224:. The removal of the methionine is more efficient when the second residue is small and uncharged (for example alanine), but inefficient when it is bulky and charged such as arginine. Once the f-Met is removed, the second residue becomes the N-terminal residue and are subject to the N-end rule. Residues with middle sized side-chains such as leucine as the second residue therefore may have a short half-life.
278:. ClpS is a bacterial adaptor protein that is responsible for recognizing protein substrates via their N-terminal residues and delivering them to a protease core for degradation. This study suggests that ClpS1 is functionally similar to ClpS, also playing a role in substrate recognition via specific N-terminal residues (
177:, positively-charged and some aliphatic and aromatic residues on the N-terminus, such as arginine, lysine, leucine, phenylalanine, tyrosine, and tryptophan, have short half-lives of around 2-minutes and are rapidly degraded. These residues (when located at the N-terminus of a protein) are referred to as
298:
were analyzed to determine the relative abundance of specific N-terminal residues. This study revealed that
Alanine, Serine, Threonine, and Valine were the most abundant N-terminal residues, while Leucine, Phenylalanine, Tryptophan, and Tyrosine (all triggers for degradation in bacteria) were among
34:
of a protein determines its half-life (time after which half of the total amount of a given polypeptide is degraded). The rule applies to both eukaryotic and prokaryotic organisms, but with different strength, rules, and outcome. In eukaryotic cells, these N-terminal residues are recognized and
302:
Furthermore, an affinity assay using ClpS1 and N-terminal residues was performed to determine whether ClpS1 did indeed have specific binding partners. This study revealed that
Phenylalanine and Tryptophan bind specifically to ClpS1, making them prime candidates for N-degrons in chloroplasts.
47:
and co-workers in 1986. However, only rough estimations of protein half-life can be deduced from this 'rule', as N-terminal amino acid modification can lead to variability and anomalies, whilst amino acid impact can also change from organism to organism. Other degradation signals, known as
252:
and a cyanobacterium, because chloroplasts share several features with the bacterium, including photosynthetic capabilities. The bacterial N-end rule is already well documented; it involves the Clp protease system which consists of the adaptor protein
1327:
LaCount DJ, Vignali M, Chettier R, Phansalkar A, Bell R, Hesselberth JR, et al. (November 2005). "A protein interaction network of the malaria parasite
Plasmodium falciparum".
690:
Erbse A, Schmidt R, Bornemann T, Schneider-Mergener J, Mogk A, Zahn R, et al. (February 2006). "ClpS is an essential component of the N-end rule pathway in
Escherichia coli".
261:
chaperone and protease core. A similar Clp system is present in the chloroplast stroma, suggesting that the N-end rule might function similarly in chloroplasts and bacteria.
381:(leucine, phenylalanine, tyrosine and tryptophan) but also N-terminal Isoleucine and hence exhibits broad specificity (in comparison to its bacterial counterpart).
189:(arginine, lysine and in a special case methionine ). Secondary destabilising residues are modified by the attachment of a Primary destabilising residue by the
364:
275:
254:
202:
999:
Dougan DA, Micevski D, Truscott KN (January 2012). "The N-end rule pathway: from recognition by N-recognins, to destruction by AAA+proteases".
792:"Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid"
282:) like its bacterial counterpart. It is posited that upon recognition, ClpS1 binds to these substrate proteins and brings them to the ClpC
193:
leucyl/phenylalanyl-tRNA-protein transferase. All other amino acids when located at the N-terminus of a protein are referred to as
1278:"Structural insights into the inactive subunit of the apicoplast-localized caseinolytic protease complex of Plasmodium falciparum"
499:
Bachmair A, Finley D, Varshavsky A (October 1986). "In vivo half-life of a protein is a function of its amino-terminal residue".
248:
organisms that can convert light into energy. It is thought that the chloroplast developed from an endosymbiosis between a
1229:"PfClpC Is an Essential Clp Chaperone Required for Plastid Integrity and Clp Protease Stability in Plasmodium falciparum"
1134:"The Arabidopsis Chloroplast Stromal N-Terminome: Complexities of Amino-Terminal Protein Maturation and Stability"
359:
contain all of the necessary components required for a
Apicoplast-localized Clp-protease, including a potential
638:"Modification of PATase by L/F-transferase generates a ClpS-dependent N-end rule substrate in Escherichia coli"
220:(f-Met). The formyl group of this methionine is quickly removed, and the methionine itself is then removed by
216:
A complicating issue is that the first residue of bacterial proteins is normally expressed with an N-terminal
1428:
743:"Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS"
306:
Further research is currently being conducted to confirm whether the N-end rule operates in chloroplasts.
