BACKGROUND: Eukaryotic gene expression is controlled by a number of RNA-binding proteins (RBP), such as the proteins from the Puf (Pumilio and FBF) superfamily (PufSF). These proteins bind to RNA via multiple Puf repeat domains, each of which specifically recognizes a single RNA base. Recently, three diversified PufSF proteins have been described in model organisms, each of which is responsible for the maturation of ribosomal RNA or the translational regulation of mRNAs; however, less is known about the role of these proteins across eukaryotic diversity. RESULTS: Here, we investigated the distribution and function of PufSF RBPs in the tree of eukaryotes. We determined that the following PufSF proteins are universally conserved across eukaryotes and can be broadly classified into three groups: (i) Nop9 orthologues, which participate in the nucleolar processing of immature 18S rRNA; (ii) 'classical' Pufs, which control the translation of mRNA; and (iii) PUM3 orthologues, which are involved in the maturation of 7S rRNA. In nearly all eukaryotes, the rRNA maturation proteins, Nop9 and PUM3, are retained as a single copy, while mRNA effectors ('classical' Pufs) underwent multiple lineage-specific expansions. We propose that the variation in number of 'classical' Pufs relates to the size of the transcriptome and thus the potential mRNA targets. We further distinguished full set of PufSF proteins in divergent metamonad Giardia intestinalis and initiated their cellular and biochemical characterization. CONCLUSIONS: Our data suggest that the last eukaryotic common ancestor (LECA) already contained all three types of PufSF proteins and that 'classical' Pufs then underwent lineage-specific expansions.

Department of Cell and Molecular Biology Science for Life Laboratory Uppsala University SE 75123 Uppsala Sweden

Department of Parasitology Faculty of Science Charles University BIOCEV Průmyslová 595 252 50 Vestec Czech Republic

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Quenault T, Lithgow T, Traven A. PUF proteins: repression, activation and mRNA localization. Trends Cell Biol. 2011;21:104–112. PubMed

Qiu C, McCann KL, Wine RN, Baserga SJ, Hall TMT. A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization. Proc Natl Acad Sci. 2014;111:18554–18559. PubMed PMC

Thomson E, Rappsilber J, Tollervey D. Nop9 is an RNA binding protein present in pre-40S ribosomes and required for 18S rRNA synthesis in yeast. Rna. 2007;13:2165–2174. PubMed PMC

Zhang B, Gallegos M, Puoti A, Durkin E, Fields S, Kimble J, et al. A conserved RNA-binding protein that regulates sexual fates in the C elegans hermaphrodite germ line. Nature. 1997;390:477–484. PubMed

Barker DD, Wang C, Moore J, Dickinson LK, Lehmann R. Pumilio is essential for function but not for distribution of the Drosophila abdominal determinant Nanos. Genes Dev. 1992;6:2312–2326. PubMed

Miller MT, Higgin JJ, Hall TM. Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p. Nat Struct Mol Biol. 2008;15:397–402. PubMed PMC

Wang Y, Opperman L, Wickens M, Hall TM. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein. Proc Natl Acad Sci U S A. 2009;106:20186–20191. PubMed PMC

Hogan GJ, Brown PO, Herschlag D. Evolutionary conservation and diversification of Puf RNA binding proteins and their mRNA targets. PLoS Biol. 2015;13:e1002307. PubMed PMC

Campbell ZT, Valley CT, Wickens M. A protein-RNA specificity code enables targeted activation of an endogenous human transcript. Nat Struct Mol Biol. 2014;21:732–738. PubMed PMC

Liang X, Hart KJ, Dong G, Siddiqui FA, Sebastian A, Li X, et al. Puf3 participates in ribosomal biogenesis in malaria parasites. J Cell Sci. 2018;131:jcs212597. PubMed PMC

Zhang C, Muench DG. A nucleolar PUF RNA-binding protein with specificity for a unique RNA sequence. J Biol Chem. 2015;290:30108–30118. PubMed PMC

Crittenden SL, Bernstein DS, Bachorik JL, Thompson BE, Gallegos M, Petcherski AG, et al. A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegans. Nature. 2002;417:660–663. PubMed

