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Werner MS, Loschko T, King T, Reich S, Theska T, Franz-Wachtel M, Macek B, Sommer RJ. Histone 4 lysine 5/12 acetylation enables developmental plasticity of Pristionchus mouth form. Nat Commun 2023; 14:2095. [PMID: 37055396 PMCID: PMC10102330 DOI: 10.1038/s41467-023-37734-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
Development can be altered to match phenotypes with the environment, and the genetic mechanisms that direct such alternative phenotypes are beginning to be elucidated. Yet, the rules that govern environmental sensitivity vs. invariant development, and potential epigenetic memory, remain unknown. Here, we show that plasticity of nematode mouth forms is determined by histone 4 lysine 5 and 12 acetylation (H4K5/12ac). Acetylation in early larval stages provides a permissive chromatin state, which is susceptible to induction during the critical window of environmental sensitivity. As development proceeds deacetylation shuts off switch gene expression to end the critical period. Inhibiting deacetylase enzymes leads to fixation of prior developmental trajectories, demonstrating that histone modifications in juveniles can carry environmental information to adults. Finally, we provide evidence that this regulation was derived from an ancient mechanism of licensing developmental speed. Altogether, our results show that H4K5/12ac enables epigenetic regulation of developmental plasticity that can be stored and erased by acetylation and deacetylation, respectively.
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Affiliation(s)
- Michael S Werner
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Thomas King
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Shelley Reich
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Tobias Theska
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, 72076, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany.
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2
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Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces. Sci Rep 2022; 12:9725. [PMID: 35697683 PMCID: PMC9192688 DOI: 10.1038/s41598-022-13235-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/13/2022] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.
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Han Z, Sieriebriennikov B, Susoy V, Lo WS, Igreja C, Dong C, Berasategui A, Witte H, Sommer RJ. Horizontally acquired cellulases assist the expansion of dietary range in Pristionchus nematodes. Mol Biol Evol 2022; 39:6493351. [PMID: 34978575 PMCID: PMC8826503 DOI: 10.1093/molbev/msab370] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) enables the acquisition of novel traits via non-Mendelian inheritance of genetic material. HGT plays a prominent role in the evolution of prokaryotes, whereas in animals, HGT is rare and its functional significance is often uncertain. Here, we investigate horizontally acquired cellulase genes in the free-living nematode model organism Pristionchus pacificus. We show that these cellulase genes 1) are likely of eukaryotic origin, 2) are expressed, 3) have protein products that are secreted and functional, and 4) result in endo-cellulase activity. Using CRISPR/Cas9, we generated an octuple cellulase mutant, which lacks all eight cellulase genes and cellulase activity altogether. Nonetheless, this cellulase-null mutant is viable and therefore allows a detailed analysis of a gene family that was horizontally acquired. We show that the octuple cellulase mutant has associated fitness costs with reduced fecundity and slower developmental speed. Furthermore, by using various Escherichia coli K-12 strains as a model for cellulosic biofilms, we demonstrate that cellulases facilitate the procurement of nutrients from bacterial biofilms. Together, our analysis of cellulases in Pristionchus provides comprehensive evidence from biochemistry, genetics, and phylogeny, which supports the integration of horizontally acquired genes into the complex life history strategy of this soil nematode.
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Affiliation(s)
- Ziduan Han
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | | | - Vladislav Susoy
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Wen-Sui Lo
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Catia Igreja
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Chuanfu Dong
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | | | - Hanh Witte
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Tuebingen, 72076, Germany
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4
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Carstensen HR, Villalon RM, Banerjee N, Hallem EA, Hong RL. Steroid hormone pathways coordinate developmental diapause and olfactory remodeling in Pristionchus pacificus. Genetics 2021; 218:6272519. [PMID: 33963848 DOI: 10.1093/genetics/iyab071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 04/26/2021] [Indexed: 12/31/2022] Open
Abstract
Developmental and behavioral plasticity allow animals to prioritize alternative genetic programs during fluctuating environments. Behavioral remodeling may be acute in animals that interact with host organisms, since reproductive adults and the developmentally arrested larvae often have different ethological needs for chemical stimuli. To understand the genes that coordinate the development and host-seeking behavior, we used the entomophilic nematode Pristionchus pacificus to characterize dauer-constitutive mutants (Daf-c) that inappropriately enter developmental diapause to become dauer larvae. We found two Daf-c loci with dauer-constitutive and cuticle exsheathment phenotypes that can be rescued by the feeding of Δ7-dafachronic acid, and that are dependent on the conserved canonical steroid hormone receptor Ppa-DAF-12. Specifically at one locus, deletions in the sole hydroxysteroid dehydrogenase (HSD) in P. pacificus resulted in Daf-c phenotypes. Ppa-hsd-2 is expressed in the canal-associated neurons (CANs) and excretory cells whose homologous cells in Caenorhabditis elegans are not known to be involved in the dauer decision. While in wildtype only dauer larvae are attracted to host odors, hsd-2 mutant adults show enhanced attraction to the host beetle pheromone, along with ectopic activation of a marker for putative olfactory neurons, Ppa-odr-3. Surprisingly, this enhanced odor attraction acts independently of the Δ7-DA/DAF-12 module, suggesting that Ppa-HSD-2 may be responsible for several steroid hormone products involved in coordinating the dauer decision and host-seeking behavior in P. pacificus.
