The blueprint of a minimal cell: MiniBacillus

Microbiology and Molecular Biology Reviews

Volumn 80, Issue 4, 2016, Pages 955-987

  Reuß, Daniel R ^a   Commichau, Fabian M ^a   Gundlach, Jan ^a   Zhu, Bingyao ^a   Stülke, Jörg ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ANTIINFECTIVE AGENT; BACTERIAL DNA; BACTERIAL PROTEIN; BACTERIAL RNA; CARBON; CHAPERONE; IRON; LIPID; MESSENGER RNA; METAL; NUCLEOTIDE; PHOSPHATE; SULFUR;

ARTICLE; ARTIFICIAL CELL; BACILLUS SUBTILIS; BACTERIAL CELL; BACTERIAL CELL WALL; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL METABOLISM; BIOSYNTHESIS; CARBON METABOLISM; CELL DIVISION; CELL ENERGY; CELL RESPIRATION; CHROMOSOME SEGREGATION; DNA REPLICATION; DRUG TARGETING; GENETIC STABILITY; GENETIC TRANSCRIPTION; NONHUMAN; PROTEIN DEGRADATION; PROTEIN QUALITY; PROTEIN SECRETION; REGULATORY MECHANISM; RNA DEGRADATION; RNA FOLDING; RNA TRANSLATION; SIGNAL TRANSDUCTION;

EID: 84995377078     PISSN: 10922172     EISSN: 10985557     Source Type: Journal    
DOI: 10.1128/MMBR.00029-16     Document Type: Article

References (177)

1. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA III, Smith HO, Venter JC. 2006. Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 103:425-430. http://dx.doi.org/10.1073/pnas.0510013103.
2. Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L. 2009. Transcriptome complexity in a genome-reduced bacterium. Science 326:1268- 1271. http://dx.doi.org/10.1126/science.1176951.
3. Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen WH, Wodke JA, Güell M, Martínez S, Bourgeois R, Kühner S, Raineri E, Letunic I, Kalinina OV, Rode M, Herrmann R, Gutiérrez-Gallego R, Russell RB, Gavin AC, Bork P, Serrano L. 2009. Impact of genome reduction on bacterial metabolism and its regulation. Science 326:1263- 1268. http://dx.doi.org/10.1126/science.1177263.
4. Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC. 2009. Proteome organization in a genome-reduced bacterium. Science 326:1235-1240. http://dx.doi.org/10.1126/science.1176343.
5. Maier T, Schmidt A, Güell M, Kühner S, Gavin AC, Aebersold R, Serrano L. 2011. Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol 7:511. http://dx.doi.org/10.1038/msb.2011.38.
6. Schmidl SR, Gronau K, Pietack N, Hecker M, Becher D, Stülke J. 2010. The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: Analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases. Mol Cell Proteomics 9:1228-1242. http://dx.doi.org/10.1074/mcp.M900267-MCP200.
7. van Noort V, Seebacher J, Bader S, Mohammed S, Vonkova I, Betts MJ, Kühner S, Kumar R, Maier T, O'Flaherty M, Rybin V, Schmeisky A, Yus E, Stülke J, Serrano L, Russell RB, Heck AJ, Bork P, Gavin AC. 2012. Cross-Talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol 8:571. http://dx.doi.org/10.1038/msb.2012.4.
8. Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L. 2015. Defining a minimal cell: Essentiality of small ORFs and ncRNAs in a genome-reduced bacterium. Mol Syst Biol 11:780. http://dx.doi.org/10.15252/msb.20145558.
9. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA III, Smith HO, Venter JC. 2010. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52-56. http://dx.doi.org/10.1126/science.1190719.
10. Hutchison CA, III, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC. 2016. Design and synthesis of a minimal bacterial genome. Science 351: Aad6253. http://dx.doi.org/10.1126/science.aad6253.
11. Xavier JC, Patil KR, Rocha I. 2014. Systems biology perspectives on minimal and simpler cells. Microbiol Mol Biol Rev 78:487-509. http://dx.doi.org/10.1128/MMBR.00050-13.
12. Blain JC, Szostak JW. 2014. Progress toward synthetic cells. Annu Rev Biochem 83:615-640. http://dx.doi.org/10.1146/annurev-biochem-080411-124036.
13. Kretschmer S, Schwille P. 2014. Toward spatially regulated division of protocells: insights into the E. coli Min system from in vitro studies. Life (Basel) 4:915-928. http://dx.doi.org/10.3390/life4040915.
14. Schwille P. 2015. Jump-starting life? Fundamental aspects of synthetic biology. J Cell Biol 210:687-690. http://dx.doi.org/10.1083/jcb.201506125.
15. Oberholzer T, Wick R, Luisi PL, Biebricher CK. 1995. Enzymatic RNA replication in self-reproducing vesicles: An approach to a minimal cell. Biochem Biophys Res Commun 207:250-257. http://dx.doi.org/10.1006/bbrc.1995.1180.
16. Szostak JW, Bartel DP, Luisi PL. 2001. Synthesizing life. Nature 409: 387-390. http://dx.doi.org/10.1038/35053176.
17. Chen IA, Roberts RW, Szostak JW. 2004. The emergence of competition between model protocells. Science 305:1474-1476. http://dx.doi.org/10.1126/science.1100757.
18. Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Kanaya S, Ara K, Ozaki K, Ogasawara N. 2008. Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res 15:73-81. http://dx.doi.org/10.1093/dnares/dsn002.
19. Wenzel M, Altenbuchner J. 2015. Development of a markerless gene deletion system for Bacillus subtilis based on the mannose phosphoenolpyruvate- dependent phosphotransferase system. Microbiology 161: 1942-1949. http://dx.doi.org/10.1099/mic.0.000150.
20. Westers H, Dorenbos R, van Dijl JM, Kabel J, Flanagan T, Devine KM, Jude F, Seror SJ, Beekman AC, Darmon E, Eschevins C, de Jong A, Bron S, Kuipers OP, Albertini AM, Antelmann H, Hecker M, Zamboni N, Sauer U, Bruand C, Ehrlich DS, Alonso JC, Salas Quax WJ. 2003. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol 20:2076-2090. http://dx.doi.org/10.1093/molbev/msg219.
