메뉴 건너뛰기




Volumn 4, Issue 3, 2017, Pages 291-305.e7

Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis

Author keywords

auxotrophic gene; Bacillus subtilis; competence; essential gene; Genome wide screening; growth; high throughput methods for transformation and double mutant analysis; ordered gene deletion mutant library; sporulation; ysaA

Indexed keywords

AMINO ACID; CARBON; NITROGEN;

EID: 85011856675     PISSN: 24054712     EISSN: 24054720     Source Type: Journal    
DOI: 10.1016/j.cels.2016.12.013     Document Type: Article
Times cited : (388)

References (78)
  • 4
    • 33745924114 scopus 로고    scopus 로고
    • Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides
    • Auchtung, J.M., Lee, C.A., Grossman, A.D., Modulation of the ComA-dependent quorum response in Bacillus subtilis by multiple Rap proteins and Phr peptides. J. Bacteriol. 188 (2006), 5273–5285.
    • (2006) J. Bacteriol. , vol.188 , pp. 5273-5285
    • Auchtung, J.M.1    Lee, C.A.2    Grossman, A.D.3
  • 5
    • 34249997536 scopus 로고    scopus 로고
    • Identification and characterization of the immunity repressor (ImmR) that controls the mobile genetic element ICEBs1 of Bacillus subtilis
    • Auchtung, J.M., Lee, C.A., Garrison, K.L., Grossman, A.D., Identification and characterization of the immunity repressor (ImmR) that controls the mobile genetic element ICEBs1 of Bacillus subtilis. Mol. Microbiol. 64 (2007), 1515–1528.
    • (2007) Mol. Microbiol. , vol.64 , pp. 1515-1528
    • Auchtung, J.M.1    Lee, C.A.2    Garrison, K.L.3    Grossman, A.D.4
  • 7
    • 84901742537 scopus 로고    scopus 로고
    • Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli
    • Babu, M., Arnold, R., Bundalovic-Torma, C., Gagarinova, A., Wong, K.S., Kumar, A., Stewart, G., Samanfar, B., Aoki, H., Wagih, O., et al. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet., 10, 2014, e1004120.
    • (2014) PLoS Genet. , vol.10 , pp. e1004120
    • Babu, M.1    Arnold, R.2    Bundalovic-Torma, C.3    Gagarinova, A.4    Wong, K.S.5    Kumar, A.6    Stewart, G.7    Samanfar, B.8    Aoki, H.9    Wagih, O.10
  • 10
    • 33646501915 scopus 로고    scopus 로고
    • A checkpoint protein that scans the chromosome for damage at the start of sporulation in Bacillus subtilis
    • Bejerano-Sagie, M., Oppenheimer-Shaanan, Y., Berlatzky, I., Rouvinski, A., Meyerovich, M., Ben-Yehuda, S., A checkpoint protein that scans the chromosome for damage at the start of sporulation in Bacillus subtilis. Cell 125 (2006), 679–690.
    • (2006) Cell , vol.125 , pp. 679-690
    • Bejerano-Sagie, M.1    Oppenheimer-Shaanan, Y.2    Berlatzky, I.3    Rouvinski, A.4    Meyerovich, M.5    Ben-Yehuda, S.6
  • 11
    • 84877060695 scopus 로고    scopus 로고
    • High-throughput approaches to understanding gene function and mapping network architecture in bacteria
    • Brochado, A.R., Typas, A., High-throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr. Opin. Microbiol. 16 (2013), 199–206.
    • (2013) Curr. Opin. Microbiol. , vol.16 , pp. 199-206
    • Brochado, A.R.1    Typas, A.2
  • 15
    • 33747367151 scopus 로고    scopus 로고
    • A strategy for extracting and analyzing large-scale quantitative epistatic interaction data
    • Collins, S.R., Schuldiner, M., Krogan, N.J., Weissman, J.S., A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol., 7, 2006, R63.
    • (2006) Genome Biol. , vol.7 , pp. R63
    • Collins, S.R.1    Schuldiner, M.2    Krogan, N.J.3    Weissman, J.S.4
  • 16
    • 84877766396 scopus 로고    scopus 로고
    • Essential genes in Bacillus subtilis: a re-evaluation after ten years
    • Commichau, F.M., Pietack, N., Stulke, J., Essential genes in Bacillus subtilis: a re-evaluation after ten years. Mol. Biosyst. 9 (2013), 1068–1075.
