Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida

Romana Petrželková, Marek Eliáš


Rab GTPases are a vast group of proteins serving a role of master regulators in membrane trafficking in eukaryotes. Previous studies delineated some 23 Rab and Rab-like paralogs ancestral for eukaryotes and mapped their current phylogenetic distribution, but the analyses relied on a limited sampling of the eukaryotic diversity. Taking advantage of the recent growth of genome and transcriptome resources for phylogenetically diverse plants and algae, we reanalyzed the evolution of the Rab family in eukaryotes with the primary plastid, collectively constituting the presumably monophyletic supergroup Archaeplastida. Our most important novel findings are as follows: (i) the ancestral set of Rabs in Archaeplastida included not only the paralogs Rab1, Rab2, Rab5, Rab6, Rab7, Rab8, Rab11, Rab18, Rab23, Rab24, Rab28, IFT27, and RTW (=Rabl2), as suggested previously, but also Rab14 and Rab34, because Rab14 exists in glaucophytes and Rab34 is present in glaucophytes and some green algae; (ii) except in embryophytes, Rab gene duplications have been rare in Archaeplastida. Most notable is the independent emergence of divergent, possibly functionally novel, in-paralogs of Rab1 and Rab11 in several archaeplastidial lineages; (iii) recurrent gene losses have been a significant factor shaping Rab gene complements in archaeplastidial species; for example, the Rab21 paralog was lost at least six times independently within Archaeplastida, once in the lineage leading to the “core” eudicots; (iv) while the glaucophyte Cyanophora paradoxa has retained the highest number of ancestral Rab paralogs among all archaeplastidial species studied so far, rhodophytes underwent an extreme reduction of the Rab gene set along their stem lineage, resulting in only six paralogs (Rab1, Rab2, Rab6, Rab7, Rab11, and Rab18) present in modern red algae. Especially notable is the absence of Rab5, a virtually universal paralog essential for the endocytic pathway, suggesting that endocytosis has been highly reduced or rewired in rhodophytes.


Archaeplastida; Chloroplastida; endocytosis; evolution; Glaucophyta; Rab GTPases; Rhodophyta

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Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol. 2009;10(8):513–525.

Woollard AA, Moore I. The functions of Rab GTPases in plant membrane traffic. Curr Opin Plant Biol. 2008;11(6):610–619.

Brighouse A, Dacks JB, Field MC. Rab protein evolution and the history of the eukaryotic endomembrane system. Cell Mol Life Sci. 2010;67(20):3449–3465.

Briguglio JS, Turkewitz AP. Tetrahymena thermophila: a divergent perspective on membrane traffic. J Exp Zool B Mol Dev Evol. 2014;322(7):500–516.

Klöpper TH, Kienle N, Fasshauer D, Munro S. Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis. BMC Biol. 2012;10:71.

Elias M, Brighouse A, Gabernet-Castello C, Field MC, Dacks JB. Sculpting the endomembrane system in deep time: high resolution phylogenetics of Rab GTPases. J Cell Sci. 2012;125(pt 10):2500–2508.

Koonin EV. The origin and early evolution of eukaryotes in the light of phylogenomics. Genome Biol. 2010;11(5):209.

Koumandou VL, Wickstead B, Ginger ML, van der Giezen M, Dacks JB, Field MC. Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit Rev Biochem Mol Biol. 2013;48(4):373–396.

Lo JC, Jamsai D, O’Connor AE, Borg C, Clark BJ, Whisstock JC, et al. RAB-like 2 has an essential role in male fertility, sperm intra-flagellar transport, and tail assembly. PLoS Genet. 2012;8(10):e1002969.

Huet D, Blisnick T, Perrot S, Bastin P. The GTPase IFT27 is involved in both anterograde and retrograde intraflagellar transport. Elife. 2014;3:e02419.

Burki F. The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb Perspect Biol. 2014;6(5):a016147.

Diekmann Y, Seixas E, Gouw M, Tavares-Cadete F, Seabra MC, Pereira-Leal JB. Thousands of rab GTPases for the cell biologist. PLoS Comput Biol. 2011;7(10):e1002217.

del Campo J, Sieracki ME, Molestina R, Keeling P, Massana R, Ruiz-Trillo I. The others: our biased perspective of eukaryotic genomes. Trends Ecol Evol. 2014;29(5):252–259.

Keeling PJ, Burki F, Wilcox HM, Allam B, Allen EE, Amaral-Zettler LA, et al. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol. 2014;12(6):e1001889.

Adl SM, Simpson AG, Farmer MA, Andersen RA, Anderson OR, Barta JR, et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 2005;52(5):399–451.

Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, et al. The revised classification of eukaryotes. J Eukaryot Microbiol. 2012;59(5):429–493.

de Clerck O, Bogaert KA, Leliaert F. Diversity and evolution of algae: primary endosymbiosis. Adv Bot Res. 2012;64:55–86.

Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, et al. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci USA. 2009;106(10):3859–3864.

Yabuki A, Kamikawa R, Ishikawa SA, Kolisko M, Kim E, Tanabe AS, et al. Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista. Sci Rep. 2014;4:4641.

Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature. 2004;428(6983):653–657.

Bhattacharya D, Price DC, Chan CX, Gross J, Steiner JM, Löffelhardt. Analysis of the genome of Cyanophora paradoxa: an algal model for understanding primary endosymbiosis. In: Löffelhardt W, editor. Endosymbiosis. Vienna: Springer; 2014. p. 135–148.