Wang X, McLachlan J, Zamore PD, Hall TM. Modular recognition of RNA by a human pumilio-homology domain. Cell. 2002;110:501–512. PubMed

Blewett NH, Goldstrohm AC. A eukaryotic translation initiation factor 4E-binding protein promotes mRNA decapping and is required for PUF repression. Mol Cell Biol. 2012;32:4181–4194. PubMed PMC

Nyikó T, Auber A, Bucher E. Functional and molecular characterization of the conserved Arabidopsis PUMILIO protein, APUM9. Plant Mol Biol. 2019;100:199–214. PubMed PMC

Goldstrohm AC, Hook BA, Seay DJ, Wickens M. PUF proteins bind Pop2p to regulate messenger RNAs. Nat Struct Mol Biol. 2006;13:533–539. PubMed

Suh N, Crittenden SL, Goldstrohm A, Hook B, Thompson B, Wickens M, et al. FBF and its dual control of gld-1 expression in the Caenorhabditis elegans germline. Genetics. 2009;181:1249–1260. PubMed PMC

Garcia-Rodriguez LJ, Gay AC, Pon LA. Puf3p, a Pumilio family RNA binding protein, localizes to mitochondria and regulates mitochondrial biogenesis and motility in budding yeast. J Cell Biol. 2007;176:197–207. PubMed PMC

Gerber AP, Herschlag D, Brown PO. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoSBiol. 2004;2:E79. PubMed PMC

Pederson T. The nucleolus. Cold Spring Harb Perspect Biol. 2011;3:1–15. PubMed PMC

Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TMT. Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA. Nat Commun. 2016;7:13085. PubMed PMC

Wang B, Ye K. Nop9 binds the central pseudoknot region of 18S rRNA. Nucleic Acids Res. 2017;45:gkw1323. PubMed PMC

Li Z, Lee I, Moradi E, Hung NJ, Johnson AW, Marcotte EM. Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol. 2009;7. PubMed PMC

Wickens M, Bernstein DS, Kimble J, Parker R. A PUF family portrait: 3’UTR regulation as a way of life. Trends Genet. 2002;18:150–157. PubMed

Tam PPC, Barrette-Ng IH, Simon DM, Tam MWC, Ang AL, Muench DG. The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization. BMC Plant Biol. 2010;10. PubMed PMC

Galgano A, Forrer M, Jaskiewicz L, Kanitz A, Zavolan M, Gerber AP. Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS One. 2008;3:e3164. PubMed PMC

O’Malley MA, Leger MM, Wideman JG, Ruiz-Trillo I. Concepts of the last eukaryotic common ancestor. Nat Ecol Evol. 2019;3:338–344. PubMed

Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, et al. Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol. 2019;66:4–119. PubMed PMC

Roger AJ, Muñoz-Gómez SA, Kamikawa R. The origin and diversification of mitochondria. Curr Biol. 2017;27:R1177–R1192. PubMed

Adam RD. Biology of Giardia lamblia. Clin Microbiol Rev. 2001;14:447–475. PubMed PMC

Jiménez-García LF. The nucleolus of Giardia lamblia. MOJ Anat Physiol. 2017;3:41–43.

Elmendorf HG, Singer SM, Nash TE. The abundance of sterile transcripts in Giardia lamblia. Nucleic Acids Res. 2001;29:4674–4683. PubMed PMC

Nixon JEJ, Wang A, Morrison HG, McArthur AG, Sogin ML, Loftus BJ, et al. A spliceosomal intron in Giardia lamblia. Proc Natl Acad Sci U S A. 2002;99:3701–3705. PubMed PMC

Kamikawa R, Inagaki Y, Tokoro M, Roger AJ, Hashimoto T. Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Curr Biol. 2011;21:311–315. PubMed

Li L, Wang CC. Capped mRNA with a single nucleotide leader is optimally translated in a primitive eukaryote, Giardia lamblia. J Biol Chem. 2004;279:14656–14664. PubMed

Hausmann S, Altura MA, Witmer M, Singer SM, Elmendorf HG, Shuman S. Yeast-like mRNA capping apparatus in Giardia lamblia. J Biol Chem. 2005;280:12077–12086. PubMed