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Affiliation(s)
- Heather R Carstensen
- Department of Biology, California State University, Northridge, Northridge, CA 91330-8303, USA
| | - Reinard M Villalon
- Department of Biology, California State University, Northridge, Northridge, CA 91330-8303, USA
| | - Navonil Banerjee
- Department of Microbiology, Immunology & Molecular Genetics and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology & Molecular Genetics and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ray L Hong
- Department of Biology, California State University, Northridge, Northridge, CA 91330-8303, USA
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5
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Ishita Y, Chihara T, Okumura M. Different combinations of serotonin receptors regulate predatory and bacterial feeding behaviors in the nematode Pristionchus pacificus. G3-GENES GENOMES GENETICS 2021; 11:6104620. [PMID: 33598706 PMCID: PMC8022940 DOI: 10.1093/g3journal/jkab011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/28/2020] [Indexed: 11/23/2022]
Abstract
Feeding behavior is one of the most fundamental behaviors in animals, and regulation of this behavior is critical for proper food intake. The nematode Pristionchus pacificus exhibits dimorphism in feeding behavior, bacterial feeding and predatory feeding on other nematodes, and the latter behavior is assumed to be an evolutionarily novel behavior. Both types of feeding behavior are modulated by serotonin; however, the downstream mechanism that modulates these behaviors is still to be clarified. Here, we focused on serotonin receptors and examined their expression patterns in P. pacificus. We also generated knockout mutants of the serotonin receptors using the CRISPR/Cas9 system and examined feeding behaviors. We found that Ppa-ser-5 mutants and the Ppa-ser-1; Ppa-ser-7 double mutant decreased predation. Detailed observation of the pharyngeal movement revealed that the Ppa-ser-1; Ppa-ser-7 double mutant reduces tooth movement, which is required for efficient predatory feeding. Conversely, Ppa-ser-7 and Ppa-mod-1 mutants decreased bacterial feeding. This study revealed that specific combinations of serotonin receptors are essential for the modulation of these distinct feeding behaviors, providing insight into the evolution of neural pathways to regulate novel feeding behavior.
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Affiliation(s)
- Yuuki Ishita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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6
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Fanelli E, Troccoli A, De Luca F. Functional Variation of Two Novel Cellulases, Pv-eng-5 and Pv-eng-8, and the Heat Shock 90 Gene, Pv-hsp-90, in Pratylenchus vulnus and Their Expression in Response to Different Temperature Stress. Int J Mol Sci 2018; 20:E107. [PMID: 30597892 PMCID: PMC6337429 DOI: 10.3390/ijms20010107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 11/18/2022] Open
Abstract
Functional characterization of two novel endoglucanase genes, Pv-eng-5 and Pv-eng-8, of the root-lesion nematode Pratylenchus vulnus was carried out. In situ-hybridization experiments revealed that Pv-eng-8 transcript was localized in the pharyngeal glands. Silencing of Pv-eng-5 and Pv-eng-8 resulted in a significant reduction of expression level (52% and 67%, respectively). Furthermore, the silencing of Pv-eng-8 determined a reduction (41%) in nematode reproduction, suggesting that treated nematodes are much less able to process food. Surprisingly, no significant difference on reproduction rate was observed with Pv-eng-5 dsRNA nematodes, suggesting a neofunctionalization of Pv-eng-5 despite the high similarity with nematode endoglucanases. Pratylenchus species are poikilothermic organisms showing close relationships with the environmental temperature. The effects of different temperature ranges revealed that the reproductive potential of P. vulnus increased with increasing temperature from 23 °C to 28 °C, but no reproduction was observed at 33 °C. In real time, increasing temperature from 23 °C to 28 °C the heat shock gene Pv-hsp-90 was differentially expressed in adult stages, while the levels of the effector genes Pv-eng-1 and Pv-eng-8 in females showed no significant differences compared to those observed at 23 °C, only in males Pv-eng-8 level decreased (45%). The upregulation of Pv-hsp-90 in both adult stages suggests a protective mechanism in order to cope with unfavorable environmental conditions.
