P. falciparum genes harboring G-quadruplexes
The striking genomic features of P. falciparum, wherein GC richness is uniquely localized in parasite's AT rich genome hint towards existence of regulatory elements in GC rich regions. G-stretches have the potential to form non Watson-Crick secondary structures called G-quadruplexes. Studies in different genomes suggest that DNA or RNA quadruplexes can regulate gene expression.
Bhartiya D, Chawla V, Ghosh S, Shankar R, Kumar N. Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics. 2016 Oct 24. pii: S0888-7543(16)30094-5.PMID: 27789319.
Functional category PFID New Annotation E.C Transcript
DNA metabolism PF3D7_0318600 cleavage and polyadenylation specificity factor, putative
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PF3D7_1425400 DEAD/DEAH box helicase, putative 3.6.4.13
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PF3D7_1117800
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DNA mismatch repair protein MLH (MLH)
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PF3D7_0726300 DNA mismatch repair protein PMS1, putative (PMS1)
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PF3D7_0411900 DNA polymerase alpha 2.7.7.7
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PF3D7_0803400 DNA repair and recombination protein RAD54, putative (RAD54) 3.6.4.12
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PF3D7_1368800 DNA repair endonuclease, putative (ERCC4) 3.1.21.1
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PF3D7_0710400 DNA repair protein RAD14, putative (RAD14) 4.2.99.18
PF3D7_1211700 DNA replication licensing factor MCM5, putative (MCM5)
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PF3D7_0814200
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DNA/RNA-binding protein Alba 1 (ALBA1)
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PF3D7_0614800 endonuclease III homologue, putative 4.2.99.18
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PF3D7_1360900 RNA-binding protein, putative
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PF3D7_1107300 polyadenylate-binding protein-interacting protein 1, putative (PAIP1)
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PF3D7_0409600 replication protein A1, large subunit (RPA1)
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PF3D7_0623900 ribonuclease H2 subunit A, putative 3.1.26.4
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RNA metabolism PF3D7_1243100 zinc finger protein, putative
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PF3D7_1031500 DEAD/DEAH box helicase, putative 3.6.4.13
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PF3D7_0318200 DNA-directed RNA polymerase II subunit RPB1 (RPB1) 2.7.7.6
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PF3D7_1472700 DNA-directed RNA polymerase, alpha subunit, putative 2.7.7.6
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PF3D7_1244000 glucose inhibited division protein a homologue, putative
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PF3D7_0611900 lsm12, putative
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PF3D7_0822100 mediator of RNA polymerase II transcription subunit 7, putative (MED7)
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PF3D7_1235500 mRNA methyltransferase, putative 2.1.1.62
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PF3D7_0917600
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pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43, putative (PRP43) 3.6.4.13
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PF3D7_0515000 pre-mRNA-splicing factor CWC2, putative (CWC2)
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PF3D7_0422500 pre-mRNA-splicing helicase BRR2, putative (BRR2) 3.6.4.13
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PF3D7_1005500 regulator of nonsense transcripts, putative
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PF3D7_0509400
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RNA polymerase I (RNAPI) 2.7.7.6
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PF3D7_0319500 RNA-binding protein, putative
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PF3D7_0416000 RNA-binding protein, putative
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PF3D7_1310700 RNA-binding protein, putative
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PF3D7_1326300 RNA-binding protein, putative
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PF3D7_1407100
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rRNA 2'-O-methyltransferase fibrillarin, putative (NOP1)
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PF3D7_0422900 methyltransferase, putative
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PF3D7_0517300
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serine/arginine-rich splicing factor 1 (SR1)
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PF3D7_1217200 snoRNA-associated small subunit rRNA processing protein, putative
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PF3D7_1234800 splicing factor 3B subunit 3, putative (SF3B3)
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PF3D7_1420000 splicing factor 3B subunit 4, putative (SF3B4)
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PF3D7_0420300 AP2 domain transcription factor
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PF3D7_1239200 transcription factor with AP2 domain(s) (ApiAP2)
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PF3D7_1317200 transcription factor with AP2 domain(s) (ApiAP2)
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PF3D7_1342900 AP2 domain transcription factor, putative
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PF3D7_1466400 AP2 domain transcription factor AP2-SP
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PF3D7_0623600 transcription or splicing factor-like protein, putative
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PF3D7_1014600 transcriptional coactivator ADA2 (ADA2)