1383:"The N-end rule adaptor protein ClpS from Plasmodium falciparum exhibits broad substrate specificity"
221:
1276:
El
Bakkouri M, Rathore S, Calmettes C, Wernimont AK, Liu K, Sinha D, et al. (January 2013).
1227:
Florentin A, Cobb DW, Fishburn JD, Cipriano MJ, Kim PS, Fierro MA, et al. (November 2017).
1082:"ClpS1 is a conserved substrate selector for the chloroplast Clp protease system in Arabidopsis"
373:
ClpS is able to recognize a variety of N-terminal primary destabilizing residues, not only the
369:
355:
341:
741:
Schuenemann VJ, Kralik SM, Albrecht R, Spall SK, Truscott KN, Dougan DA, Zeth K (May 2009).
590:
Tobias JW, Shrader TE, Rocap G, Varshavsky A (November 1991). "The N-end rule in bacteria".
1336:
803:
699:
599:
508:
291:
266:
44:
464:
8:
210:
1340:
1036:"Organization, function and substrates of the essential Clp protease system in plastids"
807:
703:
603:
512:
1360:
1304:
1277:
1253:
1228:
1158:
1133:
1106:
1081:
976:
951:
885:
767:
742:
723:
662:
637:
473:
448:
429:
416:
399:
217:
826:
791:
560:
543:
201:
are specifically recognised by the bacterial N-recognin (recognition component) ClpS.
1404:
1352:
1309:
1258:
1209:
1163:
1111:
1057:
1016:
981:
929:
889:
877:
831:
772:
715:
667:
615:
565:
524:
478:
421:
360:
335:
283:
271:
258:
1080:
Nishimura K, Asakura Y, Friso G, Kim J, Oh SH, Rutschow H, et al. (June 2013).
433:
27:
through recognition of the N-terminal residue of proteins. The rule states that the
1394:
1364:
1344:
1299:
1289:
1248:
1240:
1199:
1153:
1145:
1101:
1093:
1047:
1008:
971:
963:
919:
867:
821:
811:
762:
754:
727:
707:
657:
649:
607:
555:
516:
468:
460:
411:
173:
36:
872:
855:
542:
Gonda DK, Bachmair A, Wünning I, Tobias JW, Lane WS, Varshavsky A (October 1989).
232:
There are several reasons why it is possible that the N-end rule functions in the
43:
thereby marking the protein for degradation. The rule was initially discovered by
1244:
1052:
1035:
1012:
796:
Proceedings of the
National Academy of Sciences of the United States of America
323:
295:
245:
40:
924:
907:
1422:
241:
237:
102:-terminal residues - approximate half-life of proteins in mammalian systems
72:
1399:
1382:
1294:
1204:
1187:
816:
611:
520:
197:
and have half-lives of more than 10 hours . Proteins bearing an N-terminal
1408:
1356:
1313:
1262:
1213:
1167:
1115:
1097:
1061:
1020:
985:
933:
881:
776:
719:
671:
653:
482:
319:
206:
835:
758:
619:
569:
528:
425:
350:
330:
233:
213:, and hence ClpS delivers N-degron substrates to ClpAP for degradation.
24:
1348:
1149:
967:
711:
790:
Hirel PH, Schmitter MJ, Dessen P, Fayat G, Blanquet S (November 1989).
689:
28:
249:
1275:
636:
Ninnis RL, Spall SK, Talbo GH, Truscott KN, Dougan DA (June 2009).
236:
of plant cells as well. The first piece of evidence comes from the
326:
1326:
181:. In bacteria, destabilising residues can be further defined as
279:
190:
49:
740:
240:
which encompasses the idea that chloroplasts are derived from
1226:
1001:
Biochimica et
Biophysica Acta (BBA) - Molecular Cell Research
349:
spp. (parasites causing malaria). Similar to plants, several
78:
Met, Gly, Ala, Ser, Thr, Val, Pro - > 20 hrs (stabilizing)
589:
1132:
Rowland E, Kim J, Bhuiyan NH, van Wijk KJ (November 2015).