    • (2013) Mol. Biosyst. , vol.9 , pp. 1068-1075
    • Commichau, F.M.1    Pietack, N.2    Stulke, J.3
  • 18
    • 0032969092 scopus 로고    scopus 로고
    • Bacillus subtilis spore coat
    • Driks, A., Bacillus subtilis spore coat. Microbiol. Mol. Biol. Rev. 63 (1999), 1–20.
    • (1999) Microbiol. Mol. Biol. Rev. , vol.63 , pp. 1-20
    • Driks, A.1
  • 20
    • 84891767234 scopus 로고    scopus 로고
    • SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis
    • Eijlander, R.T., de Jong, A., Krawczyk, A.O., Holsappel, S., Kuipers, O.P., SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis. Nucleic Acids Res. 42 (2014), D685–D691.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D685-D691
    • Eijlander, R.T.1    de Jong, A.2    Krawczyk, A.O.3    Holsappel, S.4    Kuipers, O.P.5
  • 21
    • 84917682907 scopus 로고    scopus 로고
    • The molecular basis of Clostridium difficile disease and host response
    • El Feghaly, R.E., Bangar, H., Haslam, D.B., The molecular basis of Clostridium difficile disease and host response. Curr. Opin. Gastroenterol. 31 (2015), 24–29.
    • (2015) Curr. Opin. Gastroenterol. , vol.31 , pp. 24-29
    • El Feghaly, R.E.1    Bangar, H.2    Haslam, D.B.3
  • 22
    • 84855290528 scopus 로고    scopus 로고
    • Divergence and convergence in enzyme evolution
    • Galperin, M.Y., Koonin, E.V., Divergence and convergence in enzyme evolution. J. Biol. Chem. 287 (2012), 21–28.
    • (2012) J. Biol. Chem. , vol.287 , pp. 21-28
    • Galperin, M.Y.1    Koonin, E.V.2
  • 23
    • 84867988931 scopus 로고    scopus 로고
    • Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
    • Galperin, M.Y., Mekhedov, S.L., Puigbo, P., Smirnov, S., Wolf, Y.I., Rigden, D.J., Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. Environ. Microbiol. 14 (2012), 2870–2890.
    • (2012) Environ. Microbiol. , vol.14 , pp. 2870-2890
    • Galperin, M.Y.1    Mekhedov, S.L.2    Puigbo, P.3    Smirnov, S.4    Wolf, Y.I.5    Rigden, D.J.6
  • 25
    • 84940676086 scopus 로고    scopus 로고
    • Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea
    • Grazziotin, A.L., Vidal, N.M., Venancio, T.M., Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. FEBS J. 282 (2015), 3395–3411.
    • (2015) FEBS J. , vol.282 , pp. 3395-3411
    • Grazziotin, A.L.1    Vidal, N.M.2    Venancio, T.M.3
  • 26
    • 84895070168 scopus 로고    scopus 로고
    • Interlinked sister chromosomes arise in the absence of condensin during fast replication in B. subtilis
    • Gruber, S., Veening, J.W., Bach, J., Blettinger, M., Bramkamp, M., Errington, J., Interlinked sister chromosomes arise in the absence of condensin during fast replication in B. subtilis. Curr. Biol. 24 (2014), 293–298.
    • (2014) Curr. Biol. , vol.24 , pp. 293-298
    • Gruber, S.1    Veening, J.W.2    Bach, J.3    Blettinger, M.4    Bramkamp, M.5    Errington, J.6
  • 27
    • 0037261785 scopus 로고    scopus 로고
    • Controlling competence in Bacillus subtilis: shared use of regulators
    • Hamoen, L.W., Venema, G., Kuipers, O.P., Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology 149 (2003), 9–17.
    • (2003) Microbiology , vol.149 , pp. 9-17
    • Hamoen, L.W.1    Venema, G.2    Kuipers, O.P.3
  • 28
    • 0023766807 scopus 로고
    • Controlled lysis of bacterial cells utilizing mutants with defective synthesis of D-alanine
    • Heaton, M.P., Johnston, R.B., Thompson, T.L., Controlled lysis of bacterial cells utilizing mutants with defective synthesis of D-alanine. Can. J. Microbiol. 34 (1988), 256–261.
