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Christian RW, Hewitt SL, Nelson G, Roalson EH, Dhingra A. Plastid transit peptides-where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution. PeerJ 2020; 8:e9772. [PMID: 32913678 PMCID: PMC7456531 DOI: 10.7717/peerj.9772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/30/2020] [Indexed: 01/22/2023] Open
Abstract
Subcellular relocalization of proteins determines an organism's metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.
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Affiliation(s)
- Ryan W. Christian
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Seanna L. Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Grant Nelson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
| | - Eric H. Roalson
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, WA, USA
- Department of Horticulture, Washington State University, Pullman, WA, USA
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2
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Dunn CD, Paavilainen VO. Wherever I may roam: organellar protein targeting and evolvability. Curr Opin Genet Dev 2019; 58-59:9-16. [DOI: 10.1016/j.gde.2019.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 07/20/2019] [Indexed: 02/08/2023]
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3
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Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC. Cytonuclear integration and co-evolution. Nat Rev Genet 2018; 19:635-648. [PMID: 30018367 PMCID: PMC6469396 DOI: 10.1038/s41576-018-0035-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The partitioning of genetic material between the nucleus and cytoplasmic (mitochondrial and plastid) genomes within eukaryotic cells necessitates coordinated integration between these genomic compartments, with important evolutionary and biomedical implications. Classic questions persist about the pervasive reduction of cytoplasmic genomes via a combination of gene loss, transfer and functional replacement - and yet why they are almost always retained in some minimal form. One striking consequence of cytonuclear integration is the existence of 'chimeric' enzyme complexes composed of subunits encoded in two different genomes. Advances in structural biology and comparative genomics are yielding important insights into the evolution of such complexes, including correlated sequence changes and recruitment of novel subunits. Thus, chimeric cytonuclear complexes provide a powerful window into the mechanisms of molecular co-evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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4
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Río Bártulos C, Rogers MB, Williams TA, Gentekaki E, Brinkmann H, Cerff R, Liaud MF, Hehl AB, Yarlett NR, Gruber A, Kroth PG, van der Giezen M. Mitochondrial Glycolysis in a Major Lineage of Eukaryotes. Genome Biol Evol 2018; 10:2310-2325. [PMID: 30060189 PMCID: PMC6198282 DOI: 10.1093/gbe/evy164] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 12/21/2022] Open
Abstract
The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host’s metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.
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Affiliation(s)
- Carolina Río Bártulos
- Institut für Genetik, Technische Universität Braunschweig.,Fachbereich Biologie, Universität Konstanz, Germany
| | - Matthew B Rogers
- Biosciences, University of Exeter, United Kingdom.,Rangos Research Center, University of Pittsburgh, Children's Hospital, Pittsburgh, PA
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Eleni Gentekaki
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,School of Science and Human Gut Microbiome for Health Research Unit, Mae Fah Luang University, Chiang Rai, Thailand
| | - Henner Brinkmann
- Département de Biochimie, Université de Montréal C.P. 6128, Montréal, Quebec, Canada.,Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Rüdiger Cerff
- Institut für Genetik, Technische Universität Braunschweig
| | | | - Adrian B Hehl
- Institute of Parasitology, University of Zürich, Switzerland
| | - Nigel R Yarlett
- Department of Chemistry and Physical Sciences, Pace University
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, Germany.,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
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5
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Gruber A, Kroth PG. Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160402. [PMID: 28717012 PMCID: PMC5516111 DOI: 10.1098/rstb.2016.0402] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2017] [Indexed: 11/12/2022] Open
Abstract
Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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6
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Wu Z, Sloan DB, Brown CW, Rosenblueth M, Palmer JD, Ong HC. Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses. Mol Biol Evol 2017; 34:2340-2354. [PMID: 28541477 PMCID: PMC5850859 DOI: 10.1093/molbev/msx170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Colin W. Brown
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
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7
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Martin WF, Cerff R. Physiology, phylogeny, early evolution, and GAPDH. PROTOPLASMA 2017; 254:1823-1834. [PMID: 28265765 PMCID: PMC5610209 DOI: 10.1007/s00709-017-1095-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 05/23/2023]
Abstract
The chloroplast and cytosol of plant cells harbor a number of parallel biochemical reactions germane to the Calvin cycle and glycolysis, respectively. These reactions are catalyzed by nuclear encoded, compartment-specific isoenzymes that differ in their physiochemical properties. The chloroplast cytosol isoenzymes of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) harbor evidence of major events in the history of life: the origin of the first genes, the bacterial-archaeal split, the origin of eukaryotes, the evolution of protein compartmentation during eukaryote evolution, the origin of plastids, and the secondary endosymbiosis among the algae with complex plastids. The reaction mechanism of GAPDH entails phosphorolysis of a thioester to yield an energy-rich acyl phosphate bond, a chemistry that points to primitive pathways of energy conservation that existed even before the origin of the first free-living cells. Here, we recount the main insights that chloroplast and cytosolic GAPDH provided into endosymbiosis and physiological evolution.
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Affiliation(s)
- William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Rüdiger Cerff
- Institute of Genetics, Technical University of Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
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8
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Wang X, Gao B, Zhu S. Exon Shuffling and Origin of Scorpion Venom Biodiversity. Toxins (Basel) 2016; 9:toxins9010010. [PMID: 28035955 PMCID: PMC5308243 DOI: 10.3390/toxins9010010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 12/01/2022] Open
Abstract
Scorpion venom is a complex combinatorial library of peptides and proteins with multiple biological functions. A combination of transcriptomic and proteomic techniques has revealed its enormous molecular diversity, as identified by the presence of a large number of ion channel-targeted neurotoxins with different folds, membrane-active antimicrobial peptides, proteases, and protease inhibitors. Although the biodiversity of scorpion venom has long been known, how it arises remains unsolved. In this work, we analyzed the exon-intron structures of an array of scorpion venom protein-encoding genes and unexpectedly found that nearly all of these genes possess a phase-1 intron (one intron located between the first and second nucleotides of a codon) near the cleavage site of a signal sequence despite their mature peptides remarkably differ. This observation matches a theory of exon shuffling in the origin of new genes and suggests that recruitment of different folds into scorpion venom might be achieved via shuffling between body protein-coding genes and ancestral venom gland-specific genes that presumably contributed tissue-specific regulatory elements and secretory signal sequences.
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Affiliation(s)
- Xueli Wang
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
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9
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Lee DW, Woo S, Geem KR, Hwang I. Sequence Motifs in Transit Peptides Act as Independent Functional Units and Can Be Transferred to New Sequence Contexts. PLANT PHYSIOLOGY 2015; 169:471-84. [PMID: 26149569 PMCID: PMC4577419 DOI: 10.1104/pp.15.00842] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/02/2015] [Indexed: 05/04/2023]
Abstract
A large number of nuclear-encoded proteins are imported into chloroplasts after they are translated in the cytosol. Import is mediated by transit peptides (TPs) at the N termini of these proteins. TPs contain many small motifs, each of which is critical for a specific step in the process of chloroplast protein import; however, it remains unknown how these motifs are organized to give rise to TPs with diverse sequences. In this study, we generated various hybrid TPs by swapping domains between Rubisco small subunit (RbcS) and chlorophyll a/b-binding protein, which have highly divergent sequences, and examined the abilities of the resultant TPs to deliver proteins into chloroplasts. Subsequently, we compared the functionality of sequence motifs in the hybrid TPs with those of wild-type TPs. The sequence motifs in the hybrid TPs exhibited three different modes of functionality, depending on their domain composition, as follows: active in both wild-type and hybrid TPs, active in wild-type TPs but inactive in hybrid TPs, and inactive in wild-type TPs but active in hybrid TPs. Moreover, synthetic TPs, in which only three critical motifs from RbcS or chlorophyll a/b-binding protein TPs were incorporated into an unrelated sequence, were able to deliver clients to chloroplasts with a comparable efficiency to RbcS TP. Based on these results, we propose that diverse sequence motifs in TPs are independent functional units that interact with specific translocon components at various steps during protein import and can be transferred to new sequence contexts.
