Nuclear genes with apicoplast signal sequences

Nuclear genes with apicoplast signal sequences

Compiled with assistance from Stuart Ralph and checked against apicoplast proteomics

Boucher MJ, Ghosh S, Zhang L, Lal A, Jang SW, Ju A, Zhang S, Wang X, Ralph SA, Zou J, Elias JE, Yeh E. Integrative proteomics and bioinformatic prediction enable a high-confidence apicoplast proteome in malaria parasites. PLoS Biol. 2018 Sep 13;16(9):e2005895.PMID: 30212465;

Function

PfID

Formal annotation with curator's notes

Exists in proteome

Transcript

EC#

Replication and transcription

5'-3' exonuclease, N-terminal resolvase-like domain, putative

X

5'-3' exonuclease, putative

X

5'-3' exoribonuclease 1, putative

A/G-specific adenine glycosylase, putative

AP endonuclease (DNA-[apurinic or apyrimidinic site] lyase), putative

X

ATP-dependent RNA helicase ddx27, putative

X

ATP-dependent helicase, putative

X

DEAD box helicase, putative

X

DNA gyrase subunit A

X

DNA gyrase subunit B

X

DNA ligase I

crossover junction endonuclease MUS81, putative

X

DNA-directed RNA polymerase subunit alpha, putative

X

DNA-directed RNA polymerase, alpha subunit, putative

RNA polymerase beta' subunit, putative (rpoC)

