Identification of a gene involved in plasmid structural instability in Corynebacterium glutamicum

Applied Microbiology and Biotechnology

Volumn 97, Issue 18, 2013, Pages 8219-8226

  Kitade, Yukihiro ^a   Okino, Shohei ^a   Gunji, Wataru ^a   Hiraga, Kazumi ^a   Suda, Masako ^a   Suzuki, Nobuaki ^a   Inui, Masayuki ^a   Yukawa, Hideaki ^a  

^a RESEARCH INSTITUTE OF INNOVATIVE TECHNOLOGY FOR THE EARTH   (Japan)

Author keywords

Corynebacterium glutamicum; Endonuclease; Plasmid stability; Production host; Structural instability

Indexed keywords

CLOSTRIDIUM ACETOBUTYLICUM; CORYNEBACTERIUM GLUTAMICUM; ENDONUCLEASES; LABORATORY CONDITIONS; PLASMID STABILITY; STRUCTURAL INSTABILITY; STRUCTURAL STABILITIES; TRANSFORMATION EFFICIENCY;

DNA; STABILITY;

GENE EXPRESSION;

BACTERIAL PROTEIN; DEOXYRIBONUCLEASE I; DOUBLE STRANDED DNA; ENDONUCLEASE; EXODEOXYRIBONUCLEASE III; EXONUCLEASE; HELICASE; MAGNESIUM ION; METHYLTRANSFERASE; NUCLEASE; NUCLEASE S1; PLASMID DNA; TRANSPOSASE;

BACTERIUM; DNA; ENZYME; GENE; GROWTH; PLASMID; TRANSFORMATION;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM MUTANT; CLOSTRIDIUM ACETOBUTYLICUM; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; ENZYME ACTIVITY; GENE IDENTIFICATION; GENE MUTATION; GENE STRUCTURE; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OPERON; PLASMID; SEQUENCE ANALYSIS;

CLOSTRIDIUM ACETOBUTYLICUM; CORYNEBACTERIUM GLUTAMICUM;

BACTERIAL PROTEINS; CORYNEBACTERIUM GLUTAMICUM; ENDONUCLEASES; MUTATION; PLASMIDS;

EID: 84883559635     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-4934-6     Document Type: Article

References (49)

