Engineering the genome of Thermus thermophilus using a counterselectable marker

Journal of Bacteriology

Volumn 197, Issue 6, 2015, Pages 1135-1144

  Carr, Jennifer F ^a   Danziger, Michael E ^a   Huang, Athena L ^a   Dahlberg, Albert E ^a   Gregory, Steven T ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; FENCLONINE; HYDROLASE; PHENYLALANINE; PHENYLALANINE DERIVATIVE; PHENYLALANINE TRANSFER RNA; RNA 16S; BACTERIAL DNA; BACTERIAL PROTEIN; BACTERIAL RNA; GENETIC MARKER;

ADAPTIVE IMMUNITY; ALGORITHM; ALLELE; AMINO ACID SUBSTITUTION; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; CODON USAGE; COLONY FORMATION; CONTROLLED STUDY; DELETION MUTANT; DNA REPAIR; DNA REPLICATION ORIGIN; ENZYME ACTIVITY; ESSENTIAL GENE; GENE CONVERSION; GENE DELETION; GENE INSERTION SEQUENCE; GENE LOCUS; GENETIC CODE; GENETIC ENGINEERING; GENETIC RESISTANCE; HOMOLOGOUS RECOMBINATION; INVERTED TERMINAL REPEAT; LETHAL MUTANT; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OPERON; PLASMID; POINT MUTATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN HYDROLYSIS; PROTEIN SUBUNIT; THERMOPHILE; THERMUS THERMOPHILUS; CLASSIFICATION; GENE EXPRESSION REGULATION; GENETIC MARKER; GENETICS; METABOLISM; MUTATION; PHYSIOLOGY;

BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

ALLELES; AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; BETA-GALACTOSIDASE; DNA, BACTERIAL; FENCLONINE; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENETIC ENGINEERING; GENETIC MARKERS; GENOME, BACTERIAL; MUTATION; PLASMIDS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; THERMUS THERMOPHILUS;

EID: 84923294726     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.02384-14     Document Type: Article

References (56)

