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Burkhardt RN, Artyukhin AB, Aprison EZ, Curtis BJ, Fox BW, Ludewig AH, Palomino DF, Luo J, Chaturbedi A, Panda O, Wrobel CJJ, Baumann V, Portman DS, Lee SS, Ruvinsky I, Schroeder FC. Sex-specificity of the C. elegans metabolome. Nat Commun 2023; 14:320. [PMID: 36658169 PMCID: PMC9852247 DOI: 10.1038/s41467-023-36040-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Recent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative metabolomics for the analysis of wildtype animals and sex determination mutants, we show that C. elegans hermaphrodites and males exhibit pervasive metabolomic differences. Several hundred small molecules are produced exclusively or in much larger amounts in one sex, including a host of previously unreported metabolites that incorporate building blocks from nucleoside, carbohydrate, lipid, and amino acid metabolism. A subset of male-enriched metabolites is specifically associated with the presence of a male germline, whereas enrichment of other compounds requires a male soma. Further, we show that one of the male germline-dependent metabolites, an unusual dipeptide incorporating N,N-dimethyltryptophan, increases food consumption, reduces lifespan, and accelerates the last stage of larval development in hermaphrodites. Our results serve as a foundation for mechanistic studies of how the genetic sex of soma and germline shape the C. elegans metabolome and provide a blueprint for the discovery of sex-dependent metabolites in other animals.
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Affiliation(s)
- Russell N Burkhardt
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander B Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
- Chemistry Department, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Erin Z Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Andreas H Ludewig
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Diana Fajardo Palomino
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jintao Luo
- Department of Biomedical Genetics, University of Rochester, Rochester, NY, 14642, USA
- School of Life Sciences, Xiamen University, 361102, Xiamen, Fujian, China
| | - Amaresh Chaturbedi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Victor Baumann
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas S Portman
- Department of Biomedical Genetics, University of Rochester, Rochester, NY, 14642, USA
| | - Siu Sylvia Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
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Athanasouli M, Witte H, Weiler C, Loschko T, Eberhardt G, Sommer RJ, Rödelsperger C. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics 2020; 21:708. [PMID: 33045985 PMCID: PMC7552371 DOI: 10.1186/s12864-020-07100-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Background Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.
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Affiliation(s)
- Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Weiler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Tobias Loschko
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Gabi Eberhardt
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
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Umair S, Bouchet CLG, Deng Q, Palevich N, Simpson HV. Characterisation of a Teladorsagia circumcincta glutathione transferase. Mol Biochem Parasitol 2020; 239:111316. [PMID: 32889102 DOI: 10.1016/j.molbiopara.2020.111316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
A 615 bp full length cDNA encoding a Teladorsagia circumcincta glutathione transferase (TcGST) was cloned, expressed in Escherichia coli and the recombinant protein purified and its kinetic properties determined. The predicted protein consisted of 205 amino acids and was present as a single band of about 24 kDa on SDS-PAGE. Multiple alignments of the protein sequence of TcGST with homologues from other helminths showed that the highest identity of 53-68% with haem-binding nematode proteins designated as members of the nu class of GSTs. Substrate binding sites and conserved regions were identified and were generally conserved. The predicted 3-dimensional structures of TcGST and HcGST revealed highly open binding cavities typical of this class of GST, considered to allow greater accessibility to diverse ligands compared with other classes of GST. At 25 °C, the optimum pH for TcGST activity was pH 7, the Vmax was 1535 ± 33 nmoles.min-1. mg-1 protein and the apparent Km for the substrate 1-chloro-2,4-dinitrobenzene (CDNB) was 0.22 ± 0.01 mM (mean ± SD, n = 2). Antibodies in both serum and saliva from field-immune, but not nematode-naïve, sheep, recognised recombinant TcGST in enzyme-linked immunosorbent assays. The recognition of the recombinant protein by antibodies generated by exposure of sheep to the native enzyme indicates similar antigenicity of the two proteins. These findings could aid in the design of novel drugs and vaccine antigens for economically important parasites of livestock.