71:-terminal residues - approximate half-life of proteins for
541:
1131:
789:
60:
The rule may operate differently in different organisms.
1079:
635:
498:
286:
of the protease core machinery to initiate degradation.
1381:
Tan JL, Ward L, Truscott KN, Dougan DA (October 2016).
1185:
205:
is as a specific adaptor protein for the ATP-dependent
998:
185:(leucine, phenylalanine, tyrosine, and tryptophan) or
1380:
1188:"N-degron specificity of chloroplast ClpS1 in plants"
446:
1040:
Biochimica et
Biophysica Acta (BBA) - Bioenergetics
87:Leu, Phe, Asp, Lys - approx. 3 min (destabilizing)
1033:
1420:
1186:Montandon C, Dougan DA, van Wijk KJ (May 2019).
1181:
1179:
1177:
1075:
1073:
1071:
901:
899:
853:
945:
943:
849:
847:
845:
400:"The N-end rule pathway of protein degradation"
270:revealed the protein ClpS1, a possible plastid
55:
1127:
1125:
544:"Universality and structure of the N-end rule"
447:Tasaki T, Sriram SM, Park KS, Kwon YT (2012).
1174:
1068:
908:"Endosymbiosis and Eukaryotic Cell Evolution"
896:
940:
842:
585:
583:
581:
579:
1122:
1034:Nishimura K, van Wijk KJ (September 2015).
1027:
992:
494:
492:
397:
1398:
1303:
1293:
1252:
1203:
1157:
1105:
1051:
975:
923:
905:
871:
825:
815:
766:
661:
576:
559:
472:
415:
84:Tyr, Gln - approx. 10 min (destabilizing)
949:
854:Bouchnak I, van Wijk KJ (October 2019).
299:the residues that were rarely detected.
489:
81:Ile, Glu - approx. 30 min (stabilizing)
1421:
1376:
1374:
465:10.1146/annurev-biochem-051710-093308
952:"Chloroplast origin and integration"
685:
683:
681:
631:
629:
1282:The Journal of Biological Chemistry
548:The Journal of Biological Chemistry
90:Arg - approx. 2 min (destabilizing)
23:is a rule that governs the rate of
13:
1371:
417:10.1046/j.1365-2443.1997.1020301.x
14:
1440:
678:
626:
367:. In vitro data demonstrate that
52:, can also be found in sequence.
187:secondary destabilising residues
1320:
1269:
1220:
856:"N-Degron Pathways in Plastids"
227:
783:
734:
535:
440:
391:
379:Primary destabilizing residues
264:Additionally, a 2013 study in
183:Primary destabilising residues
1:
906:Archibald JM (October 2015).
873:10.1016/j.tplants.2019.06.013
561:10.1016/S0021-9258(19)84762-2
453:Annual Review of Biochemistry
398:Varshavsky A (January 1997).
384:
309:
199:Primary destabilising residue
1245:10.1016/j.celrep.2017.10.081
1053:10.1016/j.bbabio.2014.11.012
1013:10.1016/j.bbamcr.2011.07.002
950:McFadden GI (January 2001).
56:Rules in different organisms
7:
166:
10:
1445:
94:
925:10.1016/j.cub.2015.07.055
449:"The N-end rule pathway"
222:methionyl aminopeptidase
63:
1400:10.1002/1873-3468.12382
1295:10.1074/jbc.M112.416560
1205:10.1002/1873-3468.13378
860:Trends in Plant Science
817:10.1073/pnas.86.21.8247
612:10.1126/science.1962196
521:10.1126/science.3018930
1098:10.1105/tpc.113.112557
654:10.1038/emboj.2009.134
179:destabilising residues
110:Met (M), Gly (G) → 30h
759:10.1038/embor.2009.62
370:Plasmodium falciparum
356:Plasmodium falciparum
353:n species, including
342:Plasmodium falciparum
234:chloroplast organelle
1429:Protein biosynthesis
292:Arabidopsis thaliana
267:Arabidopsis thaliana
238:endosymbiotic theory
195:stabilising residues
45:Alexander Varshavsky
32:-terminal amino acid
1349:10.1038/nature04104
1341:2005Natur.438..103L
1150:10.1104/pp.15.01214
968:10.1104/pp.125.1.50
808:1989PNAS...86.8247H
712:10.1038/nature04412
704:2006Natur.439..753E
604:1991Sci...254.1374T
513:1986Sci...234..179B
25:protein degradation
289:In another study,
1393:(19): 3397–3406.