21. Hirokawa Y, Kawano H, Tanaka-Masuda K, Nakamura N, Nakagawa A, Ito M, Mori H, Oshima T, Ogasawara N. 2013. Genetic manipulation restored the growth fitness of reduced-genome Escherichia coli. J Biosci Bioeng 116:52-58. http://dx.doi.org/10.1016/j.jbiosc.2013.01.010.
22. Pósfai G, Plunkett G, III, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR. 2006. Emergent properties of reducedgenome Escherichia coli. Science 312:1044-1046. http://dx.doi.org/10.1126/science.1126439.
23. Kato J, Hashimoto M. 2008. Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome. Methods Mol Biol 416:279-293. http://dx.doi.org/10.1007/978-1-59745-321-9-18.
24. Krishnakumar R, Grose C, Haft DH, Zaveri J, Alperovich N, Gibson DG, Merryman C, Glass JI. 2014. Simultaneous non-contiguous deletions using large synthetic DNA and site-specific recombinases. Nucleic Acids Res 42:e111. http://dx.doi.org/10.1093/nar/gku509.
25. Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S. 2015. Chassis organism from Corynebacterium glutamicum-A top down approach to identify and delete irrelevant gene clusters. Biotechnol J 10: 290-301. http://dx.doi.org/10.1002/biot.201400041.
26. Leprince A, de Lorenzo V, Völler P, van Passel MWJ, Martins dos Santos VAP. 2012. Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol 14:1444-1453. http://dx.doi.org/10.1111/j.1462-2920.2012.02730.x.
27. Komatsu M, Uchiyama T, Omura S, Cane DE, Ikeda H. 2010. Genome- minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci U S A 107:2646-2651. http://dx.doi.org/10.1073/pnas.0914833107.
28. Juhas M, Reuß DR, Zhu B, Commichau FM. 2014. Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. Microbiology 160:2341-2351. http://dx.doi.org/10.1099/mic.0.079376-0
29. Sasaki M, Kumagai H, Takegawa K, Tohda H. 2013. Characterizationof genome-reduced fission yeast strains. Nucleic Acids Res 41:5382- 5399. http://dx.doi.org/10.1093/nar/gkt233.
30. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, et al. 2003. Essential Bacillus subtilis genes. Proc Natl Acad 100:4678-4683. http://dx.doi.org/10.1073/pnas.0730515100.
31. Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P. 2013. Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res 41:687-699. http://dx.doi.org/10.1093/nar/gks963.
32. Commichau FM, Pietack N, Stülke J. 2013. Essential genes in Bacillus subtilis: A re-evaluation after ten years. Mol Biosyst 9:1068-1075. http://dx.doi.org/10.1039/c3mb25595f.
33. Michna RH, Zhu B, Mäder U, Stülke J. 2016. SubtiWiki 2.0-An integrated database for the model organism Bacillus subtilis. Nucleic Acids Res 44:D654-D662. http://dx.doi.org/10.1093/nar/gkv1006.
34. Figaro S, Durand S, Gilet L, Cayet N, Sachse M, Condon C. 2013. Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence. J Bacteriol 195:2340-2348. http://dx.doi.org/10.1128/JB.00164-13.
35. Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CH, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA. 2016. A comprehensive, CRISPR-based functional analysis of essential genes in bacteria. Cell 165:1493-1506. http://dx.doi.org/10.1016/j.cell.2016.05.003.
36. Thomaides HB, Davison EJ, Burston L, Johnson H, Brown DR, Hunt AC, Errington J, Czaplewski L. 2007. Essential bacterial functions encoded by gene pairs. J Bacteriol 189:591-602. http://dx.doi.org/10.1128/JB.01381-06.
37. Mehne FMP, Gunka K, Eilers H, Herzberg C, Kaever V, Stülke J. 2013. Cyclic-di-AMP homeostasis in Bacillus subtilis: both lack and high-level accumulation of the nucleotide are detrimental for cell growth. J Biol Chem 288:2004-2017. http://dx.doi.org/10.1074/jbc.M112.395491.
38. Duman R, Ishikawa S, Celik I, Strahl H, Ogasawara N, Troc P, Löwe J, Hamoen LW. 2013. Structural and genetic analyses reveal the protein SepF as a new membrane anchor for the Z ring. Proc Natl Acad Sci U S A 110:E4601-E4610. http://dx.doi.org/10.1073/pnas.1313978110.
39. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P. 2012. The condition- dependent whole-Transcriptome reveals high-level regulatory architecture in bacteria. Science 335:1103-1106. http://dx.doi.org/10.1126/science.1206848.
40. Maaß S, Wachlin G, Bernhardt J, Eymann C, Fromion V, Riedel K, Becher D, Hecker M. 2014. Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteomics 13:2260-2276. http://dx.doi.org/10.1074/mcp.M113.035741.
41. Muntel J, Fromion V, Goelzer A, Maaß S, Mäder U, Büttner K, Hecker M, Becher D. 2014. Comprehensive absolute quantification of the cytosolic proteome of Bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (LC/MS(E)). Mol Cell Proteomics 13:1008-1019. http://dx.doi.org/10.1074/mcp.M113.032631.
42. Grosjean H, Breton M, Sirand-Pugnet P, Tardy F, Thiaucourt F, Citti C, Barré A, Yoshizawa S, Fourmy D, de Crécy-Lagard V, Blanchard A. 2014. Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PLoS Genet 10:e1004363. http://dx.doi.org/10.1371/journal.pgen.1004363.
43. Eymann C, Dreisbach A, Albrecht D, Bernhardt J, Becher D, Gentner S, Tam LT, Büttner K, Buurman G, Scharf C, Venz S, Völker U, Hecker M. 2004. A comprehensive proteome map of growing Bacillus subtilis cells. Proteomics 4:2849-2876. http://dx.doi.org/10.1002/pmic.200400907.