    • (1988) Can. J. Microbiol. , vol.34 , pp. 256-261
    • Heaton, M.P.1    Johnston, R.B.2    Thompson, T.L.3
  • 29
    • 84861889493 scopus 로고    scopus 로고
    • Isoprenoid biosynthesis in bacterial pathogens
    • Heuston, S., Begley, M., Gahan, C.G., Hill, C., Isoprenoid biosynthesis in bacterial pathogens. Microbiology 158 (2012), 1389–1401.
    • (2012) Microbiology , vol.158 , pp. 1389-1401
    • Heuston, S.1    Begley, M.2    Gahan, C.G.3    Hill, C.4
  • 30
    • 83355169571 scopus 로고    scopus 로고
    • Recent progress in Bacillus subtilis sporulation
    • Higgins, D., Dworkin, J., Recent progress in Bacillus subtilis sporulation. FEMS Microbiol. Rev. 36 (2012), 131–148.
    • (2012) FEMS Microbiol. Rev. , vol.36 , pp. 131-148
    • Higgins, D.1    Dworkin, J.2
  • 34
    • 0036428851 scopus 로고    scopus 로고
    • The structure and function of novel proteins of Bacillus anthracis and other spore-forming bacteria: development of novel prophylactic and therapeutic agents
    • Jedrzejas, M.J., The structure and function of novel proteins of Bacillus anthracis and other spore-forming bacteria: development of novel prophylactic and therapeutic agents. Crit. Rev. Biochem. Mol. Biol. 37 (2002), 339–373.
    • (2002) Crit. Rev. Biochem. Mol. Biol. , vol.37 , pp. 339-373
    • Jedrzejas, M.J.1
  • 36
    • 34547913808 scopus 로고    scopus 로고
    • Construction of consecutive deletions of the Escherichia coli chromosome
    • Kato, J., Hashimoto, M., Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol., 3, 2007, 132.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 132
    • Kato, J.1    Hashimoto, M.2
  • 37
    • 84977662492 scopus 로고    scopus 로고
    • Complex polar machinery required for proper chromosome segregation in vegetative and sporulating cells of Bacillus subtilis
    • Kloosterman, T.G., Lenarcic, R., Willis, C.R., Roberts, D.M., Hamoen, L.W., Errington, J., Wu, L.J., Complex polar machinery required for proper chromosome segregation in vegetative and sporulating cells of Bacillus subtilis. Mol. Microbiol. 101 (2016), 333–350.
    • (2016) Mol. Microbiol. , vol.101 , pp. 333-350
    • Kloosterman, T.G.1    Lenarcic, R.2    Willis, C.R.3    Roberts, D.M.4    Hamoen, L.W.5    Errington, J.6    Wu, L.J.7
  • 42
    • 1542679907 scopus 로고    scopus 로고
    • Inhibitory action of serine on growth of bacteria of the genus Bacillus on mineral synthetic media
    • Lachowicz, T.M., Morzejko, E., Panek, E., Piatkowski, J., Inhibitory action of serine on growth of bacteria of the genus Bacillus on mineral synthetic media. Folia Microbiol. 41 (1996), 21–25.
    • (1996) Folia Microbiol. , vol.41 , pp. 21-25
    • Lachowicz, T.M.1    Morzejko, E.2    Panek, E.3    Piatkowski, J.4
  • 43
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2. Nat. Methods 9 (2012), 357–359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 44
    • 85014768147 scopus 로고    scopus 로고
    • Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
    • Letunic, I., Bork, P., Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44 (2016), W242–W245.
    • (2016) Nucleic Acids Res. , vol.44 , pp. W242-W245
    • Letunic, I.1    Bork, P.2
  • 47
    • 84961369845 scopus 로고    scopus 로고
    • High-throughput genetic screens identify a large and diverse collection of new sporulation genes in Bacillus subtilis
    • Meeske, A.J., Rodrigues, C.D., Brady, J., Lim, H.C., Bernhardt, T.G., Rudner, D.Z., High-throughput genetic screens identify a large and diverse collection of new sporulation genes in Bacillus subtilis. PLoS Biol., 14, 2016, e1002341.