1. Weisburg WG, Giovannoni SJ, Woese CR. 1989. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 11:128-134. http://dx.doi.org/10.1016/S0723-2020(89)80051-7.
2. Cava F, Hidalgo A, Berenguer J. 2009. Thermus thermophilus as biological model. Extremophiles 13:213-231. http://dx.doi.org/10.1007/s00792-009-0226-6.
3. Koyama Y, Hoshino T, Tomizuka N, Furukawa K. 1986. Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166:338-340.
4. Schwarzenlander C, Averhoff B. 2006. Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273:4210-4218. http://dx.doi.org/10.1111/j.1742-4658.2006.05416.x.
5. Henne A, Brüggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk H-P, Kramer W, Merkl R, Gottschalk G, Fritz H-J. 2004. The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22:547-553. http://dx.doi.org/10.1038/nbt956.
6. Chien A, Edgar DB, Trela JM. 1976. Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. J Bacteriol 127:1550-1557.
7. Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, van der Oost J. 2014. DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507:258-261. http://dx.doi.org/10.1038/nature12971.
8. Maseda H, Hoshino T. 1998. Development of expression vectors for Thermus thermophilus. J Ferment Bioeng 86:121-124. http://dx.doi.org/10.1016/S0922-338X(98)80044-5.
9. de Grado M, Castán P, Berenguer J. 1999. A high-transformationefficiency cloning vector for Thermus thermophilus. Plasmid 42:241-245. http://dx.doi.org/10.1006/plas.1999.1427.
10. Fujita A, Misumi Y, Koyama Y. 2012. Two versatile shuttle vectors for Thermus thermophilus-Escherichia coli containing multiple cloning sites, lacZα gene and kanamycin or hygromycin resistance marker. Plasmid 67:272-275. http://dx.doi.org/10.1016/j.plasmid.2011.12.013.
11. Tamakoshi M, Uchida M, Tanabe K, Fukuyama S, Yamagishi A, Oshima T. 1997. A new Thermus-Escherichia coli shuttle integration vector system. J Bacteriol 179:4811-4814.
12. Tamakoshi M, Yaoi T, Oshima T, Yamagishi A. 1999. An efficient gene replacement and deletion system for an extreme thermophile, Thermus thermophilus. FEMS Microbiol Lett 173:431-437. http://dx.doi.org/10.1111/j.1574-6968.1999.tb13535.x.
13. Park H-S, Kilbane JJ, II. 2004. Gene expression studies of Thermus thermophilus promoters PdnaK, Parg and Pscs-mdh. Lett Appl Microbiol 38:415-422. http://dx.doi.org/10.1111/j.1472-765X.2004.01512.x.
14. Ohta T, Tokishita S-I, Imazuka R, Mori I, Okamura J, Yamagata H. 2006. ß-Glucosidase as a reporter for the gene expression studies in Thermus thermophilus and constitutive expression of DNA repair genes. Mutagenesis 21:255-260. http://dx.doi.org/10.1093/mutage/gel025.
15. Fujita A, Misumi Y, Honda S, Sato T, Koyama Y. 2013. Construction of new cloning vectors that employ the phytoene synthase encoding gene for color screening of cloned DNA inserts in Thermus thermophilus. Gene 527:655-662. http://dx.doi.org/10.1016/j.gene.2013.06.069.
16. Hoseki J, Yano T, Koyama Y, Kuramitsu S, Kagamiyama H. 1999. Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. J Biochem 126:951-956. http://dx.doi.org/10.1093/oxfordjournals.jbchem.a022539.
17. Hashimoto Y, Yano T, Kuramitsu S, Kagamiyama H. 2001. Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett 506:231-234. http://dx.doi.org/10.1016/S0014-5793(01)02926-X.
18. Nakamura A, Takakura Y, Kobayashi H, Hoshino T. 2005. In vivo directed evolution for thermostabilization of Escherichia coli hygromycin B phosphotransferase and the use of the gene as a selection marker in the host-vector system of Thermus thermophilus. J Biosci Bioeng 100:158-163. http://dx.doi.org/10.1263/jbb.100.158.
19. Brouns SJJ, Wu H, Akerboom J, Turnbull AP, de Vos WM, van der Oost J. 2005. Engineering a selectable marker for hyperthermophiles. J Biol Chem 280:11422-11431. http://dx.doi.org/10.1074/jbc.M413623200.
20. Lipscomb GL, Stirrett K, Schut GJ, Yang F, Jenney FE, Scott RA, Adams MWW, Westpheling J. 2011. Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. Appl Environ Microbiol 77:2232-2238. http://dx.doi.org/10.1128/AEM.02624-10.
21. Suzuki H, Murakami A, Yoshida KI. 2012. Counterselection system for Geobacillus kaustophilus HTA426 through disruption of pyrF and pyrR. Appl Environ Microbiol 78:7376-7383. http://dx.doi.org/10.1128/AEM.01669-12.
22. Thiel A, Michoud G, Moalic Y, Flament D, Jebbar M. 2014. Genetic manipulations of the hyperthermophilic piezophilic archaeon Thermococcus barophilus. Appl Environ Microbiol 80:2299-2306. http://dx.doi.org/10.1128/AEM.00084-14.
23. Angelov A, Li H, Geissler A, Leis B, Liebl W. 2013. Toxicity of indoxyl derivative accumulation in bacteria and its use as a new counter selection principle. Syst Appl Microbiol 36:585-592. http://dx.doi.org/10.1016/j.syapm.2013.06.001.
24. Blas-Galindo E, Cava F, López-Viñas E, Mendieta J, Berenguer J. 2007. Use of a dominant rpsL allele conferring streptomycin dependence for positive and negative selection in Thermus thermophilus. Appl Environ Microbiol 73:5138-5145. http://dx.doi.org/10.1128/AEM.00751-07.
25. Kast P, Hennecke H. 1991. Amino acid substrate specificity of Escherichia coli phenylalanyl-tRNA synthetase altered by distinct mutations. J Mol Biol 222:99-124. http://dx.doi.org/10.1016/0022-2836(91)90740-W.
26. Kast P, Wehrli C, Hennecke H. 1991. Impaired affinity for phenylalanine in Escherichia coli phenylalanyl-tRNA synthetase mutant caused by Glyto-Asp exchange in motif 2 of class II tRNA synthetases. FEBS Lett 293:160-163. http://dx.doi.org/10.1016/0014-5793(91)81176-9.
27. Kast P. 1994. pKSS-a second-generation general purpose cloning vector for efficient positive selection of recombinant clones. Gene 138:109-114. http://dx.doi.org/10.1016/0378-1119(94)90790-0.