44. Halbedel S, Hames C, Stülke J. 2004. In vivo activity of enzymatic and regulatory components of the phosphoenolpyruvate:sugar phosphotransferase system in Mycoplasma pneumoniae. J Bacteriol 186:7936- 7943. http://dx.doi.org/10.1128/JB.186.23.7936-7943.2004.
45. Sanders GM, Dallmann HG, McHenry CS. 2010. Reconstitution of the B. subtilis replisome with 13 proteins including two distinct replicases. Mol Cell 37:273-281. http://dx.doi.org/10.1016/j.molcel.2009.12.025.
46. Briggs GS, Smits WK, Soultanas P. 2012. Chromosomal replication initiation machinery of low-G-C-content Firmicutes. J Bacteriol 194: 5162-5170. http://dx.doi.org/10.1128/JB.00865-12.
47. Duggin IG, Matthews JM, Dixon NE, Wake RG, Mackay JP. 2005. A complex mechanism determines polarity of DNA replication fork arrest by the replication terminator complex of Bacillus subtilis. J Biol Chem 280:13105-13113. http://dx.doi.org/10.1074/jbc.M414187200.
48. Merrikh H, Grossman AD. 2011. Control of the replication initiator protein DnaA by an anti-cooperativity factor. Mol Microbiol 82:434- 446. http://dx.doi.org/10.1111/j.1365-2958.2011.07821.x.
49. Fukushima S, Itaya M, Kato H, Ogasawara N, Yoshikawa H. 2007. Reassessment of the in vivo functions of DNA polymerase I and RNaseH in bacterial cell growth. J Bacteriol 189:8575-8583. http://dx.doi.org/10.1128/JB.00653-07.
50. Wang X, Montero Llopis P, Rudner DZ. 2013. Organization and segregation of bacterial chromosomes. Nat Rev Genet 14:191-203. http://dx.doi.org/10.1038/nrg3375.
51. Wang X, Tang OW, Riley EP, Rudner DZ. 2014. The SMC condensing complex is required for origin segregation in Bacillus subtilis. Curr Biol 24:287-292. http://dx.doi.org/10.1016/j.cub.2013.11.050.
52. Soh YM, Bürmann F, Shin HC, Oda T, Jin KS, Toseland CP, Kim C, Lee H, Kim SJ, Kong MS, Durand-Diebold ML, Kim YG, Kim HM, Lee NK, Sato M, Oh BH, Gruber S. 2015. Molecular basis for SMC rod formation and its dissociation uponDNAbinding. Mol Cell 57:290-303. http://dx.doi.org/10.1016/j.molcel.2014.11.023.
53. Tadesse S, Mascarenhas J, Kösters B, Hasilik A, Graumann PL. 2005. Genetic interaction of the SMC complex with topoisomerase IV in Bacillus subtilis. Microbiology 151:3729-3737. http://dx.doi.org/10.1099/mic.0.28234-0.
54. Biller SJ, Burkholder WF. 2009. The Bacillus subtilis SftA (YtpS) and SpoIIIE DNA translocases play distinct roles in growing cells to ensure faithful chromosome partitioning. Mol Microbiol 74:790-809. http://dx.doi.org/10.1111/j.1365-2958.2009.06893.x.
55. Sciochetti SA, Piggot PJ, Sherratt DJ, Blakely G. 1999. The ripX locus of Bacillus subtilis encodes a site-specific recombinase involved in proper chromosome partitioning. J Bacteriol 181:6053-6062.
56. Kaimer C, Schenk K, Graumann PL. 2011. Two DNA translocases synergistically affect chromosome dimer resolution in Bacillus subtilis. J Bacteriol 193:1334-1340. http://dx.doi.org/10.1128/JB.00918-10.
57. Levine C, Hiasa H, Marians KJ. 1998. DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim Biophys Acta 1400:29-43. http://dx.doi.org/10.1016/S0167-4781(98)00126-2.
58. Fernandez S, Rojo F, Alonso JC. 1997. The Bacillus subtilis chromatinassociated protein Hbsu is involved in DNA repair and recombination. Mol Microbiol 23:1169 -1179. http://dx.doi.org/10.1046/j.1365-2958.1997.3061670.x.
59. Wiedermannová J, Sudzinová P, Koval T, Rabatinová A, Šanderova H, Ramaniuk O, Rittich Š, Dohnálek J, Fu Z, Halada P, Lewis P, Krásny L. 2014. Characterization of HelD, an interacting partner of RNA polymerase from Bacillus subtilis. Nucleic Acids Res 42:5151-5163. http://dx.doi.org/10.1093/nar/gku113.
60. Prajapati RK, Sengupta S, Rudra P, Mukhopadhyay J. 2016. Bacillus subtilis - factor functions as a transcriptional regulator by facilitating the open complex formation. J Biol Chem 291:1064-1075. http://dx.doi.org/10.1074/jbc.M115.686170.
61. Kusuya Y, Kurokawa K, Ishikawa S, Ogasawara N, Oshima T. 2011. Transcription factor GreA contributes to resolving promoter-proximalpausing of RNA polymerase in Bacillus subtilis cells. J Bacteriol 193: 3090-3099. http://dx.doi.org/10.1128/JB.00086-11.
62. Mondal S, Yakhnin AV, Sebastian A, Albert I, Babitzke P. 2016. NusA-dependent transcription termination prevents misregulation of global gene expression. Nat Microbiol 1:15007. http://dx.doi.org/10.1038/nmicrobiol.2015.7.
63. Quirk PG, Dunkey EA, Lee P, Krulwich TA. 1993. Identification of a putative Bacillus subtilis rho gene. J Bacteriol 175:647-654.
64. Lehnik-Habrink M, Lewis RJ, Mäder U, Stülke J. 2012. RNA degradation in Bacillus subtilis: An interplay of essential endo-And exoribonucleases. Mol Microbiol 84:1005-1017. http://dx.doi.org/10.1111/j.1365-2958.2012.08072.x.
65. Graumann PL, Wendrich TM, Weber MH, Schröder K, Marahiel MA. 1997. A family of cold shock proteins in Bacillus subtilis is essential for cellular growth and for efficient protein synthesis at optimal and low temperatures. Mol Microbiol 25:741-756. http://dx.doi.org/10.1046/j.1365-2958.1997.5121878.x.
