R., Ullrich, F. and Kersten, H., Structure and Organization of E. coli Genes Involved in Biosynthesis of the Deazaguanine Derivative Queuine, a Nutrient Factor for Eukaryotes. J Bacteriol 1991, 173, 2256-2264.
queCDEF refs
Reader, J., Metzgar, D., Schimmel, P. and de Crécy-lagard, V., Identification of four genes involved in the biosynthesis of Queuine by comparative genomics. J Biol Chem 2004, 279, 6280-5.
22. Van Lanen S., Reader J., Swairjo M., V. de Crécy-Lagard and D. Iwata-Reuyl. (2005). From cyclohydrolase to oxido-reductase:evolution of a new enzyme activity from a novel fold. Proc. Natl. Acad. Sci. U S A. 102:4264-9.

GluQ34 =yadB
Salazar JC, Ambrogelly A, Crain PF, McCloskey JA, Soll D. A truncated aminoacyl-tRNA synthetase modifies RNA.Proc Natl Acad Sci U S A. 2004 May 18;101(20):7536-41. Epub 2004 Apr 19.
Dubois DY, Blaise M, Becker HD, Campanacci V, Keith G, Giege R, Cambillau C, Lapointe J, Kern D.
An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7530-5. Epub 2004 Apr 19.
PMID: 15096594 [PubMed - indexed for MEDLINE]

Still one missing gene at least queB
Frey, B., McCloskey, J. A., Kersten, W. and Kersten, H., New Function of Vitamin B12: Cobamide-Dependent Reduction of Epoxyqueuosine to Queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J Bacteriol 1988, 170, 2078-2082.

k2C34=mesJ=tilS
Soma A, Ikeuchi Y, Kanemasa S, Kobayashi K, Ogasawara N, Ote T, Kato J, Watanabe K, Sekine Y, Suzuki T. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA.Mol Cell. 2003 Sep;12(3):689-98.

For all sulfur (and selenium) nucleoside coomon sulfur gransfer genes
IcsS
Nilsson K, Lundgren HK, Hagervall TG, Bjork GR. Related Articles, Links
Free in PMC The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium.
J Bacteriol. 2002 Dec;184(24):6830-5.
Mihara, H., Kato, S., Lacourciere, G. M., Stadtman, T. C., Kennedy, R. A., Kurihara, T., Tokumoto, U., Takahashi, Y. and Esaki, N., The iscS gene is essential for the biosynthesis of 2-selenouridine in tRNA and the selenocysteine-containing formate dehydrogenase H. Proc Natl Acad Sci U S A 2002, 99, 6679-83.
icsU
Fdx
IcsA
Leipuviene R, Qian Q, Bjork GR. Related Articles, Links
Formation of thiolated nucleosides present in tRNA from Salmonella enterica serovar Typhimurium occurs in two principally distinct pathways.
J Bacteriol. 2004 Feb;186(3):758-66.

se2U34
selD
Leinfelder, W., Forchhammer, K., Veprek, B., Zehelein, E. and Bock, A., In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product. Proc Natl Acad Sci U S A 1990, 87, 543-7.

ybbB
Wolfe MD, Ahmed F, Lacourciere GM, Lauhon CT, Stadtman TC, Larson TJ. Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase.
J Biol Chem. 2004 Jan 16;279(3):1801-9. Epub 2003 Oct 31.
possible missing enzyme

s2C32=TctA=ydaO
Jager, G., Leipuviene, R., Pollard, M. G., Qian, Q. and Björk, G. R., The conserved Cys-X1-X2-Cys motif present in the TtcA protein is required for the thiolation of cytidine in position 32 of tRNA from Salmonella enterica serovar Typhimurium. J Bacteriol 2004, 186, 750-7.
these last two genes are paralogs be careful for transfer of annotations normally s2C34 found in Archaea and bacteria

s4U8=thiI
Mueller, E. G., Buck, C. J., Palenchar, P. M., Barnhart, L. E. and Paulson, J. L., Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res 1998, 26, 2606-10.
117. Lauhon, C. T. and Kambampati, R., The iscS gene in Escherichia coli is required for the biosynthesis of 4-thiouridine, thiamin, and NAD. J Biol Chem 2000, 275, 20096-103.

cmnm5/mnmEU34
mnmE=trmE
Cabedo, H., Macian, F., Villarroya, M., Escudero, J. C., Martinez-Vicente, M., Knecht, E. and Armengod, M. E., The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties. Embo J 1999, 18, 7063-76.

mnmG=gidA
Bregeon, D., Colot, V., Radman, M. and Taddei, F., Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 2001, 15, 2295-306.
Scrima A, Vetter IR, Armengod ME, Wittinghofer A. The structure of the TrmE GTP-binding protein and its implications for tRNA modification.
EMBO J. 2005 Jan 12;24(1):23-33. Epub 2004 Dec 16.

mnmC=yfcK

Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.
RNA. 2004 Aug;10(8):1236-42. Epub 2004 Jul 9.

s2U34
mnmA=yfcB
Kambampati, R. and Lauhon, C. T., MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 2003, 42, 1109-17.

mnm5s2U34
tusA=yhhP
tusB=yheL
tusC=yheM
tusD=yheN
tusE=yccK
Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions.
Mol Cell. 2006 Jan 6;21(1):97-108.

i6A37=miaA
Caillet, J. and Droogmans, L., Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA. J Bacteriol 1988, 170, 4147-52.

ms2i6A37=miaB=yleA
. Esberg, B., Leung, H. C., Tsui, H. C., Björk, G. R. and Winkler, M. E., Identification of the miaB gene, involved in methylthiolation of isopentenylated A37 derivatives in the tRNA of Salmonella typhimurium and Escherichia coli. J Bacteriol 1999, 181, 7256-65.
113. Nilsson, K., Lundgren, H. K., Hagervall, T. G.

specific to Slamonella
miaE
Persson BC, Bjork GR. Related Articles,Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants.
J Bacteriol. 1993 Dec;175(24):7776-85.

Regulators
ygfZ
Ote T, Hashimoto M, Ikeuchi Y, Su'etsugu M, Suzuki T, Katayama T, Kato J. Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation.
Mol Microbiol. 2006 Jan;59(1):265-75.

mo5U34/cmo5U34/mcmo5U34
Chorismate is a precursor (so genes aro)
. Hagervall, T. G., Jonsson, Y. H., Edmonds, C. G., McCloskey, J. A. and Björk, G. R., Chorismic acid, a key metabolite in modification of tRNA. J Bacteriol 1990, 172, 252-9.

Two methylases have been identified pathway is as follows

cmoaA=yecO
cmoaB=yecP

Nasvall SJ, Chen P, Bjork GR. Related Articles, Links
Free Full Text The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo.
RNA. 2004 Oct;10(10):1662-73.

Missing
s2T/ac4A34/acp3U47Sp

Info from other bacteria
BAcillus subtilis
Gid Bacillus subtilis tRNA:m(5)U-54 MTase
Urbonavicius J, Skouloubris S, Myllykallio H, Grosjean H. Related Articles, Links
Free in PMC Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications.
Nucleic Acids Res. 2005 Jul 18;33(13):3955-64. Print 2005.

trmI

Variants
Classification:RNA Metabolism
RNA processing and modification