363:of the bacterial
336:Toxoplasma gondii
274:of the bacterial
37:ubiquitin ligases
1436:
1413:
1412:
1402:
1378:
1369:
1368:
1324:
1318:
1317:
1307:
1297:
1273:
1267:
1266:
1256:
1239:(7): 1746–1756.
1224:
1218:
1217:
1207:
1183:
1172:
1171:
1161:
1138:Plant Physiology
1129:
1120:
1119:
1109:
1077:
1066:
1065:
1055:
1031:
1025:
1024:
996:
990:
989:
979:
956:Plant Physiology
947:
938:
937:
927:
903:
894:
893:
875:
851:
840:
839:
829:
819:
787:
781:
780:
770:
738:
732:
731:
687:
676:
675:
665:
642:The EMBO Journal
633:
624:
623:
598:(5036): 1374–7.
587:
574:
573:
563:
554:(28): 16700–12.
539:
533:
532:
507:(4773): 179–86.
496:
487:
486:
476:
444:
438:
437:
419:
395:
296:stromal proteins
218:formylmethionine
174:Escherichia coli
1444:
1443:
1439:
1438:
1437:
1435:
1434:
1433:
1419:
1418:
1417:
1416:
1379:
1372:
1335:(7064): 103–7.
1325:
1321:
1274:
1270:
1225:
1221:
1184:
1175:
1130:
1123:
1092:(6): 2276–301.
1078:
1069:
1032:
1028:
997:
993:
948:
941:
918:(19): R911-21.
912:Current Biology
904:
897:
866:(10): 917–926.
852:
843:
802:(21): 8247–51.
788:
784:
739:
735:
698:(7077): 753–6.
688:
679:
648:(12): 1732–44.
634:
627:
588:
577:
540:
536:
497:
490:
445:
441:
396:
392:
387:
365:ClpS N-recognin
312:
250:eukaryotic cell
230:
169:
164:
97:
66:
58:
12:
11:
5:
1442:
1432:
1431:
1415:
1414:
1370:
1319:
1288:(2): 1022–31.
1268:
1219:
1198:(9): 962–970.
1173:
1144:(3): 1881–96.
1121:
1086:The Plant Cell
1067:
1026:
991:
939:
895:
841:
782:
733:
677:
625:
575:
534:
488:
439:
404:Genes to Cells
389:
388:
386:
383:
329:found in most
324:photosynthetic
311:
308:
246:photosynthetic
229:
226:
168:
165:
163:
162:
161:Gln (Q) → 0.8h
159:
158:Arg (R) → 1.0h
156:
155:Glu (E) → 1.0h
153:
152:Phe (F) → 1.1h
150:
149:Asp (D) → 1.1h
147:
146:Cys (C) → 1.2h
144:
143:Lys (K) → 1.3h
141:
140:Asn (N) → 1.4h
138:
137:Ser (S) → 1.9h
135:
134:Tyr (Y) → 2.8h
132:
131:Trp (W) → 2.8h
129:
128:His (H) → 3.5h
126:
125:Ala (A) → 4.4h
123:
122:Leu (L) → 5.5h
120:
119:Thr (T) → 7.2h
117:
114:
111:
108:
104:
96:
93:
92:
91:
88:
85:
82:
79:
65:
62:
57:
54:
41:ubiquitination
9:
6:
4:
3:
2:
1441:
1430:
1427:
1426:
1424:
1410:
1406:
1401:
1396:
1392:
1388:
1384:
1377:
1375:
1366:
1362:
1358:
1354:
1350:
1346:
1342:
1338:
1334:
1330:
1323:
1315:
1311:
1306:
1301:
1296:
1291:
1287:
1283:
1279:
1272:
1264:
1260:
1255:
1250:
1246:
1242:
1238:
1234:
1230:
1223:
1215:
1211:
1206:
1201:
1197:
1193:
1189:
1182:
1180:
1178:
1169:
1165:
1160:
1155:
1151:
1147:
1143:
1139:
1135:
1128:
1126:
1117:
1113:
1108:
1103:
1099:
1095:
1091:
1087:
1083:
1076:
1074:
1072:
1063:
1059:
1054:
1049:
1046:(9): 915–30.