66. Lehnik-Habrink M, Rempeters L, Kovács Á, Wrede C, Baierlein C, Krebber H, Kuipers OP, Stülke J. 2013. The DEAD-box RNA helicases in Bacillus subtilis have multiple functions and act independent from each other. J Bacteriol 195:534 -544. http://dx.doi.org/10.1128/JB.01475-12.
67. Hunt A, Rawlins JP, Thomaides HB, Errington J. 2006. Functional analysis of 11 putative essential genes in Bacillus subtilis. Microbiology 152:2895-2907. http://dx.doi.org/10.1099/mic.0.29152-0.
68. Commichau FM, Rothe FM, Herzberg C, Wagner E, Hellwig D, Lehnik-Habrink M, Hammer E, Völker U, Stülke J. 2009. Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing. Mol Cell Proteomics 8:1350- 1360. http://dx.doi.org/10.1074/mcp.M800546-MCP200.
69. Lehnik-Habrink M, Newman J, Rothe FM, Solovyova AS, Rodrigues C, Herzberg C, Commichau FM, Lewis RJ, Stülke J. 2011. RNase Y in Bacillus subtilis: A natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J Bacteriol 193:5431-5441. http://dx.doi.org/10.1128/JB.05500-11.
70. Cardenas PP, Carrasco B, Sanchez H, Deikus G, Bechhofer DH, Alonso JC. 2009. Bacillus subtilis polynucleotide phosphorylase 3=-To-5= DNase activity is involved in DNA repair. Nucleic Acids Res 37:4157- 4169. http://dx.doi.org/10.1093/nar/gkp314.
71. Nelersa CM, Schmier BJ, Malhotra A. 2011. Purification and crystallization of Bacillus subtilis NrnA, a novel enzyme involved in nanoRNA degradation. Acta Crystallogr Sect F Struct Biol CrystCommun 67:1235- 1238. http://dx.doi.org/10.1107/S1744309111026509.
72. Pelchat M, Lapointe J. 1999. Aminoacyl-TRNA synthetase genes of Bacillus subtilis: organization and regulation. Biochem Cell Biol 77:343- 347. http://dx.doi.org/10.1139/o99-040.
73. Williams-Wagner RN, Grundy FJ, Raina M, Ibba M, Henkin TM. 2015. The Bacillus subtilis tyrZ gene encodes a highly selective tyrosyltRNA synthetase and is regulated by a MarR regulator and T box riboswitch. J Bacteriol 197:1624 -1631. http://dx.doi.org/10.1128/JB.00008-15.
74. Curnow AW, Hong KW, Yuan R, Kim SI, Martins O, Winkler W, Henkin TM, Söll D. 1997. Glu-TRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc Natl Acad Sci U S A 94:11819-11826. http://dx.doi.org/10.1073/pnas.94.22.11819.
75. Akanuma G, Nanamiya H, Natori Y, Yano K, Suzuki S, Omata S, Ishizuka M, Sekine Y, Kawamura F. 2012. Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation. J Bacteriol 194: 6282-6291. http://dx.doi.org/10.1128/JB.01544-12.
76. Natori Y, Nanamiya H, Akanuma G, Kosono S, Kudo T, Ochi K, Kawamura F. 2007. A fail-safe system for the ribosome under zinclimiting conditions in Bacillus subtilis. Mol Microbiol 63:294-307. http://dx.doi.org/10.1111/j.1365-2958.2006.05513.x.
77. Gabriel SE, Helmann JD. 2009. Contributions of Zur-controlled ribosomal proteins to growth under zinc starvation conditions. J Bacteriol 191:6116-6122. http://dx.doi.org/10.1128/JB.00802-09.
78. Schmalisch M, Langbein I, Stülke J. 2002. The general stress protein Ctc of Bacillus subtilis is a ribosomal protein. J Mol Microbiol Biotechnol 4:495-501.
79. Yano K, Wada T, Suzuki S, Tagami K, Matsumoto T, Shiwa Y, Ishige T, Kawaguchi Y, Masuda K, Akanuma G, Nanamiya H, Niki H, Yoshikawa H, Kawamura F. 2013. Multiple rRNA operons are essential for cell growth and sporulation as well as outgrowth in Bacillus subtilis. Microbiology 159:2225-2236. http://dx.doi.org/10.1099/mic.0.067025-0.
80. Britton RA, Wen T, Schaefer L, Pellegrini O, Uicker WC, Mathy N, Tobin C, Daou R, Szyk J, Condon C. 2007. Maturation of the 5= end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1. Mol Microbiol 63:127-138. http://dx.doi.org/10.1111/j.1365-2958.2006.05499.x.
81. Gilet L, DiChiara JM, Figaro S, Bechhofer DH, Condon C. 2015. Small stable RNA maturation and turnover in Bacillus subtilis. Mol Microbiol 95:270-282. http://dx.doi.org/10.1111/mmi.12863.
82. Wen T, Oussenko IA, Pellegrini O, Bechhofer DH, Condon C. 2005. Ribonuclease PH plays a major role in the exonucleolytic maturation of CCA-containing tRNA precursors in Bacillus subtilis. Nucleic Acids Res 33:3636-3643. http://dx.doi.org/10.1093/nar/gki675.
83. Hartmann RK, Gössringer M, Späth B, Fischer S, Marchfelder A. 2009. The making of tRNAs and more-RNase P and tRNase Z. Prog Mol Biol Transl Sci 85:319 -368. http://dx.doi.org/10.1016/S0079-6603(08)00808-8.
84. Bylund GO, Wipemo LC, Lundberg LA, Wikström PM. 1998. RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli. J Bacteriol 180:73-82.
85. Lövgren JM, Bylund GO, Srivastava MK, Lundberg LA, Persson OP, Wingsle G, Wikström PM. 2004. The PRC-barrel domain of the ribosome maturation protein RimM mediates binding to ribosomal protein S19 in the 30S ribosomal subunits.RNA 10:1798-1812. http://dx.doi.org/10.1261/rna.7720204.
