Revised genetic map of Bacillus subtilis 168

Revised genetic map of Bacillus subtilis 168

MicrobiologyReviews32 (1985) 101-134 Published by Elsevier 101 FEMS FER 00006 Revised genetic map of Bacillus subtilis 168 (Chromosome; transposon...

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MicrobiologyReviews32 (1985) 101-134 Published by Elsevier

101

FEMS

FER 00006

Revised genetic map of Bacillus subtilis 168 (Chromosome; transposon mutagenesis; integrative mapping)

Daniel R. Zeigler * and Donald H. Dean Bacillus GeneticStock Center, Departmentof Microbiology, The Ohio State University, 484 W. 12thAvenue, Columbus, OH 43210, U.S.A.

Received8 March1985 Accepted17 April 1985

1. INTRODUCTION

2. ADVANCES IN GENETIC TECHNIQUES

During recent years, knowledge of the genetics of Bacillus subtilis has grown at an ever-increasing pace. The research leading to this growth has been directed toward several goals: the desire to compare the most thoroughly studied bacterium, the Gram-negative Escherichia coli, with a Gram-positive counterpart; the aim to explore sporulation and germination as simple model systems for the study of cellular development; and the wish to utilize the bacilli, for which a well-developed fermentation technology already exists, for the purposes of biotechnology. This research has generated an immense volume of data concerning the function and relative position of hundreds of genes located on the B. subtilis chromosome, data which in turn have fueled further research efforts. In the hope of facilitating continued growth in Bacillus research, a revised genetic map of B. subtilis 168 is presented here, accompanied by an updated listing of the genes characterized for this organism.

Two recently developed techniques, which link traditional genetic mapping with the powerful tools of molecular genetics, have found far-ranging applications during this period of growth. Using insertional mutagenesis, any mapped gene can, in principle, be cloned and its regulation can be studied. Using integrative vectors, any cloned gene can be mapped.

* Correspondence should b¢ addressed to: D.R. Zeigler,Department of Genetics,The Ohio State University,1735 Neff Avenue,Columbus,OH 43210, U.S.A.

2.1. Transposon mutagenesis

The availability of transposable dements in B. subtilis is leading to powerful new techniques for

genetic mapping, gene fusion, and gene cloning. The Streptococcus faecalis transtx)son, Tn917, has been introduced into B. subtilis and has been shown to function normally in this host [1]. Tn917

confers inducible macrolide, lincosamide, and streptogramin B (MLS) resistance. Youngman and colleagues have isolated a fragment of T n 9 1 7 from a Streptococcus plasmid and have ligated it to B. subtilis plasmid vectors containing the temperature-sensitive pE194 replication functions to produce 'a series of transposon vectors [1,2]. When a host containing one of these vectors is grown at high temperature under selection for MLS-resistance, mutants are obtained which possess Tn917 insertions in nonessential chromosomal DNA se-

0168-6445/85/$03.30 © 1985 Federationof EuropeanMicrobiologicalSocieties

102 quences. The site of the insertion can be easily mapped using the Dedonder kit of strains [3]. Tn917 appears to be generally useful for random mutagenesis of the chromosome, although an insertional hot spot exists in the gltA gene [1]. It is anticipated that insertion mutations will facilitate the mapping of genes that otherwise lack easily selectable alleles. Once an insertion is obtained in a target gene, the transposon may be replaced by modified transposons to facilitate gene cloning or studies of gene expression. One such modified transposon contains a pBR322 replicon with the ampicillin resistance gene (which is not expressed in B. subtilis) and a chloramphenicol resistance gene of Grampositive origin, all inserted into the center of Tn 917 [2]. This modified transposon, when introduced into the insertion mutant by transformation, generates a chloramphenicol-resistant transformant by replacing Tn917 [2]. One may then clone sequences adjacent to the insertion by digesting the D N A with any appropriate restriction enzyme, circularizing the fragments with DNA ligase, and introducing them into competent E. coli by transformation. Ampicillin-resistant clones possess hybrid plasmids containing B. subtilis chromosomal DNA. In order to study regulation of target genes, insertions are instead replaced by modified transposons containing a promoterless lac gene from E. coli and the selectable chloramphenicol resistance gene. Replacement generates gene fusions, placing the lacZ gene under the control of regulatory elements of the target gene. The product of the lacZ gene, fl-galactosidase, can be quantitated easily in its new host (P. Youngman, J. Perkins and Kathleen Sandman, Genetics and Biotechnology of Bacilli, Academic Press, New York, in press).

2.2. Integrative mapping A plasmid carrying chromosomal DNA in a recombination-proficient B. subtilis host cell can integrate by a Campbell-type mechanism into the host chromosome at a site homologous to the insert [4]. This phenomenon has been exploited as a means of genetically mapping cloned genes which possess no known mutant alleles. A gene of inter-

est is subcloned into an integrative vector, a plasmid that replicates only in E. coli but that possesses an antibiotic resistance marker selectable in B. subtilis. The plasmid, when introduced into competent B. subtilis cells by transformation, confers antibiotic resistance only by integrating into the chromosome. The resistance marker can be mapped by conventional techniques to reveal the chromosomal location of the cloned gene. This technique has been used to map a gene expressed during sporulation (spoVG) and genes encoding ribosomal RNA (rrnA), RNA polymerase o-factor (rpoD), and subtilisin (aprA) [4-7]. 3 Other applications for integrative vectors deserve mention. A deletion mutation can be introduced into the chromosomal copy of a cloned gene by constructing the deletion in vitro, subcloning the altered gene in an integrative vector, and transforming competent cells under selection for antibiotic resistance. In some fraction of the resistant clones, the deleted gene will have replaced the chromosomal copy [7]. Secondly, since integration of the vector at the site of a cloned fragment joins the vector to adjacent chromosomal sequences, these adjacent sequences can be easily cloned as well. Chromosomal DNA containing the integrated vector is digested with an appropriate restriction endonuclease, ligated, and introduced into competent E. coli. Resistant clones contain the vector with inserts of adjacent DNA [8]. These new fragments can in turn be used to isolate fragments adjacent to them. By repeated cycles of this process, a technique known as 'chromosome walking', an entire region of the chromosome can be isolated. Finally, integrative vectors can be used to determine whether a cloned gene is part of a larger transcriptional unit in vivo. If the insert does not contain at least one end of a transcriptional unit, it necessarily disrupts that unit upon integration and therefore abolishes gene expression. If the insert does contain sequences flanking either end of the unit, however, it can integrate within those sequences and leave the unit intact, permitting gene expression [91.

103 3. THE REVISED GENETIC MAP 3.1. Construction The revised edition of the B. subtilis 168 genetic map is presented in Fig. 1. It has been constructed after an exhaustive search for mapping data published during the period between January 1, 1960 and December 31, 1984. Only then were other editions of the map [10-12] consulted, in orderto check references and to include data cited only in those reviews. In a few cases, unpublished data received from members of the Bacillus genetic community have been used in constructing the map; these references are cited in the table of genes (Table 1). Map distances have been calculated from PBS1 and AR9 transduction data using Kemper's equations [13] following the method of Hermer and Hoch [101. Although a serious attempt has been made to reconcile all mapping data within the literature, some discrepancies exist between this map and others, both published and unpublished. It is hoped that these discrepancies will motivate careful experiments aimed to resolve them; if so, this edition of the map will have served its purpose. 3.2. Scale and origin Recent editions of the map have bee.n calibrated to a scale of 360 ° [10,11] or to summed recombination frequencies [12]. Acting upon the unanimous advice of the Advisory Committee of the Bacillus Genetic Stock Center, we have based the revised map on the more wieldy scale of 100 to bring it into conformity with the genetic map of E. coil [14]. It seems logical that the origin of replication, rather than an arbitrarily chosen auxotrophic marker, be defined as point 0/100 on the genetic map. Although the approximate map position of the replication origin (oriC) has been known for many years from density transfer analysis [15], the inability to isolate the origin in an autonomously replicating fragment [16] has prevented conventional genetic and biochemical analysis. Using pulse labeling of synchronized populations of cells, Seiki and colleagues have determined the replication order of restriction fragments in the origin region [17]. A very early replicating fragment, B7, has been cloned [16]. This fragment not only fails to replicate autono-

mously, but also suppresses the replication of vector plasmids [16] and phages [18] in both B. subtills and E. coil This phenotyp¢ is caused by the strong tandem promoters of the rrnO operon, which may adjoin oriC [19,20]. The entire promoter region has been sequenced, but it is not known whether sequences constituting oriC are included [18]. The first direct genetic mapping of fragment B7 has been reported recently by Lampe and Bott [21]. They have subcloned a smaller fragment of B7 and have mapped it by integration between gyrA and guaA. Ogasawara and colleagues have shown that guaA lies within an early replicating fragment located between rrnO and rrnA [22]. It has yet to be rigorously proved that fragment B7 in fact contains the replication origin. Unpublished data from other workers suggest that oriC may in fact lie somewhat closer to gyrA (K. B0tt, personal communication). Nevertheless, oriC has been provisionally assigned a position near rrnO, with the understanding that a slight realignment may be required when the origin has been more precisely located. 3.3. Nomenclature In general, the authors agree with Bachmann [14] that gene nomenclature should be conservative in order to maintain continuity within the literature, although we have tempered this aim with a desire to use current terminology when a consensus has bean reached among groups actively studying a gene that its nomenclature should be changed. Such changes are a logical necessity when mutations once believed to be allelic are shown to lie in different cistrons. The citF locus has been reported to code for the 3 polypeptide subunits of succinate dehydrogenase; the sdhABC nomenclature, proposed by Rutberg [23,24], has been adopted here. Likewise, 5 genes comprise argO, which was previously considered to be a single locus. These genes have been named according to their counterparts in E. coil, argABCDE [25]. Similar changes will be required for the multigene clusters spollA [9] and spoVA [26] and perhaps for other sporulation loci as well. The original terminology has been retained, however, until the alternatives are set forth in the research literature.

