The Blueprint of a Minimal Cell: MiniBacillus.
Bacillus subtilis is one of the best-studied organisms. Due to the broad knowledge and annotation and the well-developed genetic system, this bacterium is an excellent starting point for genome minimization with the aim of constructing a minimal cell. We have analyzed the genome of B. subtilis and selected all genes that are required to allow life in complex medium at 37°C. This selection is based on the known information on essential genes and functions as well as on gene and protein expression data and gene conservation. The list presented here includes 523 and 119 genes coding for proteins and RNAs, respectively. These proteins and RNAs are required for the basic functions of life in information processing (replication and chromosome maintenance, transcription, translation, protein folding, and secretion), metabolism, cell division, and the integrity of the minimal cell. The completeness of the selected metabolic pathways, reactions, and enzymes was verified by the development of a model of metabolism of the minimal cell. A comparison of the MiniBacillus genome to the recently reported designed minimal genome of Mycoplasma mycoides JCVI-syn3.0 indicates excellent agreement in the information-processing pathways, whereas each species has a metabolism that reflects specific evolution and adaptation. The blueprint of MiniBacillus presented here serves as the starting point for a successive reduction of the B. subtilis genome.
Department of General Microbiology, Institute for Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
Daniel R
DR
Reuß
Department of General Microbiology, Institute for Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
Fabian M
FM
Commichau
Department of General Microbiology, Institute for Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
Jan
J
Gundlach
Department of General Microbiology, Institute for Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany.
Bingyao
B
Zhu
Department of General Microbiology, Institute for Microbiology and Genetics, Georg August University Göttingen, Göttingen, Germany jstuelk@gwdg.de.
Jörg
J
Stülke
Science. 2009 Nov 27;326(5957):1268-71
19965477
J Bacteriol. 2003 Aug;185(16):4717-26
12896990
J Cell Biol. 2015 Aug 31;210(5):687-90
26323686
Nucleic Acids Res. 2013 Jan 7;41(1):687-99
23109554
J Biol Chem. 2013 Jan 18;288(3):2004-17
23192352
Nat Struct Mol Biol. 2013 May;20(5):604-10
23563142
Cell. 2016 Jun 2;165(6):1493-506
27238023
Microbiol Mol Biol Rev. 2012 Jun;76(2):311-30
22688815
J Bacteriol. 2010 Aug;192(15):3983-9
20511502
Science. 2013 Jan 4;339(6115):82-5
23239623
RNA. 2004 Nov;10(11):1798-812
15496525
Mol Biol Evol. 2003 Dec;20(12):2076-90
12949151
Science. 2012 Mar 2;335(6072):1103-6
22383849
Mol Microbiol. 2013 Sep;89(6):1084-98
23869552
J Biosci Bioeng. 2013 Jul;116(1):52-8
23477741
Curr Biol. 2014 Feb 3;24(3):287-92
24440393
Mol Microbiol. 2000 Jan;35(2):299-311
10652091
Mol Microbiol. 1997 Aug;25(4):741-56
9379903
DNA Res. 2008 Apr 30;15(2):73-81
18334513
Curr Opin Microbiol. 2009 Dec;12(6):683-8
19884039
Microbiology. 2015 Oct;161(10):1942-9
26238998
Mol Microbiol. 1993 May;8(4):727-37
8332065
Annu Rev Microbiol. 2011;65:239-59
21663440
Mol Syst Biol. 2015 Jan 21;11(1):780
25609650
ACS Infect Dis. 2015 Mar 13;1(3):127-129
25984568
Mol Microbiol. 2012 Dec;86(5):1031-5
23066944
Mol Cell. 2015 Jan 22;57(2):290-303
25557547
Proteomics. 2011 Jan;11(2):270-82
21204254
Biochem Biophys Res Commun. 1995 Feb 6;207(1):250-7
7531971
Genes Genet Syst. 2009 Aug;84(4):315-8
20057169