86. Schaefer L, Uicker WC, Wicker-Planquart C, Foucher AE, Jault JM, Britton RA. 2006. Multiple GTPases participate in the assembly of the large ribosomal subunit in Bacillus subtilis. J Bacteriol 188:8252-8258. http://dx.doi.org/10.1128/JB.01213-06.
87. Britton RA. 2009. Role of GTPases in ribosome assembly. Annu Rev Microbiol 63:155-176. http://dx.doi.org/10.1146/annurev.micro.091208.073225.
88. Doerfel LK, Wohlgemuth I, Kothe C, Peske F, Urlaub H, Rodnina MV. 2013. EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339:85-88. http://dx.doi.org/10.1126/science.1229017.
89. Ude S, Lassak J, Starosta AL, Kraxenberger T, Wilson DN, Jung K. 2013. Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches. Science 339:82-85. http://dx.doi.org/10.1126/science.1228985.
90. You C, Lu H, Sekowska A, Fang G, Wang Y, Gilles AM, Danchin A. 2005. The two authentic methionine aminopeptidase genes are differentially expressed in Bacillus subtilis. BMC Microbiol 5:57. http://dx.doi.org/10.1186/1471-2180-5-57.
91. Karzai AW, Roche ED, Sauer RT. 2000. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat Struct Biol 7:449-455. http://dx.doi.org/10.1038/75843.
92. Wiegert T, Schumann W. 2001. SsrA-mediated tagging in Bacillus subtilis. J Bacteriol 183:3885-3889. http://dx.doi.org/10.1128/JB.183.13.3885-3889.2001.
93. Menez J, Buckingham RH, de Zamaroczy M, Campelli CK. 2002. Peptidyl-TRNA hydrolase in Bacillus subtilis, encoded by SpoVC, is essential to vegetative growth, whereas the homologous enzyme in Saccharomyces cerevisiae is dispensable. Mol Microbiol 45:123-129. http://dx.doi.org/10.1046/j.1365-2958.2002.02992.x.
94. Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR. 2012. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-Turns but not K-loops. RNA 18:759-770. http://dx.doi.org/10.1261/rna.031518.111.
95. Beckert B, Kedrov A, Sohmen D, Kempf G, Wild K, Sinning I, Stahlberg H, Wilson DN, Beckmann R. 2015. Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions. Nat Struct Mol Biol 22:767-773. http://dx.doi.org/10.1038/nsmb.3086.
96. Von Loeffelholz O, Knoops K, Ariosa A, Zhang X, Karuppasamy M, Huard K, Schoehn G, Berger I, Shan SO, Schaffitzel C. 2013. Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex. Nat Struct Mol Biol 20:604-610. http://dx.doi.org/10.1038/nsmb.2546.
97. Nakamura K, Yahagi S, Yamazaki T, Yamane K. 1999. Bacillus subtilis histone-like protein, HBsu, is an integral component of a SRP-like par-Ticle that can bind the Alu domain of small cytoplasmic RNA. J Biol Chem 274:13569-13576. http://dx.doi.org/10.1074/jbc.274.19.13569.
98. Nakamura K, Nishiguchi M, Honda K, Yamane K. 1994. The Bacillus subtilis SRP54 homologue, Ffh, has an intrinsic GTPase activity and forms a ribonucleoprotein complex with small cytoplasmic RNA in vivo. Biochem Biophys Res Commun 199:1394-1399. http://dx.doi.org/10.1006/bbrc.1994.1385.
99. Zanen G, Antelmann H, Meima R, Jongbloed JD, Kolkman M, Hecker M, van Dijl JM, Quax WJ. 2006. Proteomic dissection of potential signal recognition particle dependence in protein secretion by Bacillus subtilis. Proteomics 6:3636-3648. http://dx.doi.org/10.1002/pmic.200500560.
100. Müller JP, Bron S, Venema G, van Dijl JM. 2000. Chaperone-like activities of the CsaA protein of Bacillus subtilis. Microbiology 146:77- 88. http://dx.doi.org/10.1099/00221287-146-1-77.
101. Zimmer J, Nam Y, Rapoport TA. 2008. Structure of a complex of the ATPase SecA and the protein-Translocation channel. Nature 455:936- 943. http://dx.doi.org/10.1038/nature07335.
102. Van der Wolk J, Klose M, Breukink E, Demel RA, de Kruiff B, Freudl R, Driessen AJ. 1993. Characterization of a Bacillus subtilis SecA mutant protein deficient in translocation ATPase and release from the membrane. Mol Microbiol 8:31-42. http://dx.doi.org/10.1111/j.1365-2958.1993.tb01200.x.
103. Saller MJ, Fusetti F, Driessen AJ. 2009. Bacillus subtilis SpoIIIJ and YqjG function in membrane protein biogenesis. J Bacteriol 191:6749-6757. http://dx.doi.org/10.1128/JB.00853-09.
104. Tjalsma H, Bron S, van Dijl JM. 2003. Complementary impact of paralogous Oxa1-like proteins of Bacillus subtilis on post-Translocational stages in protein secretion. J Biol Chem 278:15622-15632. http://dx.doi.org/10.1074/jbc.M301205200.
105. Saller MJ, Otto A, Berrelkamp-Lahpor GA, Becher D, Hecker M, Driessen A. 2011. Bacillus subtilis YqjG is required for genetic competence development. Proteomics 11:270-282. http://dx.doi.org/10.1002/pmic.201000435.
106. Tjalsma H, Bolhuis A, van Roosmalen ML, Wiegert T, Schumann W, Broekhuizen CP, Quax WJ, Venema G, Bron S, van Dijl JM. 1998. Functional analysis of the secretory precursor processing machinery of Bacillus subtilis: identification of a eubacterial homolog of archeal and eukaryotic signal peptidases. Genes Dev 12:2318-2331. http://dx.doi.org/10.1101/gad.12.15.2318.
107. van Dijl JM, de Jong A, Vehmaanperä J, Venema G, Bron S. 1992. Signal peptidase I of Bacillus subtilis: patterns of conserved amino acids in prokaryotic and eukaryotic type I signal peptidases. EMBO J 11:2819- 2828.