28. Xie Z, Okinaga T, Qi F, Zhang Z, Merritt J. 2011. Cloning-independent and counterselectable markerless mutagenesis system in Streptococcus mutans. Appl Environ Microbiol 77:8025-8033. http://dx.doi.org/10.1128/AEM.06362-11.
29. Oshima T, Imahori K. 1974. Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 24:102-112.
30. Carr JF, Gregory ST, Dahlberg AE. 20 June 2014, posting date. Transposon mutagenesis of the extremely thermophilic bacterium Thermus thermophilus HB27. Extremophiles http://dx.doi.org/10.1007/s00792-014-0663-8.
31. Kristjansson JK, Hreggvidsson GO, Alfredsson GA. 1986. Isolation of halotolerant Thermus spp. from submarine hot springs in Iceland. Appl Environ Microbiol 52:1313-1316.
32. Miller JH. 1992. A short course in bacterial genetics, p 72-74. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
33. Solovyev V, Salamov A. 2011. Automatic annotation of microbial genomes and metagenomic sequences, p 61-78. In LiRW(ed), Metagenomics and its applications in agriculture, biomedicine and environmental studies. Nova Science Publishers, Hauppauge, NY.
34. Rangannan V, Bansal M. 2011. PromBase: a Web resource for various genomic features and predicted promoters in prokaryotic genomes. BMC Res Notes 4:257. http://dx.doi.org/10.1186/1756-0500-4-257.
35. Gregory ST, Dahlberg AE. 2009. Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA. RNA 15:215-223. http://dx.doi.org/10.1261/rna.1374809.
36. Nakamura Y, Gojobori T, Ikemura T. 2000. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292. http://dx.doi.org/10.1093/nar/28.1.292.
37. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345. http://dx.doi.org/10.1038/nmeth.1318.
38. Hamilton CM, Aldea M, Washburn BK, Babitzke P, Kushner SR. 1989. New method for generating deletions and gene replacements in Escherichia coli. J Bacteriol 171:4617-4622.
39. Link AJ, Phillips D, Church GM. 1997. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol 179:6228-6237.
40. Cameron DM, Gregory ST, Thompson J, Suh M-J, Limbach PA, Dahlberg AE. 2004. Thermus thermophilus L11 methyltransferase, PrmA, is dispensable for growth and preferentially modifies free ribosomal protein L11 prior to ribosome assembly. J Bacteriol 186:5819-5825. http://dx.doi.org/10.1128/JB.186.17.5819-5825.2004.
41. Hartmann RK, Erdmann VA. 1989. Thermus thermophilus 16S rRNA is transcribed from an isolated transcription unit. J Bacteriol 171:2933-2941.
42. Gregory ST, Carr JF, Rodriguez-Correa D, Dahlberg AE. 2005. Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus. J Bacteriol 187:4804-4812. http://dx.doi.org/10.1128/JB.187.14.4804-4812.2005.
43. Gounder K, Brzuszkiewicz E, Liesegang H, Wollherr A, Daniel R, Gottschalk G, Reva O, Kumwenda B, Srivastava M, Bricio C, Berenguer J, van Heerden E, Litthauer D. 2011. Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics 12:577. http://dx.doi.org/10.1186/1471-2164-12-577.
44. Agari Y, Sakamoto K, Tamakoshi M, Oshima T, Kuramitsu S, Shinkai A. 2010. Transcription profile of Thermus thermophilus CRISPR systems after phage infection. J Mol Biol 395:270-281. http://dx.doi.org/10.1016/j.jmb.2009.10.057.
45. Brüggemann H, Chen C. 2006. Comparative genomics of Thermus thermophilus: plasticity of the megaplasmid and its contribution to a thermophilic lifestyle. J Biotechnol 124:654-661. http://dx.doi.org/10.1016/j.jbiotec.2006.03.043.
46. Gregory ST, Dahlberg AE. 2008. Transposition of an insertion sequence, ISTth7, in the genome of the extreme thermophile Thermus thermophilus HB8. FEMS Microbiol Lett 289:187-192. http://dx.doi.org/10.1111/j.1574-6968.2008.01389.x.
47. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. 2006. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32-D36. http://dx.doi.org/10.1093/nar/gkj014.
48. Takayama G, Kosuge T, Maseda H, Nakamura A, Hoshino T. 2004. Nucleotide sequence of the cryptic plasmid pTT8 from Thermus thermophilus HB8 and isolation and characterization of its high-copy-number mutant. Plasmid 51:227-237. http://dx.doi.org/10.1016/j.plasmid.2004.01.003.
49. Aoki K, Itoh T. 2007. Characterization of the ColE2-like replicon of plasmid pTT8 from Thermus thermophilus. Biochem Biophys Res Commun 353:1028-1033. http://dx.doi.org/10.1016/j.bbrc.2006.12.150.
50. Hishinuma F, Tanaka T, Sakaguchi K. 1978. Isolation of extrachromosomal deoxyribonucleic acids from extremely thermophilic bacteria. J Gen Microbiol 104:193-199. http://dx.doi.org/10.1099/00221287-104-2-193.
51. Rakowski SA, Filutowicz M. 2013. Plasmid R6K replication control. Plasmid 69:231-242. http://dx.doi.org/10.1016/j.plasmid.2013.02.003.
52. Kang SK, Cho KK, Ahn JK, Bok JD, Kang SH, Woo JH, Lee HG, You SK, Choi YJ. 2005. Three forms of thermostable lactose-hydrolase from Thermus sp. IB-21: cloning, expression, and enzyme characterization. J Biotechnol 116:337-346.
53. Morton ER, Merritt PM, Bever JD, Fuqua C. 2013. Large deletions in the pAtC58 megaplasmid of Agrobacterium tumefaciens can confer reduced carriage cost and increased expression of virulence genes. Genome Biol Evol 5:1353-1364. http://dx.doi.org/10.1093/gbe/evt095.
54. Kleckner N, Reichardt K, Botstein D. 1979. Inversions and deletions of the Salmonella chromosome generated by the translocatable tetracycline resistance element Tn10. J Mol Biol 127:89-115. http://dx.doi.org/10.1016/0022-2836(79)90461-3.
55. Ross DG, Swan J, Kleckner N. 1979. Physical structures of Tn10-promoted deletions and inversions: role of 1400 bp inverted repetitions. Cell 16:721-731. http://dx.doi.org/10.1016/0092-8674(79)90088-6.
56. Bochner BR, Huang HC, Schieven GL, Ames BN. 1980. Positive selection for loss of tetracycline resistance. J Bacteriol 143:926-933.