1045:
1041:
1037:
1030:
1022:
1018:
1014:
1010:
1006:
1002:
995:
987:
983:
978:
973:
969:
965:
961:
957:
953:
946:
944:
935:
931:
926:
921:
917:
913:
909:
902:
900:
891:
887:
883:
879:
874:
869:
865:
861:
857:
850:
848:
846:
837:
833:
828:
823:
818:
813:
809:
805:
801:
797:
793:
786:
778:
774:
769:
764:
760:
756:
753:(5): 508–14.
752:
748:
744:
737:
729:
725:
721:
717:
713:
709:
705:
701:
697:
693:
686:
684:
682:
673:
669:
664:
659:
655:
651:
647:
643:
639:
632:
630:
621:
617:
613:
609:
605:
601:
597:
593:
586:
584:
582:
580:
571:
567:
562:
557:
553:
549:
545:
538:
530:
526:
522:
518:
514:
510:
506:
502:
495:
493:
484:
480:
475:
470:
466:
462:
458:
454:
450:
443:
435:
431:
427:
423:
418:
413:
409:
405:
401:
394:
390:
382:
380:
376:
372:
371:
366:
362:
358:
357:
352:
348:
344:
343:
338:
337:
332:
328:
325:
321:
317:
307:
304:
300:
297:
294:
293:
287:
285:
281:
277:
276:ClpS recognin
273:
269:
268:
262:
260:
256:
251:
247:
243:
242:cyanobacteria
239:
235:
225:
223:
219:
214:
212:
208:
204:
200:
196:
192:
188:
184:
180:
176:
175:
160:
157:
154:
151:
148:
145:
142:
139:
136:
133:
130:
127:
124:
121:
118:
115:
113:Pro (P) → 20h
112:
109:
107:Val (V)→ 100h
106:
105:
103:
101:
89:
86:
83:
80:
77:
76:
75:
74:
73:S. cerevisiae
70:
61:
53:
51:
46:
42:
38:
33:
31:
26:
22:
20:
1390:
1387:FEBS Letters
1386:
1332:
1328:
1322:
1285:
1281:
1271:
1236:
1233:Cell Reports
1232:
1222:
1195:
1192:FEBS Letters
1191:
1141:
1137:
1089:
1085:
1043:
1039:
1029:
1007:(1): 83–91.
1004:
1000:
994:
959:
955:
915:
911:
863:
859:
799:
795:
785:
750:
747:EMBO Reports
746:
736:
695:
691:
645:
641:
595:
591:
551:
547:
537:
504:
500:
456:
452:
442:
410:(1): 13–28.
407:
403:
393:
378:
374:
368:
354:
346:
340:
334:
333:, including
315:
313:
305:
301:
290:
288:
265:
263:
231:
228:Chloroplasts
215:
198:
194:
186:
182:
178:
172:
170:
116:Ile (I)→ 20h
99:
98:
68:
67:
59:
39:, mediating
35:targeted by
29:
18:
17:
15:
962:(1): 50–3.
351:Apicomplexa
331:Apicomplexa
209:+ protease
459:: 261–89.
385:References
377:bacterial
347:Plasmodium
345:and other
316:apicoplast
310:Apicoplast
890:196351051
284:chaperone
21:-end rule
1423:Category
1409:27588721
1357:16267556
1314:23192353
1263:29141210
1214:30953344
1168:26371235
1116:23898032
1062:25482260
1021:21781991
986:11154294
934:26439354
882:31300194
777:19373253
720:16467841
672:19440203
483:22524314
434:27736735
257:and the
167:Bacteria
1365:4401702
1337:Bibcode
1305:3542988
1254:5726808
1159:4634096
1107:3723626
977:1539323
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