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Affiliation(s)
- Elena Fanelli
- Istituto per la Protezione Sostenibile delle Piante (IPSP), SS-Bari, Consiglio Nazionale delle Ricerche, (CNR), 70126 Bari, Italy.
| | - Alberto Troccoli
- Istituto per la Protezione Sostenibile delle Piante (IPSP), SS-Bari, Consiglio Nazionale delle Ricerche, (CNR), 70126 Bari, Italy.
| | - Francesca De Luca
- Istituto per la Protezione Sostenibile delle Piante (IPSP), SS-Bari, Consiglio Nazionale delle Ricerche, (CNR), 70126 Bari, Italy.
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7
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Bui LT, Ivers NA, Ragsdale EJ. A sulfotransferase dosage-dependently regulates mouthpart polyphenism in the nematode Pristionchus pacificus. Nat Commun 2018; 9:4119. [PMID: 30297689 PMCID: PMC6175886 DOI: 10.1038/s41467-018-05612-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/11/2018] [Indexed: 01/26/2023] Open
Abstract
Polyphenism, the extreme form of developmental plasticity, is the ability of a genotype to produce discrete morphologies matched to alternative environments. Because polyphenism is likely to be under switch-like molecular control, a comparative genetic approach could reveal the molecular targets of plasticity evolution. Here we report that the lineage-specific sulfotransferase SEUD-1, which responds to environmental cues, dosage-dependently regulates polyphenism of mouthparts in the nematode Pristionchus pacificus. SEUD-1 is expressed in cells producing dimorphic morphologies, thereby integrating an intercellular signalling mechanism at its ultimate target. Additionally, multiple alterations of seud-1 support it as a potential target for plasticity evolution. First, a recent duplication of seud-1 in a sister species reveals a direct correlation between genomic dosage and polyphenism threshold. Second, inbreeding to produce divergent polyphenism thresholds resulted in changes in transcriptional dosage of seud-1. Our study thus offers a genetic explanation for how plastic responses evolve.
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Affiliation(s)
- Linh T Bui
- Department of Biology, Indiana University, 915 E. 3rd St., Bloomington, IN, 47405, USA
| | - Nicholas A Ivers
- Department of Biology, Indiana University, 915 E. 3rd St., Bloomington, IN, 47405, USA
| | - Erik J Ragsdale
- Department of Biology, Indiana University, 915 E. 3rd St., Bloomington, IN, 47405, USA.
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8
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Namdeo S, Moreno E, Rödelsperger C, Baskaran P, Witte H, Sommer RJ. Two independent sulfation processes regulate mouth-form plasticity in the nematode Pristionchus pacificus. Development 2018; 145:145/13/dev166272. [PMID: 29967123 DOI: 10.1242/dev.166272] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/17/2018] [Indexed: 12/15/2022]
Abstract
Sulfation of biomolecules, like phosphorylation, is one of the most fundamental and ubiquitous biochemical modifications with important functions during detoxification. This process is reversible, involving two enzyme classes: a sulfotransferase, which adds a sulfo group to a substrate; and a sulfatase that removes the sulfo group. However, unlike phosphorylation, the role of sulfation in organismal development is poorly understood. In this study, we find that two independent sulfation events regulate the development of mouth morphology in the nematode Pristionchus pacificus. This nematode has the ability to form two alternative mouth morphologies depending on environmental cues, an example of phenotypic plasticity. We found that, in addition to a previously described sulfatase, a sulfotransferase is involved in regulating the mouth-form dimorphism in P. pacificus However, it is unlikely that both of these sulfation-associated enzymes act upon the same substrates, as they are expressed in different cell types. Furthermore, animals mutant in genes encoding both enzymes show condition-dependent epistatic interactions. Thus, our study highlights the role of sulfation-associated enzymes in phenotypic plasticity of mouth structures in Pristionchus.
