Effects on IS1 transposition frequency of a mutation in the ygjD gene involved in an essential tRNA modification in Escherichia coli
Chika Hashimoto
Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Search for more papers by this authorMasayuki Hashimoto
Institute of Molecular Medicine, Cheng Kung University Medical School, Tainan City, Taiwan
Center of Infectious Disease and Signal Transduction, National Cheng Kung University Medical school, Tainan City, Taiwan
Search for more papers by this authorHirofumi Honda
Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Search for more papers by this authorCorresponding Author
Jun-ichi Kato
Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Correspondence: Jun-ichi Kato, Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachioji, Tokyo 192-0397, Japan. Tel.: +81 42 677 2569; fax: +81 42 677 2559; e-mail: [email protected]Search for more papers by this authorChika Hashimoto
Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Search for more papers by this authorMasayuki Hashimoto
Institute of Molecular Medicine, Cheng Kung University Medical School, Tainan City, Taiwan
Center of Infectious Disease and Signal Transduction, National Cheng Kung University Medical school, Tainan City, Taiwan
Search for more papers by this authorHirofumi Honda
Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Search for more papers by this authorCorresponding Author
Jun-ichi Kato
Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Correspondence: Jun-ichi Kato, Department of Biological Sciences, Graduate Schools of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachioji, Tokyo 192-0397, Japan. Tel.: +81 42 677 2569; fax: +81 42 677 2559; e-mail: [email protected]Search for more papers by this authorAbstract
The YgjD protein is essential for the synthesis of the universal tRNA modification, N6-threonylcarbamoyladenosine (t6A), which is necessary for the decoding of ANN codons. We isolated a suppressor (ygjDsup) of the ygjDts mutant by its permissive growth at high temperature in Escherichia coli. Resequencing of the ygjDsup mutant genome showed the presence of a complicated chromosome rearrangement, an inverse insertion of a large duplicated region (c. 450 kb) into a small deleted region. The temperature-resistant growth associated with ygjDsup was due to the presence of multicopy suppressor genes, yjeE and groL, of the ygjDts mutation in the duplicated region. This DNA rearrangement was not simply mediated by IS1 transposition, but the duplicated region was flanked by IS1. We showed that the frequency of IS1 transposition was increased in ygjDts mutants. The transposase of IS1 is coded for by the insB gene, and its translation occurs through a frameshift of a ribosome translating upstream of the insA gene. We showed that this frameshifting frequency was increased by the ygjDts mutation. These results indicated that the mutation of the gene for tRNA modification, t6A, affected IS1 transposition.
Supporting Information
| Filename | Description |
|---|---|
| fml12227-sup-0001-FigS1-S4-TableS1-S2.pdfapplication/PDF, 1.3 MB | Fig. S1. Cloning of the junction regions of the isertion/deletion in the ygjDsup mutant genome. Fig. S2. The PFGE patterns predicted from the genome sequences. Fig. S3. Growth of the ygjDsup mutant with the dinG, rep, and rnhA multi-copy plasmids. Fig. S4. Junction sequences of the insertion/deletion in the ygjDsup mutant genome. Table S1. Primer sequences. Table S2. Transcription of collision-related genes in the ygjDts mutant. |
| fml12227-sup-0002-SupportingInformation.docxWord document, 1.3 MB |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- Abdullah KM, Lo RY & Mellors A (1991) Cloning, nucleotide sequence, and expression of the Pasteurella haemolytica A1 glycoprotease gene. J Bacteriol 173: 5597–5603.
- Allali-Hassani A, Campbell TL, Ho A, Schertzer JW & Brown ED (2004) Probing the active site of YjeE: a vital Escherichia coli protein of unknown function. Biochem J 384: 577–584.
- Arigoni F, Talabot F, Peitsch M, Edgerton MD, Meldrum E, Allet E, Fish R, Jamotte T, Curchod ML & Loferer H (1998) A genome-based approach for the identification of essential bacterial genes. Nat Biotechnol 16: 851–856.
- Boubakri H, de Septenville AL, Viguera E & Michel B (2010) The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J 29: 145–157.
- Brewer BJ (1988) When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell 53: 679–686.
- Butland G, Peregrín-Alvarez JM, Li J et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531–537.
- Chang AC & Cohen SN (1978) Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134: 1141–1156.
- Daugeron MC, Lenstra TL, Frizzarin M et al. (2011) Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res 39: 6148–6160.
- Deutsch C, El Yacoubi B, de Crécy-Lagard V & Iwata-Reuyl D (2012) Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 287: 13666–13673.
- Downey M, Houlsworth R, Maringele L et al. (2006) A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell 124: 1155–1168.
- El Yacoubi B, Hatin I, Deutsch C, Kahveci T, Rousset JP, Iwata-Reuyl D, Murzin AG & de Crécy-Lagard V (2011) A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 30: 882–893.