1. Ankri S, Reyes O, Leblon G (1996) Improved electro-transformation of highly DNA-restrictive corynebacteria with DNA extracted from starved Escherichia coli. FEMS Microbiol Lett 140:247-251 (Pubitemid 26228634)
2. Biswas I, Jha JK, Fromm N (2008) Shuttle expression plasmids for genetic studies in Streptococcus mutans. Microbiology 154:2275-2282
3. Bower DM, Prather KLJ (2009) Engineering of bacterial strains and vectors for the production of plasmid DNA. Appl Microbiol Biotechnol 82:805-813
4. Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA (2009) Reaction mechanism of the ε subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc 131:1550-1556
5. Dabert P, Ehrlich SD, Gruss A (1992) High-molecular-weight linear multimer formation by single-stranded DNA plasmids in Escherichia coli. J Bacteriol 174:173-178
6. Fijalkowska IJ, Schaaper RM (1996) Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc Natl Acad Sci USA 93:2856-2861 (Pubitemid 26114333)
7. Friehs K (2004) Plasmid copy number and plasmid stability. Adv Biochem Engin/Biotechnol 86:47-82
8. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM (ed) The proteomics protocols handbook. Humana, Totowa, pp 571-607
9. L-valine production by Corynebacterium glutamicum under oxygen deprivation conditions. Appl Environ Microbiol 78:865-875
10. Huang Y-P, Ito J (1999) DNA polymerase C of the thermophilic bacterium Thermus aquaticus: classification and phylogenetic analysis of the family C DNA polymerases. J Mol Evol 48:756-769 (Pubitemid 29287966)
11. Ikeda M, Katsumata R (1992) Metabolic engineering to produce tyrosine or phenylalanine in a tryptophane-producing Corynebacterium glutamicum strain. Appl Environ Microbiol 58:781-785
12. Inui M, Kawaguchi H, Murakami S, Vertès AA, Yukawa H (2004a) Metabolic engineering of Corynebacterium glutamicum for fuel ethanol production under oxygen-deprivation conditions. J Mol Microbiol Biotechnol 8:243-254 (Pubitemid 41368969)
13. Inui M, Murakami S, Okino S, Kawaguchi H, Vertès AA, Yukawa H (2004b) Metabolic analysis of Corynebacterium glutamicum during lactate and succinate productions under oxygen deprivation conditions. J Mol Microbiol Biotechnol 7:182-196 (Pubitemid 39294707)
14. Inui M, Suda M, Okino S, Nonaka H, Puskás LG, Vertès AA, Yukawa H (2007) Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions. Microbiology 153:2491-2504 (Pubitemid 47262039)
15. Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H (2008) Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol 77:1305-1316
16. Iyer RR, Pluciennik A, Rosche WA, Sinden RR, Wells RD (2000) DNA polymerase III proofreading mutants enhance the expansion and deletion of triplet repeat sequences in Escherichia coli. J Biol Chem 275:2174-2184 (Pubitemid 30060847)
17. L-alanine under oxygen deprivation. Appl Microbiol Biotechnol 87:159-165
18. Kiewiet R, Kok J, Seegers JFML, Venema G, Bron S (1993) The mode of replication is a major factor in segregational plasmid instability in Lactococcus lactis. Appl Environ Microbiol 59:358-364 (Pubitemid 23058919)
19. Kinoshita (1985) Glutamic acid bacteria. In: Demain AL, Solomon NA (eds) Biology of industrial microorganisms. Cummings, London, pp 115-146
20. Kirby TW, Harvey S, DeRose EF, Chalov S, Chikova AK, Perrino FW, Schaaper RM, London RE, Pedersen LC (2006) Structure of the Escherichia coli DNA polymerase III ε-HOT proofreading complex. J Biol Chem 281:38466-38471 (Pubitemid 46041970)
21. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37:D205-D210
22. Na S, Shen T, Jia P (1994) Studies on the plasmid instability in Corynebacteria. Chin J Biotechnol 10:187-193
23. Nakamura Y, Nishio Y, Ikeo K, Gojobori T (2003) The genome stability in Corynebacterium species due to lack of the recombinational repair system. Gene 317:149-155 (Pubitemid 37356929)
24. Nakata K, Inui M, Kos PB, Vertès AA, Yukawa H (2003) Vectors for genetic engineering of corynebacteria. In: Saha BC (ed) Fermentation biotechnology. American Chemical Society, Washington, pp 175-191
25. Nešvera J, Pátek M (2011) Tools for genetic manipulations in Corynebacterium glutamicum and their applications. Appl Microbiol Biotechnol 90:1641-1654
26. Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A (2009) Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Systems Biol 3:82
27. Okibe N, Suzuki N, Inui M, Yukawa H (2010) Isolation, evaluation and use of two strong, carbon source-inducible promoters from Corynebacterium glutamicum. Lett Appl Microbiol 50:173-180
28. Okino S, Inui M, Yukawa H (2005) Production of organic acids by Corynebacterium glutamicum under oxygen deprivation. Appl Microbiol Biotechnol 68:475-480 (Pubitemid 41549991)
29. D-lactic acid by Corynebacterium glutamicum under oxygen deprivation. Appl Microbiol Biotechnol 78:449-454
30. Oliveira PH, Prather KJ, Prazeres DMF, Monteiro GA (2009) Structural instability of plasmid biopharmaceuticals: challenges and implications. Trends Biotechnol 27:503-511
31. Sahm H, Eggeling L, de Graaf AA (2000) Pathway analysis and metabolic engineering in Corynebacterium glutamicum. Biol Chem 381:899-910
32. Sambrook J, Fritsh EF, Maniatis T (1989) Molecular cloning, a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
33. Saveson CJ, Lovett ST (1997) Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics 146:457-470 (Pubitemid 27251385)
34. Singer A, Eiteman MA, Altman E (2009) DNA plasmid production in different host strains of Escherichia coli. J Ind Microbiol Biotechnol 36:521-530
35. Suzuki N, Okayama S, Nonaka H, Tsuge Y, Inui M, Yukawa H (2005a) Large-scale engineering of the Corynebacterium glutamicum genome. Appl Environ Microbiol 71:3369-3372 (Pubitemid 40807253)
36. Suzuki N, Nonaka H, Tsuge Y, Okayama S, Inui M, Yukawa H (2005b) Multiple large segment deletion method for Corynebacterium glutamicum. Appl Microbiol Biotechnol 69:151-161 (Pubitemid 41795088)
37. Suzuki N, Okai N, Nonaka H, Tsuge Y, Inui M, Yukawa H (2006) High-throughput transposon mutagenesis of Corynebacterium glutamicum and construction of a single-gene disruptant mutant library. Appl Environ Microbiol 72:3750-3755 (Pubitemid 43728035)
38. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637 (Pubitemid 27464953)
39. Tatusova TA, Madden TL (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247-50 (Pubitemid 29217013)
40. Tauch A (2008) Genomics of industrially and medically relevant corynebacteria. In: Burkovski A (ed) Corynebacteria: genomics and molecular biology. Caister Academic, Wymondham, pp 7-32
41. Tsuchida Y, Kimura S, Suzuki N, Inui M, Yukawa H (2009) Characterization of a new 2.4-kb plasmid of Corynebacterium casei and development of stable corynebacterial cloning vector. Appl Microbiol Biotechnol 81:1107-1115
42. Udaka S (2008) The discovery of Corynebacterium glutamicum and birth of amino acid fermentation industry in Japan. In: Burkovski A (ed) Corynebacteria: genomics and molecular biology. Caister Academic, Wymondham, pp 1-6
43. Vertès AA, Inui M, Kobayashi M, Kurusu Y, Yukawa H (1993) Presence of mrr- and mcr-like restriction systems in coryneform bacteria. Res Microbiol 144:181-185
44. Wendisch VF, Bott M, Eikmanns BJ (2006) Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids. Curr Opin Microbiol 9:268-274 (Pubitemid 44183577)
45. Yamamoto S, Gunji W, Suzuki H, Toda H, Suda M, Jojima T, Inui M, Yukawa H (2012) Overexpression of genes encoding glycolytic enzymes in Corynebacterium glutamicum enhances glucose metabolism and alanine production under oxygen deprivation conditions. Appl Environ Microbiol 78:4447-4457
46. Yau SY, Keshavarz-Moore E, Ward J (2008) Host strain influences on supercoiled plasmid DNA production in Escherichia coli: implications for efficient design of large-scale processes. Biotechnol Bioeng 101:529-544
47. Yukawa H, Omumasaba CA, Nonaka H, Kós P, Okai N, Suzuki N, Suda M, Tsuge Y, Watanabe J, Ikeda Y, Vertès AA, Inui M (2007) Comparative analysis of the Corynebacterium glutamicum group and complete genome sequence of strain R. Microbiology 153:1042-1058 (Pubitemid 46605802)
48. Zhao J-B, Wei D-Z, Tong W-Y (2007) Identification of Escherichia coli host cell for high plasmid stability and improved production of antihuman ovarian carcinoma × antihuman CD3 single-chain bispecific antibody. Appl Microbiol Biotechnol 76:795-800 (Pubitemid 47340930)
49. Zuo Y, Deutscher MP (2001) Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res 29:1017-1026 (Pubitemid 32186186)