E. coli essential genes (20 sense codon recoding)

E. coli essential genes (20 sense codon recoding)

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RED20 is a so-called "fail-safe genetic code" introduced by Calles and colleagues in 2019 [1]. RED20 encodes each of the 20 canonical amino acids with exactly one sense codon and terminates translation with the canonical three stop codons. RED20 therefore leaves 41 of the 64 triplet codons unassociated with any translation machinery, meaning they are "null codons". Recoding an organism in RED20 requires recoding all of its translated genes into RED20 as well as deleting its tRNA genes associated with RED20 null codons. The Free Genes E. coli RED20 essential gene distribution represents RED20 recoded versions of 245 of the 299 translated genes in the Keio collection, which represents the set of genes essential for life in E. coli as determined by single gene deletion viability [2].

What can it be used for
The E. coli RED20 gene set can be used to research the engineering of RED20 encoded organisms and genetic systems. The E. coli RED20 gene set can also be used in E. coli based expression systems incorporating non-canonical amino acids. Because every gene in this gene set is encoded using only 20 sense codons and one of three stop codons, users of this gene set can reprogram any of the other 41 null codons using orthogonal translation machinery.

Where can I find more information

  • [1] Calles, J., Justice, I., Brinkley, D., Garcia, A. & Endy, D. Fail-safe genetic codes designed to intrinsically contain engineered organisms. Nucleic Acids Res. (2019). doi:10.1093/nar/gkz745
  • [2] Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).


All genes are present on the plate in E. coli glycerol stocks. This product is made available under the unilateral OpenMTA

Some or all of these items are for use only as permitted by a research exemption.



245 unique parts

Instructions for Use

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


Plate Layouts

Plates in Set: RED20 Plate 1 (may also be labelled ecolired20-1), RED20 Plate 2 (or ecolired20-2), RED20 Plate 3 (or ecolired20-3)

