Bacillus subtilis genes (E. coli codon optimized)

Bacillus subtilis genes (E. coli codon optimized)

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261 essential genes from Bacillus subtilis, codon optimized for Escherichia coli in MoClo-compatible high-copy ampicillin resistance backbones. Shipped in Escherichia coli Top10 in 3 96 well plates.

Discovery of genes essential for life is the first step in creating a truly synthetic organism. The Bacillus subtilis community has done an amazing job in curating a list of essential genes, and while the first published list goes back to 2003, the Bacillus subtilis community has continuously updated this list with results from new experiments. In 2016, a paper was published using a CRISPR-based method for knocking down essential genes in Bacillus subtilis. All the sgRNAs are available through the Bacillus Genetic Stock Center, which would allow for knockdown of native-sequence essential genes. We took the list of essential genes from that 2016 paper and synthesized 261 of the 289 genes through Twist Biosciences.

All the essential genes have been recorded for expression in Escherichia coli and have been made MoClo compatible. There are many possible applications for these genes: you could try to recreate essential gene pathways in-vitro, or purify the proteins for functional studies, or create a synthetic MoClo-compatible Bacillus subtilis genome using these genes and the sgRNAs available from the Bacillus Genetic Stock Center. 

Recoding was done using scripts that stochastically assigned codons to amino acids. The codon table used was the FreqB table from "Design Parameters to Control Synthetic Gene Expression in Escherichia coli", which was used because it was shown to express proteins well and was recommended to us by JCVI. All genes where inserted into the BbsI:BbsI cloning sites of pOpen_build, which is individually available through our website.

Documentation
261 of the 289 essential genes from 2016 essential gene list are included in this distribution. The essential genes included in the distribution at attached in essential_included.csv, while the essential genes not included are in essential_not_included.csv. The spreadsheet BBF_to_uniprot.csv contains links from our genes to outside resources like uniprot, as well as detailed descriptions. The spreadsheet freegenes-distribution-bacillus-subtilis-essential-genes.csv includes a plate map for each plate that gets shipped in this distribution, with information on where exactly to find any gene. In the bsub_essential.zip file are genbank files for every gene.


This product is made available under the unilateral OpenMTA. Read Terms of Service at the bottom of the page for details.

261 unique parts

Plate Layout

Instructions for Use:

Culture at 37C overnight, with shaking at around 300rpm. The selection marker for all parts is ampicillin.