104 3.4. Other significant changes in the m a p

In all, there are nearly 450 genes on the revised map, an increase of more than 100 genes over the most recent edition [11]. Although most of these additions reflect new discoveries, a significant n u m b e r has been k n o w n for m a n y years, but has been overlooked in previous compilations. A few major errors in the previous m a p have been corrected; rodB, for example, should be at position 68, not at 36 (130 °) as previously published [11]. In m a n y regions of the chromosome, a more precise map order has been determined, as indicated on the m a p (Fig. 1) and in the table of genes (Table 1).

4. U S E O F T H E G E N E T A B L E S Table 1, the table of genes, and Table 2, a list of alternative gene names, should be used in conjunction with the revised genetic map. For each entry in the table of genes, the m a p position has been estimated to the nearest 1%. The precision of this estimate is conveyed by the letter which follows it. Genes denoted by ' A ' are often used as landmark genes in m a p p i n g experiments; they are reference points for nearly all genes in their region of the chromosome. The letter ' B ' indicates that the gene has been thoroughly m a p p e d and ordered with respect to neighboring genes. M a p positions followed by ' C ' are considered reasonably certain, but the order of the gene with respect to neighboring loci has not been determined. The letter ' D ' indicates that significant discrepancies or uncertainties concerning the m a p position of the gene exist in the literature, but that the gene is p r o b a b l y located near the position given. Finally, genes that have never been m a p p e d are identified by the letter ' U ' . In all cases, primary references should be consulted whenever possible. References listed within the gene table give the most important sources of primary data for each entry; superscripts denote which references report fine-structure mapping, cloning, or D N A sequencing of the gene. If a gene of interest is not listed in Table 1, then Table 2 should be consulted to determine if it has been included under an alternative name.

ACKNOWLEDGEMENTS T h e Bacillus Genetic Stock Center is supported by the National Science F o u n d a t i o n grant D E B 7809339 and by industrial sponsors. The authors wish to thank each of their colleagues who communicated data prior to publication; their names are listed in the footnote to Table 1. Detailed c o m m e n t s concerning the map and tables, by S. Zahler and K. Bott, are especially appreciated.

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114 [303] Henner, D. and Steinberg, W. (1979) Genetic location of the Bacillus subtilis sup3 suppressor mutation. J. Bacteriol. 139, 688-670. [304] Mellado, R.P., Vinuela, E. and Salas, M. (1976) Isolation of a strong suppressor of nonsense mutations in Bacillus subtilis. Eur. J. Biochem. 65, 213-233. [305] O'Sullivan. M. and Anagnostopoulos, C. (1982) Replication terminus of the Bacillus subtilis chromosome. J. Bacteriol. 151, 135-143. [3061 Weiss, A.S. and Wake, R.G. (1983) Restriction map of DNA spanning the replication terminus of the Bacillus subtilis chromosome. J. Mol. Biol. 171, 119-138. [3071 Weiss. A.S., Smith, M.T., lismaa, T.P. and Wake, R.G. (1983) Cloning DNA from the replication terminus of the chromosome. Gene 24, 83-91. [308] Monteiro, M.J., Sargent, M.G. and Piggot, P.J. (1984) Characterization of the replication terminus of the Bacillus subtilis chromosome. J. Gen. Microbiol. 130, 2403 - 2414. [309] Weiss, A.S. and Wake, R.G. (1984) Impediment to replication fork movement in the terminus region of the Bacillus subtilis chromosome. J. Mol. Biol. 179, 745-750. [3101 lismaa, T.P., Smith, M.T. and Wake, R.G. (1984) Physical map of the Bacillus subtilis replication terminus region: its confirmation, extension, and genetic orientation. Gene 32, 171-180. [3111 Williams, G. and Smith, I. (1979) Chromosomal mutations causing resistance to tetracycline in Bacillus subtilis. Mol. Gen. Genet. 177, 23-30. [312] Naumov. L.S., Prozorov, A.A., Sauchenko, G.V., Kalinina, N.A., Chestukhin, A.V., Shemyalcin, M.F. (1973) Location of mutation rec-342, reducing ATP-dependent deoxyribonuclease activity on the chromosome map of Bacillus subtilis. Genetika 9, 171-174. [3131 Buxton, R.S. (1976) Prophage mutation causing heat inducibility of defective Bacillus subtilis bacteriophage PBSX. J. Virol. 20, 22-28. [314] Neuhard, J., Price, A.R., Schack, L. and Thomassen, E. (1978) Two thymidylate synthetases in Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 75, 1194-1198. [315] Nomura, S., Yamane, K., Sasaki, T., Yamasaki, M., Tamura, G. and Maruo, B. (1978) Tunicaycin-resistant mutants and chromosomal locations of mutational sites in Bacillus subtilis. J. Bacteriol. 136, 818-821. [316] Callister, H. and Wake, R.F. (1981) Characterization and mapping of temperature-sensitive division initiation mutations of Bacillus subtilis. J. Bacteriol. 145, 1042-1051. [317] Copeland, J.C. and Marmur, J. (1968) Identification of conserved genetic functions in Bacillus by use of temperature-sensitive mutations. Bacteriol. Rev. 32, 302-312. [318] McDonald, W.C. (1969) Linkage of a temperature sensitive locus to the streptomycin region and its use in recombination studies with streptomycin mutants of Bacillus subtilis. Can. J. Microbiol. 15, 1287-1291. [319] Anagnostopoulos, C. and Crawford, I.P. (1967) Le groupe des grnes regissant la biosynthc~,e du tryptophane chez Bacillus subtilis. C.R. Acad. Sci. Ser. D. 265, 93-96.

[320] Carlton, B.C. and Whitt, D.D. (1969) The isolation and genetic characterization of mutants of the tryptophan system of Bacillus subtilis. Genetics 62, 445-460. [3211 Band, L., Shumotsu, H. and Henner, D.J. (1984) Nucleotide sequence of the Bacillus subtilis trpE and trpD genes. Gene 27, 55-65. [322] Trowsdale, J. and Anagnostopoulos, C. (1975) Evidence for the translocation of a chromosome segment in Bacillus subtilis strains carrying the trpE26 mutation. J. Bacteriol. 122, 886-898. [3231 Steinberg, W. (1974) Temperature-induced derepression of tryptophan biosynthesis in a tryptophanyi-transfer ribonucleic acid synthetase mutant of Bacillus subtilis. J. Bacteriol. 117, 1023-1034. [324] Wawrousek, E.F. and Hansen, J.N. (1983) Structure and organization of a cluster of six tRNA genes in the space between tandem ribosomal RNA gene sets in Bacillus subtilis. J. Biol. Chem. 250, 291-298. [325] Wawrousek, E.F., Narasimhan, N. and Hansen, J.N. (1984) 2 large clusters with 37 transfer RNA genes adjacent to ribosomal RNA gene sets in Bacillus subtilis, sequence and organization of trrnD and trrnE gene clusters. J. Biol. Chem. 259, 3694-3702. [326] Lindgren, V., Holmgren, E. and Rutberg, L. (1977) Bacillus subtilis mutant with temperature-sensitive net synthesis of phosphatidylethanolamine. J. Bacteriol. 132, 473-484. [327] Galizzi, A., Siccardi, A.G., Mazza, G., Canosi, U. and Polsinelli, M. (1976) A recombination test to classify mutants of Bacillus subtilis of identical phenotype. Genet. Res. 27, 47-58. [3281 Siegel, E.C. and Marmur, J. (1969) Temperature-sensitive induction of bacteriophage in Bacillus subtilis 168. J. Virol. 4, 610-618. [329] Canosi, U., Ferrari, F.A., Ferrari, E.U., Ma77a~ G. and Siccardi, A.G. (1978) PBSX induction in a temperaturesensitive mutant of Bacillus subtilis. J. Gen. Virol. 39, 81-90. [3301 Love, P.E. and Yasbin, R.E. (1984) Genetic characterization of the inducible SOS-like system of Bacillus subtilis. J. Bacteriol. 160, 910-920. [331] Champney, W.S. and Jensen, R.A. (1969) D-tyrosine as a metabolic inhibitor of Bacillus subtilis. J. Bacteriol. 98, 205-214. [3321 Vanrandem, J. and Venema, G. (1984) Direct plasmid transfer from replica-plated E. coil colonies to competent B. subtilis cells: identification of an E. coli carrying the hisH and tyrA genes of B. subtilis. Mol. Gen. G-enet. 195, 57-61. [3331 Tamanoi, F. and Okazaki, T. (1978) Uracil incorporation into nascent DNA of thymine-requiring mutant of Bacillus subtilis 168. Proc. Natl. Acad. Sci. U.S.A. 75, 2195-2199. [3341 Makino, F. and Munakata, N. (1977) Isolation and characterization of a Bacillus subtilis mutant with a defective N-glycosidase activity for uracil-containing deoxyribonucleic acid. J. Bacteriol. 131,438-445.

