TABLE 2.

Single and double gene disruptions in B. subtilis

Gene 1aGene 2Gene(s) essential as single genebViable double knockoutcE valuedPersistent gene(s)eFunction (reference no.)fPresence in other bacteriag
S. aureusS. pneumoniaeE. coli
gyrBgrlB1 and 2NA10−1791DNA supercoiling (112)++++
gyrAgrlA1 and 2NA10−1801DNA supercoiling (112)+++++
clpCclpE+10−1781ATPases (37, 74)+++
ybeCyveA+10−832: Amino acid transporter (66)+
ybfGykuG+10−1231: Carboxylesterase (28)
ybfKnap+10−1052: Nitrate reductase (91)
ybgEywaA+10−123Aminotransferases (8)+++
lipAlipB+10−79Lipases (29)
ycdBycdC+10−79
lctPyvfH+10−1251: Lactate permease (89)+++
ycgGyqcI1NA10−71
ycgMyusM+10−86
nasDnasB+10−180Reductases (77, 80)+++
topBtopA10−3922: Chromosome partitioning (112)+++
ydbDyjqC+10−95
dalyncD1NA10−801: d-Alanine racemase (43)++++
yddSydeG+10−103
yddTyomL1 and 2NA10−131
phoBphoA+10−150Phosphatases (9, 84)+
yebBytiP+10−88Permeases (105)++
yerDgltA+10−282: Glutamate synthase (95)+++
yerFyjcD1NA10−71+++
yerQbmrU1NA10−331++++
yefAyfjO+10−1171+++
yesWyesX+10−1801: Rhamnogalacturonate lyase (79)
lplAytcQ+10−741: Lipoprotein (38)
yfnAyhdG+10−115++
yhcJyusA+10−2622: Methionine transport (46)++++
yhdHyocR+10−127+
yitAylnB+10−129
yitBcysH+10−712: Sulfotransferase (68)+
nprBnprE+10−77Proteases (54, 117)
yitSyviA+10−31+++
carApyrAA+10−882+++
carBpyrAB+10−1802+++
oppAdppE+10−1181: Oligopeptide transport (85)
yjbMywaC+10−341+++
yjbUmoeB+10−96+++
yjbVthiD+10−48HMPh kinases (83)++++
yjdDfruA+10−782: Fructose transport (24)
ykcByycA+10−178
proBproJ+10−751: Proline synthesis (73)++
ykrMyubG+10−65K+ transport (44)+++
ykvYyqhT+10−571 and 2++++
ykuApbpA+10−146Peptidoglycan synthesis (124)++
ykqCymfA1NA10−14211: RNA processing (47)+++
ctaDqoxB1NA10−180Oxidases (63, 120)++
codVripX+10−57Chromosome segregation (108)++++
kblbioF+10−962: Biotin synthesis (10)++
ymcByqeV+10−69+++
nrdEyosN1NA10−1801: Ribonucleotide reductase (41)++
nrdFyosP1NA10−10511: Ribonucleotide reductase (41)++
yncByokF+10−77Nucleases (97)+
yncFyosS+10−75++
yncMyrpD+10−78
yngEyqjD+10−91
yoaBcsbX+10−135
yoaNyvrK+10−135Oxalate decarboxylases (115)
ppsyvkC+10−741: Plipastatin synthesis (118)
yobMyokH+10−77
yocIrecQ+10−672: DNA repair (101)+++
sodFsodA+10−392: Superoxide dismutase (48)++++
yojAgntP+10−138+
ctpAyvjB+10−98+
gerCCyqiD1NA10−2621: Isoprenoid synthesis (62)+++++
ypcAyweB+10−180++
yqkJytsJ+10−74Malate utilization (65)+
ansBcitG+10−92Fumarate metabolism (126)
yqjNrocB+10−71
bmrblt+10−90Multidrug transporters (1, 7)+
brnQbraB+10−120+++
yrrOyrrN+10−44++++
ysdCytoP+10−99++++
thrSthrZ10−1801tRNA synthetases (86)+++
gapBgapA2NA10−1062Glyceraldehyde-3-phosphate dehydrogenases (32)+++
ytbEyvgN1NA10−1092: Glyoxal reductase (96)+++
ytnJyxeK+10−118+
malSywkA+10−180Malate utilization (65)+
ytrDytrC+10−81Acetoin utilization (128)
ytcCytxN+10−1082: Spore coat (113)
yufRyxkJ+10−92Malate transporters (57, 114)
yurUyurX1 and 2NA10−451++++
opuBCopuCC+10−1191: Mutation repair (102)+++
yveLywqD+10−562: Kinase (75)+++
murAAmurZ1NA10−1121+++++
fbaAiolJ1NA10−9111: Glycolysis (69); 2: myoinositol metabolism (127)+
ywhLywhK+10−1022: DNA synthesis (78)
yxjHyxjG+10−140
spo0JyyaA+10−391Chromosome binding (110)+++