108. Tjalsma H, Kontinen VP, Prágai Z, Wu H, Meima R, Venema G, Bron S, Sarvas M, van Dijl JM. 1999. The role of lipoprotein processing by signal peptidase II in the Gram-positive eubacterium Bacillus subtilis. Signal peptidase II is required for the efficient secretion of alpha-Amylase, a non-lipoprotein. J Biol Chem 274:1698-1707.
109. Okuda S, Tokuda H. 2011. Lipoprotein sorting in bacteria. Annu Rev Microbiol 65:239-259. http://dx.doi.org/10.1146/annurev-micro-090110-102859.
110. Leskelä S, Wahlstrüm E, Kontinen VP, Sarvas M. 1999. Lipid modification of prelipoproteins is dispensable for growth but essential for efficient protein secretion in Bacillus subtilis: characterization of the Lgt gene. Mol Microbiol 31:1075-1085. http://dx.doi.org/10.1046/j.1365-2958.1999.01247.x.
111. Kontinen VP, Sarvas M. 1993. The PrsA lipoprotein is essential for protein secretion in Bacillus subtilis and sets a limit for high-level secretion. Mol Microbiol 8:727-737. http://dx.doi.org/10.1111/j.1365-2958.1993.tb01616.x.
112. Hyyryläinen HL, Marciniak BC, Dahncke K, Pietiäinen M, Courtin P, Vitikainen M, Seppala R, Otto A, Becher D, Chapot-Chartier MP, Kuipers OP, Kontinen VP. 2010. Penicillin-binding protein folding is dependent on the PrsA peptidyl-prolyl cis-Trans isomerase in Bacillus subtilis. Mol Microbiol 77:108 -127. http://dx.doi.org/10.1111/j.1365-2958.2010.07188.x.
113. Tjalsma H, Antelmann H, Jongbloed JD, Braun PG, Darmon E, Dorenbos R, Dubois JY, Westers H, Zanen G, Quax WJ, Kuipers OP, Bron S, Hecker M, van Dijl JM. 2004. Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome. Microbiol Mol Biol Rev 68:207-233. http://dx.doi.org/10.1128/MMBR.68.2.207-233.2004.
114. Jongbloed JD, Grieger U, Antelmann H, Hecker M, Nijland R, Bron S, van Dijl JM. 2004. Two minimal Tat translocases in Bacillus. Mol Microbiol 54:1319-1325. http://dx.doi.org/10.1111/j.1365-2958.2004.04341.x.
115. Baptista C, Barreto HC, São-José C. 2013. High levels of DegU-P activate an ESAT-6-like secretion system in Bacillus subtilis. PLoS One 8:e67840. http://dx.doi.org/10.1371/journal.pone.0067840.
116. Hallamaa KM, Browning GF, Tang SL. 2006. Lipoprotein multigene families in Mycoplasma pneumoniae. J Bacteriol 188:5393-5399. http://dx.doi.org/10.1128/JB.01819-05.
117. Halbedel S, Hames C, Stülke J. 2007. Regulation of carbon metabolism in the mollicutes and its relation to virulence. J Mol Microbiol Biotechnol 12:147-154.
118. Lund PA. 2001. Microbial molecular chaperones. Adv Microb Physiol 44:93-140. http://dx.doi.org/10.1016/S0065-2911(01)44012-4.
119. Deuerling E, Bukau B. 2004. Chaperone-Assisted folding of newly synthesized proteins in the cytosol. Crit Rev Biochem Mol Biol 39:261-277. http://dx.doi.org/10.1080/10409230490892496.
120. Dalbey RE, Wang P, van Dijl JM. 2012. Membrane proteases in the bacterial protein secretion and quality control pathway. Microbiol Mol Biol Rev 76:311-330. http://dx.doi.org/10.1128/MMBR.05019-11.
121. Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM. 2013. Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins. Proteomics 13:3298-3308. http://dx.doi.org/10.1002/pmic.201300183.
122. Stülke J, Hillen W. 2000. Regulation of carbon catabolism in Bacillus species. Annu Rev Microbiol 54:849 - 880. http://dx.doi.org/10.1146/annurev.micro.54.1.849.
123. Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U. 2012. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 335:1099- 1103. http://dx.doi.org/10.1126/science.1206871.
124. Starai VJ, Escalante-Semerena JC. 2004. Acetyl-coenzyme A synthetase (AMP forming). Cell Mol Life Sci 61:2020-2030.
125. Rühl M, Le Coq D, Aymerich S, Sauer U. 2012. 13C flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen starving Bacillus subtilis. J Biol Chem 287:27959-27970. http://dx.doi.org/10.1074/jbc.M112.366492.
126. Winstedt L, von Wachenfeldt C. 2000. Terminal oxidases of Bacillus subtilis strain 168: one quinol oxidase, cytochrome aa3 or cytochrome bd, is required for aerobic growth. J Bacteriol 182:6557-6564. http://dx.doi.org/10.1128/JB.182.23.6557-6564.2000.
127. Härtig E, Hartmann A, Schätzle M, Albertini AM, Jahn D. 2006. The Bacillus subtilis nrdEF genes, encoding a class Ib ribonucleotide reductase, are essential for aerobic and anaerobic growth. Appl Environ Microbiol 72:5260-5265. http://dx.doi.org/10.1128/AEM.00599-06.
128. Endo T, Uratani B, Freese E. 1983. Purine salvage pathways of Bacillus subtilis and effect of guanine on growth of GMP reductase mutants. J Bacteriol 155:169-179.
129. Rodionov DA, Mironov AA, Gelfand MS. 2002. Conservation of the biotin regulon and the BirA regulatory signal in eubacteria and archaea. Genome Res 12:1507-1516. http://dx.doi.org/10.1101/gr.314502.
130. Cronan JE Jr, Waldrop GL. 2002. Multi-subunit acetyl-CoA carboxylases. Prog Lipid Res 41:407- 435. http://dx.doi.org/10.1016/S0163-7827(02)00007-3.
131. Salzberg LI, Helmann JD. 2008. Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition. J Bacteriol 190:7797-7807. http://dx.doi.org/10.1128/JB.00720-08.