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Affiliation(s)
- Saleh Umair
- AgResearch Ltd, Private Bag 11-008, Palmerston North, New Zealand.
| | | | - Qing Deng
- AgResearch Ltd, Private Bag 11-008, Palmerston North, New Zealand
| | - Nikola Palevich
- AgResearch Ltd, Private Bag 11-008, Palmerston North, New Zealand
| | - Heather V Simpson
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Sieriebriennikov B, Sun S, Lightfoot JW, Witte H, Moreno E, Rödelsperger C, Sommer RJ. Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell. PLoS Genet 2020; 16:e1008687. [PMID: 32282814 PMCID: PMC7179942 DOI: 10.1371/journal.pgen.1008687] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/23/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Environment shapes development through a phenomenon called developmental plasticity. Deciphering its genetic basis has potential to shed light on the origin of novel traits and adaptation to environmental change. However, molecular studies are scarce, and little is known about molecular mechanisms associated with plasticity. We investigated the gene regulatory network controlling predatory vs. non-predatory dimorphism in the nematode Pristionchus pacificus and found that it consists of genes of extremely different age classes. We isolated mutants in the conserved nuclear hormone receptor nhr-1 with previously unseen phenotypic effects. They disrupt mouth-form determination and result in animals combining features of both wild-type morphs. In contrast, mutants in another conserved nuclear hormone receptor nhr-40 display altered morph ratios, but no intermediate morphology. Despite divergent modes of control, NHR-1 and NHR-40 share transcriptional targets, which encode extracellular proteins that have no orthologs in Caenorhabditis elegans and result from lineage-specific expansions. An array of transcriptional reporters revealed co-expression of all tested targets in the same pharyngeal gland cell. Major morphological changes in this gland cell accompanied the evolution of teeth and predation, linking rapid gene turnover with morphological innovations. Thus, the origin of feeding plasticity involved novelty at the level of genes, cells and behavior.
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Affiliation(s)
- Bogdan Sieriebriennikov
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuai Sun
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - James W. Lightfoot
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eduardo Moreno
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ralf J. Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Rödelsperger C, Athanasouli M, Lenuzzi M, Theska T, Sun S, Dardiry M, Wighard S, Hu W, Sharma DR, Han Z. Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus. Sci Rep 2019; 9:18789. [PMID: 31827189 PMCID: PMC6906410 DOI: 10.1038/s41598-019-55359-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/20/2019] [Indexed: 01/15/2023] Open
Abstract
Nematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C. elegans facilitate the evolutionary study of biological functions using reverse genetics. However, the ability to identify orthologs of candidate genes in other species can be hampered by erroneous gene annotations. To improve gene annotation in the nematode model organism Pristionchus pacificus, we performed a genome-wide screen for C. elegans genes with potentially incorrectly annotated P. pacificus orthologs. We initiated a community-based project to manually inspect more than two thousand candidate loci and to propose new gene models based on recently generated Iso-seq and RNA-seq data. In most cases, misannotation of C. elegans orthologs was due to artificially fused gene predictions and completely missing gene models. The community-based curation raised the gene count from 25,517 to 28,036 and increased the single copy ortholog completeness level from 86% to 97%. This pilot study demonstrates how even small-scale crowdsourcing can drastically improve gene annotations. In future, similar approaches can be used for other species, gene sets, and even larger communities thus making manual annotation of large parts of the genome feasible.
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Affiliation(s)
- Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
| | - Marina Athanasouli
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Maša Lenuzzi
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Tobias Theska
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Shuai Sun
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Mohannad Dardiry
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Sara Wighard
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Wen Hu
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Devansh Raj Sharma
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ziduan Han
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
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Presence or absence? Primary structure, regioselectivity and evolution of Δ12/ω3 fatty acid desaturases in nematodes. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:1194-1205. [PMID: 31108204 DOI: 10.1016/j.bbalip.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 11/21/2022]
Abstract
For vertebrates, the adequate supply of polyunsaturated fatty acids (PUFA) by the diet, in particular ω3 long-chain PUFA, is considered essential for neural development, growth and reproduction. In contrast to aquatic ecosystems, ω3 long-chain PUFA apparently are not widely available in the terrestrial food chain. Their de novo synthesis requires the presence of Δ12 and ω3 fatty acid desaturase enzymes, which are absent in vertebrates but present, for example, in the nematode Caenorhabditis elegans (FAT-2 and FAT-1). This raises the question if soil-dwelling nematodes offer substantial supply of these valuable nutritional compounds in terrestrial food webs. BLAST searches in available nematode genomes revealed the existence of fat-2 like genes in almost all clade III-V species, but failed to identify orthologs in clade I-II nematodes. An additional RT-PCR screen across soil-dwelling nematode species identified six novel fat-2 like genes. Hints for the genetic basis of a ω3 (fat-1) desaturase activity was found only in selected clade IV-V species, but not in clades I to III nematodes. Fatty acid pattern analyses following a PUFA-free cultivation and enzymatic characterization of six selected fat-2 or fat-1 like desaturases in yeast confirmed the findings from the genetic approaches. Thus, in similar soil habitats, taxa exist that can synthesize ω3 long-chain PUFA (as Panagrolaimus, Mesorhabditis and Caenorhabditis) whereas others are unable to do so (Acrobeloides, Cephalobus and Oscheius). While these nematodes do not differ in trophic position or major diet, distinction in reproduction mode may have led to the observed variations in desaturase genes.