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PF3D7_0408900
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tRNA N6-adenosine threonylcarbamoyltransferase 2.6.99.4
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PF3D7_1105700 tRNA-splicing ligase RtcB, putative (RTCB)
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PF3D7_1306900 U1 small nuclear ribonucleoprotein A, putative
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PF3D7_0935000 U2 small nuclear ribonucleoprotein B'', putative
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PF3D7_1448000 U3 small nucleolar RNA-associated protein 12, putative (UTP12)
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PF3D7_1309300 U4/U6 small nuclear ribonucleoprotein PRP3, putative (PRPF3)
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PF3D7_1009400 zinc finger protein, putative
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Translation PF3D7_0801100 28S ribosomal RNA
PF3D7_0516200 40S ribosomal protein S11
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PF3D7_0317600 40S ribosomal protein S11, putative (RPS11)
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PF3D7_1317800 40S ribosomal protein S19 (RPS19)
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PF3D7_0705700 40S ribosomal protein S29, putative
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PF3D7_0918200 50S ribosomal protein L3, apicoplast, putative
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PF3D7_1331800 60S ribosomal protein L23, putative
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PF3D7_0509600 asparagine-tRNA ligase (AsnRS) 6.1.1.22
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PF3D7_0514300 aspartate-tRNA ligase, putative 6.1.1.12
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PF3D7_1331700 glutamine-tRNA ligase, putative 6.1.1.18
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PF3D7_1431300 large ribosomal subunit associated GTPase, putative 3.6.5.1
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PF3D7_1350100
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lysine-tRNA ligase (KRS1) 6.1.1.6
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PF3D7_1416800
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lysine-tRNA ligase, putative 6.1.1.6
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PF3D7_0212300 peptide chain release factor subunit 1, putative 3.1.1.29
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PF3D7_0704900 peptide chain release factor, putative 3.1.1.29
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PF3D7_0603700
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phenylalanine-tRNA ligase (mFRS) 6.1.1.20
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PF3D7_1213800
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proline-tRNA ligase (PRS) 6.1.1.15
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PF3D7_0203700 protein MAK16, putative (MAK16)
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PF3D7_1346100
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Sec61 alpha subunit, PfSec61 (SEC61)
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PF3D7_1010000 ribosomal protein L43, mitochondrial, putative
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PF3D7_1123400 translation elongation factor EF-1, subunit alpha, putative
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PF3D7_0828500 translation initiation factor EIF-2b alpha subunit, putative
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Post-translational modifications PF3D7_0711000
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AAA family ATPase, CDC48 subfamily 3.6.4.6
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PF3D7_1230400
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ATP-dependent protease subunit ClpQ (ClpQ) 3.5.1.98
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PF3D7_1414500
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atypical protein kinase, ABC-1 family, putative (ABCk2) 1.14.13.-
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PF3D7_1453700 co-chaperone p23 (P23)
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PF3D7_1302600
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deoxyhypusine hydroxylase (DOHH) 1.14.99.29
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PF3D7_0911900
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falstatin (ICP)
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PF3D7_0409400
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chaperone protein dnaj; heat shock protein 40
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PF3D7_1108700
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heat shock protein 40, type ii
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PF3D7_0628100
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HECT-domain (ubiquitin-transferase), putative 6.3.2.19
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PF3D7_1028000 methyltransferase, putative 2.1.1.61
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PF3D7_0109500 N-acetyltransferase, putative 2.3.1.48
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PF3D7_1228300
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NIMA related kinase 1 (NEK1) 2.7.11.1
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PF3D7_0507700 nuclear protein localization protein 4, putative (NPL4)
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PF3D7_0205400 PCI domain-containing protein, putative
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PF3D7_1349700 peptidase, putative
PF3D7_0322000
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peptidyl-prolyl cis-trans isomerase (CYP19A) 5.2.1.8
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PF3D7_0528700
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peptidyl-prolyl cis-trans isomerase (CYP23) 5.2.1.8
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PF3D7_1202400