132. Block KF, Hammond MC, Breaker RR. 2010. Evidence for widespread gene control function by the ydaO riboswitch candidate. J Bacteriol 192: 3983-3989. http://dx.doi.org/10.1128/JB.00450-10.
133. Meeske AJ, Rodrigues CD, Brady J, Lim HC, Bernhardt TG, Rudner DZ. 2016. High-Throughput genetic screens identify a large and diverse collection of new sporulation genes in Bacillus subtilis. PLoS Biol 14: E1002341. http://dx.doi.org/10.1371/journal.pbio.1002341.
134. Eitinger T, Rodionov DA, Grote M, Schneider E. 2011. Canonical and ECF-Type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev 35:3- 67. http://dx.doi.org/10.1111/j.1574-6976.2010.00230.x.
135. Slotboom DJ. 2014. Structural and mechanistic insights into prokaryotic energy-coupling factor transporters. Nat Rev Microbiol 12:79-87. http://dx.doi.org/10.1038/nrmicro3175.
136. Ollinger J, Song KB, Antelmann H, Hecker M, Helmann JD. 2006. Role of the Fur regulon in iron transport in Bacillus subtilis. J Bacteriol 188:3664-3673. http://dx.doi.org/10.1128/JB.188.10.3664-3673.2006.
137. Miethke M, Monteferrante CG, Marahiel MA, van Dijl JM. 2013. The Bacillus subtilis EfeUOB transporter is essential for high-Affinity acquisition of ferrous and ferric iron. Biochim Biophys Acta 1833:2267-2278. http://dx.doi.org/10.1016/j.bbamcr.2013.05.027.
138. Kajiyama Y, Otagiri M, Sekiguchi J, Kosono S, Kudo T. 2007. Complex formation by the mrpABCDEFG gene products, which constitute a principal Na-/H-Antiporter in Bacillus subtilis. J Bacteriol 189:7511-7514. http://dx.doi.org/10.1128/JB.00968-07.
139. Dos Santos P. 2014. Fe-S assembly in Gram-positive bacteria, p 347-366. In Rouault TA (ed), Iron-sulfur clusters in chemistry and biology. De Gruyter, Berlin, Germany.
140. Mouilleron S, Badet-Denizot MA, Badet B, Golinelli-Pimpaneau B. 2011. Dynamics of glucosamine-6-phosphate synthase catalysis. Arch Biochem Biophys 505:1-12. http://dx.doi.org/10.1016/j.abb.2010.08.008.
141. Scheffers DJ, Tol MB. 2015. LipidII: just another brick in the wall? PLoS Pathog 11:e1005213. http://dx.doi.org/10.1371/journal.ppat.1005213.
142. Meeske AJ, Sham LT, Kimsey H, Koo BM, Gross CA, Bernhardt TG, Rudner DZ. 2015. MurJ and a novel lipid II flippase are required for cell wall biogenesis in Bacillus subtilis. Proc Natl Acad Sci U S A 112:6437- 6442. http://dx.doi.org/10.1073/pnas.1504967112.
143. Kawai Y, Daniel RA, Errington J. 2009. Regulation of cell wall morphogenesis in Bacillus subtilis by recruitment of PBP1 to the MreB helix. Mol Microbiol 71:1131-1144. http://dx.doi.org/10.1111/j.1365-2958.2009.06601.x.
144. Daniel RA, Harry EJ, Errington J. 2000. Role of penicillin-binding protein PBP 2B in assembly and functioning of the division machinery in Bacillus subtilis. Mol Microbiol 35:299-311. http://dx.doi.org/10.1046/j.1365-2958.2000.01724.x.
145. Wei Y, Havasy T, McPherson DC, Popham DL. 2003. Rod shape determination by the Bacillus subtilis class B penicillin-binding proteins encoded by pbpA and pbpH. J Bacteriol 185:4717-4726. http://dx.doi.org/10.1128/JB.185.16.4717-4726.2003.
146. Vollmer W. 2012. Bacterial growth does require peptidoglycan hydrolases. Mol Microbiol 86:1031-1035. http://dx.doi.org/10.1111/mmi.12059.
147. Ohnishi R, Ishikawa S, Sekiguchi J. 1999. Peptidoglycan hydrolase LytF plays a role in cell separation with CwlF during vegetative growth of Bacillus subtilis. J Bacteriol 181:3178-3184.
148. Hashimoto M, Ooiwa S, Sekiguchi J. 2012. Synthetic lethality of the lytE cwlO genotype in Bacillus subtilis is caused by lack of D, L-endopeptidase activity at the lateral cell wall. J Bacteriol 194:796-803. http://dx.doi.org/10.1128/JB.05569-11.
149. Dominguez-Cuevas P, Porcelli I, Daniel RA, Errington J. 2013. Differentiated roles for MreB-Actin isologues and autolytic enzymes in Bacillus subtilis morphogenesis. Mol Microbiol 89:1084-1098. http://dx.doi.org/10.1111/mmi.12335.
150. Brown S, Santa Maria JP, Walker S. 2013. Wall teichoic acids of grampositive bacteria. Annu Rev Microbiol 67:313-336. http://dx.doi.org/10.1146/annurev-micro-092412-155620.
151. Matsuoka S, Chiba M, Tanimura Y, Hashimoto M, Hara H, Matsumoto K. 2011. Abnormal morphology of Bacillus subtilis ugtP mutant cells lacking glucolipids. Genes Genet Syst 86:295-304. http://dx.doi.org/10.1266/ggs.86.295.
152. Matsuoka S, Hashimoto M, Kamiya Y, Miyazawa T, Ishikawa K, Hara H, Matsumoto K. 2011. The Bacillus subtilis essential gene dgkB is dispensable in mutants with defective lipoteichoic acid biosynthesis. Genes Genet Syst 86:365-376. http://dx.doi.org/10.1266/ggs.86.365.
153. Percy MG, Gründling A. 2014. Lipoteichoic acid synthesis and function in gram-positive bacteria. Annu Rev Microbiol 68:81-100. http://dx.doi.org/10.1146/annurev-micro-091213-112949.