PlateSet: Bsubtilis-essentials-0 Bsubtilis-essentials-1 Bsubtilis-essentials-2

Genes

Gene Name NCBI ID
dnaN DNA polymerase III subunit beta NP_387883.1
gyrB DNA gyrase subunit B NP_387887.1
gyrA DNA gyrase subunit A NP_387888.1
guaB NP_387890.1
serS serine--tRNA ligase NP_387894.1
dnaX DNA polymerase III subunit gamma/tau NP_387900.2
holB DNA polymerase III subunit delta NP_387912.1
metS methionine--tRNA ligase NP_387919.1
ipk 4-diphosphocytidyl-2C-methyl-D-erythritolkinase NP_387927.1
glmU bifunctional N-acetylglucosamine-1-phosphateuridyltransferase/glucosamine-1-phosphateacetyltransferase NP_387931.1
prs ribose-phosphate pyrophosphokinase NP_387932.1
pth peptidyl-tRNA hydrolase NP_387934.1
divIC cell division protein DivIC NP_387943.1
tilS NP_387948.1
hprT hypoxanthine-guanine phosphoribosyltransferase NP_387949.1
sul dihydropteroate synthase NP_387958.1
folB dihydroneopterin aldolase NP_387959.1
folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase NP_387960.1
lysS lysine--tRNA ligase NP_387963.1
ispD 2-D-methyl-D-erythritol 4-phosphatecytidylyltransferase NP_387971.1
ispF NP_387972.1
gltX glutamate--tRNA ligase NP_387973.1
cysS cysteine--tRNA ligase NP_387975.1
secE preprotein translocase subunit SecE NP_387981.1
rplJ 50S ribosomal protein L10 NP_387985.2
rplL 50S ribosomal protein L7/L12 NP_387986.1
rpsL 30S ribosomal protein S12 NP_387991.2
rpsG 30S ribosomal protein S7 NP_387992.2
fusA elongation factor G NP_387993.2
tufA elongation factor Tu NP_387994.1
rpsJ 30S ribosomal protein S10 NP_387996.1
rplC 50S ribosomal protein L3 NP_387997.1
rplD 50S ribosomal protein L4 NP_387998.1
rplB 50S ribosomal protein L2 NP_388000.2
rpsS 30S ribosomal protein S19 NP_388001.1
rpsC 30S ribosomal protein S3 NP_388003.2
rplP 50S ribosomal protein L16 NP_388004.1
rpsQ 30S ribosomal protein S17 NP_388006.1
rplN 50S ribosomal protein L14 NP_388007.1
rplX 50S ribosomal protein L24 NP_388008.1
rplE 50S ribosomal protein L5 NP_388009.1
rpsN 30S ribosomal protein S14 NP_388010.1
rpsH 30S ribosomal protein S8 NP_388011.2
rplF 50S ribosomal protein L6 NP_388012.1
rplR 50S ribosomal protein L18 NP_388013.2
rpsE 30S ribosomal protein S5 NP_388014.1
rpmD 50S ribosomal protein L30 NP_388015.1
secY protein translocase subunit SecY NP_388017.1
adk adenylate kinase NP_388018.1
infA translation initiation factor IF-1 NP_388020.1
rpsM 30S ribosomal protein S13 NP_388022.2
rpsK 30S ribosomal protein S11 NP_388023.1
rpoA DNA-directed RNA polymerase subunit alpha NP_388024.1
rplQ 50S ribosomal protein L17 NP_388025.1
rplM 50S ribosomal protein L13 NP_388030.2
rpsI 30S ribosomal protein S9 NP_388031.1
glmM phosphoglucosamine mutase NP_388058.1
glmS glutamine--fructose-6-phosphateaminotransferase NP_388059.1
ycgG hypothetical protein NP_388192.2
nadE NP_388195.1
aroK shikimate kinase NP_388197.2
ddl D-alanine--D-alanine ligase NP_388337.1
murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase NP_388338.1
acpS holo-[acyl-carrier-protein] synthase NP_388343.1
alrA alanine racemase 1 NP_388345.1
yddT hypothetical protein NP_388391.1
ydiC hypothetical protein NP_388473.1
gcp tRNA threonylcarbamoyladenosine biosynthesisprotein Gcp NP_388475.1
groES chaperonin NP_388483.2
groEL chaperonin NP_388484.1
ydiP BsuMI modification methylase subunit YdiP NP_388488.1
ligA DNA ligase NP_388544.1
gatC NP_388549.1
gatA NP_388550.1
gatB aspartyl/glutamyl-tRNA amidotransferase subunitB NP_388551.2
yerQ diacylglycerol kinase NP_388554.1
yezG hypothetical protein YP_003097692.1
cspR NP_388774.2
yhdL anti-sigma-M factor YhdL NP_388832.1
plsC 1-acyl-sn-glycerol-3-phosphate acyltransferase NP_388835.1
prsA foldase protein PrsA NP_388876.1
hemE uroporphyrinogen decarboxylase NP_388893.1
hemH ferrochelatase NP_388894.1
hemY protoporphyrinogen oxidase NP_388895.1
yisB hypothetical protein NP_388947.1
fabF 3-oxoacyl-[acyl-carrier-protein] synthase 2 NP_389016.1
trpS tryptophan--tRNA ligase NP_389024.1
ppnK inorganic polyphosphate/ATP-NAD kinase 1 NP_389043.1
hemD hypothetical protein NP_389105.1
