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).


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245 unique parts

Instructions for Use

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


Plate Layout

PlateSet: ecolired20-1 ecolired20-2 ecolired20-3

Genes

Gene Name NCBI ID
minD inhibitor of FtsZ ring polymerization;chromosome-membrane tethering protein; membrane ATPase ofthe MinCDEE system NP_415693.1
pth peptidyl-tRNA hydrolase NP_415722.1
prs phosphoribosylpyrophosphate synthase NP_415725.1
ispE 4-diphosphocytidyl-2-C-methylerythritol kinase NP_415726.1
lolB lipoprotein localization factor NP_415727.1
hemA glutamyl tRNA reductase NP_415728.1
prfA peptide chain release factor RF-1 NP_415729.1
kdsA 3-deoxy-D-manno-octulosonate 8-phosphatesynthase NP_415733.1
topA NP_415790.1
fabI NP_415804.1
dicA Qin prophage; putative regulator for DicB NP_416088.1
ydfB Qin prophage; uncharacterized protein NP_416090.2
tyrS tyrosyl-tRNA synthetase NP_416154.1
ydiL putative HTH domain DNA-binding protein NP_416204.2
pheS NP_416229.1
rplT 50S ribosomal subunit protein L20 NP_416231.1
infC translation initiation factor IF-3 NP_416233.1
nadE NP_416254.1
tsaB NP_416321.1
aspS aspartyl-tRNA synthetase NP_416380.1
argS arginyl-tRNA synthetase NP_416390.1
pgsA phosphatidylglycerophosphate synthetase NP_416422.1
yefM antitoxin of the YoeB-YefM toxin-antitoxinsystem NP_416521.2
yejM essential inner membrane DUF3413domain-containing protein; lipid A production and membranepermeability factor NP_416693.1
gyrA NP_416734.1
folC bifunctional folylpolyglutamate synthase/dihydrofolate synthase NP_416818.1
accD NP_416819.1
fabB 3-oxoacyl-[acyl-carrier-protein] synthase I NP_416826.1
gltX glutamyl-tRNA synthetase NP_416899.1
ligA NP_416906.1
hisS histidyl tRNA synthetase NP_417009.1
ispG NP_417010.1
suhB inositol monophosphatase NP_417028.1
tadA tRNA-specific adenosine deaminase NP_417054.2
era NP_417061.1
lepB NP_417063.1
rpoE RNA polymerase sigma E factor NP_417068.1
pssA phosphatidylserine synthase;CDP-diacylglycerol-serine O-phosphatidyltransferase NP_417080.4
bamD BamABCDE complex OM biogenesis lipoprotein NP_417086.1
rplS 50S ribosomal subunit protein L19 NP_417097.1
trmD NP_417098.1
rpsP 30S ribosomal subunit protein S16 NP_417100.1
ffh NP_417101.1
grpE heat shock protein NP_417104.1
csrA pleiotropic regulatory protein for carbon sourcemetabolism NP_417176.1
alaS alanyl-tRNA synthetase NP_417177.1
ispF NP_417226.1
ispD 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase NP_417227.1
ftsB cell division protein NP_417228.1
eno enolase NP_417259.1
pyrG CTP synthetase NP_417260.1
mazE antitoxin of the ChpA-ChpR toxin-antitoxinsystem NP_417263.1
lgt phosphatidylglycerol-prolipoproteindiacylglyceryl transferase NP_417305.1
prfB peptide chain release factor RF-2 NP_417367.1
fbaA NP_417400.1
pgk phosphoglycerate kinase NP_417401.1
metK S-adenosylmethionine synthetase NP_417417.1
yqgF putative Holliday junction resolvase NP_417424.1
plsC 1-acyl-sn-glycerol-3-phosphate acyltransferase NP_417490.1
mqsA antitoxin for MqsR toxin; transcriptionalrepressor NP_417493.1
parE NP_417502.1
ribB NP_417513.1
cca NP_417528.1
tsaD NP_417536.1
rpsU 30S ribosomal subunit protein S21 NP_417537.1
dnaG DNA primase NP_417538.1
rsmI NP_417615.1
yhbV U32 peptidase family protein NP_417628.2
ftsH NP_417645.1
rpmA 50S ribosomal subunit protein L27 NP_417652.1
rplU 50S ribosomal subunit protein L21 NP_417653.1
ispB octaprenyl diphosphate synthase NP_417654.1
murA UDP-N-acetylglucosamine1-carboxyvinyltransferase NP_417656.1
lptC periplasmic membrane-anchored LPS-bindingprotein; LPS export protein NP_417666.1
lptA lipopolysaccharide export ABC transporterperiplasmic binding protein; Lipid A binding protein; LPSexport and assembly protein NP_417667.1
