51
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Li J, Singh U, Arendsee Z, Wurtele ES. Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data. Front Genet 2021; 12:722981. [PMID: 34484307 PMCID: PMC8415361 DOI: 10.3389/fgene.2021.722981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The "dark transcriptome" can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 30% of the highly transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins ("orphan-ORFs"); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph (MOG), a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally testable hypotheses about candidate genes.
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Affiliation(s)
- Jing Li
- Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Urminder Singh
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| | - Zebulun Arendsee
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| | - Eve Syrkin Wurtele
- Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
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52
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Genomic analyses of new genes and their phenotypic effects reveal rapid evolution of essential functions in Drosophila development. PLoS Genet 2021; 17:e1009654. [PMID: 34242211 PMCID: PMC8270118 DOI: 10.1371/journal.pgen.1009654] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/09/2021] [Indexed: 12/27/2022] Open
Abstract
It is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development of Drosophila. The recent progress in the genome-wide experimental testing of gene effects and improvements in the computational identification of new genes (< 40 million years ago, Mya) open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues in techniques and concepts related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including reproducibility and efficiency of knockdown experiment and difference between RNAi libraries in the knockdown efficiency and testing of phenotypic effects. We further analyzed a large data from knockdowns of 11,354 genes (~75% of the Drosophila melanogaster total genes), including 702 new genes (~66% of the species total new genes that aged < 40 Mya), revealing a similarly high proportion (~32.2%) of essential genes that originated in various Sophophora subgenus lineages and distant ancestors beyond the Drosophila genus. The transcriptional compensation effect from CRISPR knockout were detected for highly similar duplicate copies. Knockout of a few young genes detected analogous essentiality in various functions in development. Taken together, our experimental and computational analyses provide valuable data for detection of phenotypic effects of genes in general and further strong evidence for the concept that new genes in Drosophila quickly evolved essential functions in viability during development.
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53
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Hata T, Takada N, Hayakawa C, Kazama M, Uchikoba T, Tachikawa M, Matsuo M, Satoh S, Obokata J. De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome. PLoS One 2021; 16:e0252674. [PMID: 34111139 PMCID: PMC8191969 DOI: 10.1371/journal.pone.0252674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/19/2021] [Indexed: 01/16/2023] Open
Abstract
The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.
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Affiliation(s)
- Takayuki Hata
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
| | - Naoto Takada
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Chihiro Hayakawa
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Mei Kazama
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Tomohiro Uchikoba
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Makoto Tachikawa
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
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54
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Zhao Y, Lu GA, Yang H, Lin P, Liufu Z, Tang T, Xu J. Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. Mol Biol Evol 2021; 38:1544-1553. [PMID: 33306129 PMCID: PMC8042761 DOI: 10.1093/molbev/msaa317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Red Queen hypothesis depicts evolution as the continual struggle to adapt. According to this hypothesis, new genes, especially those originating from nongenic sequences (i.e., de novo genes), are eliminated unless they evolve continually in adaptation to a changing environment. Here, we analyze two Drosophila de novo miRNAs that are expressed in a testis-specific manner with very high rates of evolution in their DNA sequence. We knocked out these miRNAs in two sibling species and investigated their contributions to different fitness components. We observed that the fitness contributions of miR-975 in Drosophila simulans seem positive, in contrast to its neutral contributions in D. melanogaster, whereas miR-983 appears to have negative contributions in both species, as the fitness of the knockout mutant increases. As predicted by the Red Queen hypothesis, the fitness difference of these de novo miRNAs indicates their different fates.
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Affiliation(s)
- Yixin Zhao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guang-An Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hao Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Pei Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhongqi Liufu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jin Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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55
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Majic P, Payne JL. Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks. Mol Biol Evol 2021; 37:1165-1178. [PMID: 31845961 PMCID: PMC7086177 DOI: 10.1093/molbev/msz300] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Regulatory networks control the spatiotemporal gene expression patterns that give rise to and define the individual cell types of multicellular organisms. In eumetazoa, distal regulatory elements called enhancers play a key role in determining the structure of such networks, particularly the wiring diagram of “who regulates whom.” Mutations that affect enhancer activity can therefore rewire regulatory networks, potentially causing adaptive changes in gene expression. Here, we use whole-tissue and single-cell transcriptomic and chromatin accessibility data from mouse to show that enhancers play an additional role in the evolution of regulatory networks: They facilitate network growth by creating transcriptionally active regions of open chromatin that are conducive to de novo gene evolution. Specifically, our comparative transcriptomic analysis with three other mammalian species shows that young, mouse-specific intergenic open reading frames are preferentially located near enhancers, whereas older open reading frames are not. Mouse-specific intergenic open reading frames that are proximal to enhancers are more highly and stably transcribed than those that are not proximal to enhancers or promoters, and they are transcribed in a limited diversity of cellular contexts. Furthermore, we report several instances of mouse-specific intergenic open reading frames proximal to promoters showing evidence of being repurposed enhancers. We also show that open reading frames gradually acquire interactions with enhancers over macroevolutionary timescales, helping integrate genes—those that have arisen de novo or by other means—into existing regulatory networks. Taken together, our results highlight a dual role of enhancers in expanding and rewiring gene regulatory networks.
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Affiliation(s)
- Paco Majic
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author: E-mail:
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56
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Lange A, Patel PH, Heames B, Damry AM, Saenger T, Jackson CJ, Findlay GD, Bornberg-Bauer E. Structural and functional characterization of a putative de novo gene in Drosophila. Nat Commun 2021; 12:1667. [PMID: 33712569 PMCID: PMC7954818 DOI: 10.1038/s41467-021-21667-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/03/2021] [Indexed: 11/26/2022] Open
Abstract
Comparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard's orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard's structure appears to have been maintained with only minor changes over millions of years.
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Affiliation(s)
- Andreas Lange
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Prajal H Patel
- Department of Biology, College of the Holy Cross, Worcester, MA, USA
| | - Brennen Heames
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Adam M Damry
- Research School of Chemistry, ANU College of Science, Canberra, Australia
| | - Thorsten Saenger
- Department of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Colin J Jackson
- Research School of Chemistry, ANU College of Science, Canberra, Australia
| | | | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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57
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Structure and function of naturally evolved de novo proteins. Curr Opin Struct Biol 2021; 68:175-183. [PMID: 33567396 DOI: 10.1016/j.sbi.2020.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 01/05/2023]
Abstract
Comparative evolutionary genomics has revealed that novel protein coding genes can emerge randomly from non-coding DNA. While most of the myriad of transcripts which continuously emerge vanish rapidly, some attain regulatory regions, become translated and survive. More surprisingly, sequence properties of de novo proteins are almost indistinguishable from randomly obtained sequences, yet de novo proteins may gain functions and integrate into eukaryotic cellular networks quite easily. We here discuss current knowledge on de novo proteins, their structures, functions and evolution. Since the existence of de novo proteins seems at odds with decade-long attempts to construct proteins with novel structures and functions from scratch, we suggest that a better understanding of de novo protein evolution may fuel new strategies for protein design.
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58
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Zeng X, Li H, Li K, Yuan R, Zhao S, Li J, Luo J, Li X, Ma H, Wu G, Yan X. Evolution of the Brassicaceae-specific MS5-Like family and neofunctionalization of the novel MALE STERILITY 5 gene essential for male fertility in Brassica napus. THE NEW PHYTOLOGIST 2021; 229:2339-2356. [PMID: 33128826 PMCID: PMC7894334 DOI: 10.1111/nph.17053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 10/08/2020] [Indexed: 05/22/2023]
Abstract
New genes (or lineage-specific genes) can facilitate functional innovations. MALE STERILITY 5 (MS5) in Brassica napus is a fertility-related new gene, which has two wild-type alleles (BnMS5a and BnMS5c ) and two mutant alleles (BnMS5b and BnMS5d ) that could induce male sterility. Here, we studied the history and functional evolution of MS5 homologs in plants by phylogenetic analysis and molecular genetic experiments. We identified 727 MS5 homologs and found that they define a Brassicaceae-specific gene family that has expanded partly via multiple tandem gene duplications and also probably transpositions. The MS5 in B. napus is inherited from a basic diploid ancestor of B. rapa. Molecular genetic experiments indicate that BnMS5a and BnMS5c are functionally distinct in B. napus and that BnMS5d can inhibit BnMS5a in B. napus in a dosage-dependent manner. The BnMS5a protein can move in coordination with meiotic telomeres and interact with the nuclear envelope protein SUN1, with a possible crucial role in meiotic chromosome behavior. In summary, BnMS5 belongs to a Brassicaceae-specific new gene family, and has gained a novel function that is essential for male fertility in B. napus through neofunctionalization that has likely occurred since the origin of B. rapa.