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Łopieńska-Biernat E, Paukszto Ł, Jastrzębski JP, Makowczenko K, Stryiński R. Genes expression and in silico studies of functions of trehalases, a highly dispersed Anisakis simplex s. l. specific gene family. Int J Biol Macromol 2019; 129:957-964. [DOI: 10.1016/j.ijbiomac.2019.02.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/07/2019] [Accepted: 02/07/2019] [Indexed: 10/27/2022]
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8
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Falcke JM, Bose N, Artyukhin AB, Rödelsperger C, Markov GV, Yim JJ, Grimm D, Claassen MH, Panda O, Baccile JA, Zhang YK, Le HH, Jolic D, Schroeder FC, Sommer RJ. Linking Genomic and Metabolomic Natural Variation Uncovers Nematode Pheromone Biosynthesis. Cell Chem Biol 2018; 25:787-796.e12. [PMID: 29779955 DOI: 10.1016/j.chembiol.2018.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/28/2018] [Accepted: 04/04/2018] [Indexed: 11/17/2022]
Abstract
In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.
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Affiliation(s)
- Jan M Falcke
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Neelanjan Bose
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alexander B Artyukhin
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gabriel V Markov
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Joshua J Yim
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dominik Grimm
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
| | - Marc H Claassen
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Joshua A Baccile
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ying K Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dino Jolic
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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9
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Rapid Gene Family Evolution of a Nematode Sperm Protein Despite Sequence Hyper-conservation. G3-GENES GENOMES GENETICS 2018; 8:353-362. [PMID: 29162683 PMCID: PMC5765362 DOI: 10.1534/g3.117.300281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Reproductive proteins are often observed to be the most rapidly evolving elements within eukaryotic genomes. The major sperm protein (MSP) is unique to the phylum Nematoda and is required for proper sperm locomotion and fertilization. Here, we annotate the MSP gene family and analyze their molecular evolution in 10 representative species across Nematoda. We show that MSPs are hyper-conserved across the phylum, having maintained an amino acid sequence identity of 83.5–97.7% for over 500 million years. This extremely slow rate of evolution makes MSPs some of the most highly conserved genes yet identified. However, at the gene family level, we show hyper-variability in both gene copy number and genomic position within species, suggesting rapid, lineage-specific gene family evolution. Additionally, we find evidence that extensive gene conversion contributes to the maintenance of sequence identity within chromosome-level clusters of MSP genes. Thus, while not conforming to the standard expectation for the evolution of reproductive proteins, our analysis of the molecular evolution of the MSP gene family is nonetheless consistent with the widely repeatable observation that reproductive proteins evolve rapidly, in this case in terms of the genomic properties of gene structure, copy number, and genomic organization. This unusual evolutionary pattern is likely generated by strong pleiotropic constraints acting on these genes at the sequence level, balanced against expansion at the level of the whole gene family.
