1
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Ardern Z. Alternative Reading Frames are an Underappreciated Source of Protein Sequence Novelty. J Mol Evol 2023; 91:570-580. [PMID: 37326679 DOI: 10.1007/s00239-023-10122-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Protein-coding DNA sequences can be translated into completely different amino acid sequences if the nucleotide triplets used are shifted by a non-triplet amount on the same DNA strand or by translating codons from the opposite strand. Such "alternative reading frames" of protein-coding genes are a major contributor to the evolution of novel protein products. Recent studies demonstrating this include examples across the three domains of cellular life and in viruses. These sequences increase the number of trials potentially available for the evolutionary invention of new genes and also have unusual properties which may facilitate gene origin. There is evidence that the structure of the standard genetic code contributes to the features and gene-likeness of some alternative frame sequences. These findings have important implications across diverse areas of molecular biology, including for genome annotation, structural biology, and evolutionary genomics.
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2
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Fakhar AZ, Liu J, Pajerowska-Mukhtar KM, Mukhtar MS. The Lost and Found: Unraveling the Functions of Orphan Genes. J Dev Biol 2023; 11:27. [PMID: 37367481 PMCID: PMC10299390 DOI: 10.3390/jdb11020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
Orphan Genes (OGs) are a mysterious class of genes that have recently gained significant attention. Despite lacking a clear evolutionary history, they are found in nearly all living organisms, from bacteria to humans, and they play important roles in diverse biological processes. The discovery of OGs was first made through comparative genomics followed by the identification of unique genes across different species. OGs tend to be more prevalent in species with larger genomes, such as plants and animals, and their evolutionary origins remain unclear but potentially arise from gene duplication, horizontal gene transfer (HGT), or de novo origination. Although their precise function is not well understood, OGs have been implicated in crucial biological processes such as development, metabolism, and stress responses. To better understand their significance, researchers are using a variety of approaches, including transcriptomics, functional genomics, and molecular biology. This review offers a comprehensive overview of the current knowledge of OGs in all domains of life, highlighting the possible role of dark transcriptomics in their evolution. More research is needed to fully comprehend the role of OGs in biology and their impact on various biological processes.
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Affiliation(s)
| | | | | | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd., Birmingham, AL 35294, USA
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3
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Barrera-Redondo J, Lotharukpong JS, Drost HG, Coelho SM. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol 2023; 24:54. [PMID: 36964572 PMCID: PMC10037820 DOI: 10.1186/s13059-023-02895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.
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Affiliation(s)
- Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Jaruwatana Sodai Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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4
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Li J, Singh U, Bhandary P, Campbell J, Arendsee Z, Seetharam AS, Wurtele ES. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Res 2021; 50:e37. [PMID: 34928390 PMCID: PMC9023268 DOI: 10.1093/nar/gkab1238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Proteins encoded by newly-emerged genes ('orphan genes') share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.
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Affiliation(s)
- Jing Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA
| | - Urminder Singh
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Priyanka Bhandary
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Jacqueline Campbell
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agriculture Research Service, Ames, IA 50014, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA 50014, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
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5
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Ramos-González PL, Pons T, Chabi-Jesus C, Arena GD, Freitas-Astua J. Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:771983. [PMID: 34804105 PMCID: PMC8602818 DOI: 10.3389/fpls.2021.771983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5'-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5'-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.
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Affiliation(s)
- Pedro L. Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Tirso Pons
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriella Dias Arena
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Juliana Freitas-Astua
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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6
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Wang YW, Hess J, Slot JC, Pringle A. De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis in Amanita. Genome Biol Evol 2021; 12:2168-2182. [PMID: 32926145 PMCID: PMC7674699 DOI: 10.1093/gbe/evaa193] [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] [Accepted: 09/08/2020] [Indexed: 12/24/2022] Open
Abstract
By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer, and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the evolutionary dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM Amanita fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM Amanita species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared with genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either de novo gene birth (two gene families), horizontal gene transfer (four), or gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes a 1-aminocyclopropane-1-carboxylate deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene, a common negative regulator of plant-microbial mutualisms.
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Affiliation(s)
- Yen-Wen Wang
- Departments of Botany and Bacteriology, University of Wisconsin-Madison
| | - Jaqueline Hess
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison
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7
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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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8
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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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9
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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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