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Affiliation(s)
- Xinhua Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Hao Li
- Department of Biologythe Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Rong Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Shengbo Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Jun Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Junling Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Xiaofei Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Hong Ma
- Department of Biologythe Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Gang Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
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59
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Uncovering de novo gene birth in yeast using deep transcriptomics. Nat Commun 2021; 12:604. [PMID: 33504782 PMCID: PMC7841160 DOI: 10.1038/s41467-021-20911-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions. We find that about half of the de novo transcripts are expressed from regions which already harbor other genes in the opposite orientation; these transcripts show similar expression changes in response to stress as their overlapping counterparts, and some appear to translate small proteins. Thus, a large fraction of de novo genes in yeast are likely to co-evolve with already existing genes.
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60
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The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD + levels. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1929-1948. [PMID: 33521859 DOI: 10.1007/s11427-020-1851-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity. However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48-54 million years ago (Mya) and expanded into five duplicates (chiron1-5) in zebrafish 1-4 Mya. The chiron genes (chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD+ synthesis pathway, chirons could directly catalyze the NAD+ rate-limiting reaction and probably impact two energy metabolism genes (nmnat1 and naprt) to be under positive selection in Danioninae fishes. Together, these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD+ biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian.
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61
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Erady C, Boxall A, Puntambekar S, Suhas Jagannathan N, Chauhan R, Chong D, Meena N, Kulkarni A, Kasabe B, Prathivadi Bhayankaram K, Umrania Y, Andreani A, Nel J, Wayland MT, Pina C, Lilley KS, Prabakaran S. Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions. NPJ Genom Med 2021; 6:4. [PMID: 33495453 PMCID: PMC7835362 DOI: 10.1038/s41525-020-00167-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022] Open
Abstract
Uncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.
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Affiliation(s)
- Chaitanya Erady
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Adam Boxall
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Shraddha Puntambekar
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - N Suhas Jagannathan
- Cancer and Stem Cell Biology Programme, and Centre for Computational Biology, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Ruchi Chauhan
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - David Chong
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Narendra Meena
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Apurv Kulkarni
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | - Bhagyashri Kasabe
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, 411008, India
| | | | - Yagnesh Umrania
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Adam Andreani
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Jean Nel
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK
| | - Matthew T Wayland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Cristina Pina
- Department of Haematology, Cambridge Biomedical Campus, Cambridge, CB2 0PT, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Sudhakaran Prabakaran
- Department of Genetics, University of Cambridge, Downing Site, Cambridge, CB2 3EH, UK.
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62
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James JE, Willis SM, Nelson PG, Weibel C, Kosinski LJ, Masel J. Universal and taxon-specific trends in protein sequences as a function of age. eLife 2021; 10:e57347. [PMID: 33416492 PMCID: PMC7819706 DOI: 10.7554/elife.57347] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 01/05/2021] [Indexed: 01/12/2023] Open
Abstract
Extant protein-coding sequences span a huge range of ages, from those that emerged only recently to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be 'phylostratigraphy' trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.
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Affiliation(s)
- Jennifer E James
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
| | - Sara M Willis
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
| | - Paul G Nelson
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
| | - Catherine Weibel
- Department of Physics, University of ArizonaTucsonUnited States
- Department of Mathematics, University of ArizonaTucsonUnited States
| | - Luke J Kosinski
- Department of Molecular and Cellular Biology, University of ArizonaTucsonUnited States
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
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63
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Rödelsperger C, Ebbing A, Sharma DR, Okumura M, Sommer RJ, Korswagen HC. Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution. Mol Biol Evol 2021; 38:229-243. [PMID: 32785688 PMCID: PMC8480184 DOI: 10.1093/molbev/msaa207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Divergence of gene function and expression during development can give rise to phenotypic differences at the level of cells, tissues, organs, and ultimately whole organisms. To gain insights into the evolution of gene expression and novel genes at spatial resolution, we compared the spatially resolved transcriptomes of two distantly related nematodes, Caenorhabditis elegans and Pristionchus pacificus, that diverged 60-90 Ma. The spatial transcriptomes of adult worms show little evidence for strong conservation at the level of single genes. Instead, regional expression is largely driven by recent duplication and emergence of novel genes. Estimation of gene ages across anatomical structures revealed an enrichment of novel genes in sperm-related regions. This provides first evidence in nematodes for the "out of testis" hypothesis that has been previously postulated based on studies in Drosophila and mammals. "Out of testis" genes represent a mix of products of pervasive transcription as well as fast evolving members of ancient gene families. Strikingly, numerous novel genes have known functions during meiosis in Caenorhabditis elegans indicating that even universal processes such as meiosis may be targets of rapid evolution. Our study highlights the importance of novel genes in generating phenotypic diversity and explicitly characterizes gene origination in sperm-related regions. Furthermore, it proposes new functions for previously uncharacterized genes and establishes the spatial transcriptome of Pristionchus pacificus as a catalog for future studies on the evolution of gene expression and function.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annabel Ebbing
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht,
The Netherlands
| | - Devansh Raj Sharma
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht,
The Netherlands
- Developmental Biology, Department of Biology, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht,
The Netherlands
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64
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Weisman CM, Murray AW, Eddy SR. Many, but not all, lineage-specific genes can be explained by homology detection failure. PLoS Biol 2020; 18:e3000862. [PMID: 33137085 PMCID: PMC7660931 DOI: 10.1371/journal.pbio.3000862] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 11/12/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study. Lineage-specific gene families may arise from evolutionary innovations such as de novo gene origination, or may simply mean that a similarity search program failed to identify more distant homologs. A new computational method for modeling the expected decay of similarity search scores with evolutionary distance allows distinction between the two explanations.
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Affiliation(s)
- Caroline M. Weisman
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Andrew W. Murray
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sean R. Eddy
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
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65
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High gene space divergence contrasts with frozen vegetative architecture in the moss family Funariaceae. Mol Phylogenet Evol 2020; 154:106965. [PMID: 32956800 DOI: 10.1016/j.ympev.2020.106965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
A new paradigm has slowly emerged regarding the diversification of bryophytes, with inferences from molecular data highlighting a dynamic evolution of their genome. However, comparative studies of expressed genes among closely related taxa is so far missing. Here we contrast the dimensions of the vegetative transcriptome of Funaria hygrometrica and Physcomitrium pyriforme against the genome of their relative, Physcomitrium (Physcomitrella) patens. These three species of Funariaceae share highly conserved vegetative bodies, and are partially sympatric, growing on mineral soil in mostly temperate regions. We analyzed the vegetative gametophytic transcriptome of F. hygrometrica and P. pyriforme and mapped short reads, transcripts, and proteins to the genome and gene space of P. patens. Only about half of the transcripts of F. hygrometrica map to their ortholog in P. patens, whereas at least 90% of those of P. pyriforme align to loci in P. patens. Such divergence is unexpected given the high morphological similarity of the gametophyte but reflects the estimated times of divergence of F. hygrometrica and P. pyriforme from P. patens, namely 55 and 20 mya, respectively. The newly sampled transcriptomes bear signatures of at least one, rather ancient, whole genome duplication (WGD), which may be shared with one reported for P. patens. The transcriptomes of F. hygrometrica and P. pyriforme reveal significant contractions or expansions of different gene families. While transcriptomes offer only an incomplete estimate of the gene space, the high number of transcripts obtained suggest a significant divergence in gene sequences, and gene number among the three species, indicative of a rather strong, dynamic genome evolution, shaped in part by whole, partial or localized genome duplication. The gene ontology of their specific and rapidly-evolving protein families, suggests that the evolution of the Funariaceae may have been driven by the diversification of metabolic genes that may optimize the adaptations to environmental conditions, a hypothesis well in line with ecological patterns in the genetic diversity and structure in seed plants.