- Freiberg C, Wieland B, Spaltmann F, Ehlert K, Brötz H & Labischinski H (2001) Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria. J Mol Microbiol Biotechnol 3: 483–489.
- Galperin MY & Koonin EV (2004) ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 5452–5463.
- Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166: 557–580.
- Handford JI, Ize B, Buchanan G, Butland GP, Greenblatt J, Emili A & Palmer T (2009) Conserved network of proteins essential for bacterial viability. J Bacteriol 191: 4732–4749.
- Hashimoto C, Sakaguchi K, Taniguchi Y, Honda H, Oshima T, Ogasawara N & Kato J (2011) Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli. J Bacteriol 193: 6075–6079.
- Haussuehl K, Huesgen PF, Meier M, Dessi P, Glaser E, Adamski J & Adamska I (2009) Eukaryotic GCP1 is a conserved mitochondrial protein required for progression of embryo development beyond the globular stage in Arabidopsis thaliana. Biochem J 423: 333–341.
- Hecker A, Leulliot N, Gadelle D et al. (2007) An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res 35: 6042–6051.
- Iwadate Y, Honda H, Sato H, Hashimoto M & Kato J (2011) Oxidative stress sensitivity of engineered Escherichia coli cells with a reduced genome. FEMS Microbiol Lett 322: 25–33.
- Kato J & Hashimoto M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 3: 132.
- Kato J & Katayama T (2001) Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli. EMBO J 20: 4253–4262.
- Kisseleva-Romanova E, Lopreiato R, Baudin-Baillieu A, Rousselle JC, Ilan L, Hofmann K, Namane A, Mann C & Libri D (2006) Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J 25: 3576–3585.
- Lauhon CT (2012) Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 51: 8950–8963.
- Lerner CG, Hajduk PJ, Wagner R et al. (2007) From bacterial genomes to novel antibacterial agents: discovery, characterization, and antibacterial activity of compounds that bind to HI0065 (YjeE) from Haemophilus influenzae. Chem Biol Drug Des 69: 395–404.
- Mao DY, Neculai D, Downey M et al. (2008) Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mol Cell 32: 259–275.
- McCutcheon JP & Moran NA (2007) Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. P Natl Acad Sci USA 104: 19392–19397.
- Miller JH (1972) Experiments in Molecular Genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
- Murphy FV IV, Ramakrishnan V, Malkiewicz A & Agris PF (2004) The role of modifications in codon discrimination by tRNA(Lys)UUU. Nat Struct Mol Biol 11: 1186–1191.
- Nichols CE, Johnson C, Lockyer M, Charles IG, Lamb HK, Hawkins AR & Stammers DK (2006) Structural characterization of Salmonella typhimurium YeaZ, an M22 O-sialoglycoprotein endopeptidase homolog. Proteins 64: 111–123.
- Nichols CE, Lamb HK, Thompson P, El Omari K, Lockyer M, Charles I, Hawkins AR & Stammers DK (2013) Crystal structure of the dimer of two essential Salmonella typhimurium proteins, YgjD & YeaZ and calorimetric evidence for the formation of a ternary YgjD–YeaZ–YjeE complex. Protein Sci 22: 628–640.
- Oberto J, Breuil N, Hecker A, Farina F, Brochier-Armanet C, Culetto E & Forterre P (2009) Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. Nucleic Acids Res 37: 5343–5352.
- Perrochia L, Crozat E, Hecker A, Zhang W, Bareille J, Collinet B, van Tilbeurgh H, Forterre P & Basta T (2013) In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res 41: 1953–1964.
- Pomerantz RT & O'Donnell M (2010) Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 327: 590–592.
- Pósfai G, Koob MD, Kirkpatrick HA & Blattner FR (1997) Versatile insertion plasmids for targeted genome manipulations in bacteria: isolation, deletion, and rescue of the pathogenicity island LEE of the Escherichia coli O157:H7 genome. J Bacteriol 179: 4426–4428.
- Schmid MB & Roth JR (1983) Selection and endpoint distribution of bacterial inversion mutations. Genetics 105: 539–557.
- Sekine Y & Ohtsubo E (1989) Frameshifting is required for production of the transposase encoded by insertion sequence 1. P Natl Acad Sci USA 86: 4609–4613.
- Sekine Y, Nagasawa H & Ohtsubo E (1992) Identification of the site of translational frameshifting required for production of the transposase encoded by insertion sequence IS1. Mol Gen Genet 235: 317–324.
- Srinivasan M, Mehta P, Yu Y, Prugar E, Koonin EV, Karzai AW & Sternglanz R (2011) The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J 30: 873–881.
- Teplyakov A, Obmolova G, Tordova M, Thanki N, Bonander N, Eisenstein E, Howard AJ & Gilliland GL (2002) Crystal structure of the YjeE protein from Haemophilus influenzae: a putative ATPase involved in cell wall synthesis. Proteins 48: 220–226.