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Affiliation(s)
- Dong Wook Lee
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Seungjin Woo
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Kyoung Rok Geem
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Inhwan Hwang
- Division of Integrative Biosciences and Biotechnology (D.W.L., S.W., I.H.) and Department of Life Sciences (K.R.G., I.H.), Pohang University of Science and Technology, Pohang 790-784, Korea
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10
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Zhang C, Wang J, Marowsky NC, Long M, Wing RA, Fan C. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biol Evol 2013; 5:1038-48. [PMID: 23651622 PMCID: PMC3673630 DOI: 10.1093/gbe/evt071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa's Chr3s. Among the 28 new genes, two recently duplicated segments contained eight genes. Fourteen of the 28 new genes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ks analysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation.
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Affiliation(s)
- Chengjun Zhang
- Department of Ecology and Evolution, University of Chicago, USA
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11
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Zhu K, Gao B, Zhu S. Characterization of a chimeric antimicrobial peptide uncovers evolutionary significance of exon-shuffling. Biochem Biophys Res Commun 2012; 428:360-4. [PMID: 23103428 DOI: 10.1016/j.bbrc.2012.10.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 10/15/2012] [Indexed: 01/01/2023]
Abstract
The abaecin family comprises a class of proline-rich antimicrobial peptides (AMPs) with restricted distribution in hymenopteran insects. Intriguingly, in the parasitic wasp Nasonia vitripennis its members (termed nabaecin-1 to -3) have gained a carboxyl terminal glycine-rich antimicrobial unit through exon-shuffling. Here, we describe cDNA cloning of nabaecin-3 and the donor gene (navitripenicin) of the shuffling, and structural and functional features of nabaecin-3 and its two domains (respectively called amino-terminal abaecin unit (NtAU) and carboxyl-terminal navitripenicin unit (CtNU)). Nabaecin-3 and navitripenicin were found to be transcriptionally up-regulated in response to bacterial challenge. By using recombinant expression and chemical synthesis techniques, we produced nabaecin-3, NtAU and CtNU. Circular dichroism (CD) analyses show that these peptides remarkably differ in their structures. Functionally, nabaecin-3 displayed a wide spectrum of antimicrobial activity against an array of bacteria, yeasts and fungi at micromolar concentrations, while CtNU only had a weak antibacterial activity and NtAU completely lacked activity. Our results indicate that in Nasonia the antimicrobial function of abaecin depends on the combination of NtAU with CtNU and thus suggest a new role of exon-shuffling in buffering loss-of-function mutation of a gene.
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Affiliation(s)
- Kuanyu Zhu
- Group of Animal Innate Immunity, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, 100101 Beijing, China
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12
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França GS, Cancherini DV, de Souza SJ. Evolutionary history of exon shuffling. Genetica 2012; 140:249-57. [PMID: 22948334 DOI: 10.1007/s10709-012-9676-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 08/23/2012] [Indexed: 11/29/2022]
Abstract
Exon shuffling has been characterized as one of the major evolutionary forces shaping both the genome and the proteome of eukaryotes. This mechanism was particularly important in the creation of multidomain proteins during animal evolution, bringing a number of functional genetic novelties. Here, genome information from a variety of eukaryotic species was used to address several issues related to the evolutionary history of exon shuffling. By comparing all protein sequences within each species, we were able to characterize exon shuffling signatures throughout metazoans. Intron phase (the position of the intron regarding the codon) and exon symmetry (the pattern of flanking introns for a given exon or block of adjacent exons) were features used to evaluate exon shuffling. We confirmed previous observations that exon shuffling mediated by phase 1 introns (1-1 exon shuffling) is the predominant kind in multicellular animals. Evidence is provided that such pattern was achieved since the early steps of animal evolution, supported by a detectable presence of 1-1 shuffling units in Trichoplax adhaerens and a considerable prevalence of them in Nematostella vectensis. In contrast, Monosiga brevicollis, one of the closest relatives of metazoans, and Arabidopsis thaliana, showed no evidence of 1-1 exon or domain shuffling above what it would be expected by chance. Instead, exon shuffling events are less abundant and predominantly mediated by phase 0 introns (0-0 exon shuffling) in those non-metazoan species. Moreover, an intermediate pattern of 1-1 and 0-0 exon shuffling was observed for the placozoan T. adhaerens, a primitive animal. Finally, characterization of flanking intron phases around domain borders allowed us to identify a common set of symmetric 1-1 domains that have been shuffled throughout the metazoan lineage.
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Affiliation(s)
- Gustavo S França
- Ludwig Institute for Cancer Research, São Paulo Branch, São Paulo, Brazil
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13
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Yu D, Wang Y, Fang X, Hu S, Tang P, Fu Y. Acquisition of hydrogenosomal presequences: examples from Trichomonas vaginalis. FEMS Microbiol Lett 2012; 330:127-31. [DOI: 10.1111/j.1574-6968.2012.02541.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 03/05/2012] [Accepted: 03/05/2012] [Indexed: 12/29/2022] Open
Affiliation(s)
| | - Yue Wang
- Department of Gynecology & Obstetrics; Women's Hospital School Of Medicine Zhejiang University; Hangzhou; China
| | - Xu Fang
- Zhejiang Institute of Microbiology; Hangzhou; China
| | - Songnian Hu
- Laboratory of Genome Science and Information; Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing; China
| | - Petrus Tang
- Molecular Regulation and Bioinformatics Laboratory; Department of Parasitology; Chang Gung University; Taoyuan; Taiwan
| | - Yan Fu
- College of Animal Science; Zhejiang University; Hangzhou; China
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14
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Abstract
Gene duplication plays key roles in organismal evolution. Duplicate genes, if they survive, tend to diverge in regulatory and coding regions. Divergences in coding regions, especially those that can change the function of the gene, can be caused by amino acid-altering substitutions and/or alterations in exon-intron structure. Much has been learned about the mode, tempo, and consequences of nucleotide substitutions, yet relatively little is known about structural divergences. In this study, by analyzing 612 pairs of sibling paralogs from seven representative gene families and 300 pairs of one-to-one orthologs from different species, we investigated the occurrence and relative importance of structural divergences during the evolution of duplicate and nonduplicate genes. We found that structural divergences have been very prevalent in duplicate genes and, in many cases, have led to the generation of functionally distinct paralogs. Comparisons of the genomic sequences of these genes further indicated that the differences in exon-intron structure were actually accomplished by three main types of mechanisms (exon/intron gain/loss, exonization/pseudoexonization, and insertion/deletion), each of which contributed differently to structural divergence. Like nucleotide substitutions, insertion/deletion and exonization/pseudoexonization occurred more or less randomly, with the number of observable mutational events per gene pair being largely proportional to evolutionary time. Notably, however, compared with paralogs with similar evolutionary times, orthologs have accumulated significantly fewer structural changes, whereas the amounts of amino acid replacements accumulated did not show clear differences. This finding suggests that structural divergences have played a more important role during the evolution of duplicate than nonduplicate genes.