115 [335] Stephens, M.A., Lang, N., SandmAn, K. and Losick, R. (1984) A promoter whose utiliT~tion is temporally regulated during sporulation in Bacillus subtilis. J. Mol. Biol. 176, 333-348. [336] Cocito, C. (1979) Antibiotics of the Virginiamycin family, inhibitors which contain synergistic components. Microbiol. Rev. 43, 145-198. [337] Cocito, C. and Fraselle, G. (1973) The properties of Virginiamycin-resistant mutants of Bacillus subtilis. J. Gen. Mierobioi. 76, 115-125.

[338] Thurm, P. and Garro, A.J. (1975) Isolation and charaeterization of prophage mutants of the defective Bacillus subtilis bacteriophase PBSX. J. Virol. 16, 184-191. [339] Bernier, R., Jr., DrigueT., H. and Dcsronchas, M. (1983) Molecular cloning of a Bacillus subtilis xylanase gen¢ in Escherichia coll. Gene 26, 59-65. [340] Roncero, M. and Isabel, G. (1983) Genes controlling xylan utilization by Bacillus subtilis. J. Bacteriol. 156, 257-263.

~

/

_ _ - - - -

~

~41rR

norB

ootC rno-16 oroZ

,.r.

',to

out8

01r

glpT

~rlID

~

dM-8132 I G dim ~ N -- re¢ - - - ~ M I 526 rrnA iD

oei rrnO guaA

rWA

~DIF

--

rpsI

- - r~K

--

l

--

rplX rplV rps[ rpmD

~plE

l

- -

r p s H

crsE rpoC rpsG rpsL fun efg tuf rplC

rpoB

rplL

- -

1

1

--

1

1

l

----

l

1

- - ~WJ

-.

-

2

[9

17

16

15"

i4

13

I

I0

~

-

-

_

-

-

_

-

~

,

~

-

--

-

~

o

°

hsrR

hsrC

tsi

pigY SOp8

~uoB pur

fcuC

0o,--t

pho-I

cofA

hlrM

cam-2

fufB

ddl

~h mtlB

ksgO

i

1~4

50

29'

2B"

27'

26-

25"

24

Z3

22

21

20-

~

~

- -

--

li

P

miB

trp$

or~lABCDE orgF

metO

ospT

glyfl

red

gtoC

thlA

recH

40

39

38

37

36

35

34

32-

31.

30

phoS

-

~

/

/

-

/

-

~

-

- -

/

~

-------------___

rocA

sPo~n- E spcB poIC ch,

furR

divZ

dlvlVR

pyr rpsP

cysC

~trB tm~-12 P*g

p~A

i ~

ocIA IB f r u ~ A nP' _----1 R dope ~VF"

ipo~'r F

mete 0rg-342

pro(AB) -- ahrD

,kl ~pA

-

-

~

metA scoA

50

49-

48

47

46

45

44

43

4.2-

41

40-

SPB

-

PROPHAGE

~

--

--

--

- -

ott e - 3 T

drm

terC

gltA

Cit8

ruff

ttlyA

dnaA glnA

recE

outD

O~

J .Irn-8

8 A

J H

A

70

69

68

67.

65-

62.

~

,

~/~/

~

~

Fig. 1. The genetic map of Bacillus subtilis 168.

60

spo

m~

59

- - s#olVB ~ .~rC ~_~rvtA

~P

rib lyt

aroC

oro[ tp'A

dfrA

bfmB spoOA

t

7

~

~

58

5

52

6t

51

sP~ PROPHAGE

60-

50-

~

o~A t~

d~r - uvrll

sp4VlB

9~

~Tr8

~A

:2'**;.,

0¢f

~A

dno[ til

,poO

¢rsA

I~°

C

08

- -

~

$0¢0 corn-9

div~Z ksgO

"--"--'----,-- fib8 ms,n

bio

aro

:ii,

:~,~,

8O

79

78

i

76-

gSp-IO

¢),Sll

furor - - gerA - - spo ¢ ttG~'T'D

~vB

~o-Z " - - - - ' - - - ' - " " - aid ,rn8 trrn[ / oeCB thrA ~ s p r 8 - thrB 77~ ----'---------'--

75

74

73

72- ~

-----

70-~ J~

/I_----

~ f i b A

floB rno--~3

.re

tscC t$-341

hillA

pgk

.o* t:

tmo~P°~C

9G

89

88

87-

~

/

e~

frog-14 flaC glyC narA cfrA spoOF

- - rodC

socS

azp8 ----'------'--'---'- ahr8

95-

94.

hsr(

/

-- purA dnoC tpoCM

I00

"------------'-'- gyr8

~ecF

99. --------____ , . ~

98.

Io4

97. --------------- dna (tsA)

96.

hut

93. "--------------'----- IhiC

92"

91.

8685] ----____ --'"o,_,O"'II°"'*'~*ro°°"'*"°'

84

82-

80~81

90-

P

-,4

118 Table 1 Genes of Bacillus subtilis Gene symbol

Mnemonic

Map position a

Description and gene product

References ~'

abrA

antibiotic resistance

89 B

[27]

abrB

antibiotic resistance

1B

absC

antibiotic sensitivity

U

absD

antibiotic sensitivity

U

aceA

acetate

34 C

ac]"

acriflavine

63 B

Partial suppressor of spoO mutant phenotypes Partial suppressor of spoO mutant phenotypes; may be same as absA, absB, tolA and cpsX Partial suppressor of spoOA; ~-2 ~, #,-15 r, protease-, antibiotic ~ Partial suppressor of spoOA; ~ 2 ~, g,-15s, protease - , antibiotic s Pyruvate decarboxylase; suburtit E3 of pyruvate dehydrogenase/'branched 2-oxo acid dehydrogenas¢ complex; identical with bfmA, aceB acriflavine resistance (10/~g/ml) ATP-dependent DNase; mutation add5 (formerly recE5) leads to deficiency in recombination and repair Aminoethyl cysteine resistance (700 txg/ml); regulation of aspartokinase I I Aminoethyl cysteine resistance (700 ~tg/ml); structural gene aspartokinase II Antifolate resistance (100 t~g/ml metbotrexate) Arginine hydroxamate resistance; allele aut-1 is resistant only in the presence of ornithine Arginine hydroxamate resistance

add

U

aecA

aminoethyl cysteine

69 C

aecB

amincethyl cysteine

77 B

aft

antifolate

ahrA

arginine hydroxamate resistance

98 C

ahrB

90 B

aid

arginine hydroxamate resistance arginine hydroxamate arginine hydroxamate resistance alanine

75 A

alsA alsR

acetoin acetoin

70 B 87 C

atom

ammonia

68 D

amyE

amylase

7B

amyR

amylase

7B

aprA argABCDE argF argGH

alkafine proteas¢ arginine arginine arginine

ahrC ahrD

U

57 C 77 B

25 70 28 28

B B B B

Arginine hydroxamate resistance Arginine hydroxamate resistance in the presence of citrulline L-Aianine dehydrogenase; no growth on L-alanine as carbon source Acetolactate synthase Constitutive acetolactate synthase Glutamate requirement; marker may be spurious Amylase structural gene, ( + M) = Marburg-type amylase; ( + N) = Natto-type; (H) = hyperactivity Control of amylase synthesis, overproduction; alleles 1 and 21 are from B. subtilis 168; allele 2 is from B. subtilis hallo Subtilisin (alkafin¢ protease) Arginine requirement Arginine or citrulline requirement Arginine, ornithine or citrulline requirement

[27-29] [30,31] [30,31] [32,33]

[34] [35]

[361 [361 [371 [38]

[381 [391 [39] [401 1411

[411 [42] [43de,44,45 c 46de,47de,48]

[43de46 dc ]

[7de.49de ] [25d,50,51] [25d°50,51,52d ] [25.50,511

119 Table 1 (continued) Gene Mnemonic symbol

Map position"

