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The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas Reinhardtii

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The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas Reinhardtii cells Review The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii Ulrich Kück * and Olga Schmitt Allgemeine und Molekulare Botanik, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-234-32-28951 Abstract: In eukaryotes, RNA trans-splicing is a significant RNA modification process for the end-to- end ligation of exons from separately transcribed primary transcripts to generate mature mRNA. So far, three different categories of RNA trans-splicing have been found in organisms within a diverse range. Here, we review trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. We discuss the origin of intronic sequences and the evolutionary relationship between chloroplast ribonucleoprotein complexes and the nuclear spliceosome. Finally, we focus on the ribonucleoprotein supercomplex involved in trans-splicing of chloroplast group II introns from the green alga Chlamydomonas reinhardtii. This complex has been well characterized genetically and biochemically, resulting in a detailed picture of the chloroplast ribonucleoprotein supercomplex. This information contributes substantially to our understanding of the function of RNA-processing machineries and might provide a blueprint for other splicing complexes involved in trans- as well as cis-splicing of organellar intron RNAs. Keywords: group II intron; trans-splicing; ribonucleoprotein complex; chloroplast; Chlamydomonas reinhardtii Citation: Kück, U.; Schmitt, O. The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii. 1. Introduction Cells 2021, 10, 290. https://doi.org/ One of the unexpected and outstanding discoveries in 20th century biology was the 10.3390/cells10020290 identification of discontinuous eukaryotic genes [1,2]. Walter Gilbert introduced the terms Academic Editors: Philippe Giegé “exon” for expressed sequences and “intron” for intervening sequences [3]. In order to fuse and Laurence Marechal-Drouard exons and generate mature messenger RNA (mRNA), introns are posttranscriptionally Received: 29 December 2020 removed by splicing. Several studies revealed that splicing in nuclei of eukaryotes is Accepted: 20 January 2021 mediated by highly dynamic ribonucleoprotein machinery called the spliceosome [4]. Published: 1 February 2021 The intervening sequences in the nuclear precursor mRNA of eukaryotes are therefore described as spliceosomal introns or nuclear mRNA introns. Further intron types have been Publisher’s Note: MDPI stays neutral identified and are classified by their structural characteristics and splicing mechanisms, with regard to jurisdictional claims in i.e., archaeal introns, group I introns, and group II introns. Spliceosomal introns and published maps and institutional affil- group II introns share a common splicing mechanism (as outlined later) that is distinctly iations. different from the splicing mechanism of group I introns, which are found in genomes of bacteria and organelles as well as in nuclei of lower eukaryotes. Finally, archaeal introns are comparably small and share a pre-tRNA intron excision mechanism with eukaryotes. Here, we summarize our current knowledge about the relationship between group Copyright: © 2021 by the authors. II introns and spliceosomal introns. This includes a brief description of introns-early and Licensee MDPI, Basel, Switzerland. introns-late theories, a comparison of sequence homologies, and discussion of mechanistic This article is an open access article similarities. We describe nuclear and organellar splicing factors further and discuss how distributed under the terms and trans-spliced and degenerated group II introns may have evolved into spliceosomal introns. conditions of the Creative Commons In the second part of our review, we briefly discuss trans-spliced introns in different Attribution (CC BY) license (https:// organismal lineages and finally summarize the extensive experimental data supporting the creativecommons.org/licenses/by/ existence of a trans-splicing supercomplex in C. reinhardtii chloroplasts. 