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15
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The falsifiability of the models for the origin of eukaryotes. Curr Genet 2011; 57:367-90. [DOI: 10.1007/s00294-011-0357-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 09/29/2011] [Accepted: 09/30/2011] [Indexed: 01/13/2023]
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16
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Rödiger A, Baudisch B, Langner U, Klösgen RB. Dual targeting of a mitochondrial protein: the case study of cytochrome c1. MOLECULAR PLANT 2011; 4:679-87. [PMID: 21303841 DOI: 10.1093/mp/ssr001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
As a result of the endosymbiotic gene transfer, the majority of proteins of mitochondria and chloroplasts is encoded in the nucleus and synthesized in the cytosol as precursor molecules carrying N-terminal transit peptides for the transport into the respective target organelle. In most instances, transport takes place into either mitochondria or chloroplasts, although a few examples of dual targeting into both organelles have been described. Here, we show by a combination of three different experimental strategies that also cytochrome c(1) of potato, a component of the respiratory electron transport chain, is imported not only into mitochondria, but also into plastids. In organello import experiments with isolated mitochondria and chloroplasts, which were analyzed in both single and mixed organelle assays, demonstrate that the processing products accumulating after import within the two endosymbiotic organelles are different in size. Dual targeting of cytochrome c(1) is observed also in vivo, after biolistic transformation of leaf epidermal cells with suitable reporter constructions. Finally, Western analyses employing cytochrome c(1)-specific antiserum provide evidence that the protein accumulates in significant amounts in mitochondria and chloroplasts of both pea and spinach. The possible consequences of our findings on the relevance of the dual targeting phenomenon are discussed.
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Affiliation(s)
- Anja Rödiger
- Institute of Biology-Plant Physiology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle/Saale, Germany
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Hands P, Vosnakis N, Betts D, Irish VF, Drea S. Alternate transcripts of a floral developmental regulator have both distinct and redundant functions in opium poppy. ANNALS OF BOTANY 2011; 107:1557-66. [PMID: 21385783 PMCID: PMC3108804 DOI: 10.1093/aob/mcr045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The MADS-box transcription factor AGAMOUS (AG) is an important regulator of stamen and fruit identity as well as floral meristem determinacy in a number of core eudicots and monocots. However, its role outside of these groups has not been assessed explicitly. Examining its role in opium poppy, a basal eudicot, could uncover much about the evolution and development of flower and fruit development in the angiosperms. METHODS AG orthologues were isolated by degenerate RT-PCR and the gene sequence and structure examined; gene expression was characterized using in situ hybridization and the function assessed using virus-induced gene silencing. KEY RESULTS In opium poppy, a basal eudicot, the AGAMOUS orthologue is alternatively spliced to produce encoded products that vary at the C-terminus, termed PapsAG-1 and PapsAG-2. Both transcripts are expressed at high levels in stamens and carpels. The functional implications of this alternative transcription were examined using virus-induced gene silencing and the results show that PapsAG-1 has roles in stamen and carpel identity, reflecting those found for Arabidopsis AG. In contrast, PapsAG-2, while displaying redundancy in these functions, has a distinctive role in aspects of carpel development reflected in septae, ovule and stigma defects seen in the loss-of-function line generated. CONCLUSIONS These results describe the first explicit functional analysis of an AG-clade gene in a basal eudicot; illustrate one of the few examples of the functional consequences of alternative splicing in transcription factors and reveal the importance of alternative transcription, as well as gene duplication, as a driving force in evolution.
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Affiliation(s)
- Philip Hands
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nikolaos Vosnakis
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Donna Betts
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Vivian F. Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Sinéad Drea
- Department of Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
- For correspondence. E-mail
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Watanabe S, Wakasugi K. Module M1 of zebrafish neuroglobin acts as a structural and functional protein building block for a cell-membrane-penetrating activity. PLoS One 2011; 6:e16808. [PMID: 21304818 PMCID: PMC3033418 DOI: 10.1371/journal.pone.0016808] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 12/31/2010] [Indexed: 11/18/2022] Open
Abstract
Neuroglobin (Ngb) is a recently discovered vertebrate globin that is expressed in the brain and can reversibly bind oxygen. Mammalian Ngb is involved in neuroprotection during oxidative stress that occurs, for example, during ischemia and reperfusion. Recently, we found that zebrafish, but not human, Ngb can translocate into cells. Moreover, we demonstrated that a chimeric ZHHH Ngb protein, in which the module M1 of human Ngb is replaced by the corresponding region of zebrafish Ngb, can penetrate cell membranes and protect cells against oxidative stress-induced cell death, suggesting that module M1 of zebrafish Ngb is important for protein transduction. Furthermore, we recently showed that Lys7, Lys9, Lys21, and Lys23 in module M1 of zebrafish Ngb are crucial for protein transduction activity. In the present study, we have investigated whether module M1 of zebrafish Ngb can be used as a building block to create novel cell-membrane-penetrating folded proteins. First, we engineered a chimeric myoglobin (Mb), in which module M1 of zebrafish Ngb was fused to the N-terminus of full-length human Mb, and investigated its functional and structural properties. Our results showed that this chimeric Mb protein is stable and forms almost the same heme environment and α-helical structure as human wild-type Mb. In addition, we demonstrated that chimeric Mb has a cell-membrane-penetrating activity similar to zebrafish Ngb. Moreover, we found that glycosaminoglycan is crucial for the cell-membrane-penetrating activity of chimeric Mb as well as that of zebrafish Ngb. These results enable us to conclude that such module substitutions will facilitate the design and production of novel functional proteins.
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Affiliation(s)
- Seiji Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, Japan
- * E-mail:
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Vesteg M, Vacula R, Steiner JM, Mateásiková B, Löffelhardt W, Brejová B, Krajcovic J. A possible role for short introns in the acquisition of stroma-targeting peptides in the flagellate Euglena gracilis. DNA Res 2010; 17:223-31. [PMID: 20587589 PMCID: PMC2920757 DOI: 10.1093/dnares/dsq015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The chloroplasts of Euglena gracilis bounded by three membranes arose via secondary endosymbiosis of a green alga in a heterotrophic euglenozoan host. Many genes were transferred from symbiont to the host nucleus. A subset of Euglena nuclear genes of predominately symbiont, but also host, or other origin have obtained complex presequences required for chloroplast targeting. This study has revealed the presence of short introns (41–93 bp) either in the second half of presequence-encoding regions or shortly downstream of them in nine nucleus-encoded E. gracilis genes for chloroplast proteins (Eno29, GapA, PetA, PetF, PetJ, PsaF, PsbM, PsbO, and PsbW). In addition, the E. gracilis Pbgd gene contains two introns in the second half of presequence-encoding region and one at the border of presequence-mature peptide-encoding region. Ten of 12 introns present within presequence-encoding regions or shortly downstream of them identified in this study have typical eukaryotic GT/AG borders, are T-rich, 45–50 bp long, and pairwise sequence identities range from 27 to 61%. Thus single recombination events might have been mediated via these cis-spliced introns. A double crossing over between these cis-spliced introns and trans-spliced introns present in 5′-UTRs of Euglena nuclear genes is also likely to have occurred. Thus introns and exon-shuffling could have had an important role in the acquisition of chloroplast targeting signals in E. gracilis. The results are consistent with a late origin of photosynthetic euglenids.