    • (2016) PLoS Biol. , vol.14 , pp. e1002341
    • Meeske, A.J.1    Rodrigues, C.D.2    Brady, J.3    Lim, H.C.4    Bernhardt, T.G.5    Rudner, D.Z.6
  • 48
    • 84883464181 scopus 로고    scopus 로고
    • Accurate and universal delineation of prokaryotic species
    • Mende, D.R., Sunagawa, S., Zeller, G., Bork, P., Accurate and universal delineation of prokaryotic species. Nat. Methods 10 (2013), 881–884.
    • (2013) Nat. Methods , vol.10 , pp. 881-884
    • Mende, D.R.1    Sunagawa, S.2    Zeller, G.3    Bork, P.4
  • 50
    • 84891749330 scopus 로고    scopus 로고
    • SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information
    • Michna, R.H., Commichau, F.M., Todter, D., Zschiedrich, C.P., Stulke, J., SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information. Nucleic Acids Res. 42 (2014), D692–D698.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D692-D698
    • Michna, R.H.1    Commichau, F.M.2    Todter, D.3    Zschiedrich, C.P.4    Stulke, J.5
  • 52
    • 0017121451 scopus 로고
    • An enzyme common to histidine and aromatic amino acid biosynthesis in Bacillus subtilis
    • Nester, E.W., Montoya, A.L., An enzyme common to histidine and aromatic amino acid biosynthesis in Bacillus subtilis. J. Bacteriol. 126 (1976), 699–705.
    • (1976) J. Bacteriol. , vol.126 , pp. 699-705
    • Nester, E.W.1    Montoya, A.L.2
  • 56
    • 35848940244 scopus 로고    scopus 로고
    • High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe
    • Roguev, A., Wiren, M., Weissman, J.S., Krogan, N.J., High-throughput genetic interaction mapping in the fission yeast Schizosaccharomyces pombe. Nat. Methods 4 (2007), 861–866.
    • (2007) Nat. Methods , vol.4 , pp. 861-866
    • Roguev, A.1    Wiren, M.2    Weissman, J.S.3    Krogan, N.J.4
  • 58
    • 14844295003 scopus 로고    scopus 로고
    • CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes
    • Servant, P., Le Coq, D., Aymerich, S., CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes. Mol. Microbiol. 55 (2005), 1435–1451.
    • (2005) Mol. Microbiol. , vol.55 , pp. 1435-1451
    • Servant, P.1    Le Coq, D.2    Aymerich, S.3
  • 59
    • 84977540069 scopus 로고    scopus 로고
    • A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and Blasticidin S
    • Shiver, A.L., Osadnik, H., Kritikos, G., Li, B., Krogan, N., Typas, A., Gross, C.A., A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and Blasticidin S. PLoS Genet., 12, 2016, e1006124.
    • (2016) PLoS Genet. , vol.12 , pp. e1006124
    • Shiver, A.L.1    Osadnik, H.2    Kritikos, G.3    Li, B.4    Krogan, N.5    Typas, A.6    Gross, C.A.7
  • 61
    • 79953288485 scopus 로고    scopus 로고
    • Preparing DNA libraries for multiplexed paired-end deep sequencing for Illumina GA sequencers
    • Unit 1E.4
    • Son, M.S., Taylor, R.K., Preparing DNA libraries for multiplexed paired-end deep sequencing for Illumina GA sequencers. Curr. Protoc. Microbiol., Chapter 1, 2011 Unit 1E.4.
    • (2011) Curr. Protoc. Microbiol. , vol.Chapter 1
    • Son, M.S.1    Taylor, R.K.2
  • 62
    • 0003675244 scopus 로고    scopus 로고
    • Bacillus subtilis and Its Closest Relatives: From Genes to Cells
    • ASM Press
    • Sonenshein, A.L., Hoch, J.A., Losick, R., Bacillus subtilis and Its Closest Relatives: From Genes to Cells. 2002, ASM Press.