rplM 50S ribosomal subunit protein L13 NP_417698.1
degS NP_417702.1
mreD cell wall structural complex MreBCDtransmembrane component MreD NP_417715.1
mreC cell wall structural complex MreBCDtransmembrane component MreC NP_417716.1
mreB NP_417717.2
accB NP_417721.1
accC NP_417722.1
tsaC NP_417741.1
def peptide deformylase NP_417745.1
fmt NP_417746.1
rplQ 50S ribosomal subunit protein L17 NP_417753.1
rpoA NP_417754.1
rpsD 30S ribosomal subunit protein S4 NP_417755.1
rpsK 30S ribosomal subunit protein S11 NP_417756.1
secY preprotein translocase membrane subunit NP_417759.1
rplO 50S ribosomal subunit protein L15 NP_417760.1
rpsE 30S ribosomal subunit protein S5 NP_417762.1
rplR 50S ribosomal subunit protein L18 NP_417763.1
rpsH 30S ribosomal subunit protein S8 NP_417765.1
rpsN 30S ribosomal subunit protein S14 NP_417766.1
rplE 50S ribosomal subunit protein L5 NP_417767.1
rplX 50S ribosomal subunit protein L24 NP_417768.1
rplN 50S ribosomal subunit protein L14 NP_417769.1
rpmC 50S ribosomal subunit protein L29 NP_417771.1
rplP 50S ribosomal subunit protein L16 NP_417772.1
rpsC 30S ribosomal subunit protein S3 NP_417773.1
rplV 50S ribosomal subunit protein L22 NP_417774.1
rplB 50S ribosomal subunit protein L2 NP_417776.1
rplW 50S ribosomal subunit protein L23 NP_417777.1
rplD 50S ribosomal subunit protein L4 NP_417778.1
rpsL 30S ribosomal subunit protein S12 NP_417801.1
trpS tryptophanyl-tRNA synthetase NP_417843.1
yrfF NP_417857.1
asd NP_417891.1
ftsX putative ABC transporter permease NP_417919.1
ftsE cell division ATP-binding protein NP_417920.1
yhhQ DUF165 family inner membrane protein NP_417928.1
glyQ NP_418017.1
gpsA NP_418065.1
waaU lipopolysaccharide core biosynthesis NP_418080.1
waaA NP_418090.1
coaD pantetheine-phosphate adenylyltransferase NP_418091.1
rpmB 50S ribosomal subunit protein L28 NP_418094.1
dfp NP_418096.4
dut deoxyuridinetriphosphatase NP_418097.1
gmk guanylate kinase NP_418105.1
gyrB YP_026241.1
dnaN NP_418156.1
dnaA NP_418157.1
rpmH 50S ribosomal subunit protein L34 NP_418158.1
rnpA protein C5 component of RNase P NP_418159.1
tnaB tryptophan transporter of low affinity NP_418165.1
glmS L-glutamine:D-fructose-6-phosphateaminotransferase NP_418185.1
glmU fused N-acetyl glucosamine-1-phosphateuridyltransferase/glucosamine-1-phosphate acetyltransferase NP_418186.1
rho transcription termination factor NP_418230.1
wzyE putative ECA polysaccharide chain elongationprotein NP_418241.1
hemD uroporphyrinogen III synthase NP_418248.1
hemC hydroxymethylbilane synthase YP_026260.1
ubiB NP_418279.1
hemG NP_418292.1
yihA cell division GTP-binding protein NP_418301.3
ftsN essential cell division protein NP_418368.1
murI glutamate racemase NP_418402.2
murB NP_418403.1
birA NP_418404.1
coaA pantothenate kinase NP_418405.1
secE preprotein translocase membrane subunit NP_418408.1
nusG transcription termination factor NP_418409.1
rplJ 50S ribosomal subunit protein L10 NP_418412.1
rplL 50S ribosomal subunit protein L7/L12 NP_418413.1
rpoB NP_418414.1
ubiA p-hydroxybenzoate octaprenyltransferase NP_418464.1
plsB glycerol-3-phosphate O-acyltransferase NP_418465.4
lexA transcriptional repressor of SOS regulon NP_418467.1
dnaB replicative DNA helicase NP_418476.1
ssb single-stranded DNA-binding protein NP_418483.1
alsK D-allose kinase NP_418508.1
groS NP_418566.1
orn oligoribonuclease NP_418586.4
tsaE NP_418589.1
rpsR 30S ribosomal subunit protein S18 NP_418623.1
chpS antitoxin of the ChpBS toxin-antitoxin system NP_418645.2
ppa inorganic pyrophosphatase NP_418647.1
valS valyl-tRNA synthetase NP_418679.1
lptF lipopolysaccharide export ABC permease NP_418682.1
lptG lipopolysaccharide export ABC permease NP_418683.4