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Affiliation(s)
- Matej Vesteg
- Institute of Cell Biology and Biotechnology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, Bratislava, Slovakia
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20
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Gao B, Zhu S. Characterization of a hymenoptaecin-like antimicrobial peptide in the parasitic wasp Nasonia vitripennis. Process Biochem 2010. [DOI: 10.1016/j.procbio.2009.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 2009; 181:1183-93. [PMID: 19153256 DOI: 10.1534/genetics.108.099150] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rider is a novel and recently active Ty1-copia-like retrotransposon isolated from the T3238fer mutant of tomato. Structurally, it is delimited by a duplication of target sites and contains two long terminal direct repeats and an internal open reading frame, which encodes a Ty1-copia-type polyprotein with characteristic protein domains required for retrotransposition. The family of Rider elements has an intermediate copy number and is scattered in the chromosomes of tomato. Rider family members in the tomato genome share high sequence similarity, but different structural groups were identified (full-size elements, deletion derivatives, and solo LTRs). Southern blot analysis in Solanaceae species showed that Rider was a Lycopersicon-specific element. Sequence analysis revealed that among other plants, two Arabidopsis elements (named as Rider-like 1 and Rider-like 2) are most similar to Rider in both the coding and noncoding regions. RT-PCR analysis indicates that Rider is constitutively expressed in tomato plants. The phylogeny-based parsimony analysis and the sequence substitution analyses of these data suggest that these Rider-like elements originated from a recent introgression of Rider into the tomato genome by horizontal transfer 1-6 million years ago. Considering its transcriptional activity and the recent insertion of the element into at least two genes, Rider is a recently active retrotransposon in the tomato genome.
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Abstract
The transfer of genes from an endosymbiont to its host typically requires acquisition of targeting signals by the gene product to ensure its return to the endosymbiont for function. Many hundreds of plastid-derived genes must have acquired transit peptides for successful relocation to the nucleus. Here, we explore potential evolutionary origins of plastid transit peptides in the malaria parasite Plasmodium falciparum. We show that exons of the P. falciparum genome could serve as transit peptides after exon shuffling. We further demonstrate that numerous randomized peptides and even whimsical sequences based on English words can also function as transit peptides in vivo. Thus, facile acquisition of transit peptides from existing sequence likely expedited endosymbiont integration through intracellular gene transfer.
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23
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Kessler D, Papatheodorou P, Stratmann T, Dian EA, Hartmann-Fatu C, Rassow J, Bayer P, Mueller JW. The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae. BMC Biol 2007; 5:37. [PMID: 17875217 PMCID: PMC2031878 DOI: 10.1186/1741-7007-5-37] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 09/17/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The parvulin-type peptidyl prolyl cis/trans isomerase Par14 is highly conserved in all metazoans. The recently identified parvulin Par17 contains an additional N-terminal domain whose occurrence and function was the focus of the present study. RESULTS Based on the observation that the human genome encodes Par17, but bovine and rodent genomes do not, Par17 exon sequences from 10 different primate species were cloned and sequenced. Par17 is encoded in the genomes of Hominidae species including humans, but is absent from other mammalian species. In contrast to Par14, endogenous Par17 was found in mitochondrial and membrane fractions of human cell lysates. Fluorescence of EGFP fusions of Par17, but not Par14, co-localized with mitochondrial staining. Par14 and Par17 associated with isolated human, rat and yeast mitochondria at low salt concentrations, but only the Par17 mitochondrial association was resistant to higher salt concentrations. Par17 was imported into mitochondria in a time and membrane potential-dependent manner, where it reached the mitochondrial matrix. Moreover, Par17 was shown to bind to double-stranded DNA under physiological salt conditions. CONCLUSION Taken together, the DNA binding parvulin Par17 is targeted to the mitochondrial matrix by the most recently evolved mitochondrial prepeptide known to date, thus adding a novel protein constituent to the mitochondrial proteome of Hominidae.
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Affiliation(s)
- Daniel Kessler
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Tina Stratmann
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elke Andrea Dian
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Cristina Hartmann-Fatu
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joachim Rassow
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonathan Wolf Mueller
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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Abstract
Three decades ago Gilbert posited that novel proteins arise by re-shuffling genomic sequences encoding polypeptide domains. Today, with numerous genomes and countless genes sequenced, it is well established that recombination of sequences encoding polypeptide domains plays a major role in protein evolution. There is, however, less evidence to suggest how the novel polypeptide domains, themselves, arise. Recent comparisons of genomes from closely related species have revealed numerous species-specific exons, supporting models of domain origin based on "exonization" of intron sequences. Also, a mechanism for the origin of novel polypeptide domains has been proposed based on analyses of insertion-based polymorphisms between orthologous genes across broad phylogenetic spectra and between allelic variants of genes within species. This review discusses these processes and how each might participate in the evolutionary emergence of novel polypeptide domains.
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Affiliation(s)
- Edward E Schmidt
- Molecular Biosciences, Montana State University, Bozeman, MT 59717, USA.
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Hickford JGH, Zhou H, Fang Q. Haplotype analysis of the DQA genes in sheep: Evidence supporting recombination between the loci1. J Anim Sci 2007; 85:577-82. [PMID: 17121973 DOI: 10.2527/jas.2006-217] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The ovine class II major histocompatibility complex mediates specific immune responses to exogenous antigens in sheep. A number of ovine class II loci have been identified, and most of them appear to be polymorphic. In this study we investigated the DQA1 locus of 520 sheep and the DQA2 locus of over 40,000 sheep, finding 12 sequences and 22 sequences, respectively, using DQA1- and DQA2-specific PCR primers. Among the DQA2 sequences, 2 groups of sequences can be found: those that share homology with the DQA2 sequences from closely related species and those that cluster with bovine DQA3 and DQA4 sequences and have been called DQA2-like in sheep. The occurrence of these DQA2-like sequences was once again confirmed to correspond with the absence of detectable DQA1 sequences, suggesting that they are found at the same location as DQA1. Within the sheep studied, 37 haplotypes could be detected, 23 being haplotypes of DQA1 and DQA2 sequences and with frequencies ranging from 0.38 to 9.27%, and 14 being haplotypes of DQA2 and DQA2-like sequences and with frequencies ranging from 0.03 to 14.53%. We discovered 12 DQA1-DQA2 combinations that were derived from 5 DQA1 alleles and 4 DQA2 alleles, and 8 DQA2-DQA2-like combinations from 5 DQA2 alleles and 2 DQA2-like sequences. The frequency of occurrence of recombined DQA1-DQA2 sequences and recombined DQA2-DQA2-like sequences is similar, once again suggesting the DQA2-like sequences are found at the DQA1 locus.
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Affiliation(s)
- J G H Hickford
- Gene-Marker Laboratory, Cell Biology Group, Agriculture and Life Sciences Division, Lincoln University, Lincoln, New Zealand.
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26
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Durnford DG, Gray MW. Analysis of Euglena gracilis plastid-targeted proteins reveals different classes of transit sequences. EUKARYOTIC CELL 2006; 5:2079-91. [PMID: 16998072 PMCID: PMC1694827 DOI: 10.1128/ec.00222-06] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The plastid of Euglena gracilis was acquired secondarily through an endosymbiotic event with a eukaryotic green alga, and as a result, it is surrounded by a third membrane. This membrane complexity raises the question of how the plastid proteins are targeted to and imported into the organelle. To further explore plastid protein targeting in Euglena, we screened a total of 9,461 expressed sequence tag (EST) clusters (derived from 19,013 individual ESTs) for full-length proteins that are plastid localized to characterize their targeting sequences and to infer potential modes of translocation. Of the 117 proteins identified as being potentially plastid localized whose N-terminal targeting sequences could be inferred, 83 were unique and could be classified into two major groups. Class I proteins have tripartite targeting sequences, comprising (in order) an N-terminal signal sequence, a plastid transit peptide domain, and a predicted stop-transfer sequence. Within this class of proteins are the lumen-targeted proteins (class IB), which have an additional hydrophobic domain similar to a signal sequence and required for further targeting across the thylakoid membrane. Class II proteins lack the putative stop-transfer sequence and possess only a signal sequence at the N terminus, followed by what, in amino acid composition, resembles a plastid transit peptide. Unexpectedly, a few unrelated plastid-targeted proteins exhibit highly similar transit sequences, implying either a recent swapping of these domains or a conserved function. This work represents the most comprehensive description to date of transit peptides in Euglena and hints at the complex routes of plastid targeting that must exist in this organism.