yjzJ hypothetical protein YP_003097711.1
xkdB phage-like element PBSX protein XkdB NP_389134.2
xkdC phage-like element PBSX protein XkdC NP_389135.2
mgtE magnesium transporter MgtE NP_389213.1
patA N-acetyl-LL-diaminopimelate aminotransferase NP_389283.2
dapH NP_389301.2
dapL N-acetyldiaminopimelate deacetylase NP_389302.1
rnjA ribonuclease J 1 NP_389336.1
pdhA pyruvate dehydrogenase E1 component subunitalpha NP_389341.1
ylaN hypothetical protein NP_389367.1
ftsW lipid II flippase FtsW NP_389368.1
coaD phosphopantetheine adenylyltransferase NP_389385.1
ftsL cell division protein FtsL NP_389398.1
pbpB penicillin-binding protein 2B NP_389399.2
murE NP_389401.1
mraY phospho-n-acetylmuramoyl-pentapeptide-transferase NP_389402.2
murD UDP-N-acetylmuramoylalanine--D-glutamate ligase NP_389403.1
murG NP_389405.2
murB UDP-N-acetylenolpyruvoylglucosamine reductase NP_389406.1
divIB cell division protein DivIB NP_389407.1
ftsA cell division protein FtsA NP_389411.2
ftsZ cell division protein FtsZ NP_389412.2
ileS isoleucine--tRNA ligase NP_389426.2
coaBC coenzyme A biosynthesis bifunctional proteinCoaBC NP_389452.1
priA NP_389453.1
yloU hypothetical protein NP_389465.1
plsX phosphate acyltransferase NP_389471.1
fabD malonyl CoA-acyl carrier protein transacylase NP_389472.1
fabG 3-oxoacyl-[acyl-carrier-protein] reductase FabG NP_389473.1
acpP acyl carrier protein NP_389474.1
rnc ribonuclease 3 NP_389475.1
ffh signal recognition particle protein NP_389480.1
rpsP 30S ribosomal protein S16 NP_389481.1
trmD NP_389485.1
rplS 50S ribosomal protein L19 NP_389486.1
rbgA ribosome biogenesis GTPase A NP_389487.1
rpsB 30S ribosomal protein S2 NP_389531.1
tsf elongation factor Ts NP_389532.1
pyrH uridylate kinase NP_389533.2
frr ribosome-recycling factor NP_389534.1
uppS undecaprenyl pyrophosphate synthase NP_389535.1
cdsA phosphatidate cytidylyltransferase NP_389536.1
dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase NP_389537.2
proS proline--tRNA ligase NP_389539.1
nusA transcription termination/antiterminationprotein NusA NP_389542.1
infB translation initiation factor IF-2 NP_389545.1
ribC riboflavin biosynthesis protein RibC NP_389549.1
rpsO 30S ribosomal protein S15 NP_389550.1
dapG aspartokinase 1 NP_389558.2
pgsA CDP-diacylglycerol--glycerol-3-phosphate3-phosphatidyltransferase NP_389574.2
ymdA ribonuclease Y NP_389578.1
nrdI ribonucleotide reductase stimulatory proteinNrdI NP_389619.1
nrdF ribonucleoside-diphosphate reductase subunitbeta NP_389621.1
yneF hypothetical protein NP_389674.1
yneS glycerol-3-phosphate acyltransferase NP_389689.1
odhB dihydrolipoyllysine-residue succinyltransferasecomponent of 2-oxoglutarate dehydrogenase complex NP_389818.2
yomL hypothetical protein NP_390015.1
sunI hypothetical protein NP_390032.1
dfrA dihydrofolate reductase NP_390064.1
dnaD DNA replication protein DnaD NP_390116.1
panC pantothenate synthetase NP_390123.1
birA bifunctional protein BirA NP_390125.1
cca CCA-adding enzyme NP_390126.1
dapB 4-hydroxy-tetrahydrodipicolinate reductase NP_390130.1
aroE 3-phosphoshikimate 1-carboxyvinyltransferase NP_390141.1
aroF chorismate synthase NP_390152.3
hepT heptaprenyl diphosphate synthase component 2 NP_390155.1
ubiE demethylmenaquinone methyltransferase NP_390156.1
hepS heptaprenyl diphosphate synthase component 1 NP_390157.1
folE GTP cyclohydrolase 1 NP_390159.1
hbs DNA-binding protein HU 1 NP_390160.1
gpsA glycerol-3-phosphate dehydrogenase NP_390164.1
engA GTPase Der NP_390165.1
cmk cytidylate kinase NP_390170.1
resC cytochrome c biogenesis protein ResC NP_390194.2
scpA segregation and condensation protein A NP_390203.1
ypuF hypothetical protein NP_390204.1
yqjK ribonuclease Z NP_390265.1
dxs 1-deoxy-D-xylulose-5-phosphate synthase NP_390307.1
folD bifunctional protein FolD NP_390311.1
yqhY hypothetical protein NP_390313.2
accC acetyl-CoA carboxylase biotin carboxylasesubunit NP_390314.2
accB acetyl-CoA carboxylase biotin carboxyl carrierprotein subunit NP_390315.1
ispG NP_390386.1
ispH 4-hydroxy-3-methylbut-2-enyl diphosphatereductase NP_390395.2