Description and gene product

References b

arg-342

arginine

32 C

[53]

aroA

aromatic

71 B

aroB

aromatic

55 B

aroC

aromatic

55 B

aroD

aromatic

62 A

aroE

aromatic

54 B

aroF

aromatic

55 B

aroG

aromatic

71 A

aroH

aromatic

55 B

arol

aromatic

8A

aroJ

asaA

aromatic arsenate

U 62 B

asp B asp H asp T

aspartate aspartate aspanate

54 B 56 C 27 B

ath attck- 3 T

adenine-thiamine attachment

17 C 49 C

att ep- 105 art S P 0 2

attachment attachment

68 B 5B

dZC

azetidin carboxylic acid

azi azlA

azide azaleucine

83 C 68 B

az/B azlD azp B

azaleucine azaleucine azopyrimidine

65 C 69 B 90 B

b/mB

branched fatty acids

57 C

Arginine, omithine or citrulline requirement 3-Deoxy-o-arabinoheptalosonic 7-phosphate synthase; requires shikimic acid or phenylalanine, tyrosifie and tryptophan Dehydroquinate synthase; requires shikimic acid or phenylalanine, tyrosine and tryptophan Dehydroquinate dehydratase; requires shikimic acid or phenylalanine, tyrosine, and tryptophan Shikimate dehydrogenase; requires shikimic acid 3-Enolpyruvyl shikimate-5-phosphate synthase; requires phenylalanine, tyrosine and tryptophan Chorismate synthase; requires phenylalanine, tyrosine and tryptophan Chorisrnate mutase, isozyme 3 requires phenylalanine tyrosine and tryptophan Chorismate mutase, isozyme 1, 2 (from B. subtilis W23) requires phenylalanine, tyrosine and tryptophan Shikimate kinase; requires phenylalanine, tyrosine and tryptophan Requires tyrosine and phenylalanine Arsenate sensitive (1 raM) asaA2 is a large deletion Aspartate aminotransferase Constitutive aspartase Deficient in high affinity aspartate transport Adenine-thiamine requirement Integration site for ~3T; probably identical to att-SP# Integration site for 4,-105 and a-ll Integration site for SPO2; prophage responsible for the RecC phenotype Resistance to L-azetidin-2-carboxyfic acid (500 ttg/ml) Resistance to sodium azide 4-Azaleucine resistance (40 ag/ml); may be promoter of iivBC-leu operon 4-Azaleucine resistance (40 ~tg/ml) 4-Azaleucine resistance (40 ~tg/ml) Resistance to azopyrimidines (50/~g/ml hydtoxyphenylazouracil HPUra) Requires branched chain fatty acid or valine or isoleucine

8C

[54,551

[54- 56,57 d ]

[54,55,57d,58 d ]

[54,55,59]

[54-561

|54,55l 154,551 [54,551 [43d,46d,55]

[55,601 [61,62] [53,631 [64] [631 [651 [66,67~] [68,69]

[70-72] [731

[111 [74,75d,76]

[741 [A] [771 [32]

120 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

bioA bioB bio-112 but cafA cara-2

biotin biotin biotin bromouracil tolerance caffeine chloramphenicoi

71 B 71 B 71 B U 16 C 15 C

[78] [781 [781 [79] 180] [81]

catA

catabolite

26 B

cdd cer che

cytidine deaminase cerulenin chemotaxis

U U 39 C

cheR citB

chemotaxis citric acid cycle

55 C 43 A

citC

citric acid cycle

70 B

citG citK

citric acid cycle citric acid cycle

79 B 48 A

citL

citric acid cycle

34 C

corn-9

competence

75 C

corn-30

competence

U

corn-71

competence

57 C

com-104

competence

95 C

7-KAP:DAP aminotransferase Biotin synthetase Early defect in biotin synthesis 5-Bromouracil tolerance Caffeine resistance Chloramiphenicol resistance. probably altered permeability Hyperproduction of extracellular proteases; same as scoC, possibly same as hpr Deoxycytidine-cytidine deaminase Cerulenin resistance (40 p.g/mi) Chemotaxis, cluster of 32 linked mutations Chemotaxis Aconitate hydratase; autolytic. requires glutamate lsocitrate dehydrogenase; autolytic, requires glutamate Fumarate hydratase; autolytic a-Ketoglutarate dehydrogenase complex, enzyme E1 Lipoamide dehydrogenase; subunit E3 of both the a-ketoglutarate dehydrogenase, pyruvate dehydrogenase/branched 2-oxo acid dehydrogenase complexes Reduced DNA binding and transformation; normal transduction and protoplast transformation Reduced DNA binding and transformation; normal transduction and protoplast transformation Reduced DNA binding and transformation; normal transduction and protoplast transformation Reduced DNA binding and transformation; normal transduction and protoplast transformation Carbamoyl phosphate synthetase. arginine-regulated Carbamoyl phosphate synthetase. uracil-regulated Cytidine kinase Catabolite resistant sporulation Catabolite resistant sporulation Catabolite resistant sporulafion; smooth colony morphology on TBAB Catabolite resistant sporulation; resistance to several antibiotics during sporulation; part of rpo operon Catabolite resistant sporulation Cysteine sensitivity

cpa

28 C

cpu

28 C

crk crsB crsC crsD

18 C 59 C

crsE

3B

crsF css

U

1C

cysteine

34 C 2C

[82,83]

184,851 IB] 186al 1861 [87] 1871 [87,88a,89 a ] 187.90] 187,911

[921

1921

[921

[921

[25a,931 [25a,931 [84,851 [941 [941 [941

[94,95] [94I [96]

121 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

ctrA

cytidine

89 A

[97]

cyc cym cysA

cycloserine cyst¢ine-methionine cysteine

26 C 2C 2A

cysB cysC

cysteine cysteine

79 B 34 C

dal dapE dcd dck ddd

D-alanine diaminopimelate dCMP

12 A 35 C U U U

Requirement for cytidine in the absence of ammonium ion Cycloserine resistance Requirement of cysteine or methionine Serine transacetylase; cysteine requirement Cysteine requirement Cysteine, methionine, sulfite, or sulfide requirement D-Alanine racemase N-AcetyI-L-diaminopimilate deacylase dCMP dehydrogenase Deoxycytidine kinase Deoxycytidine diphosphate deaminase D-Alanine figase Confers kasugamycin or spectinomycin dependence on some resistant strains Dihydrofolate reductase, trimethoprim resistance (0.5 pg/ml) Excretion of inhibitor of sporulation exonuclease; mutants are phenotypically Spo + Temperature-sensitive cell division Temperature-sensitive cell division Minicell production Minicell production Minicell production Temperature-sensitive cell division S¢ptum initiation mutant DNA synthesis; ribonucleotide reduction DNA synthesis; initiation of chromosome replication DNA synthesis DNA synthesis; initiation of chromosome replication DNA synthesis; homologous to E. coli DNA pdmase DNA synthesis DNA synthesis DNA synthesis DNA synthesis DNA synthesis DNA elongation; cell filarnentation DNA synthesis; initiation of chromosome replication Requirement for dAdo or dGuo plus dCyd, suppressed by cdd, ddd. or cdg thy8 Deoxyriboaldolase; unable to use dcoxyribonucl¢otides for growth

ddl dep

dependence

12 C 3C

dfrA

dihydrofolate reductase

53 C

din

DNase inhibitor

MC

dwl divll dwlVA divlVB divlVC div V div-355 dnaA

division division division division division division division DNA

37 C 87 C 37 C 68 B 4C 75 C 1C 42 B

dnaB

DNA

69 C

dnaC dnaD

DNA DNA

98 B 55 C

dnaE

DNA

61 D

dnaG dnaH dnal dna(ts)A dna(ts)B dna-526 dna-8132

DNA DNA DNA DNA DNA DNA DNA

1C 0B 68 C 97 C 97 C 0C 0B

dns

deoxyribonuclcoside

dra

dcoxyfiboaldolase

U

95 C

[11 ] [96,98] [96] [42] [53,99] [91,97] [100] [101] [84,85] [84,85] [100] [102]

[103] [104]

[105] [105] [106[ [106] [105] [105] [107] [108-110] [108,110] [108,110,111] [ 108,111 ] [108,111,C ~] [108,110] [108,110] [108,110] [15,110] [15,110] [107] [11,112] [M]

[113]