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Affiliation(s)
- Dion G Durnford
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada E3B 5A3.
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27
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Drea SC, Lao NT, Wolfe KH, Kavanagh TA. Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 46:723-35. [PMID: 16709189 DOI: 10.1111/j.1365-313x.2006.02741.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
OEP16, a channel protein of the outer membrane of chloroplasts, has been implicated in amino acid transport and in the substrate-dependent import of protochlorophyllide oxidoreductase A. Two major clades of OEP16-related sequences were identified in land plants (OEP16-L and OEP16-S), which arose by a gene duplication event predating the divergence of seed plants and bryophytes. Remarkably, in angiosperms, OEP16-S genes evolved by gaining an additional exon that extends an interhelical loop domain in the pore-forming region of the protein. We analysed the sequence, structure and expression of the corresponding Arabidopsis genes (atOEP16-S and atOEP16-L) and demonstrated that following duplication, both genes diverged in terms of expression patterns and coding sequence. AtOEP16-S, which contains multiple G-box ABA-responsive elements (ABREs) in the promoter region, is regulated by ABI3 and ABI5 and is strongly expressed during the maturation phase in seeds and pollen grains, both desiccation-tolerant tissues. In contrast, atOEP-L, which lacks promoter ABREs, is expressed predominantly in leaves, is induced strongly by low-temperature stress and shows weak induction in response to osmotic stress, salicylic acid and exogenous ABA. Our results indicate that gene duplication, exon gain and regulatory sequence evolution each played a role in the divergence of OEP16 homologues in plants.
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Affiliation(s)
- Sinéad C Drea
- Plant Molecular Genetics Laboratory, Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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28
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Sargeant TJ, Marti M, Caler E, Carlton JM, Simpson K, Speed TP, Cowman AF. Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol 2006; 7:R12. [PMID: 16507167 PMCID: PMC1431722 DOI: 10.1186/gb-2006-7-2-r12] [Citation(s) in RCA: 324] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 12/20/2005] [Accepted: 01/23/2006] [Indexed: 11/23/2022] Open
Abstract
A new software was used to predict exported proteins that are conserved between malaria parasites infecting rodents and those infecting humans, revealing a lineage-specific expansion of exported proteins. Background The apicomplexan parasite Plasmodium falciparum causes the most severe form of malaria in humans. After invasion into erythrocytes, asexual parasite stages drastically alter their host cell and export remodeling and virulence proteins. Previously, we have reported identification and functional analysis of a short motif necessary for export of proteins out of the parasite and into the red blood cell. Results We have developed software for the prediction of exported proteins in the genus Plasmodium, and identified exported proteins conserved between malaria parasites infecting rodents and the two major causes of human malaria, P. falciparum and P. vivax. This conserved 'exportome' is confined to a few subtelomeric chromosomal regions in P. falciparum and the synteny of these and surrounding regions is conserved in P. vivax. We have identified a novel gene family PHIST (for Plasmodium helical interspersed subtelomeric family) that shares a unique domain with 72 paralogs in P. falciparum and 39 in P. vivax; however, there is only one member in each of the three species studied from the P. berghei lineage. Conclusion These data suggest radiation of genes encoding remodeling and virulence factors from a small number of loci in a common Plasmodium ancestor, and imply a closer phylogenetic relationship between the P. vivax and P. falciparum lineages than previously believed. The presence of a conserved 'exportome' in the genus Plasmodium has important implications for our understanding of both common mechanisms and species-specific differences in host-parasite interactions, and may be crucial in developing novel antimalarial drugs to this infectious disease.
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Affiliation(s)
- Tobias J Sargeant
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Matthias Marti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
| | - Elisabet Caler
- The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA
| | - Jane M Carlton
- The Institute for Genomic Research (TIGR), Rockville, Maryland 20850, USA
| | - Ken Simpson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
| | - Terence P Speed
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
| | - Alan F Cowman
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
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Vibranovski MD, Sakabe NJ, de Souza SJ. A possible role of exon-shuffling in the evolution of signal peptides of human proteins. FEBS Lett 2006; 580:1621-4. [PMID: 16487520 DOI: 10.1016/j.febslet.2006.01.094] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Revised: 01/23/2006] [Accepted: 01/31/2006] [Indexed: 11/22/2022]
Abstract
It was recently shown that there is a predominance of phase 1 introns near the cleavage site of signal peptides encoded by human genes. It was suggested that this biased distribution was due to intron insertion at AGmid R:G proto-splice sites. However, we found that there is no disproportional excess of AGmid R:G that would support insertion at proto-splice sites. In fact, all nGmid R:G sites are enriched in the vicinity of the cleavage site. Additional analyses support an alternative scenario in which exon-shuffling is largely responsible for such excess of phase 1 introns.
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Affiliation(s)
- Maria Dulcetti Vibranovski
- Laboratory of Computational Biology, Ludwig Institute for Cancer Research, Sao Paulo Branch, Rua Prof. Antonio Prudente 109, CEP 01509-010, São Paulo, SP, Brazil
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Harb OS, Chatterjee B, Fraunholz MJ, Crawford MJ, Nishi M, Roos DS. Multiple functionally redundant signals mediate targeting to the apicoplast in the apicomplexan parasite Toxoplasma gondii. EUKARYOTIC CELL 2005; 3:663-74. [PMID: 15189987 PMCID: PMC420125 DOI: 10.1128/ec.3.3.663-674.2004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Most species of the protozoan phylum Apicomplexa harbor an endosymbiotic organelle--the apicoplast--acquired when an ancestral parasite engulfed a eukaryotic plastid-containing alga. Several hundred proteins are encoded in the parasite nucleus and are posttranslationally targeted to the apicoplast by a distinctive bipartite signal. The N-terminal 20 to 30 amino acids of nucleus-encoded apicoplast targeted proteins function as a classical signal sequence, mediating entry into the secretory pathway. Cleavage of the signal sequence exposes a transit peptide of variable length (50 to 200 amino acids) that is required for directing proteins to the apicoplast. Although these peptides are enriched in basic amino acids, their structural and functional characteristics are not well understood, which hampers the identification of apicoplast proteins that may constitute novel chemotherapeutic targets. To identify functional domains for a model apicoplast transit peptide, we generated more than 80 deletions and mutations throughout the transit peptide of Toxoplasma gondii ferredoxin NADP+ reductase (TgFNR) and examined the ability of these altered transit peptides to mediate proper targeting and processing of a fluorescent protein reporter. These studies revealed the presence of numerous functional domains. Processing can take place at multiple sites in the protein sequence and may occur outside of the apicoplast lumen. The TgFNR transit peptide contains at least two independent and functionally redundant targeting signals, each of which contains a subdomain that is required for release from or proper sorting within the endoplasmic reticulum. Certain deletion constructs traffic to multiple locations, including the apicoplast periphery, the rhoptries, and the parasitophorous vacuole, suggesting a common thread for targeting to these specialized compartments.