Genes

Gene Name NCBI ID Freegenes ID
minD inhibitor of FtsZ ring polymerization;chromosome-membrane tethering protein; membrane ATPase ofthe MinCDEE system NP_415693.1 BBF10K_001035
pth peptidyl-tRNA hydrolase NP_415722.1 BBF10K_001036
prs phosphoribosylpyrophosphate synthase NP_415725.1 BBF10K_001037
ispE 4-diphosphocytidyl-2-C-methylerythritol kinase NP_415726.1 BBF10K_001038
lolB lipoprotein localization factor NP_415727.1 BBF10K_001039
hemA glutamyl tRNA reductase NP_415728.1 BBF10K_001040
prfA peptide chain release factor RF-1 NP_415729.1 BBF10K_001041
kdsA 3-deoxy-D-manno-octulosonate 8-phosphatesynthase NP_415733.1 BBF10K_001043
topA DNA topoisomerase 1 NP_415790.1 BBF10K_001044
fabI Enoyl-[acyl-carrier-protein] reductase [NADH] FabI NP_415804.1 BBF10K_001046
dicA Qin prophage; putative regulator for DicB NP_416088.1 BBF10K_001048
ydfB Qin prophage; uncharacterized protein NP_416090.2 BBF10K_001049
tyrS tyrosyl-tRNA synthetase NP_416154.1 BBF10K_001050
ydiL putative HTH domain DNA-binding protein NP_416204.2 BBF10K_001052
pheS Phenylalanine--tRNA ligase alpha subunit NP_416229.1 BBF10K_001054
rplT 50S ribosomal subunit protein L20 NP_416231.1 BBF10K_001055
infC translation initiation factor IF-3 NP_416233.1 BBF10K_001056
nadE NH(3)-dependent NAD(+) synthetase NP_416254.1 BBF10K_001058
tsaB tRNA threonylcarbamoyladenosine biosynthesis protein TsaB NP_416321.1 BBF10K_001059
aspS aspartyl-tRNA synthetase NP_416380.1 BBF10K_001060
argS arginyl-tRNA synthetase NP_416390.1 BBF10K_001061
pgsA phosphatidylglycerophosphate synthetase NP_416422.1 BBF10K_001062
yefM antitoxin of the YoeB-YefM toxin-antitoxinsystem NP_416521.2 BBF10K_001063
yejM essential inner membrane DUF3413domain-containing protein; lipid A production and membranepermeability factor NP_416693.1 BBF10K_001065
gyrA DNA gyrase subunit A NP_416734.1 BBF10K_001066
folC bifunctional folylpolyglutamate synthase/dihydrofolate synthase NP_416818.1 BBF10K_001069
accD Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta NP_416819.1 BBF10K_001070
fabB 3-oxoacyl-[acyl-carrier-protein] synthase I NP_416826.1 BBF10K_001071
gltX glutamyl-tRNA synthetase NP_416899.1 BBF10K_001072
ligA DNA ligase NP_416906.1 BBF10K_001073
hisS histidyl tRNA synthetase NP_417009.1 BBF10K_001076
ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) NP_417010.1 BBF10K_001077
suhB inositol monophosphatase NP_417028.1 BBF10K_001078
tadA tRNA-specific adenosine deaminase NP_417054.2 BBF10K_001079
era GTPase Era NP_417061.1 BBF10K_001081
lepB Signal peptidase I NP_417063.1 BBF10K_001082
rpoE RNA polymerase sigma E factor NP_417068.1 BBF10K_001083
pssA phosphatidylserine synthase;CDP-diacylglycerol-serine O-phosphatidyltransferase NP_417080.4 BBF10K_001084
bamD BamABCDE complex OM biogenesis lipoprotein NP_417086.1 BBF10K_001085
rplS 50S ribosomal subunit protein L19 NP_417097.1 BBF10K_001086
trmD tRNA (guanine-N(1)-)-methyltransferase NP_417098.1 BBF10K_001087
rpsP 30S ribosomal subunit protein S16 NP_417100.1 BBF10K_001088
ffh Signal recognition particle protein NP_417101.1 BBF10K_001089
grpE heat shock protein NP_417104.1 BBF10K_001090
csrA pleiotropic regulatory protein for carbon sourcemetabolism NP_417176.1 BBF10K_001092
alaS alanyl-tRNA synthetase NP_417177.1 BBF10K_001093
ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase NP_417226.1 BBF10K_001094