dnaC DNA biosynthesis protein NP_418781.1
ribF bifunctional riboflavin kinase/FAD synthetase NP_414566.1
ileS isoleucyl-tRNA synthetase NP_414567.1
lspA NP_414568.1
ispH NP_414570.1
folA dihydrofolate reductase NP_414590.1
lptD NP_414596.1
ftsL membrane bound cell division leucine zipperseptum protein NP_414625.1
ftsI transpeptidase involved in septal peptidoglycansynthesis; penicillin-binding protein 3 NP_414626.1
murF UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase NP_414628.1
mraY phospho-N-acetylmuramoyl-pentapeptidetransferase NP_414629.1
murD UDP-N-acetylmuramoyl-L-alanine:D-glutamateligase NP_414630.1
ftsW putative lipid II flippase; integral membraneprotein; FtsZ ring stabilizer NP_414631.1
murG N-acetylglucosaminyl transferase NP_414632.1
ftsQ NP_414635.1
ftsA ATP-binding cell division FtsK recruitmentprotein NP_414636.1
ftsZ GTP-binding tubulin-like cell division protein NP_414637.1
lpxC UDP-3-O-acyl N-acetylglucosamine deacetylase NP_414638.1
secM regulator of secA translation NP_414639.2
secA NP_414640.1
can carbonic anhydrase NP_414668.1
folK 2-amino-4-hydroxy-6-hydroxymethyldihyropteridinepyrophosphokinase NP_414684.1
hemL NP_414696.1
erpA iron-sulfur cluster insertion protein NP_414698.1
rpsB 30S ribosomal subunit protein S2 NP_414711.1
tsf translation elongation factor EF-Ts NP_414712.1
pyrH uridylate kinase NP_414713.1
frr ribosome recycling factor NP_414714.1
dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase NP_414715.1
ispU undecaprenyl pyrophosphate synthase NP_414716.1
cdsA CDP-diglyceride synthase NP_414717.2
rseP NP_414718.1
bamA BamABCDE complex OM biogenesis outer membranepore-forming assembly factor NP_414719.1
lpxD NP_414721.1
lpxA UDP-N-acetylglucosamine acetyltransferase NP_414723.1
lpxB tetraacyldisaccharide-1-P synthase NP_414724.1
accA NP_414727.1
tilS NP_414730.1
proS prolyl-tRNA synthetase NP_414736.1
yafN antitoxin of the YafO-YafN toxin-antitoxinsystem NP_414767.1
yagG CP4-6 prophage; putative sugar transporter NP_414804.1
hemB NP_414903.4
secD SecYEG protein translocase auxillary subunit NP_414942.1
secF SecYEG protein translocase auxillary subunit NP_414943.1
ribD NP_414948.1
ribE riboflavin synthase beta chain NP_414949.1
thiL thiamine monophosphate kinase NP_414951.1
dxs NP_414954.1
ispA geranyltranstransferase NP_414955.1
dnaX NP_415003.1
adk adenylate kinase NP_415007.1
hemH ferrochelatase NP_415008.1
lpxH NP_415057.1
cysS cysteinyl-tRNA synthetase NP_415059.1
folD NP_415062.1
entD phosphopantetheinyltransferase component ofenterobactin synthase multienzyme complex NP_415115.2
mrdB cell wall shape-determining protein NP_415167.1
mrdA NP_415168.1
nadD NP_415172.1
holA NP_415173.1
lptE NP_415174.1
lnt apolipoprotein N-acyltransferase NP_415190.1
glnS glutamyl-tRNA synthetase NP_415206.1
fldA flavodoxin 1 NP_415210.1
cydA NP_415261.2
infA translation initiation factor IF-1 NP_415404.1
serS seryl-tRNA synthetase NP_415413.1
msbA lipid ABC transporter permease/ATPase NP_415434.1
lpxK NP_415435.1
kdsB 3-deoxy-manno-octulosonate cytidylyltransferase NP_415438.1
mukF NP_415442.1
mukE NP_415443.2
asnS asparaginyl tRNA synthetase NP_415450.1
fabA beta-hydroxydecanoyl thioester dehydrase NP_415474.1
yceQ uncharacterized protein NP_415603.2
fabD malonyl-CoA-[acyl-carrier-protein] transacylase NP_415610.1
fabG 3-oxoacyl-[acyl-carrier-protein] reductase NP_415611.1
acpP NP_415612.1
tmk thymidylate kinase NP_415616.1
holB NP_415617.1
lolC lipoprotein-releasing system transmembraneprotein NP_415634.1
lolE lipoprotein-releasing system transmembraneprotein NP_415636.1
purB adenylosuccinate lyase NP_415649.1
minE cell division topological specificity factor NP_415692.1

 

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