Williams CW, Elmendorf HG. Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach. BMC Genomics. 2011;12:586. PubMed PMC

Frickey T, Lupas A. CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics. 2004;20:3702–3704. PubMed

Almagro Armenteros JJ, Sønderby CK, Sønderby SK, Nielsen H, Winther O. DeepLoc: prediction of protein subcellular localization using deep learning. Bioinformatics. 2017;33:3387–3395. PubMed

Dolezal P, Smíd O, Rada P, Zubácová Z, Bursać D, Suták R, et al. Giardia mitosomes and trichomonad hydrogenosomes share a common mode of protein targeting. Proc Natl Acad Sci U S A. 2005;102:10924–10929. PubMed PMC

Martincová E, Voleman L, Pyrih J, Žárský V, Vondráčková P, Kolísko M, et al. Probing the biology of Giardia intestinalis mitosomes using in vivo enzymatic tagging. Mol Cell Biol. 2015;35:2864–2874. PubMed PMC

Hall TMT. Expanding the RNA-recognition code of PUF proteins. Nat Struct Mol Biol. 2014;21:653–655. PubMed

Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, et al. A quantitative and predictive model for RNA binding by human Pumilio proteins. Mol Cell. 2019;74:966–981. PubMed PMC

Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, et al. Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science. 2007;317:1921–1926. PubMed

Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27:1017–1018. PubMed PMC

Kershner AM, Kimble J. Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator. Proc Natl Acad Sci U S A. 2010;107:3936–3941. PubMed PMC

Yang YT, Ting YH, Liang KJ, Lo KY. The roles of Puf6 and Loc1 in 60S biogenesis are interdependent, and both are required for efficient accommodation of Rpl43. J Biol Chem. 2016;291:19312–19323. PubMed PMC

Gu W, Deng Y, Zenklusen D, Singer RH. A new yeast PUF family protein, Puf6p, represses ASH1 mRNA translation and is required for its localization. Genes Dev. 2004;18:1452–1465. PubMed PMC

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Di B, Juzokaite L, Vancaester E, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 2017;541:353–358. PubMed

Qiu C, Dutcher RC, Porter DF, Arava Y, Wickens M, Hall TMT. Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Nucleic Acids Res. 2019;47:8770–8784. PubMed PMC

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin E V., et al. The COG database: an updated vesion includes eukaryotes. BMC Bioinformatics. 2003;4:1–14. PubMed PMC

Vosseberg J, van Hooff JJE, Marcet-Houben M, van Vlimmeren A, van Wijk LM, Gabaldón T, et al. Timing the origin of eukaryotic cellular complexity with ancient duplications. bioRxiv. 2019;:823484:1–18. PubMed PMC

Ankarklev J, Jerlström-Hultqvist J, Ringqvist E, Troell K, Svärd SG. Behind the smile: cell biology and disease mechanisms of Giardia species. Nat Rev Microbiol. 2010;8:413–422. PubMed

Prucca CG, Slavin I, Quiroga R, Elías EV, Rivero FD, Saura A, et al. Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature. 2008;456:750–754. PubMed

Andersen JS, Lyon CE, Fox AH, Leung AKL, Lam YW, Steen H, et al. Directed proteomic analysis of the human nucleolus. Curr Biol. 2002;12:1–11. PubMed

Narcisi EM, Glover CVC, Fechheimer M. Fibrillarin, a conserved pre-ribosomal RNA processing protein of Giardia. J. Eukaryot. Microbiol. 1998;45:105–11. PubMed

Jiménez-García LF, Zavala G, Chávez-Munguía B, Ramos-Godínez M d P, López-Velázquez G, Segura-Valdez M d L, et al. Identification of nucleoli in the early branching protist Giardia duodenalis. Int J Parasitol. 2008;38:1297–1304. PubMed

Tian XF, Yang ZH, Shen H, Adam RD, Lu SQ. Identification of the nucleoli of Giardia lamblia with TEM and CFM. Parasitol Res. 2010;106:789–793. PubMed

Li L, Wang CC. Identification in the ancient protist Giardia lamblia of two eukaryotic translation initiation factor 4E homologues with distinctive functions. Eukaryot Cell. 2005;4:948–959. PubMed PMC