ispD 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase NP_417227.1 BBF10K_001095
ftsB cell division protein NP_417228.1 BBF10K_001096
eno enolase NP_417259.1 BBF10K_001097
pyrG CTP synthetase NP_417260.1 BBF10K_001098
mazE antitoxin of the ChpA-ChpR toxin-antitoxinsystem NP_417263.1 BBF10K_001099
lgt phosphatidylglycerol-prolipoproteindiacylglyceryl transferase NP_417305.1 BBF10K_001100
prfB peptide chain release factor RF-2 NP_417367.1 BBF10K_001101
fbaA Fructose-bisphosphate aldolase NP_417400.1 BBF10K_001102
pgk phosphoglycerate kinase NP_417401.1 BBF10K_001103
metK S-adenosylmethionine synthetase NP_417417.1 BBF10K_001104
yqgF putative Holliday junction resolvase NP_417424.1 BBF10K_001105
plsC 1-acyl-sn-glycerol-3-phosphate acyltransferase NP_417490.1 BBF10K_001106
mqsA antitoxin for MqsR toxin; transcriptionalrepressor NP_417493.1 BBF10K_001108
parE DNA topoisomerase 4 subunit B NP_417502.1 BBF10K_001109
ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase NP_417513.1 BBF10K_001110
cca Multifunctional CCA protein NP_417528.1 BBF10K_001111
tsaD tRNA N6-adenosine threonylcarbamoyltransferase NP_417536.1 BBF10K_001112
rpsU 30S ribosomal subunit protein S21 NP_417537.1 BBF10K_001113
dnaG DNA primase NP_417538.1 BBF10K_001114
rsmI Ribosomal RNA small subunit methyltransferase I NP_417615.1 BBF10K_001117
yhbV U32 peptidase family protein NP_417628.2 BBF10K_001118
ftsH ATP-dependent zinc metalloprotease FtsH NP_417645.1 BBF10K_001122
rpmA 50S ribosomal subunit protein L27 NP_417652.1 BBF10K_001124
rplU 50S ribosomal subunit protein L21 NP_417653.1 BBF10K_001125
ispB octaprenyl diphosphate synthase NP_417654.1 BBF10K_001126
murA UDP-N-acetylglucosamine1-carboxyvinyltransferase NP_417656.1 BBF10K_001127
lptC periplasmic membrane-anchored LPS-bindingprotein; LPS export protein NP_417666.1 BBF10K_001128
lptA lipopolysaccharide export ABC transporterperiplasmic binding protein; Lipid A binding protein; LPSexport and assembly protein NP_417667.1 BBF10K_001129
rplM 50S ribosomal subunit protein L13 NP_417698.1 BBF10K_001131
degS Serine endoprotease DegS NP_417702.1 BBF10K_001132
mreD cell wall structural complex MreBCDtransmembrane component MreD NP_417715.1 BBF10K_001133
mreC cell wall structural complex MreBCDtransmembrane component MreC NP_417716.1 BBF10K_001134
mreB Cell shape-determining protein MreB NP_417717.2 BBF10K_001135
accB Biotin carboxyl carrier protein of acetyl-CoA carboxylase NP_417721.1 BBF10K_001136
accC Biotin carboxylase NP_417722.1 BBF10K_001137
tsaC Threonylcarbamoyl-AMP synthase NP_417741.1 BBF10K_001138
def peptide deformylase NP_417745.1 BBF10K_001139
fmt Methionyl-tRNA formyltransferase NP_417746.1 BBF10K_001140
rplQ 50S ribosomal subunit protein L17 NP_417753.1 BBF10K_001141
rpoA DNA-directed RNA polymerase subunit alpha NP_417754.1 BBF10K_001142
rpsD 30S ribosomal subunit protein S4 NP_417755.1 BBF10K_001143
rpsK 30S ribosomal subunit protein S11 NP_417756.1 BBF10K_001144
secY preprotein translocase membrane subunit NP_417759.1 BBF10K_001145
rplO 50S ribosomal subunit protein L15 NP_417760.1 BBF10K_001146
rpsE 30S ribosomal subunit protein S5 NP_417762.1 BBF10K_001148
rplR 50S ribosomal subunit protein L18 NP_417763.1 BBF10K_001149
rpsH 30S ribosomal subunit protein S8 NP_417765.1 BBF10K_001151
rpsN 30S ribosomal subunit protein S14 NP_417766.1 BBF10K_001152
rplE 50S ribosomal subunit protein L5 NP_417767.1 BBF10K_001153