TFIIH basal transcription factor complex helicase XBP subunit, putative

DNA (cytosine-5)-methyltransferase

X

pseudouridine synthase, putative

X

pseudouridylate synthase, putative

RNA pseudouridylate synthase, putative

X

dihydrouridine synthase, putative

X

single-stranded DNA-binding protein

X

ribosomal RNA small subunit methyltransferase a2, putative

X

TatD-like deoxyribonuclease

nd6 protein, putative

X

met-10+ like protein, putative

X

queuine tRNA-ribosyltransferase, putative

tRNA (guanine(26)-n(2))-dimethyltransferase, putative

X

rRNA methyltransferase, putative

X

tRNA nucleotidyltransferase, putative

X

DNA-(apurinic or apyrimidinic site) lyase 1

X

plastid replication-repair enzyme

X

bacterial histone-like protein

F-box only protein 9 homolog, putative

X

apicoplast calcium binding protein 1

Translation

ribosomal protein S4, putative

40S ribosomal protein S4, putative

X

apicoplast ribosomal protein S6, putative

X

30S ribosomal protein S9, putative

X

ribosomal protein S10, apicoplast, putative

X

ribosomal protein s14, apicoplast, putative

X

ribosomal protein s15, apicoplast, putative

40S ribosomal protein S25

X

50S ribosomal protein L1, apicoplast, putative

50s ribosomal protein l2, putative

X

50S ribosomal protein L3, apicoplast, putative

ribosomal protein l12, mitochondrial, putative

X

50S ribosomal protein L10, putative

X

50S ribosomal protein L12, apicoplast, putative

60S ribosomal protein L14, putative

X

ribosomal protein l15, apicoplast, putative

X

50S ribosomal protein L17, apicoplast, putative

X

50s ribosomal protein l18, apicoplast, putative

X

ribosomal protein l21, apicoplast, putative

X

50S ribosomal protein L22, apicoplast, putative

X

ribosomal protein l27, putative

50S ribosomal protein L28, apicoplast, putative

X

ribosomal protein L29, apicoplast, putative

X

ribosomal protein L35, apicoplast, putative

X

translation initiation factor IF-1

X

elongation factor Ts

X

elongation factor G

X

peptide chain release factor 2

X

peptide chain release factor 1

X

peptide chain release factor 2

X

peptide chain release factor 1

X

ribosome-recycling factor

X

peptide deformylase

X

alanine--tRNA ligase

arginine-tRNA ligase; arginyl-tRNA synthetase

X

arginine--tRNA ligase, putative

X

asparagine--tRNA ligase

X

aspartate--tRNA ligase, putative

X

cysteine--tRNA ligase, putative

X

glutamate--tRNA ligase

X

glutamyl-tRNA(Gln) amidotransferase subunit A

X

glycine--tRNA ligase

X

isoleucine--tRNA ligase, putative

X

histidine--tRNA ligase, putative

X

leucine--tRNA ligase, putative

X

lysine--tRNA ligase, putative

X

methionyl-tRNA formyltransferase, putative

X

phenylalanine--tRNA ligase

X

proline--tRNA ligase, putative

serine--tRNA ligase, putative

X

serine--tRNA ligase, putative

X

threonine--tRNA ligase

X

tRNA dimethylallyltransferase, putative

X

methionine--tRNA ligase, putative

X

tRNA pseudouridine synthase, putative

tryptophanyl-tRNA synthetase tryptophan--tRNA ligase

X

tryptophanyl-tRNA synthetase, putative tryptophan--tRNA ligase, putative

X

tyrosine--tRNA ligase

X

valine--tRNA ligase, putative

translation initiation factor IF-3

X

peptidyl-tRNA hydrolase 2, putative

histone acetyltransferase, putative

Isoprenoid biosynthesis

1-deoxy-D-xylulose 5-phosphate reductoisomerase

X

1-deoxy-D-xylulose 5-phosphate reductoisomerase

X

1-deoxy-D-xylulose 5-phosphate synthase

X

2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

X

4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, putative

X

4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), putative

X

4-hydroxy-3-methylbut-2-enyl diphosphate reductase

Fatty acid and phospholipid metabolism

3-oxoacyl-(acyl-carrier protein) reductase, putative

X

3-oxoacyl-[acyl-carrier-protein] reductase

X

3-oxoacyl-acyl-carrier protein synthase I/II

X

acyl carrier protein

acyl-CoA synthetase

acyl-CoA synthetase

acyl-CoA synthetase

X

beta-hydroxyacyl-ACP dehydratase

X

beta-ketoacyl-ACP synthase III oxoacyl-ACP synthase FABH

X

acetyl-coa carboxylase

X

dephospho-CoA kinase

diacylglycerol kinase, putative

X

dihydrolipoamide acyltransferase component E2

X

enoyl-acyl carrier reductase

X

glycerol-3-phosphate 1-O-acyltransferase, putative

X

holo-[acyl-carrier-protein] synthase, putative

phosphatidylserine synthase, putative

X

dihydrolipoyl dehydrogenase, apicoplast

X

lipoyl synthase

X

malonyl CoA-acyl carrier protein transacylase precursor

X

acyl-CoA synthetase

X

GTP-binding protein ENGA

steroid dehydrogenase, putative

X

patatin-like phospholipase, putative

patatin-like phospholipase, putative

phospholipid or glycerol acyltransferase, putative

phosphatidic acid phosphatase 2; phospholipid phosphatase pap2

stearoyl-CoA desaturase

X

pyruvate dehydrogenase E1 component subunit beta

X

pyruvate dehydrogenase E1 component subunit alpha

X

NADP-specific glutamate dehydrogenase

X

pyruvate kinase 2, pyrkii

triosephosphate isomerase, putative

P-loop containing nucleoside triphosphate hydrolase, putative

Transport

ABC transporter, putative

X

ABC transporter B family member 4, putative, ABCB4

ABC transporter B family member 6, putative, ABCB6

X

ABC transporter F family member 1, putative, ABCF1

cation-transporting ATPase 1

cation transporting P-ATPase, ATPase3

cation transporting ATPase, putative

X

phosphoenolpyruvate/phosphate translocator, PPT

X

ABC transporter B family member 3, putative. ABCB3

X

triose phosphate transporter, TPT

copper transporter, CTR1

Antoxidant defense

1-cys peroxiredoxin

X

1-cys peroxiredoxin

X

glutathione peroxidase-like thioredoxin peroxidase

thioredoxin-like mero protein

X

glyoxalase I-like protein gilp

NAD(P) transhydrogenase, putative, nth

X

aldehyde reductase, putative

X

superoxide dismutase [Fe]