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10
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Abstract
Nematodes, such as Caenorhabditis elegans, form one of the most species-rich animal phyla. By now more than 30 nematode genomes have been published allowing for comparative genomic analyses at various different time-scales. The majority of a nematode's gene repertoire is represented by either duplicated or so-called orphan genes of unknown origin. This indicates the importance of mechanisms that generate new genes during the course of evolution. While it is certain that nematodes have acquired genes by horizontal gene transfer from various donors, this process only explains a small portion of the nematode gene content. As evolutionary genomic analyses strongly support that most orphan genes are indeed protein-coding, future studies will have to decide, whether they are result from extreme divergence or evolved de novo from previously noncoding sequences. In this contribution, I summarize several studies investigating gene loss and gain in nematodes and discuss the strengths and weaknesses of individual approaches and datasets. These approaches can be used to ask nematode-specific questions such as associated with the evolution of parasitism or with switches in mating systems, but also can complement studies in other animal phyla like vertebrates and insects to broaden our general view on genome evolution.
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Affiliation(s)
- Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany.
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11
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Serotonin Drives Predatory Feeding Behavior via Synchronous Feeding Rhythms in the Nematode Pristionchus pacificus. G3-GENES GENOMES GENETICS 2017; 7:3745-3755. [PMID: 28903981 PMCID: PMC5677172 DOI: 10.1534/g3.117.300263] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Feeding behaviors in a wide range of animals are regulated by the neurotransmitter serotonin, although the exact neural circuits and associated mechanism are often unknown. The nematode Pristionchus pacificus can kill other nematodes by opening prey cuticles with movable teeth. Previous studies showed that exogenous serotonin treatment induces a predatory-like tooth movement and slower pharyngeal pumping in the absence of prey; however, physiological functions of serotonin during predation and other behaviors in P. pacificus remained completely unknown. Here, we investigate the roles of serotonin by generating mutations in Ppa-tph-1 and Ppa-bas-1, two key serotonin biosynthesis enzymes, and by genetic ablation of pharynx-associated serotonergic neurons. Mutations in Ppa-tph-1 reduced the pharyngeal pumping rate during bacterial feeding compared with wild-type. Moreover, the loss of serotonin or a subset of serotonergic neurons decreased the success of predation, but did not abolish the predatory feeding behavior completely. Detailed analysis using a high-speed camera revealed that the elimination of serotonin or the serotonergic neurons disrupted the timing and coordination of predatory tooth movement and pharyngeal pumping. This loss of synchrony significantly reduced the efficiency of successful predation events. These results suggest that serotonin has a conserved role in bacterial feeding and in addition drives the feeding rhythm of predatory behavior in Pristionchus.
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12
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Sanghvi GV, Baskaran P, Röseler W, Sieriebriennikov B, Rödelsperger C, Sommer RJ. Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts. PLoS One 2016; 11:e0164881. [PMID: 27741297 PMCID: PMC5065204 DOI: 10.1371/journal.pone.0164881] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 10/03/2016] [Indexed: 11/20/2022] Open
Abstract
Nematodes, the earth's most abundant metazoa are found in all ecosystems. In order to survive in diverse environments, they have evolved distinct feeding strategies and they can use different food sources. While some nematodes are specialists, including parasites of plants and animals, others such as Pristionchus pacificus are omnivorous feeders, which can live on a diet of bacteria, protozoans, fungi or yeast. In the wild, P. pacificus is often found in a necromenic association with beetles and is known to be able to feed on a variety of microbes as well as on nematode prey. However, in laboratory studies Escherichia coli OP50 has been used as standard food source, similar to investigations in Caenorhabditis elegans and it is unclear to what extent this biases the obtained results and how relevant findings are in real nature. To gain first insight into the variation in traits induced by a non-bacterial food source, we study Pristionchus-fungi interactions under laboratory conditions. After screening different yeast strains, we were able to maintain P. pacificus for at least 50-60 generations on Cryptococcus albidus and Cryptococcus curvatus. We describe life history traits of P. pacificus on both yeast strains, including developmental timing, survival and brood size. Despite a slight developmental delay and problems to digest yeast cells, which are both reflected at a transcriptomic level, all analyses support the potential of Cryptococcus strains as food source for P. pacificus. In summary, our work establishes two Cryptococcus strains as alternative food source for P. pacificus and shows change in various developmental, physiological and morphological traits, including the transcriptomic profiles.