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66
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Suenaga Y, Nakatani K, Nakagawara A. De novo evolved gene product NCYM in the pathogenesis and clinical outcome of human neuroblastomas and other cancers. Jpn J Clin Oncol 2020; 50:839-846. [PMID: 32577751 DOI: 10.1093/jjco/hyaa097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022] Open
Abstract
NCYM is an antisense transcript of MYCN oncogene and promotes tumor progression. NCYM encodes a de novo protein whose open reading frame evolved from noncoding genomic regions in the ancestor of Homininae. Because of its topology, NCYM is always co-amplified with MYCN oncogene, and the mutual regulations between NCYM and MYCN maintain their expressions at high levels in MYCN-amplified tumors. NCYM stabilizes MYCN by inhibiting GSK3β, whereas MYCN stimulates transcription of both NCYM and MYCN. NCYM mRNA and its noncoding transcript variants MYCNOS have been shown to stimulate MYCN expression via direct binding to MYCN promoter, indicating that both coding and noncoding transcripts of NCYM induce MYCN expression. In contrast to the noncoding functions of NCYM, NCYM protein also promotes calpain-mediated cleavage of c-MYC. The cleaved product called Myc-nick inhibits cell death and promotes cancer cell migration. Furthermore, NCYM-mediated inhibition of GSK3β results in the stabilization of β-catenin, which promotes aggressiveness of bladder cancers. These MYCN-independent functions of NCYM showed their clinical significance in MYCN-non-amplified tumors, including adult tumors. This year is the 30th anniversary of the identification of NCYM/MYCNOS gene. On this special occasion, we summarize the current understanding of molecular functions and the clinical significance of NCYM and discuss future directions to achieve therapeutic strategies targeting NCYM.
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67
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Shi T, Rahmani RS, Gugger PF, Wang M, Li H, Zhang Y, Li Z, Wang Q, Van de Peer Y, Marchal K, Chen J. Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants. Mol Biol Evol 2020; 37:2394-2413. [PMID: 32343808 PMCID: PMC7403625 DOI: 10.1093/molbev/msaa105] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K-pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein-protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein-protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.
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Affiliation(s)
- Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD
| | - Muhua Wang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hui Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhizhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Centre for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDLab, IMEC, Ghent University, Ghent, Belgium
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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68
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Zile K, Dessimoz C, Wurm Y, Masel J. Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence. Genome Biol Evol 2020; 12:1355-1366. [PMID: 32589737 PMCID: PMC8059200 DOI: 10.1093/gbe/evaa127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.
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Affiliation(s)
- Karina Zile
- Division of Biosciences, University College London, United Kingdom
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Switzerland
- Center for Integrative Genomics, University of Lausanne, Switzerland
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Department of Computer Science, University College London, United Kingdom
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
- Alan Turing Institute, London, United Kingdom
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona
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69
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Jasti N, Sebagh D, Riaz M, Wang X, Koripella B, Palanisamy V, Mohammad N, Chen Q, Friedrich M. Towards reconstructing the dipteran demise of an ancient essential gene: E3 ubiquitin ligase Murine double minute. Dev Genes Evol 2020; 230:279-294. [PMID: 32623522 DOI: 10.1007/s00427-020-00663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Genome studies have uncovered many examples of essential gene loss, raising the question of how ancient genes transition from essentiality to dispensability. We explored this process for the deeply conserved E3 ubiquitin ligase Murine double minute (Mdm), which is lacking in Drosophila despite the conservation of its main regulatory target, the cellular stress response gene p53. Conducting gene expression and knockdown experiments in the red flour beetle Tribolium castaneum, we found evidence that Mdm has remained essential in insects where it is present. Using bioinformatics approaches, we confirm the absence of the Mdm gene family in Drosophila, mapping its loss to the stem lineage of schizophoran Diptera and Pipunculidae (big-headed flies), about 95-85 million years ago. Intriguingly, this gene loss event was preceded by the de novo origin of the gene Companion of reaper (Corp), a novel p53 regulatory factor that is characterized by functional similarities to vertebrate Mdm2 despite lacking E3 ubiquitin ligase protein domains. Speaking against a 1:1 compensatory gene gain/loss scenario, however, we found that hoverflies (Syrphidae) and pointed-wing flies (Lonchopteridae) possess both Mdm and Corp. This implies that the two p53 regulators have been coexisting for ~ 150 million years in select dipteran clades and for at least 50 million years in the lineage to Schizophora and Pipunculidae. Given these extensive time spans of Mdm/Corp coexistence, we speculate that the loss of Mdm in the lineage to Drosophila involved further acquisitions of compensatory gene activities besides the emergence of Corp. Combined with the previously noted reduction of an ancestral P53 contact domain in the Mdm homologs of crustaceans and insects, we conclude that the loss of the ancient Mdm gene family in flies was the outcome of incremental functional regression over long macroevolutionary time scales.
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Affiliation(s)
- Naveen Jasti
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.,Institute for Protein Design, Washington University, 1959 NE Pacific Street, Seattle, WA, 98195, USA
| | - Dylan Sebagh
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Mohammed Riaz
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Xin Wang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Bharat Koripella
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Vasanth Palanisamy
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Nabeel Mohammad
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Qing Chen
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA. .,Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI, 48201, USA.
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70
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Understanding the proteome encoded by "non-coding RNAs": new insights into human genome. SCIENCE CHINA. LIFE SCIENCES 2020; 63:986-995. [PMID: 32318910 DOI: 10.1007/s11427-019-1677-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/12/2020] [Indexed: 01/19/2023]
Abstract
A great number of non-coding RNAs (ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling (Ribo-seq), full length translating RNA analysis (RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.
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71
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Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES. phylostratr: a framework for phylostratigraphy. Bioinformatics 2020; 35:3617-3627. [PMID: 30873536 DOI: 10.1093/bioinformatics/btz171] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. This is done by searching for homologs within increasingly broad clades. The deepest clade that contains a homolog of the protein(s) encoded by a gene is that gene's phylostratum. RESULTS We have created a general R-based framework, phylostratr, to estimate the phylostratum of every gene in a species. The program fully automates analysis: selecting species for balanced representation, retrieving sequences, building databases, inferring phylostrata and returning diagnostics. Key diagnostics include: detection of genes with inferred homologs in old clades, but not intermediate ones; proteome quality assessments; false-positive diagnostics, and checks for missing organellar genomes. phylostratr allows extensive customization and systematic comparisons of the influence of analysis parameters or genomes on phylostrata inference. A user may: modify the automatically generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae. AVAILABILITY AND IMPLEMENTATION Source code available at https://github.com/arendsee/phylostratr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zebulun Arendsee
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
| | - Jing Li
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Arun Seetharam
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Department of Statistics, Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
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72
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Evolution of novel genes in three-spined stickleback populations. Heredity (Edinb) 2020; 125:50-59. [PMID: 32499660 PMCID: PMC7413265 DOI: 10.1038/s41437-020-0319-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes frequently acquire new protein-coding genes which may significantly impact an organism’s fitness. Novel genes can be created, for example, by duplication of large genomic regions or de novo, from previously non-coding DNA. Either way, creation of a novel transcript is an essential early step during novel gene emergence. Most studies on the gain-and-loss dynamics of novel genes so far have compared genomes between species, constraining analyses to genes that have remained fixed over long time scales. However, the importance of novel genes for rapid adaptation among populations has recently been shown. Therefore, since little is known about the evolutionary dynamics of transcripts across natural populations, we here study transcriptomes from several tissues and nine geographically distinct populations of an ecological model species, the three-spined stickleback. Our findings suggest that novel genes typically start out as transcripts with low expression and high tissue specificity. Early expression regulation appears to be mediated by gene-body methylation. Although most new and narrowly expressed genes are rapidly lost, those that survive and subsequently spread through populations tend to gain broader and higher expression levels. The properties of the encoded proteins, such as disorder and aggregation propensity, hardly change. Correspondingly, young novel genes are not preferentially under positive selection but older novel genes more often overlap with FST outlier regions. Taken together, expression of the surviving novel genes is rapidly regulated, probably via epigenetic mechanisms, while structural properties of encoded proteins are non-debilitating and might only change much later.
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73
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Zelhof AC, Mahato S, Liang X, Rylee J, Bergh E, Feder LE, Larsen ME, Britt SG, Friedrich M. The brachyceran de novo gene PIP82, a phosphorylation target of aPKC, is essential for proper formation and maintenance of the rhabdomeric photoreceptor apical domain in Drosophila. PLoS Genet 2020; 16:e1008890. [PMID: 32579558 PMCID: PMC7340324 DOI: 10.1371/journal.pgen.1008890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/07/2020] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
The Drosophila apical photoreceptor membrane is defined by the presence of two distinct morphological regions, the microvilli-based rhabdomere and the stalk membrane. The subdivision of the apical membrane contributes to the geometrical positioning and the stereotypical morphology of the rhabdomeres in compound eyes with open rhabdoms and neural superposition. Here we describe the characterization of the photoreceptor specific protein PIP82. We found that PIP82's subcellular localization demarcates the rhabdomeric portion of the apical membrane. We further demonstrate that PIP82 is a phosphorylation target of aPKC. PIP82 localization is modulated by phosphorylation, and in vivo, the loss of the aPKC/Crumbs complex results in an expansion of the PIP82 localization domain. The absence of PIP82 in photoreceptors leads to misshapped rhabdomeres as a result of misdirected cellular trafficking of rhabdomere proteins. Comparative analyses reveal that PIP82 originated de novo in the lineage leading to brachyceran Diptera, which is also characterized by the transition from fused to open rhabdoms. Taken together, these findings define a novel factor that delineates and maintains a specific apical membrane domain, and offers new insights into the functional organization and evolutionary history of the Drosophila retina.