122 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

drm

deoxyribomutase

49 C

[1131

durR ebr ecp

duramycin ethidium bromide

5C 90B 57 C

efg

elongation factor G

3B

estA estB fdp

esterase esterase fructose biphosphate

U 84 C

fibA

fiber

84C

fibB

fiber

74 C

flaA

flagella

84C

flaB flaC fnd-15 frag-14

flagella flagella fluoroindol fragment

/rag-33

fragment

83 C

fruA

fructose fructose

34 C 34 C 17C 78 C 3C

Phosphodeoxyribomutase; unable to use deoxyribonucleotides or ribonucleotides for growth Duramycin resistance Ethidium bromide resistance (10 ttg/mi) Resistance to 2-amino-5-ethoxycarbonyi pyrimidine-4(3H)-one (300-800/~g/ml) Elongation factor G; fusidic acid resistance Esterase A defect Esterase B defect Deficient in o-fructose-l,6-bisphosphate 1-phosphohydrolase; fails to grow on gluconeogenic carbon sources in the presence of the bypass mutation bfd Helical macrofiber production, transient division suppression Helical macrofiber production, persistent division suppression Defect in flageilar synthesis; group of 21 linked mutations, possibly including the hag locus Defect in flagellar synthesis Defect in flagellar synthesis Fluoroindol resistance (50/tg/mi) 2.05 kB Restriction fragment; contains post-exponential promoter 3.32 kb Restriction fragment; contains post-exponential promoter Fructose transport Fructose 1-phosphate kinase Fructokinase Regulation of fumarase Streptomycin resistance (100 ttg/ml); higher resistance in conjunction with rspL1 (475/tg/ml) and strR ( > 1 mg/ml) 5-Fluorouracil resistance (1/~g/ml) 5-Fluorouracil resistance (40 p,g/ml) in the presence of 40/tg/mi uracil 5-Fiuorouracil resistance (40/~g/ml) in the presence of 40/tg/ml uracil 5-Fluorouracil resistance (40/~g/ml) in the presence of 40/tg/ml uracil 5-Fiuorouracil resistance (40/~g/mi) in the presence of 40/tg/ml uracil Glutamine binding protein; common subunit to anthranilate synthetase and p-amino-benzoate synthetase Glucose dehydrogenase L-Glutamine-D- fructose-6-phosphate aminotransferase

fruB fruC furoR

fructose

fumarase

98 B

85 C 87 C 100 C 88 C

furA furB

fluorouracil fluorouracil

37 B 13 D

furC

fluorouracii

89 B

/urE

fluorouracil

89 B

furl:

fluorouracil

42 C

gat

glutamate anthranilate

2B

gdh

glucose dehydrogenase glucosamine

10 B U

gcaA

[A] [114] [1151 [116-118,119 c]

[12o] [12o] [121,122]

[1231 [1231 [1241

I124] [1241 [125] [126 d ] [126d ]

[127,128] [127,128] [127,128] [II] [129]

[1301 [651 [27] [27] [1311 [28,103,132,133] [134a,135] [1361

123 Table 1 (continued) Oene symbol

Mnemonic

Map position *

Description and gene product

References b

gerA

germination

79 B

[88a,137-139,D e ]

gerB gerC gerD gerE gerF gerH gerl gerJ

germination germination ges'mination germination germination germination germination germination

85 C 55 B 3C 69 B 83 C 68 C 83 C 55 B

gerM glnA

germination glutamine

68 C 43 B

glpD gipK gipP glpT

glycerol phosphate glycerol phosphate glycerol phosphate glycerol phosphate

23 B 23 B 23 B 6B

gltA

glutamate

46 A

gltB glyA glyB glyC grit gsp-lO

glutamate glycine glycine glycine glucanate

U 55 D 25 A 88 B 98 B 80 C

gtaA

glucoteichoic acid

85 B

gtaB gtaC

glucoteichoic acid glucoteichoic acid

85 B 24 B

guaA guaB gutA gutB gutR

guanine guanine glucitol glucitol glucitol

0A 17 B 16 C 16 C 16 C

gyrA

gyrase

99 B

gyrB

gyrase

99 B

hag

H antigen

84 C

hds

host DNA suppressor

hem/I

heine biosynthesis

Germination defective probably polycistronic Germination defective Germination defective Germination defective Germination defective Germination defective Germination defective Germination defective Germination defective, allelic to tzm; spores are heat sensitive Germination defective Glutamine synthetase; glutamine auxotroph, pleiotropically relieved of catabolite repression Glycerol-3-phosphate dehydrogenase Glycerol kinase Positive regulation ofglpD and glpK Fosfomycin resistance (200 #g/aft); glycerol phosphate transport defect Glutamate-2-ketoglutarate amino transfarase; glutamate or aspartate requirement Glutamate requirement Glycine requirement Glycine requirement Glycine requirement Unable to grow on glucanate Outgrowth defective, may belong to gerA locus Lacks U DP-glucose-poly-(glycerol phosphate)-glucosyltransferase Glucosylation of teichoic acid Giucosylation of teichoic acid lacks phosphoglucomutase 1MP dehydrogenase Guanine requirement D-Glucitol permease D-Glucitoi dehydrogenase Regulation of gtaA, gutB; constitutive mutation allows for growth on xylitol DNA gyrase, subunit A; naladixic acid resistance DNA gyrase, subunit B; novobiocin resistance Flagellar antigen, allele 1 = 168, allele 2 = W23, allele 3 - straight filament Extragenic suppressor of several DNA mutations; resistance to arylaxopyrimidines 8-Aminokvulinic acid synthetase; requires heine

2C

68 C

[137,138] [137.138] [137,1381 [137,1381 [137,1381

[140] [140[ [57d,137,141]

[El [142= 144,145d,146 ~]

[147] [147] [147,148] [149] [53,131]

[150] [151] [1521 [1531 [121,1221 [140,154] [ 155,156] [155,156] [155,1561 [27,28] [111 [157,1581 [157,158] [157,158] [21d,159] [159,Fd[ [124]

[160]

[161,162]

124 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

heraB hemC heroD heine hemF hemG hlsA

heme biosynthesis heme biosynthesis heme biosynthesis heme biosynthesis heme biosynthesis heme biosynthesis histidine

68 C 68 C 68 C 26 C 26 C 26 C 83 A 83 D

[ 162-164] [162 - 1641 [162,163] [164,165] [164,1651 [164,165] [97,153,166 a ] [167]

hisH

histidine

55 B

hom hsrB hsrC hsrE

homoserine restriction restriction restriction

77 B 98 C 18C 96 C

hsrM

restriction

16C

hts

H2S

hutC

histidine utilization

93 B

hutG

histidine utilization

93 B

hutH hurl hutP

histidine utilization histidine utilization histidine utilization

93 B 93 B 93 B

hutR

histidine utilization

93 B

hutU ifm ilvA

histidine utilization flagella isoleucine-valine

93 B 84 C 53 B

iloB ilvC

isoleucine-valine isoleucine-valine

68 B 68 B

ilvD iol iur

isoleucine-valine inositol inhibition uracil

53 B 98 B U

kauA kdpA kr-7 ksgA ksgB

keto-acid uptake potassium kasugamycin kasugamycin kasugamycin

49 B U 0C 1B 74 B

ksgC

kasugamycin

3-Aminolevulinic acid dehydrase Prophobilinogen deaminase Uroporphyrinogen 1I! cosynthase Uroporphyrinogen decarboxylase Coproporphyrinogen oxidase Ferrochelatase Histidine requirement Histidine synthetic genes, except for hisH, are probably all linked to hisA Histidinol phosphate aminotransferase, tyrosine-phenylalanine aminotransferase Homoserine dehydrogenase Restriction enzyme Bsu 1247I Restriction enzyme Bsu 124711 Restriction enzyme Bsu 12311 B. subtilis Marburg restriction enzyme; allele nonB, in conjunction with nonA, allows infection by SP10 Overproduction of hydrogen sulfide; probably regulation of cysteine desulfhydrylase Constitutive histidine-degrading enzymes Formiminoglutamic acid (FGA)-hydrolase Histidase Defective in histidine utilization Pleiotropic loss of histidine-degrading enzymes Resistance of histidine-degrading enzymes to catabolite repression Orocanase Increased flagella and motility Threonine dehydratase; vas allele causes valine sensitivity Condensing enzyme fl-Hydroxy-a-ketoacid reductoisomerase Dihydroxyacid dehydratase Unable to grow on inositol Inhibition by iracil, relation to cpu unknown Branched chain a-keto acid transport Requires 0.25 M K ~ for growth Kasugamycin resistance High-level kasugamycin resistance Kasugamycin resistance permeabil-, ity; cross resistance to gentamycin, kanamycin Frumarase defective, kasugamycin resistance

his cluster

U

1601

[168] [1691 [169] I169] [169,1701

[96]

[171,172] [171-173] [171~,172] [172] [1711 [171] [172.1731 [124] [91,174,175] [75a,76d176,177] [75a,76a,176,1771

11761 [121,122] [GI

[1781 [AI [1021 [179] [1791 in]

125 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

ksgD ktaR

kasugamycin

10 C 68 C

[11]

leuA

leucine

Kasugamycin resistance Resistance to ketothiaisoleucine; possibly isoleueyi-tRNA synthetase a-lsopropylmalate synthase

