Plasmodium ubiquitin-protein conjugates
Ponts N, Saraf A, Chung DW, Harris A, Prudhomme J, Washburn MP, Florens L, Le Roch KG. Unraveling the ubiquitome of the human malaria parasite. J Biol Chem. 2011 286(46):40320-30. PMID: 21930698
Green JL, Wu Y, Encheva V, Lasonder E, Prommaban A, Kunzelmann S, Christodoulou E, Grainger M, Truongvan N, Bothe S, Sharma V, Song W, Pinzuti I, Uthaipibull C, Srichairatanakool S, Birault V,Langsley G, Schindelin H, Stieglitz B, Snijders AP, Holder AA.Ubiquitin activation is essential for schizont maturation in Plasmodium falciparum blood-stage development. PLoS Pathog. 2020 Jun 22;16(6):e1008640. PMID: 32569299   
There are a number of differences between the two studies, some technological, some methodological and some biological. First, most of Green et ak Ub sites (light grey background) are in extracellular merozoites and this stage was not examined in the Ponts et al study (white background).  Second, Green et al used a very different technology that is likely more sensitive, involving immune-purification of the Ub remnant peptide(s) from each protein and then identifying them directly by MS. Third, Ponts et al. purified proteins using a Ub-antibody and then analysed all the proteins in that fraction. This may over-represent proteins that are polyubiquitylated (whereas Geen et al was blind to whether or not substrates were polyubiquitylated) but also Ponts et al  method was indirect in that other proteins (for examples those in complexes with ubiquitylated proteins) would also be purified and potentially identified. Fourth, there may be many de-ubiquitinases active during the long purification procedures used in the earlier study, whereas Green et al first step was to deactivate such enzymes by making the lysate in 9M urea.
Functional group PfID Annotation EC# Transcript
25381 DNA metabolism PF3D7_0903400 ATP-dependent RNA helicase ddx60, putative
25398 PF3D7_1409300
DNA damage-inducible protein 1 3.4.23.-
25434 PF3D7_0505500
DNA mismatch repair protein MSH6, putative
25409 PF3D7_1011700 DNA repair protein RAD23, putative
25393 PF3D7_1417800
DNA replication licensing factor MCM2
25397 PF3D7_0705400 DNA replication licensing factor MCM7
25414 PF3D7_0814200
DNA/RNA-binding protein Alba 1
25410 PF3D7_1346300
DNA/RNA-binding protein Alba 2
25428 PF3D7_1010200 DNA2/NAM7 helicase, putative
25363 PF3D7_0525400
G-protein coupled receptor, putative
25372 PF3D7_1224300
polyadenylate-binding protein 1, putative
25379 PF3D7_1361900
proliferating cell nuclear antigen 1
25374 PF3D7_0904800 replication protein A1, small fragment
25422 PF3D7_1023900
SNF2 helicase, putative chromodomain-helicase-DNA-binding protein 1 homolog, putative
25364 PF3D7_0510500
topoisomerase I
25413 RNA metabolism PF3D7_1123900
13 kda ribonucleoprotein-associated protein, putative
25368 PF3D7_1368200
ABC transporter E family member 1, putative
25382 PF3D7_0420300 AP2 domain transcription factor
29754 PF3D7_0730300 AP2 domain transcription factor AP2-L, putative
25383 PF3D7_1143100
AP2 domain transcription factor AP2-O
25415 PF3D7_0209800
ATP-dependent RNA helicase UAP56
25370 PF3D7_1236100 clustered-asparagine-rich protein
25408 PF3D7_1409800 CUGBP Elav-like family member 2
25389 PF3D7_0215700 DNA-directed RNA polymerase II subunit RPB2
25391 PF3D7_1027400 DNA-directed RNA polymerase II subunit RPB7, putative
25427 PF3D7_1213700 DNA-directed RNA polymerases I, II, and III subunit RPABC3, putative
25373 PF3D7_1358200 RNA polymerase III transcription initiation factor B
25417 PF3D7_1104300 RNA poymerase III transcription initiatin factor B
25420 PF3D7_1026600 Armadillo-type fold
25407 PF3D7_1034500 armadillo repeat protein, putative
33719 PF3D7_1202900
high mobility group protein B1
25380 PF3D7_0730400 imp1-like protein, putative
25423 PF3D7_1128200
multiprotein bridging factor type 1, putative
25366 PF3D7_1439500 oocyst rupture protein 2, putative
25406 PF3D7_0923900 polyadenylate-binding protein 2, putative
25405 PF3D7_1011800 PRE-binding protein
25430 PF3D7_0405400 pre-mRNA-processing-splicing factor 8, putative
25388 PF3D7_0515000 pre-mRNA-splicing factor CWC2, putative
25384 PF3D7_0916700 RNA-binding protein musashi, putative
25404 PF3D7_1110400 RNA-binding protein, putative
25390 PF3D7_1310700
PhIL1-interacting protein PhIP
25411 PF3D7_1360900 RNA-binding protein, putative
25418 PF3D7_0517300
serine/arginine-rich splicing factor 1
25369 PF3D7_0503300
serine/arginine-rich splicing factor 12
25416 PF3D7_1006800
G-strand-binding protein 2
25400 PF3D7_0604100
SPE2-interacting protein transcription factor with AP2 domain(s)
25403 PF3D7_1309300 U4/U6 small nuclear ribonucleoprotein PRP3, putative
25402 PF3D7_1317400 zinc finger protein, putative
25371 PF3D7_0812500 RNA-binding protein, putative