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Affiliation(s)
- Andrew C. Zelhof
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Simpla Mahato
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Xulong Liang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Jonathan Rylee
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Emma Bergh
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Lauren E. Feder
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Matthew E. Larsen
- Department of Neurology and Ophthalmology, Dell Medical School, University of Texas, Austin, Texas, United States of America
| | - Steven G. Britt
- Department of Neurology and Ophthalmology, Dell Medical School, University of Texas, Austin, Texas, United States of America
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
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74
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Brunet MA, Leblanc S, Roucou X. Reconsidering proteomic diversity with functional investigation of small ORFs and alternative ORFs. Exp Cell Res 2020; 393:112057. [PMID: 32387289 DOI: 10.1016/j.yexcr.2020.112057] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 04/21/2020] [Accepted: 05/02/2020] [Indexed: 12/13/2022]
Abstract
The discovery of functional yet non-annotated open reading frames (ORFs) throughout the genome of several species presents an unprecedented challenge in current genome annotation. These novel ORFs are shorter than annotated ones and many can be found on the same RNA, in opposition to current assumptions in annotation methodologies. Whilst the literature lacks consensus, these novel ORFs are commonly referred to as small ORFs (sORFs) or alternative ORFs (alt-ORFs). Unannotated ORFs represent an overlooked layer of complexity in the coding potential of genomes and are transforming our current vision of the nature of coding genes. In this review, we outline what constitutes a sORF or an alt-ORF and emphasize differences between both nomenclatures. We then describe complementary large-scale methods to accurately discover novel ORFs as well as yield functional insights on the novel proteins they encode. While serendipitous discoveries highlighted the functional importance of some novel ORFs, omics methods facilitate and improve their characterization to better understand physiological and pathological pathways. Functional annotation of sORFs, alt-ORFs and their corresponding microproteins will likely help fundamental and clinical research.
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Affiliation(s)
- Marie A Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada.
| | - Sebastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada; PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada.
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75
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Pascual-Carreras E, Marin-Barba M, Herrera-Úbeda C, Font-Martín D, Eckelt K, de Sousa N, García-Fernández J, Saló E, Adell T. Planarian cell number depends on blitzschnell, a novel gene family that balances cell proliferation and cell death. Development 2020; 147:dev.184044. [PMID: 32122990 DOI: 10.1242/dev.184044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/19/2020] [Indexed: 01/14/2023]
Abstract
Control of cell number is crucial to define body size during animal development and to restrict tumoral transformation. The cell number is determined by the balance between cell proliferation and cell death. Although many genes are known to regulate those processes, the molecular mechanisms underlying the relationship between cell number and body size remain poorly understood. This relationship can be better understood by studying planarians, flatworms that continuously change their body size according to nutrient availability. We identified a novel gene family, blitzschnell (bls), that consists of de novo and taxonomically restricted genes that control cell proliferation:cell death ratio. Their silencing promotes faster regeneration and increases cell number during homeostasis. Importantly, this increase in cell number leads to an increase in body size only in a nutrient-rich environment; in starved planarians, silencing results in a decrease in cell size and cell accumulation that ultimately produces overgrowths. bls expression is downregulated after feeding and is related to activity of the insulin/Akt/mTOR network, suggesting that the bls family evolved in planarians as an additional mechanism for restricting cell number in nutrient-fluctuating environments.
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Affiliation(s)
- Eudald Pascual-Carreras
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Marta Marin-Barba
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Daniel Font-Martín
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Kay Eckelt
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Nidia de Sousa
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Jordi García-Fernández
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Emili Saló
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
| | - Teresa Adell
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine, Universitat de Barcelona, Barcelona 08028, Catalunya, Spain .,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona 08028, Catalunya, Spain
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76
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Heames B, Schmitz J, Bornberg-Bauer E. A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila. J Mol Evol 2020; 88:382-398. [PMID: 32253450 PMCID: PMC7162840 DOI: 10.1007/s00239-020-09939-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/13/2020] [Indexed: 12/13/2022]
Abstract
Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Drosophila genus. Across the annotated proteomes of twelve species, we find 6297 orphan genes within 4953 taxon-specific clusters of orthologs. By inferring the ancestral DNA as non-coding for between 550 and 2467 (8.7-39.2%) of these genes, we describe for the first time how de novo emergence contributes to the abundance of clade-specific Drosophila genes. In support of them having functional roles, we show that de novo genes have robust expression and translational support. However, the distinct nucleotide sequences of de novo genes, which have characteristics intermediate between intergenic regions and conserved genes, reflect their recent birth from non-coding DNA. We find that de novo genes encode more disordered proteins than both older genes and intergenic regions. Together, our results suggest that gene emergence from non-coding DNA provides an abundant source of material for the evolution of new proteins. Following gene birth, gradual evolution over large evolutionary timescales moulds sequence properties towards those of conserved genes, resulting in a continuum of properties whose starting points depend on the nucleotide sequences of an initial pool of novel genes.
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Affiliation(s)
- Brennen Heames
- Institute for Evolution and Biodiversity, 48149, Münster, Germany
| | - Jonathan Schmitz
- Institute for Evolution and Biodiversity, 48149, Münster, Germany
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77
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Abrahams L, Hurst LD. A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences. Mol Biol Evol 2020; 37:1148-1164. [PMID: 31841162 PMCID: PMC7086181 DOI: 10.1093/molbev/msz299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Although the constraints on a gene’s sequence are often assumed to reflect the functioning of that gene, here we propose transfer selection, a constraint operating on one class of genes transferred to another, mediated by shared binding factors. We show that such transfer can explain an otherwise paradoxical depletion of stop codons in long intergenic noncoding RNAs (lincRNAs). Serine/arginine-rich proteins direct the splicing machinery by binding exonic splice enhancers (ESEs) in immature mRNA. As coding exons cannot contain stop codons in one reading frame, stop codons should be rare within ESEs. We confirm that the stop codon density (SCD) in ESE motifs is low, even accounting for nucleotide biases. Given that serine/arginine-rich proteins binding ESEs also facilitate lincRNA splicing, a low SCD could transfer to lincRNAs. As predicted, multiexon lincRNA exons are depleted in stop codons, a result not explained by open reading frame (ORF) contamination. Consistent with transfer selection, stop codon depletion in lincRNAs is most acute in exonic regions with the highest ESE density, disappears when ESEs are masked, is consistent with stop codon usage skews in ESEs, and is diminished in both single-exon lincRNAs and introns. Owing to low SCD, the maximum lengths of pseudo-ORFs frequently exceed null expectations. This has implications for ORF annotation and the evolution of de novo protein-coding genes from lincRNAs. We conclude that not all constraints operating on genes need be explained by the functioning of the gene but may instead be transferred owing to shared binding factors.
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Affiliation(s)
- Liam Abrahams
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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78
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Beeby M, Ferreira JL, Tripp P, Albers SV, Mitchell DR. Propulsive nanomachines: the convergent evolution of archaella, flagella and cilia. FEMS Microbiol Rev 2020; 44:253-304. [DOI: 10.1093/femsre/fuaa006] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Echoing the repeated convergent evolution of flight and vision in large eukaryotes, propulsive swimming motility has evolved independently in microbes in each of the three domains of life. Filamentous appendages – archaella in Archaea, flagella in Bacteria and cilia in Eukaryotes – wave, whip or rotate to propel microbes, overcoming diffusion and enabling colonization of new environments. The implementations of the three propulsive nanomachines are distinct, however: archaella and flagella rotate, while cilia beat or wave; flagella and cilia assemble at their tips, while archaella assemble at their base; archaella and cilia use ATP for motility, while flagella use ion-motive force. These underlying differences reflect the tinkering required to evolve a molecular machine, in which pre-existing machines in the appropriate contexts were iteratively co-opted for new functions and whose origins are reflected in their resultant mechanisms. Contemporary homologies suggest that archaella evolved from a non-rotary pilus, flagella from a non-rotary appendage or secretion system, and cilia from a passive sensory structure. Here, we review the structure, assembly, mechanism and homologies of the three distinct solutions as a foundation to better understand how propulsive nanomachines evolved three times independently and to highlight principles of molecular evolution.