68 A

[1801 [75c,76d,176, 177c,181d,182d,183a,

leuB

leucine

68 B

leuC

leucine

68 B

leuD lin

leucine lincomycin lysine

68 B 7B 56 A

lysS menB

lysine menaqulnone

2B 74 B

menC, D

menaqumone

7,1 B

menE

menaqulnone

74 B

metA

methionine

30 B

metB

methionine

53B

metC metD mit

methionine methionine mitomycin

32 A 28 B U

mpo

membrane proteins

59 C

mtlA mtlB mtr

mannitol mannitol 5-methyltryptophan

10D 10B 55 B

narA

nitrate

89 B

narB

nitrate

8B

lsopropylmalate isomerase; leucine requirement /]-Isopropylmalate dehydrogenase Probably isopropylmalate isomerase Lincomycin resistance Diaminopimelate decarboxylase; lysine requirement Lysyl-tRNA synthase Napthoate synthase; menaquinone deficiency Multiple aminoglycoside resistance; menaquinone deficiency OSB-coenzyme A synthetase; menaquinone deficiency Requirement for methionine, cystathionine, or homocysteine Requirement for methionine or bomocysteine Requirement for methionine Requirement for metbionine Resistance to mitomycin C (0.25 pg/ml) Overproduction of membrane proteins MP32 and MP18; temperature-sensitive sporulation Deficiency in mannitol transport Mannitol-l-phosphate dehydrogenase Resistance to 5-methyl-tryptophan (1 mg/ml); derepression of the tryptophan biosynthetic pathway Inability to use nitrate as nitrogen source Inability to use nitrate as nitrogen

184a,185] [75c,76d,177¢,183d] [75d.76d,176, 177c,183d l [75d,76d,186] [187,1881 [64,75d,151, 166d.189 d ]

[19o1 [181d,191]

[191] [1911 [971 [97,181d,192] [97,181 d ]

11561 [192,1931 [194]

[11] [97] [125,195,1961

[41,97] [41,97]

soUrce

nic nonA

neomycin nicotinic acid non-permissive

U 67 B U

nov B nprE nprR oriC

novobiocin neutral proteas¢ neutral protease origin

78 B 3,1 C 34C OD

outA

outgrowth

3C

outB

outgrowth

7C

lleO

Neomycin resistance (0.5/lg/ml) Nicotinic acid requirement Permissive for SP10 and NR2 infection in hsrM1 background. Resistance to novobiocin (2 pg/ml) Structural gene for neutral protease Regulatory gene for neutral protease Origin of replication of the chromosome Temperature-sensitive outgrowth; impaired division Temperature-sensitive outgrowth; no resumption of RNA synthesis

[187,1881

D301 [1971 [1591

[198,H d ] [198,Hdl [16,1821,1741

11403541 1z40,1991

126 Table 1 (continued) Gene symbol

Mnemonic

outC

outgrowth

8C

outD

outgrowth

41 C

outE

outgrowth

86 D

outF

outgrowth

85 C

oxr

oxolinic acid

6B

pab

p-aminobenzoic acid

2B

p£1C

pactamycin

pap p/k pgk

Map position a

1B U 70 C 82 B

pha-I pha-2 pheA

phosphofructokinase phosphoglycerol kinase kinase phage phage phenylalanine

16 C 75 C 67 A

phoP

phosphatase

70 B

phoR phoS

phosphatase phosphatase

70 B 32 B

phoT pigY polA polC

phosphatase pigment polymerase polymerase

68 C 17 C 70 C 39 C

pro(A B) ptg ptm ptsl

proline peptidoglycan pyrithymine phosphotransferase

32 B 36 C 29 C 34 C

purA purB

pufine pufine

98 A 17 A

purC purD purE purF

pufine pufine pufine punne

17 B 17 B 17 B U

purH pycA

purine pyruvate carboxylase

U 35 C

pyrA pyrB

pyrimidine pyrimidine

37 B 37 B

Description and gene product

References h

Temperature-sensitive outgrowth; no resumption of DNA synthesis Temperat ure-sensitive outgrowth; incomplete resumption of protein synthesis Temperature-sensitive outgrowth; incomplete resumption of prorein synthesis Temperature-sensitive outgrowth; no resumption of RNA synthesis Oxolinic acid resistance; reduced permeability p-Aminobenzoic synthase, subunit A; p-aminobenzoic acid requirement Resistance to pactamycin (5/ag/ml) Pyrimidine nucleotide phosphorylase Phosphofructokinase 3-Phosphoglycerol kinase; germination defective Resistance to phage SPOI Resistance to phage SPP1 Prephrenate dehydratase; phenylalanine requirement Regulation of alkaline phosphatase and alkaline phosphodiesterase Regulation of alkaline phosphatase Constitutive alkaline phosphatase; probably negative regulator Constitutive alkaline phosphatase Sporulation-associated pigment DNA polymerase I DNA polymerase 111, azp alleles are resistant to azopyrimidines; rout alleles increase the mutation rate Proline requirement Defect in peptidoglycan synthesis Pyrithymine resistance Phosphoenolpyruvate phosphotransferase enzyme I; no growth on most sugars Adenine requirement Adenine, guanine, or hypoxanthine requirement Adenine or hypoxanthine requirement Adenine or hypoxanthine requirement Adenine requirement Glutamine pbosphoribosyl pyrophosphate amidotransferase Adenine requirement Pyruvate carboxylase; temperaturesensitive requirement for aspartate Carbamyl phosphate synthetase Aspartate transcarbamylase

[140,199] I140,1541

[140,1991

[140,1~1 [2001 [1331

[1881 1111 [128] [137,1401 [97]

[2011 [54,181d,202,203 a l [204~,2051 [204c,2061 [207,2081 [1401 [2091 [210,211] [108,211-215]

[208,216]

11001 Illl 1128,217,2181 [lO,181d,219d l [lO,181dl [220,221]

I220,2211 [220,221,222 dc]

1111 12231 [224,1d ] [224,225d,Id ]

127 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

pyrC pyrD pyrE

pyrimidine pyrimidine pyrimidine

37 B 37 A 37 B

[224,1d ] [I81d,224,225d,ld ] [224,225did ]

pyrF

pyrimidine

37 B

pyrG recA

pyrimidine recombination

U 39 A

recB

recombination

67 B

recD

recombination

0B

recE

recombination

39 C

recF

recombination

0B

recG

recombination

54 C

recH

recombination

22 B

recl

recombination

24 C

recL

recombination

9D

recM

recombination

0B

recN

recombination

40 C

red relG rev

r.ed relaxed relaxed revertant

83 C 67 C 3D 89 C

ribA ribB

riboflavin riboflavin

55 B 55 B

ribC

riboflavin

55 B

ribD ribF ribH

riboflavin riboflavin riboflavin

55 B 55 B 55 B

ribO ribT

riboflavin

riboflavin

55 B 55 B

rib-627

riboflavin

55 B

rib-850

riboflavin

55 B

Dihydroorotase Dihydroorotate dehydrogenase Orotidine-5-rnonophosphate pyrophosphorylase Orotidine-5-monophosphate decarboxylase CTP synthetase Transformation defective, transduction proficient, repair defective Transformation and transduction defective, repair defective Transformation and transduction defective, repair defective Transformation and transduction defective, repair defective Transformation proficient, repair defective Transformation proficient, transduction defective, repair defective ATP-dependent nuclease; recombination and repair defective Transformation defective, repair defective Recombination defective, repair defective Recombination defective, repair defective Recombination defective, repair defective, possibly allelic to recE Red or red-purple colony Relaxed RNA synthesis Relaxed RNA synthesis Restoration of Spo + phenotype to antibiotic resistant, Spo- strains; catabolite resistant sporulation Riboflavin requirement Riboflavin synthetase; riboflavin requirement Prototroph, accumulates riboflavin; lumichrome, lumiflavin resistance Riboflavin requirement Constitutive production of MERL Riboflavin requirement; accumulates fibulose-substituted pteridines Prototroph; accumulates riboflavin Riboflavin requirement; accumulates ribityl-suhstituted pteridines Riboflavin requirement probably one of first two enzymes of riboflavin synthesis Riboflavin requirement; probably ' one of first 2 enzymes of riboflavin synthesis

re/A

[224,225d Id ] [85] [I30,226] [I30,226] [226] [226] [226] [226] [I37.227] [110,140] [110,226] [110] [11,110] [1 ] [228,229] [230] [95,231]

[232] [232] [232-234] [231,234 c ] [234] [234c ] [232] [234 c] [2351

[235]

128 Table 1 (continued) Gene symbol

Mnemonic

Map position a

rna-16

RNA

rna-53 rodB rodC rplA

RNA rod rod ribosomal protein

85 C 68 B 87 C 3B

rplC

ribosomal protein

3B

rplE rplF rpLl rplK

ribosomal protein ribosomal protein ribosomal protein ribosomal protein

3C 3C 3B 3B

rplL rplO

ribosomal protein ribosomal protein

3B 3C

rplU rplV

ribosomal protein ribosomal protein

67 C 3C

rplX rpmA rpmD

ribosomal protein ribosomal protein ribosomal protein

3C 67 C 3B

rpoB

RNA polymerase

3B

rpoC

RNA polymerase

3B

rpoD

RNA polymerase

61 C

rpsD

ribosomal protein

70 C

rpsE rpsF rpsG rpsH rpsl rpsJ rpsK rpsL rpsP rps T

ribosomal ribosomal ribosomal ribosomal ribosomal ribosomal ribosomal ribosomal ribosomal ribosomal ribosomal

3B 0D 3B 3C 3B 3C 3B 3B 36 B 3C 3C

rrnA

ribosomal RNA

rrnB

rRNA

8C

~rotein 9rotem 3rotem arotem ~rotem arotem arotem ~rotem arotem arotem 9rotein cluster