Protein folding

mitochondrial import inner membrane translocase subunit TIM14, putative

mitochondrial import inner membrane translocase subunit TIM14, putative

DnaJ protein, putative

X

60 kDa chaperonin

X

20 kDa chaperonin

heat shock protein 101 chaperone protein ClpB2

heat shock protein 40, type ii

DnaJ protein, putative

X

heat shock protein 90, putative

tetratricopeptide repeat protein, putative

Fe-S cluster production

cysteine desulfurase, putative; SufS-like

X

cysteine desulfurase

cysteine desulfurase ISCS

X

NifU-like scaffold protein

X

sulfur cluster assembly protein SufD

X

ABC transporter I family member 1 FeS assembly ATPase SufC

X

cysteine desulfuration protein SufE

X

ferredoxin, putative

X

ferredoxin--NADP reductase

protein ISD11, putative

X

cytosolic Fe-S cluster assembly factor NBP35, putative

Porphyrin biosynthesis

delta-aminolevulinic acid dehydratase, porphobilinogen synthase

X

delta-aminolevulinic acid dehydratase porphobilinogen synthase, HemB

X

porphobilinogen deaminase

X

uroporphyrinogen III decarboxylase

Post-translational modification and Proteolysis

N6-adenine-specific methylase, putative

X

N6-adenine-specific methylase, putative

PEXEL protease plasmepsin V

X

ATP-dependent Clp protease proteolytic subunit

X

ATP-dependent Clp protease proteolytic subunit

X

ATP-dependent Clp protease regulatory subunit Clpc, putative

X

ATP-dependent Clp protease adaptor protein ClpS, putative

X

chaperone protein ClpB1

protein-s-isoprenylcysteine o-methyltransferase

X

M17 leucyl aminopeptidase

M1-family alanyl aminopeptidase

X

stromal-processing peptidase, putative

X

methionine aminopeptidase 1c, putative

aminopeptidase P

dipeptidyl aminopeptidase 3

X

apicoplast-minus ipp-rescued 4

dipeptidyl aminopeptidase 1 cathepsin C, homolog

OTU-like cysteine protease

serine/threonine protein kinase, putative

shewanella-like protein phosphatase 1, putative

protein tyrosine phosphatase, putative

X

S-adenosyl-methyltransferase, putative

serine palmitoyltransferase, putative

adenylyltransferase and sulfurtransferase uba4, putative

X

ubiquitin-conjugating enzyme E2

X

ubiquitin-activating enzyme

X

apicoplast ubiquitin-like protein aubl

palmitoyltransferase, putative

Unknown function in apicoplast (16.5 % of all gen

cysteine repeat modular protein 2 homologue

cysteine repeat modular protein 2

glutamine--fructose-6-phosphate aminotransferase [isomerizing], putative

X

GTP-binding protein protein obg1

X

pdz domain-containing protein, putative

X

serine/threonine protein kinase, putative

X

UMP-CMP kinase, putative

aspartate carbamoyltransferase

transmembrane emp24 domain-containing protein, putative

X

AAA family ATPase, CDC48 subfamily

PIR protein rifin

rifin PIR protein

rifin PIR protein

rifin

rifin

PIR protein rifin

rifin

rifin PIR protein

PIR protein rifin

rifin PIR protein

PIR protein rifin

PIR protein rifin

rifin PIR protein

rifin

rifin

stevor

rifin, pseudogene

rifin, pseudogene

PIR protein stevor

PIR protein stevor

stevor PIR protein

PIR protein stevor

PIR protein stevor

PIR protein stevor

PIR protein stevor

stevor PIR protein

PIR protein stevor

stevor PIR protein

stevor, pseudogene

stevor, pseudogene

stevor, pseudogene

PIR protein stevor

apyrase

early transcribed membrane protein 10., ETRAMP10.1

early transcribed membrane protein 11.1

early transcribed membrane protein 11.2

erythrocyte membrane protein 3

X

conserved Plasmodium protein, unknown function

reticulocyte binding protein homologue 3, pseudogene

circumsporozoite (CS) protein

parasitophorous vacuole membrane antigen QF 116 exported protein 1 circumsporozoite-related antigen

glutamate-rich protein GLURP

transmembrane emp24 domain-containing protein, putative

merozoite surface protein 2

serine repeat antigen 6

6-cysteine protein p230

liver stage antigen 3

erythrocyte membrane protein 1 (PfEMP1), pseudogene

X

ribosome biogenesis GTPase A, putative

X

GTP-binding protein, putative

X

GTP-binding protein, putative

glideosome-associated protein 50 secreted acid phosphatase

X

added_product=dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit wbp1, putative

NIMA related kinase 3

X

glucose inhibited division protein a homologue, putative

chitinase

plasmepsin X

plasmepsin VII

plasmepsin I

COX11 cytochrome c oxidase assembly protein putative

cysteine proteinase falcipain 2a falcipain 2

falcipain 2' cysteine proteinase falcipain 2b

GPI-anchor transamidase

plasmepsin III histo-aspartic protease

thrombospondin-related sporozoite protein

thrombospondin-related apical membrane protein

X

ccr4 domain-containing protein 4, putative

apical sushi protein

perforin-like protein 1

X

tRNA N6-adenosine threonylcarbamoyltransferase

X

conserved Plasmodium protein, unknown function

X

t-cell immunomodulatory protein homolog, putative

LCCL domain-containing protein

signal recognition particle receptor subunit beta, putative

osmiophilic body protein g377

X

translation initiation factor IF-2 sporozoite surface antigen MB2

+ 283 Hypothetical proteins

Online articles related to Nuclear genes with apicoplast signal sequences retrieved from PubMed

Drugs affecting pathway with unknown specific target

Drug Name	PubMed Articles (year of publication)
15-Desoxyspergualin	15-deoxyspergualin primarily targets the trafficking of apicoplast proteins in Plasmodium falciparum

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