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Affiliation(s)
- Morgan Beeby
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Josie L Ferreira
- Department of Life Sciences, Frankland Road, Imperial College of London, London, SW7 2AZ, UK
| | - Patrick Tripp
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology, University of Freiburg, Schaenzlestrasse 1, 79211 Freiburg, Germany
| | - David R Mitchell
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, 750 E. Adams St., Syracuse, NY 13210, USA
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79
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Vakirlis N, Carvunis AR, McLysaght A. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife 2020; 9:e53500. [PMID: 32066524 PMCID: PMC7028367 DOI: 10.7554/elife.53500] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
The origin of 'orphan' genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special circumstance of conserved synteny to estimate the contribution of complete divergence to the pool of orphan genes. By separately comparing yeast, fly and human genes to related taxa using conservative criteria, we find that complete divergence accounts, on average, for at most a third of eukaryotic orphan and taxonomically restricted genes. We observe that complete divergence occurs at a stable rate within a phylum but at different rates between phyla, and is frequently associated with gene shortening akin to pseudogenization.
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Affiliation(s)
- Nikolaos Vakirlis
- Smurfit Institute of GeneticsTrinity College Dublin, University of DublinDublinIreland
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of MedicineUniversity of PittsburghPittsburghUnited States
| | - Aoife McLysaght
- Smurfit Institute of GeneticsTrinity College Dublin, University of DublinDublinIreland
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80
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Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun 2020; 11:781. [PMID: 32034123 PMCID: PMC7005711 DOI: 10.1038/s41467-020-14500-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/20/2019] [Indexed: 11/14/2022] Open
Abstract
Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast. Disruption of emerging sequences is generally inconsequential for fitness in the laboratory and in natural populations. Overexpression of emerging sequences, however, is enriched in adaptive fitness effects compared to overexpression of established genes. We find that adaptive emerging sequences tend to encode putative transmembrane domains, and that thymine-rich intergenic regions harbor a widespread potential to produce transmembrane domains. These findings, together with in-depth examination of the de novo emerging YBR196C-A locus, suggest a novel evolutionary model whereby adaptive transmembrane polypeptides emerge de novo from thymine-rich non-genic regions and subsequently accumulate changes molded by natural selection. There is increasing evidence that protein-coding genes can emerge de novo from noncoding genomic regions. Vakirlis et al. propose that sequences encoding transmembrane polypeptides can emerge de novo in thymine-rich genomic regions and provide organisms with fitness benefits.
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Affiliation(s)
- Nikolaos Vakirlis
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, 2, Ireland
| | - Omer Acar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Brian Hsu
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - Nelson Castilho Coelho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - S Branden Van Oss
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Kate Medetgul-Ernar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - Ray W Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States
| | - Cameron P Hines
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States
| | - John Iannotta
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Saurin Bipin Parikh
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, 2, Ireland
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States
| | - Allyson F O'Donnell
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States. .,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, United States.
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA, 92093, United States.
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States. .,Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, United States.
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81
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Ritschard EA, Whitelaw B, Albertin CB, Cooke IR, Strugnell JM, Simakov O. Coupled Genomic Evolutionary Histories as Signatures of Organismal Innovations in Cephalopods: Co-evolutionary Signatures Across Levels of Genome Organization May Shed Light on Functional Linkage and Origin of Cephalopod Novelties. Bioessays 2019; 41:e1900073. [PMID: 31664724 DOI: 10.1002/bies.201900073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/05/2019] [Indexed: 12/07/2023]
Abstract
How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction with many species-specific organs, coleoid cephalopods (octopuses, squids, cuttlefishes) provide exciting model systems to investigate how organismal novelties evolve. However, dissecting these processes requires novel approaches that enable deeper interrogation of genome evolution. Here, the existence of specific sets of genomic co-evolutionary signatures between expanded gene families, genome reorganization, and novel genes is posited. It is reasoned that their co-evolution has contributed to the complex organization of cephalopod nervous systems and the emergence of ecologically unique organs. In the course of reviewing this field, how the first cephalopod genomic studies have begun to shed light on the molecular underpinnings of morphological novelty is illustrated and their impact on directing future research is described. It is argued that the application and evolutionary profiling of evolutionary signatures from these studies will help identify and dissect the organismal principles of cephalopod innovations. By providing specific examples, the implications of this approach both within and beyond cephalopod biology are discussed.
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Affiliation(s)
- Elena A Ritschard
- Department for Molecular Evolution and Development, University of Vienna, Austria
| | - Brooke Whitelaw
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
| | | | - Ira R Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland, 4811, Australia
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, Queensland, 4811, Australia
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Oleg Simakov
- Department for Molecular Evolution and Development, University of Vienna, Austria
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82
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Rödelsperger C, Prabh N, Sommer RJ. New Gene Origin and Deep Taxon Phylogenomics: Opportunities and Challenges. Trends Genet 2019; 35:914-922. [DOI: 10.1016/j.tig.2019.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/29/2019] [Indexed: 01/22/2023]
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83
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Keeling DM, Garza P, Nartey CM, Carvunis AR. The meanings of 'function' in biology and the problematic case of de novo gene emergence. eLife 2019; 8:e47014. [PMID: 31674305 PMCID: PMC6824840 DOI: 10.7554/elife.47014] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/11/2019] [Indexed: 12/24/2022] Open
Abstract
The word function has many different meanings in molecular biology. Here we explore the use of this word (and derivatives like functional) in research papers about de novo gene birth. Based on an analysis of 20 abstracts we propose a simple lexicon that, we believe, will help scientists and philosophers discuss the meaning of function more clearly.
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Affiliation(s)
- Diane Marie Keeling
- Department of Communication Studies, College of Arts & SciencesUniversity of San DiegoSan DiegoUnited States
| | | | | | - Anne-Ruxandra Carvunis
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghUnited States
- Pittsburgh Center for Evolutionary Biology and MedicineUniversity of Pittsburgh School of MedicinePittsburghUnited States
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84
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Surm JM, Stewart ZK, Papanicolaou A, Pavasovic A, Prentis PJ. The draft genome of Actinia tenebrosa reveals insights into toxin evolution. Ecol Evol 2019; 9:11314-11328. [PMID: 31641475 PMCID: PMC6802032 DOI: 10.1002/ece3.5633] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
Sea anemones have a wide array of toxic compounds (peptide toxins found in their venom) which have potential uses as therapeutics. To date, the majority of studies characterizing toxins in sea anemones have been restricted to species from the superfamily, Actinioidea. No highly complete draft genomes are currently available for this superfamily, however, highlighting our limited understanding of the genes encoding toxins in this important group. Here we have sequenced, assembled, and annotated a draft genome for Actinia tenebrosa. The genome is estimated to be approximately 255 megabases, with 31,556 protein-coding genes. Quality metrics revealed that this draft genome matches the quality and completeness of other model cnidarian genomes, including Nematostella, Hydra, and Acropora. Phylogenomic analyses revealed strong conservation of the Cnidaria and Hexacorallia core-gene set. However, we found that lineage-specific gene families have undergone significant expansion events compared with shared gene families. Enrichment analysis performed for both gene ontologies, and protein domains revealed that genes encoding toxins contribute to a significant proportion of the lineage-specific genes and gene families. The results make clear that the draft genome of A. tenebrosa will provide insight into the evolution of toxins and lineage-specific genes, and provide an important resource for the discovery of novel biological compounds.
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Affiliation(s)
- Joachim M. Surm
- Faculty of HealthSchool of Biomedical SciencesQueensland University of TechnologyKelvin GroveQldAustralia
- Institute of Health and Biomedical InnovationQueensland University of TechnologyKelvin GroveQldAustralia
| | - Zachary K. Stewart
- Science and Engineering FacultySchool of Earth, Environmental and Biological SciencesQueensland University of TechnologyBrisbaneQldAustralia
- Institute for Future EnvironmentsQueensland University of TechnologyBrisbaneQldAustralia
| | | | - Ana Pavasovic
- Faculty of HealthSchool of Biomedical SciencesQueensland University of TechnologyKelvin GroveQldAustralia
| | - Peter J. Prentis
- Science and Engineering FacultySchool of Earth, Environmental and Biological SciencesQueensland University of TechnologyBrisbaneQldAustralia
- Institute for Future EnvironmentsQueensland University of TechnologyBrisbaneQldAustralia
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85
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Perochon A, Kahla A, Vranić M, Jia J, Malla KB, Craze M, Wallington E, Doohan FM. A wheat NAC interacts with an orphan protein and enhances resistance to Fusarium head blight disease. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1892-1904. [PMID: 30821405 PMCID: PMC6737021 DOI: 10.1111/pbi.13105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 05/05/2023]
Abstract
Taxonomically-restricted orphan genes play an important role in environmental adaptation, as recently demonstrated by the fact that the Pooideae-specific orphan TaFROG (Triticum aestivum Fusarium Resistance Orphan Gene) enhanced wheat resistance to the economically devastating Fusarium head blight (FHB) disease. Like most orphan genes, little is known about the cellular function of the encoded protein TaFROG, other than it interacts with the central stress regulator TaSnRK1α. Here, we functionally characterized a wheat (T. aestivum) NAC-like transcription factor TaNACL-D1 that interacts with TaFROG and investigated its' role in FHB using studies to assess motif analyses, yeast transactivation, protein-protein interaction, gene expression and the disease response of wheat lines overexpressing TaNACL-D1. TaNACL-D1 is a Poaceae-divergent NAC transcription factor that encodes a Triticeae-specific protein C-terminal region with transcriptional activity and a nuclear localisation signal. The TaNACL-D1/TaFROG interaction was detected in yeast and confirmed in planta, within the nucleus. Analysis of multi-protein interactions indicated that TaFROG could form simultaneously distinct protein complexes with TaNACL-D1 and TaSnRK1α in planta. TaNACL-D1 and TaFROG are co-expressed as an early response to both the causal fungal agent of FHB, Fusarium graminearum and its virulence factor deoxynivalenol (DON). Wheat lines overexpressing TaNACL-D1 were more resistant to FHB disease than wild type plants. Thus, we conclude that the orphan protein TaFROG interacts with TaNACL-D1, a NAC transcription factor that forms part of the disease response evolved within the Triticeae.