dnaG DNA primase NP_390400.2
glyS glycine--tRNA ligase beta subunit NP_390404.2
glyQ glycine--tRNA ligase alpha subunit NP_390405.1
era GTPase Era NP_390407.1
holA hypothetical protein NP_390434.1
nadD nicotinate-nucleotide adenylyltransferase NP_390442.1
yqeH hypothetical protein NP_390445.1
yqaE XRE family transcriptional regulator NP_390512.1
alaS alanine--tRNA ligase NP_390618.1
mnmA tRNA-specific 2-thiouridylase MnmA NP_390627.3
aspS aspartate--tRNA ligase NP_390633.1
nifS cysteine desulfurase NifS NP_390666.1
rpmA 50S ribosomal protein L27 NP_390672.1
rplU 50S ribosomal protein L21 NP_390674.1
mreD rod shape-determining protein MreD NP_390679.1
mreC cell shape-determining protein MreC NP_390680.2
mreB rod shape-determining protein MreB NP_390681.2
folC folylpolyglutamate synthase NP_390686.1
hemB delta-aminolevulinic acid dehydratase NP_390691.1
hemC porphobilinogen deaminase NP_390693.1
hemA glutamyl-tRNA reductase NP_390695.1
engB GTP-binding protein EngB NP_390697.1
racE glutamate racemase NP_390717.2
trxA thioredoxin NP_390728.1
pheT phenylalanine--tRNA ligase beta subunit NP_390741.1
pheS phenylalanine--tRNA ligase alpha subunit NP_390742.1
ysgA tRNA/rRNA methyltransferase YsgA NP_390743.1
rplT 50S ribosomal protein L20 NP_390763.1
infC translation initiation factor IF-3 NP_390765.1
dnaI primosomal protein DnaI NP_390776.1
dnaB replication initiation and membrane attachmentprotein NP_390777.1
coaE dephospho-CoA kinase NP_390784.1
accA acetyl-CoA carboxylase carboxyltransferasesubunit alpha NP_390798.1
accD acetyl-CoA carboxylase carboxyltransferasesubunit beta NP_390799.2
rpsD 30S ribosomal protein S4 NP_390844.1
tyrS tyrosine--tRNA ligase 1 NP_390845.1
murC UDP-N-acetylmuramate--L-alanine ligase NP_390857.1
asnB asparagine synthetase 1 NP_390932.1
metK S-adenosylmethionine synthase NP_390933.1
mntA manganese-binding lipoprotein MntA NP_390955.1
menC o-succinylbenzoate synthase NP_390956.1
menE 2-succinylbenzoate-CoA ligase NP_390957.1
menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase NP_390960.1
mrpA NP_391038.2
mrpB NP_391039.1
mrpC NP_391040.2
mrpD NP_391041.3
mrpE YP_054591.2
mrpF NP_391043.2
mrpG NP_391044.1
yumC ferredoxin--NADP reductase 2 NP_391091.2
dapF diaminopimelate epimerase NP_391097.1
sufB FeS cluster assembly protein SufB NP_391146.1
iscU NifU-like protein NP_391147.1
sufS cysteine desulfurase NP_391148.1
sufD FeS cluster assembly protein SufD NP_391149.1
sufC ABC transporter ATP-binding protein NP_391150.1
rghRA HTH-type transcriptional repressor RghR NP_391246.1
eno enolase NP_391270.1
pgm NP_391271.1
gapA glyceraldehyde-3-phosphate dehydrogenase 1 NP_391274.1
trxB thioredoxin NP_391359.1
prfB peptide chain release factor 2 NP_391409.1
secA protein translocase subunit SecA NP_391410.1
tagO undecaprenyl-phosphate N-acetylglucosaminyl1-phosphate transferase NP_391433.1
tuaB teichuronic acid biosynthesis protein TuaB NP_391440.1
mnaA UDP-N-acetylglucosamine 2-epimerase NP_391446.1
tagH teichoic acids export ATP-binding protein TagH NP_391451.1
tagG teichoic acid translocation permease proteinTagG NP_391452.1
tagF CDP-glycerol:poly NP_391453.1
tagD glycerol-3-phosphate cytidylyltransferase NP_391455.1
tagA N-acetylmannosaminyltransferase NP_391456.1
tagB CDP-glycerol:glycerophosphateglycerophosphotransferase NP_391457.1
mbl MreB-like protein NP_391522.2
murAA UDP-N-acetylglucosamine1-carboxyvinyltransferase 1 NP_391557.1
prfA peptide chain release factor 1 NP_391582.1
pyrG CTP synthase NP_391596.1
rodA rod shape-determining protein RodA NP_391691.1
menA NP_391728.1
yxlC hypothetical protein NP_391748.1
walK sensor histidine kinase NP_391920.1
walR transcriptional regulator NP_391921.1
dnaC replicative DNA helicase NP_391924.2
ppaC manganese-dependent inorganic pyrophosphatase NP_391935.1
rpsR 30S ribosomal protein S18 NP_391969.2
ssbA single-stranded DNA-binding protein NP_391970.1
rnpA ribonuclease P protein component NP_391985.1
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