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Affiliation(s)
- Omar S Harb
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018, USA
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Nassoury N, Morse D. Protein targeting to the chloroplasts of photosynthetic eukaryotes: getting there is half the fun. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1743:5-19. [PMID: 15777835 DOI: 10.1016/j.bbamcr.2004.09.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 08/10/2004] [Accepted: 09/17/2004] [Indexed: 11/19/2022]
Abstract
The plastids of many algae are surrounded by three or four membranes, thought to be a consequence of their evolutionary origin through secondary endosymbiosis between photosynthetic and non-photosynthetic eukaryotes. Each membrane constitutes a barrier to the passage of proteins, so protein targeting in these complex plastids has an extra level of difficulty when compared to higher plants. In the latter, protein translocation across the two membranes uses multi-protein complexes that together import proteins possessing an N-terminal leader sequence rich in serine and threonine (S/T). In contrast, while targeting to most complex plastids also involves an S/T-rich region, this region is preceded by an N-terminal hydrophobic signal peptide. This arrangement of peptide sequences suggests that proteins directed to complex plastids pass through the ER, as do other proteins with hydrophobic signal peptides. However, this simplistic view is not always easy to reconcile with what is known about the different secondary plastids. In the first group, with plastids bounded by three membranes, plastid-directed proteins do indeed arrive in Golgi-derived vesicles, but a second hydrophobic region follows the S/T-rich region in all leaders. In the second group, where four membranes completely surround the plastids, it is still not known how the proteins arrive at the plastids, and in addition, one member of this group uses a targeting signal rich in asparagine and lysine in place of the S/T-rich region. In the third group, the fourth bounding membrane is contiguous with the ER, but it is not clear what distinguishes plastid membranes from others in the endomembrane system. Knowing what to expect is important, as genomic sequencing programs may soon be turning up some of the missing pieces in these translocation puzzles.
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Affiliation(s)
- Nasha Nassoury
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke est, Montreal, Quebec, Canada H1X 2B2
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Kilian O, Kroth PG. Presequence acquisition during secondary endocytobiosis and the possible role of introns. J Mol Evol 2004; 58:712-21. [PMID: 15461428 DOI: 10.1007/s00239-004-2593-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Targeting of nucleus-encoded proteins into chloroplasts is mediated by N-terminal presequences. During evolution of plastids from formerly free-living cyanobacteria by endocytobiosis, genes for most plastid proteins have been transferred from the plastid genome to the nucleus and subsequently had to be equipped with such plastid targeting sequences. So far it is unclear how the gene domains coding for presequences and the respective mature proteins may have been assembled. While land plant plastids are supposed to originate from a primary endocytobiosis event (a prokaryotic cyanobacterium was taken up by a eukaryotic cell), organisms with secondary plastids like diatoms experienced a second endocytobiosis step involving a eukaryotic alga taken up by a eukaryotic host cell. In this group of algae, apparently most genes encoding chloroplast proteins have been transferred a second time (from the nucleus of the endosymbiont to the nucleus of the secondary host) and thus must have been equipped with additional targeting signals. We have analyzed cDNAs and the respective genomic DNA fragments of seven plastid preproteins from the diatom Phaeodactylum tricornutum. In all of these genes we found single spliceosomal introns, generally located within the region coding for the N-terminal plastid targeting sequences or shortly downstream of it. The positions of the introns can be related to the putative phylogenetic histories of the respective genes, indicating that the bipartite targeting sequences in these secondary algae might have evolved by recombination events via introns.
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Affiliation(s)
- Oliver Kilian
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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33
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Timmis JN, Ayliffe MA, Huang CY, Martin W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 2004; 5:123-35. [PMID: 14735123 DOI: 10.1038/nrg1271] [Citation(s) in RCA: 926] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeremy N Timmis
- School of Molecular and Biomedical Science, The University of Adelaide, South Australia 5005, Australia.
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Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nat Rev Genet 2003; 4:865-75. [PMID: 14634634 DOI: 10.1038/nrg1204] [Citation(s) in RCA: 641] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.
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Affiliation(s)
- Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA.
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36
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Zhu S, Darbon H, Dyason K, Verdonck F, Tytgat J. Evolutionary origin of inhibitor cystine knot peptides. FASEB J 2003; 17:1765-7. [PMID: 12958203 DOI: 10.1096/fj.02-1044fje] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The inhibitor cystine knot (ICK) fold is an evolutionarily conserved structural motif shared by a large group of polypeptides with diverse sequences and bioactivities. Although found in different phyla (animal, plant, and fungus), ICK peptides appear to be most prominent in venoms of cone snail and spider. Recently, two scorpion toxins activating a calcium release channel have been found to adopt an ICK fold. We have isolated and identified both cDNA and genomic clones for this family of ICK peptides from the scorpion Opistophthalmus carinatus. The gene characterized by three well-delineated exons respectively coding for three structural and functional domains in the toxin precursors illustrates the correlation between exon and module as suggested by the "exon theory of genes." Based on the analysis of precursor organization and gene structure combined with the 3-D fold and functional data, our results highlight a common evolutionary origin for ICK peptides from animals. In contrast, ICK peptides from plant and fungus might be independently evolved from another ancestor.
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Affiliation(s)
- Shunyi Zhu
- Laboratory of Toxicology, University of Leuven, Belgium
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37
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Jozefowicz C, McClintock J, Prince V. The fates of zebrafish Hox gene duplicates. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2003; 3:185-94. [PMID: 12836697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
In his 1970 book, Susumu Ohno stressed the importance of gene duplication in the evolution of the vertebrate genome and body plan. He elaborated the idea that duplication events provide novel genetic material on which evolution may act. Data are accumulating to show that extensive duplication events, perhaps incorporating the duplication of entire genomes, occurred in the lineage leading to teleost fishes. These duplications may have been pivotal in the explosive radiation of this highly successful vertebrate group. Thus, the teleosts provide us with an ideal opportunity to investigate the fates and functions of duplicated genes. A convenient system for these studies is the zebrafish, Danio rerio, which has become a popular genetic and embryological model.
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Affiliation(s)
- Chris Jozefowicz
- The Committees on Evolutionary Biology, The University of Chicago, Chicago, IL 60637, USA
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38
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Petersen J, Brinkmann H, Cerff R. Origin, evolution, and metabolic role of a novel glycolytic GAPDH enzyme recruited by land plant plastids. J Mol Evol 2003; 57:16-26. [PMID: 12962302 DOI: 10.1007/s00239-002-2441-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
NAD-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a cytosolic marker enzyme of eukaryotes (GapC; EC 1.2.1.12). Land plants possess an additional NADP+-dependent enzyme (EC 1.2.1.13) within their chloroplasts which is composed of two subunits, GapA and GapB. Another plastid GAPDH enzyme (GapCp) was recently discovered in gymnosperms and ferns. This novel GapCp is closely related to cytosolic GapC and displays glycolytic NAD+ cosubstrate specificity. Here we show that this new gene GapCp is also present and actively expressed in angiosperms, mosses, and liverworts. Phylogenetic analyses of the available GapC and GapCp sequences suggest that the gene duplication giving rise to GapCp occurred in ancestral charophyte algae. The data are also consistent with a monophyletic origin of charophytes and land plants and further support the view that land plants arose from a Coleochaete-like green alga. Northern hybridizations were employed to study the expression of the genes GapCp, GapC, GapA, and GapB in green and nongreen tissues from pepper (Capsicum annuum). The results demonstrate that GapCp mRNAs are mainly expressed in red pepper fruit and roots, in which the transcript levels of photosynthetic GapA and GapB are downregulated. This suggests that in flowering plants GapCp plays a specific role in glycolytic energy production of nongreen plastids such as chromoplasts and leukoplasts and that angiosperms may be the only land plants where glycolysis is absent in green chloroplasts.