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Affiliation(s)
- Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Amal Kahla
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Monika Vranić
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Jianguang Jia
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Keshav B. Malla
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | | | | | - Fiona M. Doohan
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
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86
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Xie C, Bekpen C, Künzel S, Keshavarz M, Krebs-Wheaton R, Skrabar N, Ullrich KK, Tautz D. A de novo evolved gene in the house mouse regulates female pregnancy cycles. eLife 2019; 8:44392. [PMID: 31436535 PMCID: PMC6760900 DOI: 10.7554/elife.44392] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/21/2019] [Indexed: 12/16/2022] Open
Abstract
The de novo emergence of new genes has been well documented through genomic analyses. However, a functional analysis, especially of very young protein-coding genes, is still largely lacking. Here, we identify a set of house mouse-specific protein-coding genes and assess their translation by ribosome profiling and mass spectrometry data. We functionally analyze one of them, Gm13030, which is specifically expressed in females in the oviduct. The interruption of the reading frame affects the transcriptional network in the oviducts at a specific stage of the estrous cycle. This includes the upregulation of Dcpp genes, which are known to stimulate the growth of preimplantation embryos. As a consequence, knockout females have their second litters after shorter times and have a higher infanticide rate. Given that Gm13030 shows no signs of positive selection, our findings support the hypothesis that a de novo evolved gene can directly adopt a function without much sequence adaptation. Different species have specific genes that set them apart from other species. Yet exactly how these species-specific genes originate is not fully known. The traditional view is that existing old genes are duplicated to make a ‘spare’ copy, which can change through mutations into a new gene with a new role gradually over time. Despite there being lots of evidence supporting this theory, not all new genes found in recent years can be traced back to older genes. This led to an alternative view – that recently evolved genes can also appear ‘de novo’, and come from regions of random DNA sequences that did not previously code for a protein. So far, the possibility of genes forming de novo during evolution has largely been supported by comparing and analyzing the genomes of related species. However, very little is known about the biological role these de novo genes play. Now, Xie et al. have generated a list of recently evolved de novo mouse genes, and carried out a detailed analysis of one de novo gene expressed in females at the time when embryos implant into the uterus wall. To study the role of this gene, Xie et al. created a strain of knock-out mice that have a defunct version of the protein coded by the gene. Loss of this protein caused female mice to have their second litter after a shorter period of time and increased the likelihood that female mice would terminate their newborn pups. This suggests that this newly discovered de novo gene is involved in regulating the female reproductive cycles of mice. Further analysis showed that this de novo gene counteracts the action of an older gene that promotes the implantation of embryos. This gene has therefore likely evolved due to the benefit it offers mothers, as it protects them from experiencing the increased physiological stress caused by a premature second pregnancy. These findings support the idea that genes which have evolved de novo can have an essential biological purpose despite coming from random DNA sequences. This establishes that de novo evolution of genes is the second major mechanism of how new genes with significant biological roles can form in the genome.
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Affiliation(s)
- Chen Xie
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cemalettin Bekpen
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Maryam Keshavarz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Rebecca Krebs-Wheaton
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Neva Skrabar
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Kristian Karsten Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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87
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Witt E, Benjamin S, Svetec N, Zhao L. Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila. eLife 2019; 8:e47138. [PMID: 31418408 PMCID: PMC6697446 DOI: 10.7554/elife.47138] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/06/2019] [Indexed: 12/25/2022] Open
Abstract
The testis is a peculiar tissue in many respects. It shows patterns of rapid gene evolution and provides a hotspot for the origination of genetic novelties such as de novo genes, duplications and mutations. To investigate the expression patterns of genetic novelties across cell types, we performed single-cell RNA-sequencing of adult Drosophila testis. We found that new genes were expressed in various cell types, the patterns of which may be influenced by their mode of origination. In particular, lineage-specific de novo genes are commonly expressed in early spermatocytes, while young duplicated genes are often bimodally expressed. Analysis of germline substitutions suggests that spermatogenesis is a highly reparative process, with the mutational load of germ cells decreasing as spermatogenesis progresses. By elucidating the distribution of genetic novelties across spermatogenesis, this study provides a deeper understanding of how the testis maintains its core reproductive function while being a hotbed of evolutionary innovation.
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Affiliation(s)
- Evan Witt
- Laboratory of Evolutionary Genetics and GenomicsThe Rockefeller UniversityNew YorkUnited States
| | - Sigi Benjamin
- Laboratory of Evolutionary Genetics and GenomicsThe Rockefeller UniversityNew YorkUnited States
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and GenomicsThe Rockefeller UniversityNew YorkUnited States
| | - Li Zhao
- Laboratory of Evolutionary Genetics and GenomicsThe Rockefeller UniversityNew YorkUnited States
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88
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Pouvreau B, Fenske R, Ivanova A, Murcha MW, Mylne JS. An interstitial peptide is readily processed from within seed proteins. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:175-183. [PMID: 31203882 DOI: 10.1016/j.plantsci.2019.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/25/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
The importance of de novo protein evolution is apparent, but most examples are de novo coding transcripts evolving from silent or non-coding DNA. The peptide macrocycle SunFlower Trypsin Inhibitor 1 (SFTI-1) evolved over 45 million years from genetic expansion within the N-terminal 'discarded' region of an ancestral seed albumin precursor. SFTI-1 and its adjacent albumin are both processed into separate, mature forms by asparaginyl endopeptidase (AEP). Here to determine whether the evolution of SFTI-1 in a latent region of its precursor was critical, we used a transgene approach in A. thaliana analysed by peptide mass spectrometry and RT-qPCR. SFTI could emerge from alternative locations within preproalbumin as well as emerge with precision from unrelated seed proteins via AEP-processing. SFTI production was possible with the adjacent albumin, but peptide levels dropped greatly without the albumin. The ability for SFTI to be processed from multiple sequence contexts and different proteins suggests that to make peptide, it was not crucial for the genetic expansion that gave rise to SFTI and its family to be within a latent protein region. Interstitial peptides, evolving like SFTI within existing proteins, might be more widespread and as a mechanism, SFTI exemplifies a stable, new, functional peptide that did not need a new gene to evolve de novo.
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Affiliation(s)
- Benjamin Pouvreau
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Ricarda Fenske
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Aneta Ivanova
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia
| | - Joshua S Mylne
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia; The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.
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89
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Nielly-Thibault L, Landry CR. Differences Between the Raw Material and the Products of de Novo Gene Birth Can Result from Mutational Biases. Genetics 2019; 212:1353-1366. [PMID: 31227545 PMCID: PMC6707459 DOI: 10.1534/genetics.119.302187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/14/2019] [Indexed: 12/03/2022] Open
Abstract
Proteins are among the most important constituents of biological systems. Because all protein-coding genes have a noncoding ancestral form, the properties of noncoding sequences and how they shape the birth of novel proteins may influence the structure and function of all proteins. Differences between the properties of young proteins and random expectations from noncoding sequences have previously been interpreted as the result of natural selection. However, interpreting such deviations requires a yet-unattained understanding of the raw material of de novo gene birth and its relation to novel functional proteins. We mathematically show that the average properties and selective filtering of the "junk" polypeptides of which this raw material is composed are not the only factors influencing the properties of novel functional proteins. We find that in some biological scenarios, they also depend on the variance of the properties of junk polypeptides and their correlation with the rate of allelic turnover, which may itself depend on mutational biases. This suggests for instance that any property of polypeptides that accelerates their exploration of the sequence space could be overrepresented in novel functional proteins, even if it has a limited effect on adaptive value. To exemplify the use of our general theoretical results, we build a simple model that predicts the mean length and mean intrinsic disorder of novel functional proteins from the genomic GC content and a single evolutionary parameter. This work provides a theoretical framework that can guide the prediction and interpretation of results when studying the de novo emergence of protein-coding genes.