J Mol Microbiol Biotechnol. 2007;12(1-2):147-54
17183222
Nature. 2008 Oct 16;455(7215):936-43
18923516
Biotechnol J. 2015 Feb;10(2):290-301
25139579
J Bacteriol. 2007 Jan;189(2):591-602
17114254
Nature. 2009 Feb 12;457(7231):849-53
19212404
Biochem Cell Biol. 1999;77(4):343-7
10546897
Arch Biochem Biophys. 2011 Jan 1;505(1):1-12
20709015
Mol Syst Biol. 2011 Jul 19;7:511
21772259
Microbiology. 2013 Nov;159(Pt 11):2225-36
23970567
Microbiology. 2005 Nov;151(Pt 11):3729-37
16272394
Science. 2012 Mar 2;335(6072):1099-103
22383848
J Bacteriol. 1993 Feb;175(3):647-54
8423140
Mol Microbiol. 1997 Jun;24(5):905-15
9219999
Mol Microbiol. 2015 Jul;97(2):189-204
25869574
Chem Commun (Camb). 2016 Mar 7;52(19):3754-7
26824279
RNA. 2012 Apr;18(4):759-70
22355167
J Bacteriol. 2011 Mar;193(6):1334-40
21239579
J Bacteriol. 2000 Dec;182(23):6557-64
11073895
J Bacteriol. 2012 Oct;194(19):5162-70
22797751
Mol Microbiol. 1999 Feb;31(4):1075-85
10096076
Annu Rev Microbiol. 2000;54:849-80
11018147
Curr Opin Microbiol. 2013 Dec;16(6):745-51
24094808
Genes Genet Syst. 2011;86(5):295-304
22362028
Mol Microbiol. 2011 Oct;82(2):434-46
21895792
Mol Microbiol. 2007 Jan;63(1):294-307
17163968
J Microbiol Methods. 2013 Dec;95(3):350-2
24140578
Mol Microbiol. 2004 Dec;54(5):1319-25
15554971
J Biol Chem. 2003 May 2;278(18):15622-32
12586834
J Bacteriol. 1998 Jan;180(1):73-82
9422595
Nature. 2001 Jan 18;409(6818):387-90
11201752
Annu Rev Biochem. 2014;83:615-40
24606140
Proc Natl Acad Sci U S A. 2015 May 19;112(20):6437-42
25918422
Genes Dev. 1998 Aug 1;12(15):2318-31
9694797
Nat Rev Genet. 2013 Mar;14(3):191-203
23400100
Mol Cell Proteomics. 2014 Apr;13(4):1008-19
24696501
J Mol Microbiol Biotechnol. 2002 Sep;4(5):495-501
12432960
J Bacteriol. 2013 May;195(10):2340-8
23504012
Science. 2016 Mar 25;351(6280):aad6253
27013737
Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2646-51
20133795
J Bacteriol. 2012 Nov;194(22):6282-91
23002217
J Bacteriol. 1999 May;181(10):3178-84
10322020
Science. 2004 Sep 3;305(5689):1474-6
15353806
Nucleic Acids Res. 2016 Jan 4;44(D1):D654-62
26433225
Mol Biosyst. 2013 Jun;9(6):1068-75
23420519
PLoS One. 2013 Jul 04;8(7):e67840
23861817
PLoS Pathog. 2015 Dec 17;11(12):e1005213
26679002
Mol Cell Proteomics. 2010 Jun;9(6):1228-42
20097688
Methods Mol Biol. 2008;416:279-93
18392974
FEMS Microbiol Rev. 2011 Jan;35(1):3-67
20497229
Mol Microbiol. 2012 Feb;83(3):623-39
22211522
Life (Basel). 2014 Dec 11;4(4):915-28
25513760
Prog Mol Biol Transl Sci. 2009;85:319-68
19215776
J Bacteriol. 2009 Oct;191(19):6116-22
19648245
J Bacteriol. 2011 Jun;193(12):3090-9
21515770
Mol Microbiol. 2009 Mar;71(5):1131-44
19192185
Mol Cell Proteomics. 2014 Sep;13(9):2260-76
24878497
Mol Microbiol. 2008 Dec;70(6):1307-22
19019149
Genome Res. 2002 Oct;12(10):1507-16
12368242
Mol Microbiol. 2002 Oct;46(1):25-36
12366828
J Bacteriol. 2011 Feb;193(4):896-908
21169496
Biochim Biophys Acta. 2013 Oct;1833(10):2267-78
23764491
J Biol Chem. 1999 May 7;274(19):13569-76
10224127
Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):E4601-10
24218584
Nat Struct Mol Biol. 2015 Oct;22(10):767-73
26344568
J Bacteriol. 2006 May;188(10):3664-73
16672620
BMC Microbiol. 2012 Dec 19;12:298
23249255
Science. 2009 Nov 27;326(5957):1235-40
19965468
J Bacteriol. 2009 Nov;191(21):6749-57
19717609
Microbiol Mol Biol Rev. 2004 Jun;68(2):207-33
15187182
Nat Microbiol. 2016 Jan 11;1:15007
27571753
Science. 2006 May 19;312(5776):1044-6
16645050
Cell Mol Life Sci. 2004 Aug;61(16):2020-30
15316652
J Bacteriol. 2007 Oct;189(20):7511-4
17693497