0C 76 D

Description and gene product

References b

Temperature-sensitive RNA synthesis; delayed spore outgrowth at permissive temperature Temperature-sensitive R N A synthesis Cell wall defective; salt dependence Cell wall defective; salt dependence Protein BLI ( = E. coli L1); chloramphenicoi resistance 11 Protein BL7 ( = E. coli L3); possible micrococcin resistance Protein BL6 ( = E. coil L5) Protein BL8 ( = E. coil L6) Protein BL5 ( = E. coli L10) Protein BLII ( = E. coil LII); bryamycin (thiostrepton) resistance; some mutants have relaxed phenotype Protein BL9 ( = 17, coli LI2) Protein BLI5; chloramphenicol resistance II1 Protein L20 Protein BL22; erythromycin resistance Protein BL23 ( = E. coli L24) Protein L24 Protein BL27 ( = E. coli L30); kasugamycin resistance RNA polymerase subunit ,8; rifampin resistance RNA polymerase subunit ,8'; lipiarmycin and streptolydigin resistant; crsE may be allelic RNA polymerase subunit 043; allelic to crsA Protein $4; restores fun, strR mutants to Spo + phenotype Protein $5, spectinomycin resistance Protein $6 Protein $7 Protein $8 Protein $9 Protein S10; tetracycline resistance Protein S11; kasugamycin resistance Protein SI 2, streptomycin resistance Protein SI 6 Protein $20 Proteins BL4, BL14, BLI6, BL17, BL25, $3, S17, S19; resistance to bryamycin, kanamycin, neamycin, oleandomycin, streptomycin Ribosomal RNA gene set; relationship to trrn gene sets unknown Ribosomal RNA gene set; linked to trrnE

[236]

[228,236] [237,2381 [237,238] [239,240] [239] [239] [239] [239,240] [229,239-2411

[240,242,243] [243] [244] [243,245] /2391 12441 1239,2461 [247] I95,248,2491

[6d,Jc] 12501 [239,251,252] [2531 II 17,2391 1239] [239,2461 [2541 [239,2461 [2391 [2531 [2541 [243]

[5,18dc,255] [256,25: c]

129 Table 1 (continued) Gene symbol

Mnemonic

Map position •

rrnG rrnH rrnl rrnO

rRNA rRNA rRNA rRNA

rmA

revertant

57 C

sacA sacB sacL sacP sacQ

sucrose sucrose sucrose sucrose sucrose

91 A 82 A 65 C 91 B 75 B

sacR

sucrose

82 B

2B 2B 2B 0B

Description and gene product

References b

Ribosomal RNA gene set Ribosomal RNA gene set Ribosomal RNA gene set Ribosomal RNA gene set, located adjacent to origin Restores wild type sporogeny to spoOF; partial reversion of spoOB, spoOE; suppression of sporulation by alcohols Sucrase Levansucrase Levanase Sucrose transport Hyperproduction of levansucrase and proteascs Constitutive sucras¢ a n d / o r ievan-

[F] [F] IF] [16d,18de19d~,20] [258]

[259c,260 c ] [259,261,262,263 d ] [264] [264] [261,265] [259,261.263 d ]

sucrasc

sacS sacT

sucrose sucrose

93 B

Constitutive sucrase a n d / o r levan-

[259,2661

91 B

sucrase Constitutive sucrase and/or levan-

[259,266]

sacU

sucrose

84 C

sapA

suppressor alkaline pho~phatase

30 B

sapB

17 C

scoA

suppressor alkaline phosphatase spornlation control

31 B

scaB

sporulation control

34 C

sdhA sa~B

suceinate dehydrogenase 69 B succinate dehydrogenase 69 B

$dhC

succinate dehydrogenase 69 B

set serC serR smo

serine scrine serine resistant smooth

55 B 69 C 8C 81 B

spcB

spectinomycin

39 C

spcD spg

spectinomycin sporangiomycin

spoOA

sporulation

59 B

spoOB

sporulation

68 B

U U

sucrase ( - ) Allele abolishes ievansucrase; (h) alleles overproduce levansucrase, proteases and amylase; allelic to pap Allows synthesis of alkaline phosphatase in spa- mutants; possibly allelic to scoA, phoS Allows synthesis of alkaline phosphatase in spa- mutants Delayed sporulation; elevated proteolytic activity Delayed sporulation; elevated proteolytic activity Cytochrome bsss Iron protein subunit of succinate dehydrogenase Flavoprotein protein subunit of succinate dehydrogenase Requirement for serine Requirement for serine Resistance to serine Smooth-rough colony morphology; long chains of small, oval ceils Resistance to spectinomycin (100 ttg/ml) Spectinomycin dependence Sporangiomycin resistance:50S ribosome alteration Stage 0 sporulation; allelic to spoOC, sol" Stage 0 sporulation

[44.259,267]

[207]

[207] [83] [83] [23] [23] [23] [57d,195] [A] [A] [237.263 d ] [215.268] [269] [270] [53.94.181 d. 271,272,273 d, 274,K ¢] [53,181d,272. 275d,276 d ]

130 Table 1 (continued) Gene symbol

Mnemonic

Map position a

spoOE spoOF

sporulation sporulation

34 C 89 C

spoOG spoOH

sporulation sporulation

59 C 2B

spoOJ spoOK spoOL spollA

sporulation sporulation sporulation sporulation

99 C 29 C 29 C 56 B

spollB spoliC spoliD spollE spollF spollG

sporulation sporulation sporulation sporulation sporulation sporulation

68 B 81C 86 C 2B 33 C 35 C

spoliH spollIA spolllB spoiIIC spolllD spolllE spolllF spol VA spol VB spol VC

sporulation sporulation sporulation sporulation sporulation sporulation sporulation sporulation sporulation sporulation

1B 59 C 59 C 65 C 78 C 39 C 66 B 55 B 57 C 64C

spol VD spol VE spoi VF spol VG spo VA

sporulation sporulation sporulation sporulation sporulation

65 C 66C 68 B 29 C 56 B

spo VB spo VC spo VE spo VF

sporulation sporulation sporulation sporulation

66 C 1C 35 C 35 C

spo VG spoVH

sporulation sporulation

IB 68 B

spo VJ

sporulation

60 B

spo VIA

sporulation

69 C

spo VI B

sporulation

68 C

Description and gene product Stage 0 sporulation Stage 0 sporulation; mutants fail to synthesize P3 AP3 Stage 0 sporulation Stage 0 sporulation; reported to be structural gene for sporulation nuclease Stage 0 sporulation Stage 0 sporulation Stage 0 sporulation Stage II sporulation; operon with 2-3 cistrons Stage II sporulation Stage II sporulation Stage II sporulation Stage II sporulation Stage II sporulation Stage II sporulation; possibly encodes a sporulation o-factor Stage I[ sporulation Stage III sporulation Stage Ill sporulation Stage Ill sporulation Stage IiI sporulation Stage III sporulation Stage Ill sporulation Stage IV sporulation S~age IV sporulation Stage IV sporulation; two complementation groups reported Stage IV sporulation Stage IV sporulation Stage IV sporulation Stage IV sporulation Stage V sporulation; as many as 6 cistrons Stage V sporulation Stage V sporulation Stage V sporulation Stage V sporulation; requires dipicolonic acid for heat-resistant spores Stage V sporulation Stage V sporulation; defective DPA; lysozyme resistant, heat-sensitive spores Stage V sporulation; lysozyme resistant, heat-sensitive spores Stage VI sporulation; coat lacks 36kDa peptide; lysozyme-sensitive spores, delayed germination Stage VI sporulation; coat has reduced amounts of 36kDa peptide, delayed germination

References b

[2721 [166d,272,277,278 a ]

[272] [272,279,280 d ] [140,272]

12721 []401 [9,272,281,282 ¢, 283a,284c,285 e ]

I2721 [2721 [2721 [2721 [2721 [272,276a,La= I I2721 12721 [180d,272] [272]

12721 [2721 [2021 [57 d,2721 12721 [272,2861 I272] I2721 I202,272] 12721 [570,272,287d,M =] [202,272] [272,288]