rplX 50S ribosomal subunit protein L24 NP_417768.1 BBF10K_001154
rplN 50S ribosomal subunit protein L14 NP_417769.1 BBF10K_001155
rpmC 50S ribosomal subunit protein L29 NP_417771.1 BBF10K_001156
rplP 50S ribosomal subunit protein L16 NP_417772.1 BBF10K_001157
rpsC 30S ribosomal subunit protein S3 NP_417773.1 BBF10K_001158
rplV 50S ribosomal subunit protein L22 NP_417774.1 BBF10K_001159
rplB 50S ribosomal subunit protein L2 NP_417776.1 BBF10K_001161
rplW 50S ribosomal subunit protein L23 NP_417777.1 BBF10K_001162
rplD 50S ribosomal subunit protein L4 NP_417778.1 BBF10K_001163
rpsL 30S ribosomal subunit protein S12 NP_417801.1 BBF10K_001168
trpS tryptophanyl-tRNA synthetase NP_417843.1 BBF10K_001169
yrfF Putative membrane protein IgaA homolog NP_417857.1 BBF10K_001170
asd Aspartate-semialdehyde dehydrogenase NP_417891.1 BBF10K_001171
ftsX putative ABC transporter permease NP_417919.1 BBF10K_001172
ftsE cell division ATP-binding protein NP_417920.1 BBF10K_001173
yhhQ DUF165 family inner membrane protein NP_417928.1 BBF10K_001175
glyQ Glycine--tRNA ligase alpha subunit NP_418017.1 BBF10K_001178
gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase NP_418065.1 BBF10K_001179
waaU lipopolysaccharide core biosynthesis NP_418080.1 BBF10K_001180
waaA 3-deoxy-D-manno-octulosonic acid transferase NP_418090.1 BBF10K_001181
coaD pantetheine-phosphate adenylyltransferase NP_418091.1 BBF10K_001182
rpmB 50S ribosomal subunit protein L28 NP_418094.1 BBF10K_001183
dfp Coenzyme A biosynthesis bifunctional protein CoaBC NP_418096.4 BBF10K_001184
dut deoxyuridinetriphosphatase NP_418097.1 BBF10K_001185
gmk guanylate kinase NP_418105.1 BBF10K_001186
gyrB DNA gyrase subunit B YP_026241.1 BBF10K_001188
dnaN Beta sliding clamp NP_418156.1 BBF10K_001189
dnaA Chromosomal replication initiator protein DnaA NP_418157.1 BBF10K_001190
rpmH 50S ribosomal subunit protein L34 NP_418158.1 BBF10K_001191
rnpA protein C5 component of RNase P NP_418159.1 BBF10K_001192
tnaB tryptophan transporter of low affinity NP_418165.1 BBF10K_001194
glmS L-glutamine:D-fructose-6-phosphateaminotransferase NP_418185.1 BBF10K_001195
glmU fused N-acetyl glucosamine-1-phosphateuridyltransferase/glucosamine-1-phosphate acetyltransferase NP_418186.1 BBF10K_001196
rho transcription termination factor NP_418230.1 BBF10K_001197
wzyE putative ECA polysaccharide chain elongationprotein NP_418241.1 BBF10K_001198
hemD uroporphyrinogen III synthase NP_418248.1 BBF10K_001199
hemC hydroxymethylbilane synthase YP_026260.1 BBF10K_001200
ubiB Probable protein kinase UbiB NP_418279.1 BBF10K_001201
hemG Protoporphyrinogen IX dehydrogenase [menaquinone] NP_418292.1 BBF10K_001203
yihA cell division GTP-binding protein NP_418301.3 BBF10K_001205
ftsN essential cell division protein NP_418368.1 BBF10K_001206
murI glutamate racemase NP_418402.2 BBF10K_001207
murB UDP-N-acetylenolpyruvoylglucosamine reductase NP_418403.1 BBF10K_001208
birA Bifunctional ligase/repressor BirA NP_418404.1 BBF10K_001209
coaA pantothenate kinase NP_418405.1 BBF10K_001210
secE preprotein translocase membrane subunit NP_418408.1 BBF10K_001211
nusG transcription termination factor NP_418409.1 BBF10K_001212
rplJ 50S ribosomal subunit protein L10 NP_418412.1 BBF10K_001213
rplL 50S ribosomal subunit protein L7/L12 NP_418413.1 BBF10K_001214
rpoB DNA-directed RNA polymerase subunit beta NP_418414.1 BBF10K_001215