Collén J, Porcel B, Carré W, Ball SG, Chaparro C, Tonon T, et al. Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci USA. 2013;110(13):5247–5252.

Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, et al. Genome of the red alga Porphyridium purpureum. Nat Commun. 2013;4:1941.

Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, et al. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science. 2013;339(6124):1207–1210.

Nakamura Y, Sasaki N, Kobayashi M, Ojima N, Yasuike M, Shigenobu Y, et al. The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PLoS One. 2013;8(3):e57122.

Price DC, Chan CX, Yoon HS, Yang EC, Qiu H, Weber AP, et al. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science. 2012;335(6070):843–847.

Saito C, Ueda T. Functions of RAB and SNARE proteins in plant life. Int Rev Cell Mol Biol. 2009;274:183–233.

Zhang Z, Hill DR, Sylvester AW. Diversification of the RAB guanosine triphosphatase family in dicots and monocots. J Integr Plant Biol. 2007;49(8):1129–1141.

Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science. 2008;319(5859):64–69.

Huber H, Beyser K, Fabry S. Small G proteins of two green algae are localized to exocytic compartments and to flagella. Plant Mol Biol. 1996;31(2):279–293.

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–3402.

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780.

Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–1313.

Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the gateway computing environments workshop (GCE). New Orleans, LA; 2010. p. 1–8.

Quang LS, Gascuel O, Lartillot N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics. 2008;24(20):2317–2323.

Letunic I, Bork P. Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39(web server issue):W475–W478.

Rogozin IB, Basu MK, Csürös M, Koonin EV. Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. Genome Biol Evol. 2009;1:99–113.

Finet C, Timme RE, Delwiche CF, Marlétaz F. Multigene phylogeny of the green lineage reveals the origin and diversification of land plants. Curr Biol. 2010;20(24):2217–2222.

Laurin-Lemay S, Brinkmann H, Philippe H. Origin of land plants revisited in the light of sequence contamination and missing data. Curr Biol. 2012;22(15):R593–R594.

Ueda T, Yamaguchi M, Uchimiya H, Nakano A. Ara6, a plant-unique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana. EMBO J. 2001;20(17):4730–4741.

Hoepflinger MC, Geretschlaeger A, Sommer A, Hoeftberger M, Nishiyama T, Sakayama H, et al. Molecular and biochemical analysis of the first ARA6 homologue, a RAB5 GTPase, from green algae. J Exp Bot. 2013;64(18):5553–5568.

Vanneste K, Maere S, van de Peer Y. Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos Trans R Soc Lond B Biol Sci. 2014;369(1648).

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science. 2011;332(6032):960–963.

Yoon HS, Müller KM, Sheath RG, Ott FD, Bhattacharya D. Defining the major lineages of red algae (Rhodophyta). J Phycol. 2006;42(2):482–492.

Verbruggen H, Maggs CA, Saunders GW, Le Gall L, Yoon HS, de Clerck O. Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evol Biol. 2010;10:16.

Rutherford S, Moore I. The Arabidopsis Rab GTPase family: another enigma variation. Curr Opin Plant Biol. 2002;5(6):518–528.

Elias M, Patron NJ, Keeling PJ. The RAB family GTPase Rab1A from Plasmodium falciparum defines a unique paralog shared by Chromalveolates and Rhizaria. J Eukaryot Microbiol. 2009;56(4):348–356.

Elias M. Patterns and processes in the evolution of the eukaryotic endomembrane system. Mol Membr Biol. 2010;27(8):469–489.

Reyes-Prieto A, Bhattacharya D. Phylogeny of nuclear-encoded plastid-targeted proteins supports an early divergence of glaucophytes within Plantae. Mol Biol Evol. 2007;24(11):2358–2361.

Deschamps P, Moreira D. Signal conflicts in the phylogeny of the primary photosynthetic eukaryotes. Mol Biol Evol. 2009;26(12):2745–2753.

Marin B, Melkonian M. Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons. Protist. 2010;161(2):304–336.

Lemieux C, Otis C, Turmel M. Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species. BMC Genomics. 2014;15:857.

Umen JG. Green algae and the origins of multicellularity in the plant kingdom. Cold Spring Harb Perspect Biol. 2014;6(11).

Ali M, Leung KF, Field MC. The ancient small GTPase Rab21 functions in intermediate endocytic steps in trypanosomes. Eukaryot Cell. 2014;13(2):304–319.

Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, et al. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. 2009;324(5924):268–272.

Lumb JH, Field MC. Rab23 is a flagellar protein in Trypanosoma brucei. BMC Res Notes. 2011;4:190.

Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, et al. The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell. 2010;22(9):2943–2955.

Lewis LA, McCourt RM. Green algae and the origin of land plants. Am J Bot. 2004;91(10):1535–1556.

Hodges ME, Wickstead B, Gull K, Langdale JA. The evolution of land plant cilia. New Phytol. 2012;195(3):526–540.

Woodman PG. Biogenesis of the sorting endosome: the role of Rab5. Traffic. 2000;1(9):695–701.

Maruyama S, Kim E. A modern descendant of early green algal phagotrophs. Curr Biol. 2013;23(12):1081–1084.

Lemieux C, Otis C, Turmel M. Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae. BMC Evol Biol. 2014;14:211.