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Affiliation(s)
- Jörn Petersen
- Institute of Genetics, University of Braunschweig, D-38106 Braunschweig, Germany
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Bruce BD. The paradox of plastid transit peptides: conservation of function despite divergence in primary structure. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1541:2-21. [PMID: 11750659 DOI: 10.1016/s0167-4889(01)00149-5] [Citation(s) in RCA: 180] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Transit peptides are N-terminal extensions that facilitate the targeting and translocation of cytosolically synthesized precursors into plastids via a post-translational mechanism. With the complete Arabidopsis genome in hand, it is now evident that transit peptides direct more than 3500 different proteins into the plastid during the life of a typical plant. Deciphering a common mechanism for how this multitude of targeting sequences function has been hampered by the realization that at a primary sequence level, transit peptides are highly divergent in length, composition, and organization. This review addresses recent findings on several of the diverse functions that transit peptides must perform, including direct interaction with envelope lipids, association with a cis-acting guidance complex, recognition by envelope receptors, insertion into the Toc/Tic translocon, interaction with molecular motors, and finally, recognition/cleavage by the stromal processing peptidase. In addition to higher plants, transit peptides also direct the import of proteins into complex plastids derived from secondary endosymbiosis. An emerging concept suggests that transit peptides contain multiple domains that provide either distinct or possibly overlapping functions. Although still poorly characterized, evolutionary processes could yield transit peptides with alternative domain organizations.
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Affiliation(s)
- B D Bruce
- Department of Biochemistry, Cellular and Molecular Biology, Center of Excellence in Structural Biology, Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, TN 37917, USA.
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40
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Abstract
Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.
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Affiliation(s)
- M Long
- Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago Illinois 60637, USA.
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41
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Adams KL, Rosenblueth M, Qiu YL, Palmer JD. Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution. Genetics 2001; 158:1289-300. [PMID: 11454775 PMCID: PMC1461739 DOI: 10.1093/genetics/158.3.1289] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Unlike in animals, the functional transfer of mitochondrial genes to the nucleus is an ongoing process in plants. All but one of the previously reported transfers in angiosperms involve ribosomal protein genes. Here we report frequent transfer of two respiratory genes, sdh3 and sdh4 (encoding subunits 3 and 4 of succinate dehydrogenase), and we also show that these genes are present and expressed in the mitochondria of diverse angiosperms. Southern hybridization surveys reveal that sdh3 and sdh4 have been lost from the mitochondrion about 40 and 19 times, respectively, among the 280 angiosperm genera examined. Transferred, functional copies of sdh3 and sdh4 were characterized from the nucleus in four and three angiosperm families, respectively. The mitochondrial targeting presequences of two sdh3 genes are derived from preexisting genes for anciently transferred mitochondrial proteins. On the basis of the unique presequences of the nuclear genes and the recent mitochondrial gene losses, we infer that each of the seven nuclear sdh3 and sdh4 genes was derived from a separate transfer to the nucleus. These results strengthen the hypothesis that angiosperms are experiencing a recent evolutionary surge of mitochondrial gene transfer to the nucleus and reveal that this surge includes certain respiratory genes in addition to ribosomal protein genes.
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Affiliation(s)
- K L Adams
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
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42
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Adams KL, Daley DO, Qiu YL, Whelan J, Palmer JD. Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 2000; 408:354-7. [PMID: 11099041 DOI: 10.1038/35042567] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A central component of the endosymbiotic theory for the bacterial origin of the mitochondrion is that many of its genes were transferred to the nucleus. Most of this transfer occurred early in mitochondrial evolution; functional transfer of mitochondrial genes has ceased in animals. Although mitochondrial gene transfer continues to occur in plants, no comprehensive study of the frequency and timing of transfers during plant evolution has been conducted. Here we report frequent loss (26 times) and transfer to the nucleus of the mitochondrial gene rps10 among 277 diverse angiosperms. Characterization of nuclear rps10 genes from 16 out of 26 loss lineages implies that many independent, RNA-mediated rps10 transfers occurred during recent angiosperm evolution; each of the genes may represent a separate functional gene transfer. Thus, rps10 has been transferred to the nucleus at a surprisingly high rate during angiosperm evolution. The structures of several nuclear rps10 genes reveal diverse mechanisms by which transferred genes become activated, including parasitism of pre-existing nuclear genes for mitochondrial or cytoplasmic proteins, and activation without gain of a mitochondrial targeting sequence.
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Affiliation(s)
- K L Adams
- Department of Biology, Indiana University, Bloomington 47405, USA
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43
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Abstract
It is thought that two to three thousand different proteins are targeted to the chloroplast, and the 'transit peptides' that act as chloroplast targeting sequences are probably the largest class of targeting sequences in plants. At a primary structural level, transit peptide sequences are highly divergent in length, composition and organization. An emerging concept suggests that transit peptides contain multiple domains that provide either distinct or overlapping functions. These functions include direct interaction with envelope lipids, chloroplast receptors and the stromal processing peptidase. The genomic organization of transit peptides suggests that these domains might have originated from distinct exons, which were shuffled and streamlined throughout evolution to yield a modern, multifunctional transit peptide. Although still poorly characterized, this evolutionary process could yield transit peptides with different domain organizations. The plasticity of transit peptide design is consistent with the diverse biological functions of chloroplast proteins.
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Affiliation(s)
- B D Bruce
- Dept of Biochemistry, Cellular and Molecular Biology Department, The Center for Legume Research, University of Tennessee-Knoxville, USA.
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44
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Wang W, Zhang J, Alvarez C, Llopart A, Long M. The origin of the Jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol Biol Evol 2000; 17:1294-301. [PMID: 10958846 DOI: 10.1093/oxfordjournals.molbev.a026413] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Jingwei (jgw) is the first gene found to be of sufficiently recent origin in Drosophila to offer insights into the origin of a gene. While its chimerical gene structure was partially resolved as including a retrosequence of alcohol dehydrogenase (ADH:), the structure of its non-ADH: parental gene, the donor of the N-terminal domain of jgw, is unclear. We characterized this non-ADH: parental locus, yellow emperor (ymp), by cloning it, mapping it onto the polytene chromosomes, sequencing the entire locus, and examining its expression patterns in Drosophila melanogaster. We show that ymp is located in the 96-E region; the N-terminal domain of ymp has donated the non-ADH: portion of jgw via a duplication. The similar 5' portions of the gene and its regulatory sequences give rise to similar testis-specific expression patterns in ymp and jgw in Drosophila teissieri. Furthermore, between-species comparison of ymp revealed purifying selection in the protein sequence, suggesting a functional constraint in ymp. While the structure of ymp provides clear information for the molecular origin of the new gene jgw, it unexpectedly casts a new light on the concept of genes. We found, for the first time, that the single locus of the ymp gene encompasses three major molecular mechanisms determining structure of eukaryotic genes: (1) the 5' exons of ymp are involved in an exon-shuffling event that has created the portion recruited by jgw; (2) using alternative cleavage sites and alternative splicing sites, the 3' exon groups of ymp produce two proteins with nonhomologous C-terminal domains, both exclusively in the testis; and (3) in the opposite strand of the third intron of ymp is an essential gene, musashi (msi), which encodes an RNA-binding protein. The composite gene structure of ymp manifests the complexity of the gene concept, which should be considered in genomic research, e.g., gene finding.