4.0/). Cells 2021, 10, 290. https://doi.org/10.3390/cells10020290 https://www.mdpi.com/journal/cells Cells 2021, 10, x FOR PEER REVIEW 2 of 23 In the second part of our review, we briefly discuss trans-spliced introns in different organismal lineages and finally summarize the extensive experimental data supporting the existence of a trans-splicing supercomplex in C. reinhardtii chloroplasts. Cells 2021, 10, 290 2. Introns-Early or Introns-Late Debate 2 of 23 Very soon after the discovery of spliceosomal introns, several theories arose about their origin and evolution. The introns-early theory published around the same time is closely2. Introns-Early coupled to or the Introns-Late exon theory Debate of genes [5–7]. The main hypothesis is that the split structureVery of soongenes after is ancie the discoverynt and occurs of spliceosomal in all domains introns, of several life, and theories that arose exons about are theirancestral geneticorigin elements and evolution. encoding The introns-early proteins with theory small published domains. around Thus, the samemultidomain time is closely proteins coupled to the exon theory of genes [5–7]. The main hypothesis is that the split structure evolved by recombination of neighboring exons that were connected by noncoding se- of genes is ancient and occurs in all domains of life, and that exons are ancestral genetic quenceselements [8,9]. encoding Subsequentl proteinsy, with these small noncoding domains. sequences Thus, multidomain became proteinsintrons. evolvedHowever, by fur- therrecombination investigations of neighboringshowed inconsistent exons that correlation were connected between by noncoding exons and sequences protein [8 ,domain9]. unitsSubsequently, [10]. these noncoding sequences became introns. However, further investigations showedAn alternative, inconsistent the correlation introns-late between theory exons, was and proposed protein domainby different units authors [10]. [11,12]. Ac- cordingAn to alternative,this hypothesis, the introns-late spliceosomal theory, introns was proposed are unique by different to eukaryotes, authors introduced [11,12]. Ac- into thecording host genome to this hypothesis, by an endosymbiont spliceosomal ( intronsFigure are1). uniqueThe endosymbiosis to eukaryotes, introducedof α-proteobacteria into α entailedthe host massive genome genomic by an endosymbiont transfer accompanied (Figure1). The by endosymbiosis invasion of ofthe -proteobacteriahost genome with entailed massive genomic transfer accompanied by invasion of the host genome with group group II introns. This type of intron has the ability to self-splice and invade DNA, and it II introns. This type of intron has the ability to self-splice and invade DNA, and it is found is foundin abundance in abundance in eubacterial in eubacterial genomes [genomes13,14]. Strong [13,14]. selective Strong pressure selective on thepressure archaeal on the archaealhost may host have may initiated have initiated the fragmentation the fragmentation of group II of intron group RNA II intron into five RNA small into nuclear five small nuclearRNAs RNAs (snRNAs) (snRNAs) and the and mRNA the mRNA intron, whichintron, now which function now infunction splicing in of splicing spliceosomal of spliceo- somalintrons introns [15]. Consistent[15]. Consistent with this with idea ofthis intron idea evolution of intron is theevolution distribution is the of groupdistribution II in- of grouptrons II [ 13introns]. They [13]. are frequentlyThey are frequently found in bacterial found genomes in bacterial and weregenomes most and likely were introduced most likely introducedby horizontal by horizontal transfer to eukaryotictransfer to nuclei eukaryotic [16]. nuclei [16]. FigureFigure 1. The 1. intronsThe introns-late-late theory theory explains explains the the evolution of of spliceosomal spliceosomal introns. introns. The endosymbiosisThe endosymbiosis of a group of a II group intron-rich II intron- rich αα-proteobacteria-proteobacteria intointo thethe archaeal archaeal intronless intronless host host was was followed followed by the by invasionthe invasion of the of host the genomehost genome by mobile by mobile group IIgroup II introns.introns. The The resulting resulting discontinuous discontinuous genes genes provoked provoked aa strongstrong selective selective pressure pressure toward toward evolving evolving intron intron removal. removal. This This includedincluded the degradation the degradation of group of group II intron II intron RNA RNA into into mRNA mRNA intronsintrons and and small small nucleolar nucleolar RNAs RNAs (snRNAs). (snRNAs). Separation Separation of of the inefficientthe inefficient splicing splicing reaction reaction from from translation translation was was achieved achieved byby developing developing a nucleara nuclear envelope. envelope. Cells 2021, 10, 290 3 of 23 So far, group II introns have not been found in nuclear genomes of eukaryotes, which indicates that they were efficiently transformed into spliceosomal introns during evolution. The introns-late theory was further expanded by proposing that the invasion of group II introns was one of the major driving forces for nucleus–cytoplasm compartmentaliza- tion [17]. Accordingly, the “turbulent phase” of gene transfer, including
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