    • (2002)
    • Sonenshein, A.L.1    Hoch, J.A.2    Losick, R.3
  • 64
    • 0027474353 scopus 로고
    • Multisensory activation of the phosphorelay initiating sporulation in Bacillus subtilis: identification and sequence of the protein kinase of the alternate pathway
    • Trach, K.A., Hoch, J.A., Multisensory activation of the phosphorelay initiating sporulation in Bacillus subtilis: identification and sequence of the protein kinase of the alternate pathway. Mol. Microbiol. 8 (1993), 69–79.
    • (1993) Mol. Microbiol. , vol.8 , pp. 69-79
    • Trach, K.A.1    Hoch, J.A.2
  • 66
    • 84946069451 scopus 로고    scopus 로고
    • UniProt: a hub for protein information
    • UniProt Consortium, UniProt: a hub for protein information. Nucleic Acids Res. 43 (2015), D204–D212.
    • (2015) Nucleic Acids Res. , vol.43 , pp. D204-D212
    • UniProt Consortium1
  • 69
    • 70349130412 scopus 로고    scopus 로고
    • Homologues of the Bacillus subtilis SpoVB protein are involved in cell wall metabolism
    • Vasudevan, P., McElligott, J., Attkisson, C., Betteken, M., Popham, D.L., Homologues of the Bacillus subtilis SpoVB protein are involved in cell wall metabolism. J. Bacteriol. 191 (2009), 6012–6019.
    • (2009) J. Bacteriol. , vol.191 , pp. 6012-6019
    • Vasudevan, P.1    McElligott, J.2    Attkisson, C.3    Betteken, M.4    Popham, D.L.5
  • 71
    • 34250849031 scopus 로고    scopus 로고
    • Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape
    • Xu, L., Sedelnikova, S.E., Baker, P.J., Hunt, A., Errington, J., Rice, D.W., Crystal structure of S. aureus YlaN, an essential leucine rich protein involved in the control of cell shape. Proteins 68 (2007), 438–445.
    • (2007) Proteins , vol.68 , pp. 438-445
    • Xu, L.1    Sedelnikova, S.E.2    Baker, P.J.3    Hunt, A.4    Errington, J.5    Rice, D.W.6
  • 74
    • 50949129295 scopus 로고    scopus 로고
    • Cre/lox system and PCR-based genome engineering in Bacillus subtilis
    • Yan, X., Yu, H.J., Hong, Q., Li, S.P., Cre/lox system and PCR-based genome engineering in Bacillus subtilis. Appl. Environ. Microbiol. 74 (2008), 5556–5562.
    • (2008) Appl. Environ. Microbiol. , vol.74 , pp. 5556-5562
    • Yan, X.1    Yu, H.J.2    Hong, Q.3    Li, S.P.4
  • 75
    • 0037709014 scopus 로고    scopus 로고
    • Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box
    • Yoshida, K., Yamaguchi, H., Kinehara, M., Ohki, Y.H., Nakaura, Y., Fujita, Y., Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. Mol. Microbiol. 49 (2003), 157–165.
    • (2003) Mol. Microbiol. , vol.49 , pp. 157-165
    • Yoshida, K.1    Yamaguchi, H.2    Kinehara, M.3    Ohki, Y.H.4    Nakaura, Y.5    Fujita, Y.6
  • 77
    • 84946925898 scopus 로고    scopus 로고
    • Essentiality drives the orientation bias of bacterial genes in a continuous manner
    • Zheng, W.X., Luo, C.S., Deng, Y.Y., Guo, F.B., Essentiality drives the orientation bias of bacterial genes in a continuous manner. Sci. Rep., 5, 2015, 16431.
    • (2015) Sci. Rep. , vol.5 , pp. 16431
    • Zheng, W.X.1    Luo, C.S.2    Deng, Y.Y.3    Guo, F.B.4
  • 78
    • 84888004411 scopus 로고    scopus 로고
    • Metabolic suppression identifies new antibacterial inhibitors under nutrient limitation
    • Zlitni, S., Ferruccio, L.F., Brown, E.D., Metabolic suppression identifies new antibacterial inhibitors under nutrient limitation. Nat. Chem. Biol. 9 (2013), 796–804.
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 796-804
    • Zlitni, S.1    Ferruccio, L.F.2    Brown, E.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.