25365 PF3D7_1248700 conserved protein, unknown function
25395 Translation PF3D7_0516200 40S ribosomal protein S11
25375 PF3D7_1130200
60S ribosomal protein P0
25432 PF3D7_0317600 40S ribosomal protein S11, putative
25421 PF3D7_0307100 40S ribosomal protein S12, putative
25401 PF3D7_1358800 40S ribosomal protein S15
25376 PF3D7_0316800 40S ribosomal protein S15A, putative
25399 PF3D7_0813900 40S ribosomal protein S16, putative
25392 PF3D7_1242700 40S ribosomal protein S17, putative
25424 PF3D7_1126200 40S ribosomal protein S18, putative
25367 PF3D7_1144000 40S ribosomal protein S21
25435 PF3D7_0705700 40S ribosomal protein S29, putative
25386 PF3D7_1465900 40S ribosomal protein S3
25429 PF3D7_0322900 40S ribosomal protein S3A, putative
25394 PF3D7_1447000 40S ribosomal protein S5
25378 PF3D7_1342000 40S ribosomal protein S6
25396 PF3D7_1302800 40S ribosomal protein S7, putative
25433 PF3D7_0309600
60S acidic ribosomal protein P2
25385 PF3D7_0719600 60S ribosomal protein L11a, putative
25431 PF3D7_0517000 60S ribosomal protein L12, putative
25426 PF3D7_0814000 60S ribosomal protein L13-2, putative
25412 PF3D7_1351400 60S ribosomal protein L17, putative
25377 PF3D7_1341200 60S ribosomal protein L18, putative
25419 PF3D7_0614500 60S ribosomal protein L19
PF3D7_0516900 60S ribosomal protein L2
PF3D7_1426000 60S ribosomal protein L21
PF3D7_1331800 60S ribosomal protein L23, putative
PF3D7_1309100 60S ribosomal protein L24, putative
PF3D7_0312800 60S ribosomal protein L26, putative
PF3D7_0618300 60S ribosomal protein L27a, putative
PF3D7_0503800 60S ribosomal protein L31
PF3D7_0710600 60S ribosomal protein L34
PF3D7_1142600 60S ribosomal protein L35ae, putative
PF3D7_1424100 60S ribosomal protein L5, putative
PF3D7_1338200 60s ribosomal protein l6, putative
PF3D7_1323100 60S ribosomal protein L6, putative
PF3D7_1338200 60s ribosomal protein l6, putative
PF3D7_0307200 60S ribosomal protein L7, putative
PF3D7_1357100 elongation factor 1-alpha
PF3D7_0913200 elongation factor 1-beta
elongation factor 2
eukaryotic initiation factor 4A helicase 45
PF3D7_0422700 eukaryotic initiation factor 4A-III, putative
PF3D7_0517700 eukaryotic translation initiation factor 3 subunit B, putative
PF3D7_1206200 eukaryotic translation initiation factor 3 subunit C, putative
PF3D7_0716800 eukaryotic translation initiation factor 3 subunit I, putative
PF3D7_1438000 eukaryotic translation initiation factor eIF2A, putative
PF3D7_1019000 eukaryotic translation initiation factor subunit eIF2A, putative
PF3D7_1003500 40S ribosomal protein S20e, putative
PF3D7_1125700 kelch domain-containing protein, putative
PF3D7_1125800 kelch domain-containing protein, putative
PF3D7_1019400 60S ribosomal protein L30e, putative
PF3D7_0722400 OBG-like ATPase 1, putative
prolyl-tRNA synthetase proline--tRNA ligase
replication factor c subunit 1
PF3D7_1402500 ribosomal protein s27a, putative
PF3D7_1146000 ribosome assembly protein 4, putative
ribosome associated membrane protein RAMP4, putative
rRNA 2'-O-methyltransferase fibrillarin, putative
PF3D7_0914600 transcription elongation factor 1, putative
PF3D7_1335600 wd repeat-containing protein, putative
translation-enhancing factor
Post translational modifications PF3D7_1211800 polyubiquitin
14-3-3 protein
20 kDa chaperonin
26S protease regulatory subunit 6A, putative
26S protease regulatory subunit 7, putative; 26S proteasome AAA-ATPase subunit RPT1, putative
26S protease regulatory subunit 10B, putative; 26S proteasome AAA-ATPase subunit RPT4, putative
26S protease regulatory subunit 4, putative
26S protease regulatory subunit 8, putative
PF3D7_0205900 26S proteasome regulatory subunit RPN1, putative
PF3D7_0807800 26S proteasome regulatory subunit RPN10, putative
PF3D7_1368100 26S proteasome regulatory subunit RPN11, putative
PF3D7_1414000 26S proteasome regulatory subunit RPN13, putative
PF3D7_1466300 26S proteasome regulatory subunit RPN2, putative
PF3D7_1338100 26S proteasome regulatory subunit RPN3, putative
PF3D7_1030500 26S proteasome regulatory subunit RPN9, putative
PF3D7_0807800 26S proteasome regulatory subunit RPN10, putative
adenylate kinase-like protein 1
ADP-ribosylation factor 1
PF3D7_1244600 ADP-ribosylation factor GTPase-activating protein 1, arfgap1
ADP-ribosylation factor, putative
PF3D7_0403800 alpha/beta hydrolase, putative
PF3D7_1328500 alpha/beta-hydrolase, putative
aminopeptidase P
autophagy-related protein 8
PF3D7_1248500 bax inhibitor 1, putative
PF3D7_1459800 bax inhibitor 1, putative
Calcium-dependent protein kinases; CDPK1
PF3D7_1238100 calcyclin binding protein, putative
cAMP-dependent protein kinase catalytic subunit
PF3D7_0811000 cullin-1, putative
PF3D7_0629800 cullin-2, putative
cysteine proteinase falcipain 2a falcipain 2 3.4.22.-