154. Robson SA, Michie KA, Mackay JP, Harry E, King GF. 2002. The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components. Mol Microbiol 44:663-674. http://dx.doi.org/10.1046/j.1365-2958.2002.02920.x.
155. Szwedziak P, Löwe J. 2013. Do the divisome and elongasome share a common evolutionary past? Curr Opin Microbiol 16:745-751. http://dx.doi.org/10.1016/j.mib.2013.09.003.
156. Edwards DH, Errington J. 1997. The Bacillus subtilis DivIVA protein targets to the division septum and controls the site specificity of cell division. Mol Microbiol 24:905-915. http://dx.doi.org/10.1046/j.1365-2958.1997.3811764.x.
157. Bramkamp M, van Baarle S. 2009. Division site selection in rod-shaped bacteria. Curr Opin Microbiol 12:683-688. http://dx.doi.org/10.1016/j.mib.2009.10.002.
158. Biller SJ, Wayne KJ, Winkler ME, Burkholder WF. 2011. The putative hydrolase YycJ (WalJ) affects the coordination of cell division with DNA replication in Bacillus subtilis and may play a conserved role in cell wall metabolism. J Bacteriol 193:896 -908. http://dx.doi.org/10.1128/JB.00594-10.
159. Lluch-Senar M, Querol E, Piñol J. 2010. Cell division in a minimal bacterium in the absence of ftsZ. Mol Microbiol 78:278-289. http://dx.doi.org/10.1111/j.1365-2958.2010.07306.x.
160. Leaver M, Dominguez-Cuevas P, Coxhead JM, Daniel RA, Errington J. 2009. Life without a wall or division machine in Bacillus subtilis. Nature 457:849-853. http://dx.doi.org/10.1038/nature07742.
161. Mercier R, Kawai Y, Errington J. 2014. General principles for the formation and proliferation of a wall-free (L-form) state in bacteria. eLife 3:e04629. http://dx.doi.org/10.7554/eLife.04629.
162. Bisicchia P, Noone D, Lioliou E, Howell A, Quigley S, Jensen T, Jarmer H, Devine KM. 2007. The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis. Mol Microbiol 65: 180-200. http://dx.doi.org/10.1111/j.1365-2958.2007.05782.x.
163. Dubrac S, Bisicchia P, Devine KM, Msadek T. 2008. A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway. Mol Microbiol 70:1307-1322. http://dx.doi.org/10.1111/j.1365-2958.2008.06483.x.
164. Luo Y, Helmann JD. 2012. Analysis of the role of Bacillus subtilis -M in lactam resistance reveals an essential role for c-di-AMP in peptidoglycan synthesis. Mol Microbiol 83:623-639. http://dx.doi.org/10.1111/j.1365-2958.2011.07953.x.
165. Commichau FM, Dickmanns A, Gundlach J, Ficner R, Stülke J. 2015. A jack of all trades: The multiple roles of the unique essential second messenger cyclic di-AMP. Mol Microbiol 97:189-204. http://dx.doi.org/10.1111/mmi.13026.
166. Gundlach J, Mehne FM, Herzberg C, Kampf J, Valerius O, Kaever V, Stülke J. 2015. An essential poison: synthesis and degradation of cyclic di-AMP in Bacillus subtilis. J Bacteriol 197:3265-3274. http://dx.doi.org/10.1128/JB.00564-15.
167. Dempwolff F, Wischhusen HM, Specht M, Graumann PL. 2012. The deletion of bacterial dynamin and flotillin genes results in pleiotropic effects on cell division, cell growth, and in cell shape maintenance. BMC Microbiol 12:298. http://dx.doi.org/10.1186/1471-2180-12-298.
168. Rosenberg J, Dickmanns A, Neumann P, Gunka K, Arens J, Kaever V, Stülke J, Ficner R, Commichau FM. 2015. Structural and biochemical analysis of the essential diadenylate cyclase CdaA from Listeria monocytogenes. J Biol Chem 290:6596-6606. http://dx.doi.org/10.1074/jbc.M114.630418.
169. Bai Y, Yang J, Zarella TM, Zhang Y, Metzger DW, Bai G. 2014. Cyclic di-AMP impairs potassium uptake mediated by a cyclic di-AMP binding protein in Streptococcus pneumoniae. J Bacteriol 196:614-623. http://dx.doi.org/10.1128/JB.01041-13.
170. Opoku-Temeng C, Sintim HO. 2016. Potent inhibition of cyclic diadenylate monophosphate cyclase by the antiparasite drug, suramin. Chem Commun (Camb) 52:3754-3757. http://dx.doi.org/10.1039/C5CC10446G.
171. Stacy R, Anderson WF, Myler PJ. 2015. Structural genomics support for infectious disease drug design. ACS Infect Dis 1:127-129. http://dx.doi.org/10.1021/id500048p.
172. Rahmer R, Heravi KM, Altenbuchner J. 2015. Construction of a supercompetent Bacillus subtilis 168 using the pmtlA-comKS inducible cassette. Front Microbiol 6:1431. http://dx.doi.org/10.3389/fmicb.2015.01431.
173. Kumpfmüller J, Kabisch J, Schweder T. 2013. An optimized technique for rapid genome modifications of Bacillus subtilis. J Microbiol Methods 95:350-352. http://dx.doi.org/10.1016/j.mimet.2013.10.003.
174. Morimoto T, Ara K, Ozaki K, Ogasawara N. 2009. A new simple method to introduce marker-free deletions in the Bacillus subtilis ge-nome. Genes Genet Syst 84:315-318. http://dx.doi.org/10.1266/ggs.84.315.
175. Fabret C, Ehrlich SD, Noirot P. 2002. A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol Microbiol 46:25- 36. http://dx.doi.org/10.1046/j.1365-2958.2002.03140.x.
176. Gibson DG, Young L, Chuang RY, 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.
177. de Kok S, Stanton LH, Slaby T, Durot M, Holmes VF, Patel KG, Platt D, Shapland EB, Serber Z, Dean J, Newman JD, Chandran SS. 2014. Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth Biol 3:97-106. http://dx.doi.org/10.1021/sb4001992.