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Affiliation(s)
- Gaurav V. Sanghvi
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Praveen Baskaran
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Waltraud Röseler
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, Tübingen, Germany
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13
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Meyer JM, Markov GV, Baskaran P, Herrmann M, Sommer RJ, Rödelsperger C. Draft Genome of the Scarab Beetle Oryctes borbonicus on La Réunion Island. Genome Biol Evol 2016; 8:2093-105. [PMID: 27289092 PMCID: PMC4987105 DOI: 10.1093/gbe/evw133] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Beetles represent the largest insect order and they display extreme morphological, ecological and behavioral diversity, which makes them ideal models for evolutionary studies. Here, we present the draft genome of the scarab beetle Oryctes borbonicus, which has a more basal phylogenetic position than the two previously sequenced pest species Tribolium castaneum and Dendroctonus ponderosae providing the potential for sequence polarization. Oryctes borbonicus is endemic to La Réunion, an island located in the Indian Ocean, and is the host of the nematode Pristionchus pacificus, a well-established model organism for integrative evolutionary biology. At 518 Mb, the O. borbonicus genome is substantially larger and encodes more genes than T. castaneum and D. ponderosae. We found that only 25% of the predicted genes of O. borbonicus are conserved as single copy genes across the nine investigated insect genomes, suggesting substantial gene turnover within insects. Even within beetles, up to 21% of genes are restricted to only one species, whereas most other genes have undergone lineage-specific duplications and losses. We illustrate lineage-specific duplications using detailed phylogenetic analysis of two gene families. This study serves as a reference point for insect/coleopteran genomics, although its original motivation was to find evidence for potential horizontal gene transfer (HGT) between O. borbonicus and P. pacificus. The latter was previously shown to be the recipient of multiple horizontally transferred genes including some genes from insect donors. However, our study failed to provide any clear evidence for additional HGTs between the two species.
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Affiliation(s)
- Jan M Meyer
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Gabriel V Markov
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany Present address: Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227 Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff Cedex, France
| | - Praveen Baskaran
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Matthias Herrmann
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany
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14
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Gyawali P, Beale DJ, Ahmed W, Karpe AV, Magalhaes RJS, Morrison PD, Palombo EA. Determination of Ancylostoma caninum ova viability using metabolic profiling. Parasitol Res 2016; 115:3485-92. [PMID: 27236650 DOI: 10.1007/s00436-016-5112-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/04/2016] [Indexed: 01/05/2023]
Abstract
Differentiation between viable and non-viable hookworm ova in environmental samples is necessary in order to implement strategies to mitigate re-infections in endemic regions. In this study, an untargeted metabolic profiling method was developed that utilised gas chromatography-mass spectrometry (GC-MS) in order to investigate hookworm ova viability. Ancylostoma caninum was used to investigate the metabolites within viable and non-viable ova. Univariate and multivariate statistical analyses of the data resulted in the identification of 53 significant metabolites across all hookworm ova samples. The major compounds observed in viable and non-viable hookworm ova were tetradecanoic acid, commonly known as myristic acid [fold change (FC) = 0.4], and dodecanoic acid, commonly known as lauric acid (FC = 0.388). Additionally, the viable ova had self-protecting metabolites such as prostaglandins, a typical feature absent in non-viable ova. The results of this study demonstrate that metabolic profiling using GC-MS methods can be used to determine the viability of canine hookworm ova. Further studies are needed to assess the applicability of metabolic profiling using GC-MS to detect viable hookworm ova in the mixed (viable and non-viable) populations from environmental samples and identify the metabolites specific to human hookworm species.
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Affiliation(s)
- P Gyawali
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, Queensland, 4102, Australia. .,School of Public Health, University of Queensland, Herston Road, Brisbane, Queensland, 4006, Australia.