fabLfabI10−18Fatty acid biosynthesis (42)
yccCansA+10−181l-Asparaginases (33)++++
ycdHmntA2NA10−18Mn2+ transporters (11, 88)++
nasAnarK+10−341: Nitrate transport (80); 2: nitrite excretion (18)++
ydfAywrK+10−55++
purNykkE+10−2211: Purine metabolism (103)++++
yfnBysaA+10−14+++++
yaaOspeA+10−702: Polyamine synthesis (109)+++
nhaCmleN+10−62Na+/H+ antiporters (123)++
fabHBfabHA10−66Fatty acid biosynthesis (15)+++
yisQyojI+10−27++
yjbDyqgZ+10−291: Competence (76)++
yjbGyusX+10−2411: Sporulation (52)++
tenIthiE+10−202: Thiamine synthesis (61)++++
ylaKphoH+10−232++++
ylmByodQ+10−55++
pyrCpucH+10−3411: Pyrimidine metabolism (64); 2: purine metabolism (107)+++
yloUyqhY1 and 2NA10−131 and 2++++
recGmfd+10−691 and 2Recombination (5)++++++
yacOysgA2NA10−201 and 2++++++
yocJyvaB+10−46++
ypvAdinG+10−43+
rluBytzF+10−221++++
yqjMyqiG+10−351: Detoxification (34)++
yqjEpepT+10−2122: Aminopeptidase (13)++++
pstApstC+10−301 and 2Phosphate uptake (87)++++
yrhGywcJ+10−17++++
amyXglgB+10−141: Pullulanase (67)+++
ythAcydA+10−512: Cytochrome subunit (125)+++
glgDglgC+10−27+++
yvfKyvdG+10−60Dextrin transport (51, 106)++++
yvfCtuaA+10−182: Teichuronic acid synthesis (30)++++
hisFhisA+10−19++++
yoaEyyaE+10−80+
gamAnagB+10−642: Glucosamine-6-phosphate deaminase (121)++++
yfkNyhcR1NA10−391: Nucleotidase (14); 2: nuclease (81)++++
yfjRykwC+10−25++
xylRglcK+10−2021: Repressor (19); 2: kinase (111)++++
yqjGspoIIIJ10−342Secretion (116)+++
purTpurK+10−301: Purine metabolism (104)++++
hemNhemZ+10−301Heme biosynthesis (45)+++
htrAyyxA+10−1151: Protease (22)++++
opuEycgO+10−1531: Proline transport (122)+++
yodRscoB+10−542: Protease (6)+
yodSscoA+10−442: Protease (6)++
ypcPpolA10−4922: DNA repair (71)+++++
  • a Pairs are ordered according to the chromosomal position of gene 1, proceeding clockwise from oriC, as in the published genome sequence (24).

  • b Each gene was disrupted by transformation of 168CA with a recombinant derivative of either pMUTIN4 or pHT35, enabling single crossover integration into the chromosome. The gene that could not be disrupted after repeated attempts is annotated as 1 (gene 1) and/or 2 (gene 2).

  • c Double knockouts were created by transformation of viable single knockout strains with the plasmid used to disrupt the partner gene. Growth of transformants was examined on antibiotic selective media diagnostic for both constructs (+, double mutant viable; −, double mutant inviable). For the pairs in which individual genes were essential, double knockouts were not attempted (NA).

  • d Level of protein sequence similarity within each pair.

  • e Genes conserved (persistent) in the gram-positive clade, as defined by Fang et al. (31). Genes are annotated as 1 (gene 1) and/or 2 (gene 2).

  • f Functions experimentally established for B. subtilis outside this study. Where the function is not common to both genes or if it is known for only one, the description is preceded by the relevant gene annotation (1 for gene 1 or 2 for gene 2).

  • g Shown is whether the encoded protein pair is reciprocally similar to one protein (+) or a pair of proteins (++) in S. aureus, S. pneumoniae, or E. coli.

  • h HMP, 4-amino-5-hydroxymethyl-2-methylpyrimidine.