ubiA p-hydroxybenzoate octaprenyltransferase NP_418464.1 BBF10K_001217
plsB glycerol-3-phosphate O-acyltransferase NP_418465.4 BBF10K_001218
lexA transcriptional repressor of SOS regulon NP_418467.1 BBF10K_001219
dnaB replicative DNA helicase NP_418476.1 BBF10K_001220
ssb single-stranded DNA-binding protein NP_418483.1 BBF10K_001221
alsK D-allose kinase NP_418508.1 BBF10K_001222
groS 10 kDa chaperonin NP_418566.1 BBF10K_001223
orn oligoribonuclease NP_418586.4 BBF10K_001226
tsaE tRNA threonylcarbamoyladenosine biosynthesis protein TsaE NP_418589.1 BBF10K_001227
rpsR 30S ribosomal subunit protein S18 NP_418623.1 BBF10K_001228
chpS antitoxin of the ChpBS toxin-antitoxin system NP_418645.2 BBF10K_001229
ppa inorganic pyrophosphatase NP_418647.1 BBF10K_001230
valS valyl-tRNA synthetase NP_418679.1 BBF10K_001231
lptF lipopolysaccharide export ABC permease NP_418682.1 BBF10K_001232
lptG lipopolysaccharide export ABC permease NP_418683.4 BBF10K_001233
dnaC DNA biosynthesis protein NP_418781.1 BBF10K_001234
ribF bifunctional riboflavin kinase/FAD synthetase NP_414566.1 BBF10K_003118
ileS isoleucyl-tRNA synthetase NP_414567.1 BBF10K_003119
lspA Lipoprotein signal peptidase NP_414568.1 BBF10K_003120
ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase NP_414570.1 BBF10K_003121
folA dihydrofolate reductase NP_414590.1 BBF10K_003122
lptD LPS-assembly protein LptD NP_414596.1 BBF10K_003123
ftsL membrane bound cell division leucine zipperseptum protein NP_414625.1 BBF10K_003124
ftsI transpeptidase involved in septal peptidoglycansynthesis; penicillin-binding protein 3 NP_414626.1 BBF10K_003125
murF UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase NP_414628.1 BBF10K_003127
mraY phospho-N-acetylmuramoyl-pentapeptidetransferase NP_414629.1 BBF10K_003128
murD UDP-N-acetylmuramoyl-L-alanine:D-glutamateligase NP_414630.1 BBF10K_003129
ftsW putative lipid II flippase; integral membraneprotein; FtsZ ring stabilizer NP_414631.1 BBF10K_003130
murG N-acetylglucosaminyl transferase NP_414632.1 BBF10K_003131
ftsQ Cell division protein FtsQ NP_414635.1 BBF10K_003133
ftsA ATP-binding cell division FtsK recruitmentprotein NP_414636.1 BBF10K_003134
ftsZ GTP-binding tubulin-like cell division protein NP_414637.1 BBF10K_003135
lpxC UDP-3-O-acyl N-acetylglucosamine deacetylase NP_414638.1 BBF10K_003136
secM regulator of secA translation NP_414639.2 BBF10K_003137
secA Protein translocase subunit SecA NP_414640.1 BBF10K_003138
can carbonic anhydrase NP_414668.1 BBF10K_003140
folK 2-amino-4-hydroxy-6-hydroxymethyldihyropteridinepyrophosphokinase NP_414684.1 BBF10K_003141
hemL Glutamate-1-semialdehyde 2,1-aminomutase NP_414696.1 BBF10K_003142
erpA iron-sulfur cluster insertion protein NP_414698.1 BBF10K_003143
rpsB 30S ribosomal subunit protein S2 NP_414711.1 BBF10K_003145
tsf translation elongation factor EF-Ts NP_414712.1 BBF10K_003146
pyrH uridylate kinase NP_414713.1 BBF10K_003147
frr ribosome recycling factor NP_414714.1 BBF10K_003148
dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase NP_414715.1 BBF10K_003149
ispU undecaprenyl pyrophosphate synthase NP_414716.1 BBF10K_003150
cdsA CDP-diglyceride synthase NP_414717.2 BBF10K_003151
rseP Regulator of sigma-E protease RseP NP_414718.1 BBF10K_003152
bamA BamABCDE complex OM biogenesis outer membranepore-forming assembly factor NP_414719.1 BBF10K_003153
lpxD UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase NP_414721.1 BBF10K_003154