12721 [272,2891 14,290] [175] [1751 [291] [2921

131 Table 1 (continued) Gene symbol

Mnemonic

spoCM

sporulation

99C

spoLl sprA

sporulation suppressor

62 B U

sprB

suppressor

77 B

srh

suppressor recH

34D

$1'Tn

spectinomycin resistance modifier

Map

position *

3C

$$a

58 C

ssp- 1

35 C

strB strC

streptomycin streptomycin

35 C 59 C

strD

streptomycin

3C

strR

streptomycin

4C

sui sup-3 tag

sulfonilamide suppressor suppressor tcichoic acid

2B 9C 9C 85 B

tern-1

temperature-sensitive

ler

terminus

tetB

tetracycline

thL4 thiB thiC thrA thrB

thiamine thiamine thiamine threonine threonine

22 B 29 B 93 B 77B 77 B

thyA

thymidine

42 B

thyB

thymidine

53 A

til tmrA

tilerone tunicamycin

62 C 7B

tmrB tins-12

tunicamycin temperature-sensitive

8B 36C

tma-26

temperature-sensitive

IB

~¢-44

U

46C 2C

Description and gene product

References b

Stage 0 spomlation, possibly identical to spoOJ ' Decadent' sporulation Derepression of homo~'rine kinase, h o ~ dehydrogenase and the minor threonine dehydratase Suppression of isolencine auxotrophy; sensitivity to methionine Restores recH mutants to near wildtype transformation efficiency Growth and sporulation of rpsE mutants Ability to sporulate in the pr~ence of aliphatic alcohols Endonuciease excising spore photoproducts Streptomycin resistance (200 pg/ml) Streptomycin resistance (1 mg/ml); requires glucose for growth Streptomycin dependence (0.5 mg/ml); probably allelic to rpsL Streptomycin dependence; lethal unless in thepresence of fun or rpr-21 Sulfanilamide resistance Nonsense suppressor Nonsense suppressor Decreased synthesis of teichoic acid; temperature-sensitive growth Temperature-sensitive protein and RNA synthesis; cotransduees with purB Replication terminus

[28]

Resistance to tetracycline (20/,g/ml); permeability Thiamine requirement Thiamine requirement Thiamine requirement Homoserine kinase Threonine synthetase with minor threonine dehydrogenase activity Thymidylate synthetase A; aminopterin sensitive, 46 ° resistant Thymidylate synthetase B; 46 ° m f i v e T'flerone resistance Tunicamycin resistance; hyperproduction of a-amylases Tunicamycin resistance Temperature-sensitive septum initiation; alletic to ts-12 Temperature-sensitive growth; rigidity

[293]

[2941 [294,295]

[2961 [2521 [297,298] [299] [300] {300] [301] [129]

[70,133,302d ]

13o31 [3o4] {1531

[GI [305-307,308d, 309,310]

[3111 [312] [53,313]

[169] [168,184 d ] [168,295] [314] [314] [11] [315]

[46d,315] [107,316] [181d,319,318]

132 Table 1 (continued) Gene symbol

Mnemonic

Map position a

Description and gene product

References b

tolB tre

tolerance trehalose

U 20 A

[30,31] [971

trpA trpB trpC trpD

tryptophan tryptophan tryptophan tryptophan

55 55 55 55

trpE

tryptophan

55 B

Tolerance to ~29 in spoO strains Inability to utilize trehalose as carbon source Tryptophan synthase Tryptophan synthase lndoleglyceroi phosphate synthase Anthranilate phosphoribosyltransferase Anthranilate synthase

trpF

tryptophan

55 B

trpS

tryptophan

29 B

trrnA

tRNA, rRNA

U

trrnB

tRNA, rRNA

U

trrnC

tRNA, rRNA

U

trrnD

tRNA, rRNA

U

trrnE

tRNA, rRNA

76 C

B B A B

N-(5'-Phosphoribosyl) anthranilate isomerase Tryptophanyl-tRNA synthase; resistance to 5-fluorotryptophan (50 #g/ml) 2-3 tRNA Genes, probably flanked by rRNA gene sets 6 tRNA Genes, flanked by rRNA gene sets, including the major 5S rRNA species gene 8-12 tRNA Genes, probably flanked by rRNA gene sets 16 tRNA Genes, linked to an rRNA set containing the minor 5S rRNA species gene 21 tRNA Genes, linked to rrnB

[319.320 c ] [319,320] [57d,319,321 a ] [319,320,321 d`] [296,319,320 c, 321de,3221 [320 ~] [323]

[324d1 [324de1

[324] [325 de]

[257de,325dl

rrnn is-39

temperature-sensitive

62 C

is-341

temperature-sensitive

84 C

tscA

temperature-sensitive

4C

tscB

temperature-sensitive

7C

tscC

temperature-sensitive

84 C

tscD

temperature-sensitive

68 C

tscE

temperature-sensitive

67 C

tscF

temperature-sensitive

7C

tscG

temperature-sensitive

7C

tscH

temperature-sensitive

8C

tsi

temperature-sensitive

18 C

tuf

Tu-factor

3B

Temperature-sensitive synthesis of phosphatidylethanolamine Temperature-sensitive septum initiation mutant Temperature-sensitive growth; delayed stop of DNA, protein synthesis at 45 ° Temperature-sensitive growth; delayed stop of DNA. protein synthesis at 45 ° Temperature-sensitive growth; protein and DNA synthesis at 45 ° Temperature-sensitive growth; normal protein and DNA synthesis at 45 ° Temperature-sensitive growth; normal protein and DNA synthesis at 45 ° Temperature-sensitive growth; normal DNA synthesis, delayed stop of protein synthesis at 45 ° Temperature-sensitive growth; normal DNA and protein synthesis at 45 ° Temperature-sensitive growth; normal DNA and protein synthesis at 45°C Temperature-sensitive induction of PBSX Elongation factor Tu; kirromycin resistance (200/~ g/ml)

[326] {107] [327]

[3271 [327] [327] [327] [327]

[327] [327] [328-330] [17]

133 Table 1 (continued) Gene symbol

Mnemonic

Map position •

Description and gene product

Refere~es

tyrA

tyrosine

54 B

[42,54,56, 57J,331,332 d ]

urg uvrA

UV repair

U 83 B

uvrB

UV repair

69 C

uvrC

UV repair

83 B

veg

vegetative

1B

virM

virginamycin M

U

virS

virginamycin S

U

wrd

weird

56 C

xhd xhi xin xki xtl xynA xynB 0.3 kb

PBSX head PBSX heat inducibility PBSX induction PBSX kill PBSX tail xylan xylan

31 B 31 B 31 B 31 B 31 B 15 C 15 C I B

Prephenate dehydrogenase; may mutate to auxotrophy (tyr), to D-tyrosine resistance (D- tyrR ), to aminotyrosine resistance (amt) N-Glycosidase Excision repair defective; no initial incision Excision of UV-induced pyrimidine dimers in DNA Excision repair defective; gaps not closed Transcribed actively during growth and sporulation Resistance to virginamycin M (50/~g/ml) Resistance to virginamycin S (13/t g/ml) Slow growth on PGYE medium, normal on MA medium Induced PBSX lacks heads Heat inducible PBSX Induction defective PBSX Fails to kill B. subtilis W23 Induced PBSX lacks tails .B-Xylanase ,8-Xylosidase Expressed during sporulation beginning at t4, encodes 61 amino acid polypeptide

b

[333,334] [299 C,N] [299,N] [N] [335] [335,336] [335,336] [137] [338] [313] [338] [223] [338] [339d,340] [340] [335 ~]

The letters A - D following each position refer to the degree of precision with which the map position is known (see text). b References: Abstr. 9th Int. Spores Conference: [C] Wang, L., Price, C. and Doi, R.; [D] Feavers, I., Miles, 3. and Moir, A.; [H] Yang, M. and Henner, D.; [I]Lerner, C. and Switzer, R.; [J] Price C., Gitt, M. and Wang, L.; [K] Ferrari, F., Trach, IC, LeC¢~, D. and Hoch, J. [L] Straiger, P., Bouvier, J., Bonamy, C. and Szuimajster, J.; [M] Errington, J. and Fort, P. Personal communication: [A] Zahler, S.; [B] Zeigler, D., [E] Smith, D.A.; [F] Bott, K. [G] Siegel, E., [N] Yasbin, R. c Reference reports fine structure genetic map. d Reference reports molecular cloning of the gene. e Reference reports DNA sequence data for the gene. "

134 Table 2 Alternative gene symbols Alternative

Preferred

Alternative

symbol

symbol

symbol

aceB amt amyA amy B amy H

aceA tyrA amyE sac U amy R argGH argF arg,4BCDE pycA polC bfmB aceA hsrR gyrA rplA rplO rplL sdh rplA rplO rplL abr B rpoD pyrR divl VC div V divll dw l polC polC

lpm mdh mic rout- 1 nalA non B nova pap pyrX rm

argA argC argO aspA azpA bfa bfmA bsr cafB chill chilli chil V cit F cml-7 cml- I 1 cml-91 cps X crsA cytR divA divB dioC dio D dnaF dnaP dpa drp D- tyrR ery fus gsp hisB hcr- 1 hcr- 114 hsdR kir

spo VF

rpoB tyrA rpl V efg out hisH uvrC1 uvrB114 hsrR tuf

r168 recC recE 5 recN4 recO rfro rif rou scoA scoC sol s orR spcA spoOC sprE std strA suh trap trp X is- 1 ts-5 tsA tsB

ts-8132 tsp tzm urs uvrAl vas O.4 kb

Preferred symbol rpoC citH rplC polC gyrA hsrM gyrB sacU pyre hsrM hsrM att- SP02 add-5 recE4 recB rpoB rpoB smo sapA catA spoOA gut R rpsE spoOA aprA rpoC rpsL hisH dfrA gat tmsA tmsB dna( tsA) dna( tsB) dna-8132 rplK gerJ cpu uorCl ilvA spo VG