| | - D J Beale
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, Queensland, 4102, Australia
| | - W Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, Queensland, 4102, Australia
| | - A V Karpe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, Queensland, 4102, Australia.,Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, 3122, Australia
| | - R J Soares Magalhaes
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, 4343, Australia.,Children's Health Research Centre, The University of Queensland, South Brisbane, Queensland, 4101, Australia
| | - P D Morrison
- Australian Centre for Research on Separation Science (ACROSS), School of Applied Sciences, RMIT University, Melbourne, Victoria, 3001, Australia
| | - E A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, Victoria, 3122, Australia
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15
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Markov GV, Meyer JM, Panda O, Artyukhin AB, Claaßen M, Witte H, Schroeder FC, Sommer RJ. Functional Conservation and Divergence of daf-22 Paralogs in Pristionchus pacificus Dauer Development. Mol Biol Evol 2016; 33:2506-14. [PMID: 27189572 DOI: 10.1093/molbev/msw090] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Small-molecule signaling in nematode dauer formation has emerged as a major model to study chemical communication in development and evolution. Developmental arrest as nonfeeding and stress-resistant dauer larvae represents the major survival and dispersal strategy. Detailed studies in Caenorhabditis elegans and Pristionchus pacificus revealed that small-molecule communication changes rapidly in evolution resulting in extreme structural diversity of small-molecule compounds. In C. elegans, a blend of ascarosides constitutes the dauer pheromone, whereas the P. pacificus dauer pheromone includes additional paratosides and integrates building blocks from diverse primary metabolic pathways. Despite this complexity of small-molecule structures and functions, little is known about the biosynthesis of small molecules in nematodes outside C. elegans Here, we show that the genes encoding enzymes of the peroxisomal β-oxidation pathway involved in small-molecule biosynthesis evolve rapidly, including gene duplications and domain switching. The thiolase daf-22, the most downstream factor in C. elegans peroxisomal β-oxidation, has duplicated in P. pacificus, resulting in Ppa-daf-22.1, which still contains the sterol-carrier-protein (SCP) domain that was lost in C. elegans daf-22, and Ppa-daf-22.2. Using the CRISPR/Cas9 system, we induced mutations in both P. pacificus daf-22 genes and identified an unexpected complexity of functional conservation and divergence. Under well-fed conditions, ascaroside biosynthesis proceeds exclusively via Ppa-daf-22.1 In contrast, starvation conditions induce Ppa-daf-22.2 activity, resulting in the production of a specific subset of ascarosides. Gene expression studies indicate a reciprocal up-regulation of both Ppa-daf-22 genes, which is, however, independent of starvation. Thus, our study reveals an unexpected functional complexity of dauer development and evolution.
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Affiliation(s)
- Gabriel V Markov
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Jan M Meyer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Oishika Panda
- Boyce Thompson Institute, Cornell University Department of Chemistry and Chemical Biology, Cornell University
| | | | - Marc Claaßen
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Hanh Witte
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
| | - Frank C Schroeder
- Boyce Thompson Institute, Cornell University Department of Chemistry and Chemical Biology, Cornell University
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, Germany
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Haemonchus contortus: Genome Structure, Organization and Comparative Genomics. ADVANCES IN PARASITOLOGY 2016; 93:569-98. [PMID: 27238013 DOI: 10.1016/bs.apar.2016.02.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model.
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Microevolution of Duplications and Deletions and Their Impact on Gene Expression in the Nematode Pristionchus pacificus. PLoS One 2015; 10:e0131136. [PMID: 26125626 PMCID: PMC4488370 DOI: 10.1371/journal.pone.0131136] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/27/2015] [Indexed: 11/19/2022] Open
Abstract
The evolution of diversity across the animal kingdom has been accompanied by tremendous gene loss and gain. While comparative genomics has been fruitful to characterize differences in gene content across highly diverged species, little is known about the microevolution of structural variations that cause these differences in the first place. In order to investigate the genomic impact of structural variations, we made use of genomic and transcriptomic data from the nematode Pristionchus pacificus, which has been established as a satellite model to Caenorhabditis elegans for comparative biology. We exploit the fact that P. pacificus is a highly diverse species for which various genomic data including the draft genome of a sister species P. exspectatus is available. Based on resequencing coverage data for two natural isolates we identified large (> 2kb) deletions and duplications relative to the reference strain. By restriction to completely syntenic regions between P. pacificus and P. exspectatus, we were able to polarize the comparison and to assess the impact of structural variations on expression levels. We found that while loss of genes correlates with lack of expression, duplication of genes has virtually no effect on gene expression. Further investigating expression of individual copies at sites that segregate between the duplicates, we found in the majority of cases only one of the copies to be expressed. Nevertheless, we still find that certain gene classes are strongly depleted in deletions as well as duplications, suggesting evolutionary constraint acting on synteny. In summary, our results are consistent with a model, where most structural variations are either deleterious or neutral and provide first insights into the microevolution of structural variations in the P. pacificus genome.
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