lpxA UDP-N-acetylglucosamine acetyltransferase NP_414723.1 BBF10K_003156
lpxB tetraacyldisaccharide-1-P synthase NP_414724.1 BBF10K_003157
accA Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha NP_414727.1 BBF10K_003159
tilS tRNA(Ile)-lysidine synthase NP_414730.1 BBF10K_003160
proS prolyl-tRNA synthetase NP_414736.1 BBF10K_003161
yafN antitoxin of the YafO-YafN toxin-antitoxinsystem NP_414767.1 BBF10K_003162
yagG CP4-6 prophage; putative sugar transporter NP_414804.1 BBF10K_003163
hemB Delta-aminolevulinic acid dehydratase NP_414903.4 BBF10K_003164
secD SecYEG protein translocase auxillary subunit NP_414942.1 BBF10K_003165
secF SecYEG protein translocase auxillary subunit NP_414943.1 BBF10K_003166
ribD Riboflavin biosynthesis protein RibD NP_414948.1 BBF10K_003167
ribE riboflavin synthase beta chain NP_414949.1 BBF10K_003168
thiL thiamine monophosphate kinase NP_414951.1 BBF10K_003169
dxs 1-deoxy-D-xylulose-5-phosphate synthase NP_414954.1 BBF10K_003170
ispA geranyltranstransferase NP_414955.1 BBF10K_003171
dnaX DNA polymerase III subunit tau NP_415003.1 BBF10K_003172
adk adenylate kinase NP_415007.1 BBF10K_003173
hemH ferrochelatase NP_415008.1 BBF10K_003174
lpxH UDP-2,3-diacylglucosamine hydrolase NP_415057.1 BBF10K_003175
cysS cysteinyl-tRNA synthetase NP_415059.1 BBF10K_003176
folD Bifunctional protein FolD NP_415062.1 BBF10K_003177
entD phosphopantetheinyltransferase component ofenterobactin synthase multienzyme complex NP_415115.2 BBF10K_003178
mrdB cell wall shape-determining protein NP_415167.1 BBF10K_003179
mrdA Peptidoglycan D,D-transpeptidase MrdA NP_415168.1 BBF10K_003180
nadD Nicotinate-nucleotide adenylyltransferase NP_415172.1 BBF10K_003181
holA DNA polymerase III subunit delta NP_415173.1 BBF10K_003182
lptE LPS-assembly lipoprotein LptE NP_415174.1 BBF10K_003183
lnt apolipoprotein N-acyltransferase NP_415190.1 BBF10K_003185
glnS glutamyl-tRNA synthetase NP_415206.1 BBF10K_003186
fldA flavodoxin 1 NP_415210.1 BBF10K_003187
cydA Cytochrome bd-I ubiquinol oxidase subunit 1 NP_415261.2 BBF10K_003188
infA translation initiation factor IF-1 NP_415404.1 BBF10K_003189
serS seryl-tRNA synthetase NP_415413.1 BBF10K_003193
msbA lipid ABC transporter permease/ATPase NP_415434.1 BBF10K_003195
lpxK Tetraacyldisaccharide 4'-kinase NP_415435.1 BBF10K_003196
kdsB 3-deoxy-manno-octulosonate cytidylyltransferase NP_415438.1 BBF10K_003197
mukF Chromosome partition protein MukF NP_415442.1 BBF10K_003198
mukE Chromosome partition protein MukE NP_415443.2 BBF10K_003199
asnS asparaginyl tRNA synthetase NP_415450.1 BBF10K_003201
fabA beta-hydroxydecanoyl thioester dehydrase NP_415474.1 BBF10K_003202
yceQ uncharacterized protein NP_415603.2 BBF10K_003205
fabD malonyl-CoA-[acyl-carrier-protein] transacylase NP_415610.1 BBF10K_003206
fabG 3-oxoacyl-[acyl-carrier-protein] reductase NP_415611.1 BBF10K_003207
acpP Acyl carrier protein NP_415612.1 BBF10K_003208
tmk thymidylate kinase NP_415616.1 BBF10K_003209
holB DNA polymerase III subunit delta' NP_415617.1 BBF10K_003210
lolC lipoprotein-releasing system transmembraneprotein NP_415634.1 BBF10K_003211
lolE lipoprotein-releasing system transmembraneprotein NP_415636.1 BBF10K_003213
purB adenylosuccinate lyase NP_415649.1 BBF10K_003214
minE cell division topological specificity factor NP_415692.1 BBF10K_003216

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