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Affiliation(s)
- Lou Nielly-Thibault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biologie, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec, Quebec G1V 0A6, Canada
- PROTEO, Quebec, Quebec G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biologie, Université Laval, Quebec, Quebec G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec, Quebec G1V 0A6, Canada
- PROTEO, Quebec, Quebec G1V 0A6, Canada
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90
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Rahi ML, Mather PB, Ezaz T, Hurwood DA. The Molecular Basis of Freshwater Adaptation in Prawns: Insights from Comparative Transcriptomics of Three Macrobrachium Species. Genome Biol Evol 2019; 11:1002-1018. [PMID: 30840062 PMCID: PMC6450038 DOI: 10.1093/gbe/evz045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/17/2022] Open
Abstract
Elucidating the molecular basis of adaptation to different environmental conditions is important because adaptive ability of a species can shape its distribution, influence speciation, and also drive a variety of evolutionary processes. For crustaceans, colonization of freshwater habitats has significantly impacted diversity, but the molecular basis of this process is poorly understood. In the current study, we examined three prawn species from the genus Macrobrachium (M. australiense, M. tolmerum, and M. novaehollandiae) to better understand the molecular basis of freshwater adaptation using a comparative transcriptomics approach. Each of these species naturally inhabit environments with different salinity levels; here, we exposed them to the same experimental salinity conditions (0‰ and 15‰), to compare expression patterns of candidate genes that previously have been shown to influence phenotypic traits associated with freshwater adaptation (e.g., genes associated with osmoregulation). Differential gene expression analysis revealed 876, 861, and 925 differentially expressed transcripts under the two salinities for M. australiense, M. tolmerum, and M. novaehollandiae, respectively. Of these, 16 were found to be unannotated novel transcripts and may be taxonomically restricted or orphan genes. Functional enrichment and molecular pathway mapping revealed 13 functionally enriched categories and 11 enriched molecular pathways that were common to the three Macrobrachium species. Pattern of selection analysis revealed 26 genes with signatures of positive selection among pairwise species comparisons. Overall, our results indicate that the same key genes and similar molecular pathways are likely to be involved with freshwater adaptation widely across this decapod group; with nonoverlapping sets of genes showing differential expression (mainly osmoregulatory genes) and signatures of positive selection (genes involved with different life history traits).
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Affiliation(s)
- Md Lifat Rahi
- Science and Engineering Faculty, School of Earth Environment and Biological Sciences (EEBS), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Peter B Mather
- Science and Engineering Faculty, School of Earth Environment and Biological Sciences (EEBS), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Tariq Ezaz
- Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Australian Capital Territory, Australia
| | - David A Hurwood
- Science and Engineering Faculty, School of Earth Environment and Biological Sciences (EEBS), Queensland University of Technology (QUT), Brisbane, Queensland, Australia
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91
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Prabh N, Rödelsperger C. De Novo, Divergence, and Mixed Origin Contribute to the Emergence of Orphan Genes in Pristionchus Nematodes. G3 (BETHESDA, MD.) 2019; 9:2277-2286. [PMID: 31088903 PMCID: PMC6643871 DOI: 10.1534/g3.119.400326] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/11/2019] [Indexed: 12/30/2022]
Abstract
Homology is a fundamental concept in comparative biology. It is extensively used at the sequence level to make phylogenetic hypotheses and functional inferences. Nonetheless, the majority of eukaryotic genomes contain large numbers of orphan genes lacking homologs in other taxa. Generally, the fraction of orphan genes is higher in genomically undersampled clades, and in the absence of closely related genomes any hypothesis about their origin and evolution remains untestable. Previously, we sequenced ten genomes with an underlying ladder-like phylogeny to establish a phylogenomic framework for studying genome evolution in diplogastrid nematodes. Here, we use this deeply sampled data set to understand the processes that generate orphan genes in our focal species Pristionchus pacificus Based on phylostratigraphic analysis and additional bioinformatic filters, we obtained 29 high-confidence candidate genes for which mechanisms of orphan origin were proposed based on manual inspection. This revealed diverse mechanisms including annotation artifacts, chimeric origin, alternative reading frame usage, and gene splitting with subsequent gain of de novo exons. In addition, we present two cases of complete de novo origination from non-coding regions, which represents one of the first reports of de novo genes in nematodes. Thus, we conclude that de novo emergence, divergence, and mixed mechanisms contribute to novel gene formation in Pristionchus nematodes.
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Affiliation(s)
- Neel Prabh
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, August Thienemann Str. 2, 24306 Plön, Germany
| | - Christian Rödelsperger
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
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92
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Hilgers L, Hartmann S, Hofreiter M, von Rintelen T. Novel Genes, Ancient Genes, and Gene Co-Option Contributed to the Genetic Basis of the Radula, a Molluscan Innovation. Mol Biol Evol 2019; 35:1638-1652. [PMID: 29672732 PMCID: PMC5995198 DOI: 10.1093/molbev/msy052] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.
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Affiliation(s)
- Leon Hilgers
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Corresponding author: E-mail:
| | - Stefanie Hartmann
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Adaptive Evolutionary Genomics Department, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Thomas von Rintelen
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
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93
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Durand É, Gagnon-Arsenault I, Hallin J, Hatin I, Dubé AK, Nielly-Thibault L, Namy O, Landry CR. Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations. Genome Res 2019; 29:932-943. [PMID: 31152050 PMCID: PMC6581059 DOI: 10.1101/gr.239822.118] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 05/13/2019] [Indexed: 12/17/2022]
Abstract
Little is known about the rate of emergence of de novo genes, what their initial properties are, and how they spread in populations. We examined wild yeast populations (Saccharomyces paradoxus) to characterize the diversity and turnover of intergenic ORFs over short evolutionary timescales. We find that hundreds of intergenic ORFs show translation signatures similar to canonical genes, and we experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Compared with canonical genes, intergenic ORFs have lower translation efficiency, which could imply a lack of optimization for translation or a mechanism to reduce their production cost. Translated intergenic ORFs also tend to have sequence properties that are generally close to those of random intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared <110 kya, already show gene-like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary timescales.
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Affiliation(s)
- Éléonore Durand
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Johan Hallin
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Isabelle Hatin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Lou Nielly-Thibault
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada
| | - Olivier Namy
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Centre de Recherche en Données Massives de l'Université Laval, Pavillon Charles-Eugène-Marchand, Université Laval, G1V 0A6 Québec, Québec, Canada.,Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, G1V 0A6 Québec, Québec, Canada
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94
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Surm JM, Smith HL, Madio B, Undheim EA, King GF, Hamilton BR, Burg CA, Pavasovic A, Prentis PJ. A process of convergent amplification and tissue‐specific expression dominates the evolution of toxin and toxin‐like genes in sea anemones. Mol Ecol 2019; 28:2272-2289. [DOI: 10.1111/mec.15084] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/09/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Joachim M. Surm
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
- Institute of Health and Biomedical Innovation Queensland University of Technology Kelvin Grove Queensland Australia
| | - Hayden L. Smith
- Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane Queensland Australia
- Institute for Future Environments Queensland University of Technology Brisbane Queensland Australia
| | - Bruno Madio
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Eivind A.B. Undheim
- Centre for Advanced Imaging University of Queensland Saint Lucia Queensland Australia
| | - Glenn F. King
- Institute for Molecular Bioscience University of Queensland Brisbane Queensland Australia
| | - Brett R. Hamilton
- Centre for Advanced Imaging University of Queensland Saint Lucia Queensland Australia
- Centre for Microscopy and Microanalysis University of Queensland Saint Lucia Queensland Australia
| | - Chloé A. Burg
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
- Institute of Health and Biomedical Innovation Queensland University of Technology Kelvin Grove Queensland Australia
| | - Ana Pavasovic
- Faculty of Health, School of Biomedical Sciences Queensland University of Technology Kelvin Grove Queensland Australia
| | - Peter J. Prentis
- Science and Engineering Faculty, School of Earth, Environmental and Biological Sciences Queensland University of Technology Brisbane Queensland Australia
- Institute for Future Environments Queensland University of Technology Brisbane Queensland Australia
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95
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Affiliation(s)
- Stephen Branden Van Oss
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
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96
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Foy SG, Wilson BA, Bertram J, Cordes MHJ, Masel J. A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution. Genetics 2019; 211:1345-1355. [PMID: 30692195 PMCID: PMC6456324 DOI: 10.1534/genetics.118.301719] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/25/2019] [Indexed: 01/06/2023] Open
Abstract
To detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare "more evolved" to "less evolved" entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer. To be retained during evolution, a protein must not only have a function, but must also avoid toxic dysfunction such as protein aggregation. There is conflict between the two requirements: hydrophobic amino acids form the cores of protein folds, but also promote aggregation. Young genes avoid strongly hydrophobic amino acids, which is presumably the simplest solution to the aggregation problem. Here we show that young genes' few hydrophobic residues are clustered near one another along the primary sequence, presumably to assist folding. The higher aggregation risk created by the higher hydrophobicity of older genes is counteracted by more subtle effects in the ordering of the amino acids, including a reduction in the clustering of hydrophobic residues until they eventually become more interspersed than if distributed randomly. This interspersion has previously been reported to be a general property of proteins, but here we find that it is restricted to old genes. Quantitatively, the index of dispersion delineates a gradual trend, i.e., a decrease in the clustering of hydrophobic amino acids over billions of years.