J Biol Chem. 2012 Aug 10;287(33):27959-70
22740702
Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):425-30
16407165
Nat Rev Microbiol. 2014 Feb;12 (2):79-87
24362466
Annu Rev Microbiol. 2014;68:81-100
24819367
Genes Genet Syst. 2011;86(6):365-76
22451476
Mol Microbiol. 2002 Jul;45(1):123-9
12100553
Microbiology. 2000 Jan;146 ( Pt 1):77-88
10658654
Biochem Biophys Res Commun. 1994 Mar 30;199(3):1394-9
7511896
Adv Microb Physiol. 2001;44:93-140
11407116
Microbiology. 2006 Oct;152(Pt 10):2895-907
17005971
J Bacteriol. 1983 Jul;155(1):169-79
6408059
Annu Rev Microbiol. 2009;63:155-76
19575570
Mol Microbiol. 2012 Jun;84(6):1005-17
22568516
Nucleic Acids Res. 2014 Apr;42(8):5151-63
24520113
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4678-83
12682299
Mol Microbiol. 1993 Apr;8(1):31-42
8497195
Nucleic Acids Res. 2009 Jul;37(12):4157-69
19433509
Nucleic Acids Res. 2013 May 1;41(10):5382-99
23563150
Microbiology. 2014 Nov;160(Pt 11):2341-51
25092907
Mol Microbiol. 2015 Jan;95(2):270-82
25402410
PLoS Biol. 2016 Jan 06;14(1):e1002341
26735940
Science. 2010 Jul 2;329(5987):52-6
20488990
Mol Cell. 2010 Jan 29;37(2):273-81
20122408
Microbiol Mol Biol Rev. 2014 Sep;78(3):487-509
25184563
Mol Microbiol. 2007 Jan;63(1):127-38
17229210
J Bacteriol. 2013 Feb;195(3):534-44
23175651
J Bacteriol. 2006 Dec;188(23):8252-8
16997968
BMC Microbiol. 2005 Oct 05;5:57
16207374
J Bacteriol. 1999 Oct;181(19):6053-62
10498718
J Bacteriol. 2014 Feb;196(3):614-23
24272783
Science. 2009 Nov 27;326(5957):1263-8
19965476
Mol Microbiol. 1997 Mar;23(6):1169-79
9106208
J Bacteriol. 2001 Jul;183(13):3885-9
11395451
Mol Cell Proteomics. 2009 Jun;8(6):1350-60
19193632
Nucleic Acids Res. 2005 Jun 27;33(11):3636-43
15983136
Environ Microbiol. 2012 Jun;14(6):1444-53
22429517
J Bacteriol. 2006 Aug;188(15):5393-9
16855228
Biochim Biophys Acta. 1998 Oct 1;1400(1-3):29-43
9748489
Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):11819-26
9342321
J Bacteriol. 2007 Dec;189(23):8575-83
17905985
Prog Lipid Res. 2002 Sep;41(5):407-35
12121720
Nat Methods. 2009 May;6(5):343-5
19363495
Elife. 2014 Oct 30;3:null
25358088
Proteomics. 2013 Nov;13(22):3298-308
24115457
J Biol Chem. 1999 Jan 15;274(3):1698-707
9880550
Mol Microbiol. 2010 Jul 1;77(1):108-27
20487272
Annu Rev Microbiol. 2013;67:313-36
24024634
EMBO J. 1992 Aug;11(8):2819-28
1639057
Front Microbiol. 2015 Dec 21;6:1431
26732353
J Bacteriol. 2015 Oct;197(20):3265-74
26240071
J Bacteriol. 2004 Dec;186(23):7936-43
15547265
Proteomics. 2004 Oct;4(10):2849-76
15378759
J Biol Chem. 2005 Apr 1;280(13):13105-13
15657033
J Bacteriol. 2008 Dec;190(23):7797-807
18820022
J Bacteriol. 2012 Feb;194(4):796-803
22139507
Proteomics. 2006 Jun;6(12):3636-48
16705751
Mol Syst Biol. 2012 Feb 28;8:571
22373819
Nat Struct Biol. 2000 Jun;7(6):449-55
10881189
J Biol Chem. 2016 Jan 15;291(3):1064-75
26546673
J Bacteriol. 2011 Oct;193(19):5431-41
21803996
Crit Rev Biochem Mol Biol. 2004 Sep-Dec;39(5-6):261-77
15763705
Mol Microbiol. 2010 Oct;78(2):278-89
20735775
J Biol Chem. 2015 Mar 6;290(10):6596-606
25605729
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1235-8
22102036
Mol Microbiol. 2002 May;44(3):663-74
11994149
Science. 2013 Jan 4;339(6115):85-8
23239624
Appl Environ Microbiol. 2006 Aug;72(8):5260-5
16885274
PLoS Genet. 2014 May 08;10(5):e1004363
24809820
J Bacteriol. 2015 May;197(9):1624-31
25733610
Mol Microbiol. 2009 Nov;74(4):790-809
19788545
Nucleic Acids Res. 2014 Aug;42(14):e111
24914053
ACS Synth Biol. 2014 Feb 21;3(2):97-106
24932563
Mol Microbiol. 2007 Jul;65(1):180-200
17581128