YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

The rRNAs in Escherichia coli contain methylations at 24 nucleotides, which collectively are important for ribosome function. Three of these methylations are m5C modifications located at nucleotides C967 and C1407 in 16S rRNA and at nucleotide C1962 in 23S rRNA. Bacterial rRNA modifications generally require specific enzymes, and only one m5C rRNA methyltransferase, RsmB (formerly Fmu) that methylates nucleotide C967, has previously been identified. BLAST searches of the E.coli genome revealed a single gene, yebU, with sufficient similarity to rsmB to encode a putative m5C RNA methyltransferase. This suggested that the yebU gene product modifies C1407 and/or C1962. Here, we analysed the E.coli rRNAs by matrix assisted laser desorption/ionization mass spectrometry and show that 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. Nucleotide C1407 is located at a functionally active region of the 30 S subunit interface close to the P site, and YebU-directed methylation of this nucleotide seems to be conserved in bacteria. The yebU knockout strains display slower growth and reduced fitness in competition with wild-type cells. We suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF, and that the nomenclature system be extended to include the rRNA methyltransferases that still await identification.

OriginalsprogEngelsk
TidsskriftJournal of Molecular Biology
Vol/bind359
Udgave nummer3
Sider (fra-til)777-786
Antal sider10
ISSN0022-2836
DOI
StatusUdgivet - 2006

Fingeraftryk

Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
Recombinant Proteins
Terminology
m(5)C rRNA methyltransferase
RNA
Enzymes
Growth
In Vitro Techniques

Citer dette

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title = "YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407",
abstract = "The rRNAs in Escherichia coli contain methylations at 24 nucleotides, which collectively are important for ribosome function. Three of these methylations are m5C modifications located at nucleotides C967 and C1407 in 16S rRNA and at nucleotide C1962 in 23S rRNA. Bacterial rRNA modifications generally require specific enzymes, and only one m5C rRNA methyltransferase, RsmB (formerly Fmu) that methylates nucleotide C967, has previously been identified. BLAST searches of the E.coli genome revealed a single gene, yebU, with sufficient similarity to rsmB to encode a putative m5C RNA methyltransferase. This suggested that the yebU gene product modifies C1407 and/or C1962. Here, we analysed the E.coli rRNAs by matrix assisted laser desorption/ionization mass spectrometry and show that 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. Nucleotide C1407 is located at a functionally active region of the 30 S subunit interface close to the P site, and YebU-directed methylation of this nucleotide seems to be conserved in bacteria. The yebU knockout strains display slower growth and reduced fitness in competition with wild-type cells. We suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF, and that the nomenclature system be extended to include the rRNA methyltransferases that still await identification.",
keywords = "Amino Acid Sequence, Escherichia coli, Escherichia coli Proteins, Genome, Bacterial, Methylation, Methyltransferases, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Nucleotides, RNA, Ribosomal, 16S, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Journal Article, Research Support, Non-U.S. Gov't",
author = "Andersen, {Niels M{\o}ller} and Stephen Douthwaite",
year = "2006",
doi = "10.1016/j.jmb.2006.04.007",
language = "English",
volume = "359",
pages = "777--786",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Heinemann",
number = "3",

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YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. / Andersen, Niels Møller; Douthwaite, Stephen.

I: Journal of Molecular Biology, Bind 359, Nr. 3, 2006, s. 777-786.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407

AU - Andersen, Niels Møller

AU - Douthwaite, Stephen

PY - 2006

Y1 - 2006

N2 - The rRNAs in Escherichia coli contain methylations at 24 nucleotides, which collectively are important for ribosome function. Three of these methylations are m5C modifications located at nucleotides C967 and C1407 in 16S rRNA and at nucleotide C1962 in 23S rRNA. Bacterial rRNA modifications generally require specific enzymes, and only one m5C rRNA methyltransferase, RsmB (formerly Fmu) that methylates nucleotide C967, has previously been identified. BLAST searches of the E.coli genome revealed a single gene, yebU, with sufficient similarity to rsmB to encode a putative m5C RNA methyltransferase. This suggested that the yebU gene product modifies C1407 and/or C1962. Here, we analysed the E.coli rRNAs by matrix assisted laser desorption/ionization mass spectrometry and show that 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. Nucleotide C1407 is located at a functionally active region of the 30 S subunit interface close to the P site, and YebU-directed methylation of this nucleotide seems to be conserved in bacteria. The yebU knockout strains display slower growth and reduced fitness in competition with wild-type cells. We suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF, and that the nomenclature system be extended to include the rRNA methyltransferases that still await identification.

AB - The rRNAs in Escherichia coli contain methylations at 24 nucleotides, which collectively are important for ribosome function. Three of these methylations are m5C modifications located at nucleotides C967 and C1407 in 16S rRNA and at nucleotide C1962 in 23S rRNA. Bacterial rRNA modifications generally require specific enzymes, and only one m5C rRNA methyltransferase, RsmB (formerly Fmu) that methylates nucleotide C967, has previously been identified. BLAST searches of the E.coli genome revealed a single gene, yebU, with sufficient similarity to rsmB to encode a putative m5C RNA methyltransferase. This suggested that the yebU gene product modifies C1407 and/or C1962. Here, we analysed the E.coli rRNAs by matrix assisted laser desorption/ionization mass spectrometry and show that 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. Nucleotide C1407 is located at a functionally active region of the 30 S subunit interface close to the P site, and YebU-directed methylation of this nucleotide seems to be conserved in bacteria. The yebU knockout strains display slower growth and reduced fitness in competition with wild-type cells. We suggest that a more appropriate designation for yebU would be the rRNA small subunit methyltransferase gene rsmF, and that the nomenclature system be extended to include the rRNA methyltransferases that still await identification.

KW - Amino Acid Sequence

KW - Escherichia coli

KW - Escherichia coli Proteins

KW - Genome, Bacterial

KW - Methylation

KW - Methyltransferases

KW - Models, Molecular

KW - Molecular Sequence Data

KW - Nucleic Acid Conformation

KW - Nucleotides

KW - RNA, Ribosomal, 16S

KW - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1016/j.jmb.2006.04.007

DO - 10.1016/j.jmb.2006.04.007

M3 - Journal article

VL - 359

SP - 777

EP - 786

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 3

ER -