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Affiliation(s)
- Scott G Foy
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Benjamin A Wilson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Jason Bertram
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
| | - Matthew H J Cordes
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721
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97
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Du K, Wuertz S, Adolfi M, Kneitz S, Stöck M, Oliveira M, Nóbrega R, Ormanns J, Kloas W, Feron R, Klopp C, Parrinello H, Journot L, He S, Postlethwait J, Meyer A, Guiguen Y, Schartl M. The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system. Sci Rep 2019; 9:5293. [PMID: 30923320 PMCID: PMC6439221 DOI: 10.1038/s41598-019-41457-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/27/2019] [Indexed: 01/18/2023] Open
Abstract
We have sequenced the genome of the largest freshwater fish species of the world, the arapaima. Analysis of gene family dynamics and signatures of positive selection identified genes involved in the specific adaptations and unique features of this iconic species, in particular it's large size and fast growth. Genome sequences from both sexes combined with RAD-tag analyses from other males and females led to the isolation of male-specific scaffolds and supports an XY sex determination system in arapaima. Whole transcriptome sequencing showed that the product of the gland-like secretory organ on the head surface of males and females may not only provide nutritional fluid for sex-unbiased parental care, but that the organ itself has a more specific function in males, which engage more in parental care.
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Affiliation(s)
- Kang Du
- University of Wuerzburg, Physiological Chemistry, Biocenter, 97074, Wuerzburg, Germany
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sven Wuertz
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, D-12587, Berlin, Germany
| | - Mateus Adolfi
- University of Wuerzburg, Physiological Chemistry, Biocenter, 97074, Wuerzburg, Germany
| | - Susanne Kneitz
- University of Wuerzburg, Physiological Chemistry, Biocenter, 97074, Wuerzburg, Germany
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, D-12587, Berlin, Germany
| | - Marcos Oliveira
- University of Wuerzburg, Physiological Chemistry, Biocenter, 97074, Wuerzburg, Germany
- Reproductive and Molecular Biology Group, Departament of Morphology, Institute of Biosciences, UNESP, Botucatu, Brazil
| | - Rafael Nóbrega
- Reproductive and Molecular Biology Group, Departament of Morphology, Institute of Biosciences, UNESP, Botucatu, Brazil
| | - Jenny Ormanns
- University of Wuerzburg, Physiological Chemistry, Biocenter, 97074, Wuerzburg, Germany
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, D-12587, Berlin, Germany
| | - Romain Feron
- INRA, UR1037 LPGP, Fish Physiology and Genomics, F-35042, Rennes, France
| | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094, Montpellier Cedex 05, France
| | - Laurent Journot
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094, Montpellier Cedex 05, France
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, OR, 97401, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstraße 10, 78457, Konstanz, Germany
| | - Yann Guiguen
- INRA, UR1037 LPGP, Fish Physiology and Genomics, F-35042, Rennes, France
| | - Manfred Schartl
- University of Wuerzburg, Physiological Chemistry, Biocenter, 97074, Wuerzburg, Germany.
- Comprehensive Cancer Center Mainfranken, University Hospital, 97080, Würzburg, Germany.
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, 77843, USA.
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98
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Shao Y, Chen C, Shen H, He BZ, Yu D, Jiang S, Zhao S, Gao Z, Zhu Z, Chen X, Fu Y, Chen H, Gao G, Long M, Zhang YE. GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes. Genome Res 2019; 29:682-696. [PMID: 30862647 PMCID: PMC6442393 DOI: 10.1101/gr.238733.118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
The origination of new genes contributes to phenotypic evolution in humans. Two major challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we created GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes. Genome-wide comparison of the age inference methods revealed that the synteny-based pipeline (SBP) is most suited for recently duplicated genes, whereas the protein-family–based methods are useful for ancient genes. For SBP-dated primate-specific protein-coding genes (PSGs), we performed manual evaluation based on published PSG lists and showed that SBP generated a conservative data set of PSGs by masking less reliable syntenic regions. After assessing the coding potential based on evolutionary constraint and peptide evidence from proteomic data, we curated a list of 254 PSGs with different levels of protein evidence. This list also includes 41 candidate misannotated pseudogenes that encode primate-specific short proteins. Coexpression analysis showed that PSGs are preferentially recruited into organs with rapidly evolving pathways such as spermatogenesis, immune response, mother–fetus interaction, and brain development. For brain development, primate-specific KRAB zinc-finger proteins (KZNFs) are specifically up-regulated in the mid-fetal stage, which may have contributed to the evolution of this critical stage. Altogether, hundreds of PSGs are either recruited to processes under strong selection pressure or to processes supporting an evolving novel organ.
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Affiliation(s)
- Yi Shao
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Shen
- College of Computers, Hunan University of Technology, Zhuzhou Hunan 412007, China
| | - Bin Z He
- FAS Center for Systems Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Shilei Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhiqiang Gao
- University of Chinese Academy of Sciences, Beijing 100049, China.,National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhenglin Zhu
- School of Life Sciences, Chongqing University, Chongqing 400044, China
| | - Xi Chen
- Wuhan Institute of Biotechnology, Wuhan 430072, China.,Medical Research Institute, Wuhan University, Wuhan 430072, China
| | - Yan Fu
- University of Chinese Academy of Sciences, Beijing 100049, China.,National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hua Chen
- University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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99
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Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol 2019; 3:679-690. [PMID: 30858588 DOI: 10.1038/s41559-019-0822-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection.
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100
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Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids. Proc Natl Acad Sci U S A 2019; 116:4400-4405. [PMID: 30765531 PMCID: PMC6410882 DOI: 10.1073/pnas.1817138116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The diverse antifreeze proteins enabling the survival of different polar fishes in freezing seas offer unparalleled vistas into the breadth of genetic sources and mechanisms that produce crucial new functions. Although most new genes evolved from preexisting genic ancestors, some are deemed to have arisen from noncoding DNA. However, the pertinent mechanisms, functions, and selective forces remain uncertain. Our paper presents clear evidence that the antifreeze glycoprotein gene of the northern codfish originated from a noncoding region. We further describe the detailed mechanism of its evolutionary transformation into a full-fledged crucial life-saving gene. This paper is a concrete dissection of the process of a de novo gene birth that has conferred a vital adaptive function directly linked to natural selection. A fundamental question in evolutionary biology is how genetic novelty arises. De novo gene birth is a recently recognized mechanism, but the evolutionary process and function of putative de novo genes remain largely obscure. With a clear life-saving function, the diverse antifreeze proteins of polar fishes are exemplary adaptive innovations and models for investigating new gene evolution. Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence. We constructed genomic DNA libraries for AFGP-bearing and AFGP-lacking species across the gadid phylogeny and performed fine-scale comparative analyses of the AFGP genomic loci and homologs. We identified the noncoding founder region and a nine-nucleotide (9-nt) element therein that supplied the codons for one Thr-Ala-Ala unit from which the extant repetitive AFGP-coding sequence (cds) arose through tandem duplications. The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal. Through a 1-nt frameshift mutation, these two parts formed a single read-through open reading frame (ORF). It became functionalized when a putative translocation event conferred the essential cis promoter for transcriptional initiation. We experimentally proved that all genic components of the extant gadid AFGP originated from entirely nongenic DNA. The gadid AFGP evolutionary process also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF existed before the regulatory element to activate transcription was acquired.
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