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Affiliation(s)
- W Wang
- Department of Ecology and Evolution, University of Chicago. Department of Molecular and Cellular Biology, Harvard University
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45
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Abstract
A very small fraction of the proteins required for the propagation and function of mitochondria are coded by their genomes, while nuclear genes code the vast majority. We studied the migration of genes between the two genomes when transfer mechanisms mediate this exchange. We could calculate the influence of differential mutation rates, as well as that of biased transfer rates, on the partitioning of genes between the two genomes. We observe no significant difference in partitioning for haploid and diploid cell populations, but the effective size of cell populations is important. For infinitely large effective populations, higher mutation rates in mitochondria than in nuclear genomes are required to drive mitochondrial genes to the nuclear genome. In the more realistic case of finite populations, gene transfer favoring the nucleus and/or higher mutation rates in the mitochondrion will drive mitochondrial genes to the nucleus. We summarize experimental data that identify a gene transfer process mediated by vacuoles that favors the accumulation of mitochondrial genes in the nuclei of modern cells. Finally, we compare the behavior of mitochondrial genes for which transfer to the nucleus is neutral or influenced by purifying selection.
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Affiliation(s)
- O G Berg
- Department of Molecular Evolution, Uppsala University Evolutionary Biology Centre, Uppsala, Sweden.
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46
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de GREY AUBREYD. Noncorrelation Between Maximum Life Span and Antioxidant Enzyme Levels Among Homeotherms: Implications for Retarding Human Aging. ACTA ACUST UNITED AC 2000. [DOI: 10.1089/rej.1.2000.3.25] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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Abstract
The bacterial origins of plastid division and protein import by plastids are beginning to emerge - thanks largely to the availability of a total genome sequence for a cyanobacterium. Despite existing for hundreds of millions of years within the plant cell host, the chloroplast endosymbiont retains clear hallmarks of its bacterial ancestry. Plastid division relies on proteins that are also responsible for bacterial division, although may of the genes for these proteins have been confiscated by the host. Plastid protein import on the other hand relies on proteins that seem to have functioned originally as exporters but that have now been persuaded to operate in the reverse direction to traffic proteins from the host cell into the endosymbiont.
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Affiliation(s)
- G I McFadden
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, VIC 3010, Australia. . edu.au
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48
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Adams KL, Song K, Roessler PG, Nugent JM, Doyle JL, Doyle JJ, Palmer JD. Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc Natl Acad Sci U S A 1999; 96:13863-8. [PMID: 10570164 PMCID: PMC24156 DOI: 10.1073/pnas.96.24.13863] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The respiratory gene cox2, normally present in the mitochondrion, was previously shown to have been functionally transferred to the nucleus during flowering plant evolution, possibly during the diversification of legumes. To search for novel intermediate stages in the process of intracellular gene transfer and to assess the evolutionary timing and frequency of cox2 transfer, activation, and inactivation, we examined nuclear and mitochondrial (mt) cox2 presence and expression in over 25 legume genera and mt cox2 presence in 392 genera. Transfer and activation of cox2 appear to have occurred during recent legume evolution, more recently than previously inferred. Many intermediate stages of the gene transfer process are represented by cox2 genes in the studied legumes. Nine legumes contain intact copies of both nuclear and mt cox2, although transcripts could not be detected for some of these genes. Both cox2 genes are transcribed in seven legumes that are phylogenetically interspersed with species displaying only nuclear or mt cox2 expression. Inactivation of cox2 in each genome has taken place multiple times and in a variety of ways, including loss of detectable transcripts or transcript editing and partial to complete gene loss. Phylogenetic evidence shows about the same number (3-5) of separate inactivations of nuclear and mt cox2, suggesting that there is no selective advantage for a mt vs. nuclear location of cox2 in plants. The current distribution of cox2 presence and expression between the nucleus and mitochondrion in the studied legumes is probably the result of chance mutations silencing either cox2 gene.
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Affiliation(s)
- K L Adams
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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49
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Long M, Wang W, Zhang J. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 1999; 238:135-41. [PMID: 10570991 DOI: 10.1016/s0378-1119(99)00229-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This paper deals with a general question posed by the origin of new processed chimerical genes: when a new retrosequence inserts into a new genome position, how does it become activated and acquire novel protein function by recruiting new functional domains and regulatory elements? Jingwei (jgw), a newly evolved functional gene with a chimerical structure in Drosophila, provides an opportunity to examine such questions. The source of its exon encoding C-terminal peptide has been identified as an Adh retrosequence, which extends the concept of exon shuffling from recombination to retroposition as a general molecular mechanism for the origin of a new gene. However, the origin of 5' exons remains unclear. We examined two hypotheses concerning the origin of these non-Adh-derived jgw exons: (i) these exons might originate from a unique genomic sequence that fortuitously evolved a standard intron-exon structure and regulatory sequence for jgw; (ii) these exons might be a duplicate of an unrelated previously existing gene. Genomic Southern analysis, in conjunction with construction and screening of a genomic bookshelf (sub-library), was conducted in a group of Drosophila species. The results demonstrated that there are duplicate genes containing the same structure as the recruited portion of jgw. We name this duplicate gene in Drosophila teissieri and Drosophila yakuba and its orthologous gene in Drosophila melanogaster as yellow-emperor (ymp). Thus, the 5' exons/introns originated from a previously existing gene that provided new modules with specific sub-function to create jgw.
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Affiliation(s)
- M Long
- Department of Ecology and Evolution, The University of Chicago, IL 60637, USA.
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50
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Abstract
Plastids with two bounding membranes--as exemplified by red algae, green algae, plants, and glaucophytes--derive from primary endosymbiosis; a process involving engulfment and retention of a cyanobacterium by a phagotrophic eukaryote. Plastids with more than two bounding membranes (such as those of euglenoids, dinoflagellates, heterokonts, haptopytes, apicomplexa, cryptomonads, and chlorarachniophytes) probably arose by secondary endosymbiosis, in which a eukaryotic alga (itself the product of primary endosymbiosis) was engulfed and retained by a phagotroph. Secondary endosymbiosis transfers photosynthetic capacity into heterotrophic lineages, has apparently occurred numerous times, and has created several major eukaryotic lineages comprising upwards of 42,600 species. Plastids acquired by secondary endosymbiosis are sometimes referred to as "second-hand." Establishment of secondary endosymbioses has involved transfer of genes from the endosymbiont nucleus to the secondary host nucleus. Limited gene transfer could initially have served to stabilise the endosymbioses, but it is clear that the transfer process has been extensive, leading in many cases to the complete disappearance of the endosymbiont nucleus. One consequence of these gene transfers is that gene products required in the plastid must be targeted into the organelle across multiple membranes: at least three for stromal proteins in euglenoids and dinoflagellates, and across five membranes in the case of thylakoid lumen proteins in plastids with four bounding membranes. Evolution of such targeting mechanisms was obviously a key step in the successful establishment of each different secondary endosymbiosis. Analysis of targeted proteins in the various organisms now suggests that a similar system is used by each group. However, rather than interpreting this similarity as evidence of an homologous origin, I believe that targeting has evolved convergently by combining and recycling existing protein trafficking mechanisms already existing in the endosymbiont and host. Indeed, by analyzing the multiple motifs in targeting sequences of some genes it is possible to infer that they originated in the plastid genome, transferred from there into the primary host nucleus, and subsequently moved into the secondary host nucleus. Thus, each step of the targeting process in "second-hand" plastids recapitulates the gene's previous intracellular transfers.
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Affiliation(s)
- G I McFadden
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, Vic., Australia.
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