Saraiya AA, Wang CC. snoRNA, a novel precursor of microRNA in Giardia lamblia. PLOS Pathog. 2008;4:e1000224. PubMed PMC

Lamanna AC, Karbsteina K. Nob1 binds the single-stranded cleavage site D at the 3′-end of 18S rRNA with its PIN domain. Proc Natl Acad Sci U S A. 2009;106:14259–14264. PubMed PMC

Teodorovic S, Walls CD, Elmendorf HG. Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res. 2007;35:2544–2553. PubMed PMC

Vanacova S, Liston DR, Tachezy J, Johnson PJ. Molecular biology of the amitochondriate parasites, Giardia intestinalis, Entamoeba histolytica and Trichomonas vaginalis. Int J Parasitol. 2003;33:235–255. PubMed

Filipovska A, Razif MF, Nygard KK, Rackham O. A universal code for RNA recognition by PUF proteins. Nat Chem Biol. 2011;7:425–427. PubMed

Burki F, Roger AJ, Brown MW, Simpson AGB. The new tree of eukaryotes. Trends Ecol Evol. 2020;35:43–55. PubMed

Zimmermann L, Stephens A, Nam SZ, Rau D, Kübler J, Lozajic M, et al. A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core. J Mol Biol. 2018;430:2237–43. PubMed

Bailey TL, Johnson J, Grant CE, Noble WS. The MEME suite. Nucleic Acids Res. 2015;43:W39–W49. PubMed PMC

Aurrecoechea C, Barreto A, Basenko EY, Brestelli J, Brunk BP, Cade S, et al. EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Res. 2017;45:D581–D591. PubMed PMC

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6. PubMed PMC

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

Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25:1189–1191. PubMed PMC

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Bioinformatics 2009;25:1972–1973. PubMed PMC

Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490. PubMed PMC

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020. PubMed PMC

Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–522. PubMed PMC

Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, et al. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data. Nature. 2018;556:452–456. PubMed PMC

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–589. PubMed PMC

Wang H-C, Minh BQ, Susko E, Roger AJ. Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst Biol. 2018;67:216–235. PubMed

Keister DB. Axenic culture of Giardia lamblia in TYI-S-33 medium supplemented with bile. Trans R Soc Trop Med Hyg. 1983;77:487–488. PubMed

Pyrihová E, Motyčková A, Voleman L, Wandyszewska N, Fišer R, Seydlová G, et al. A single Tim translocase in the mitosomes of Giardia intestinalis illustrates convergence of protein import machines in anaerobic eukaryotes. Genome Biol Evol. 2018;10:2813–2822. PubMed PMC

Masuda T, Tomita M, Ishihama Y. Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res. 2008;7:731–740. PubMed

Hebert AS, Richards AL, Bailey DJ, Ulbrich A, Coughlin EE, Westphall MS, et al. The one hour yeast proteome. Mol Cell Proteomics. 2014;13:339–347. PubMed PMC

Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014;13:2513–2526. PubMed PMC

Tyanova S, Temu T, Sinitcyn P, Carlson A, Hein MY, Geiger T, et al. The Perseus computational platform for comprehensive analysis of (prote) omics data. Nat Methods. 2016;13:731–740. PubMed

Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 2016;44:11033–11033. PubMed PMC

Voleman L, Najdrová V, Ástvaldsson Á, Tůmová P, Einarsson E, Švindrych Z, et al. Giardia intestinalis mitosomes undergo synchronized fission but not fusion and are constitutively associated with the endoplasmic reticulum. BMC Biol. 2017;15:27. PubMed PMC

: Najdrova V, Stairs CW, Vinopalová M, Voleman L, Dolezal P. The evolution of Puf superfamily proteins for rRNA maturation and mRNA translational regulation across the tree of eukaryotes. Supporting datasets. 2020. Figshare. DOI: 10.6084/m9.figshare.12097692. PubMed PMC

Mlf mediates proteotoxic response via formation of cellular foci for protein folding and degradation in Giardia

Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis

Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3

Efficient CRISPR/Cas9-mediated gene disruption in the tetraploid protist Giardia intestinalis

The evolution of the Puf superfamily of proteins across the tree of eukaryotes

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10.6084/m9.figshare.12097692