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Affiliation(s)
- Suryesh Namdeo
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Eduardo Moreno
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Praveen Baskaran
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Hanh Witte
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
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9
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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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10
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Werner MS, Sieriebriennikov B, Loschko T, Namdeo S, Lenuzzi M, Dardiry M, Renahan T, Sharma DR, Sommer RJ. Environmental influence on Pristionchus pacificus mouth form through different culture methods. Sci Rep 2017; 7:7207. [PMID: 28775277 PMCID: PMC5543044 DOI: 10.1038/s41598-017-07455-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/28/2017] [Indexed: 12/29/2022] Open
Abstract
Environmental cues can impact development to elicit distinct phenotypes in the adult. The consequences of phenotypic plasticity can have profound effects on morphology, life cycle, and behavior to increase the fitness of the organism. The molecular mechanisms governing these interactions are beginning to be elucidated in a few cases, such as social insects. Nevertheless, there is a paucity of systems that are amenable to rigorous experimentation, preventing both detailed mechanistic insight and the establishment of a generalizable conceptual framework. The mouth dimorphism of the model nematode Pristionchus pacificus offers the rare opportunity to examine the genetics, genomics, and epigenetics of environmental influence on developmental plasticity. Yet there are currently no easily tunable environmental factors that affect mouth-form ratios and are scalable to large cultures required for molecular biology. Here we present a suite of culture conditions to toggle the mouth-form phenotype of P. pacificus. The effects are reversible, do not require the costly or labor-intensive synthesis of chemicals, and proceed through the same pathways previously examined from forward genetic screens. Different species of Pristionchus exhibit different responses to culture conditions, demonstrating unique gene-environment interactions, and providing an opportunity to study environmental influence on a macroevolutionary scale.
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Affiliation(s)
- Michael S Werner
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Tobias Loschko
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Suryesh Namdeo
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Masa Lenuzzi
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Mohannad Dardiry
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Tess Renahan
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Devansh Raj Sharma
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
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12
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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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13
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Prabh N, Rödelsperger C. Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs? BMC Bioinformatics 2016; 17:226. [PMID: 27245157 PMCID: PMC4888513 DOI: 10.1186/s12859-016-1102-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/24/2016] [Indexed: 12/26/2022] Open
Abstract
Background Current genome sequencing projects reveal substantial numbers of taxonomically restricted, so called orphan genes that lack homology with genes from other evolutionary lineages. However, it is not clear to what extent orphan genes are real, genomic artifacts, or represent non-coding RNAs. Results Here, we use a simple set of assumptions to test the nature of orphan genes. First, a sequence that is transcribed is considered a real biological entity. Second, every sequence that is supported by proteome data or shows a depletion of non-synonymous substitutions is a protein-coding gene. Using genomic, transcriptomic and proteomic data for the nematode Pristionchus pacificus, we show that between 4129–7997 (42–81 %) of predicted orphan genes are expressed and 3818–7545 (39–76 %) of orphan genes are under negative selection. In three cases that exhibited strong evolutionary constraint but lacked expression evidence in 14 RNA-seq samples, we could experimentally validate the predicted gene structures. Comparing different data sets to infer selection on orphan gene clusters, we find that the presence of a closely related genome provides the most powerful resource to robustly identify evidence of negative selection. However, even in the absence of other genomic data, the availability of paralogous sequences was enough to show negative selection in 8–10 % of orphan genes. Conclusions Our study shows that the great majority of previously identified orphan genes in P. pacificus are indeed protein-coding genes. Even though this work represents a case study on a single species, our approach can be transferred to genomic data of other non-model organisms in order to ascertain the protein-coding nature of orphan genes.
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Affiliation(s)
- Neel Prabh
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany.
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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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Baskaran P, Rödelsperger C, Prabh N, Serobyan V, Markov GV, Hirsekorn A, Dieterich C. Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus. BMC Evol Biol 2015; 15:185. [PMID: 26370559 PMCID: PMC4570658 DOI: 10.1186/s12862-015-0466-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/14/2015] [Indexed: 12/28/2022] Open
Abstract
Background The development of multicellular organisms is accompanied by gene expression changes in differentiating cells. Profiling stage-specific expression during development may reveal important insights into gene sets that contributed to the morphological diversity across the animal kingdom. Results We sequenced RNA-seq libraries throughout a developmental timecourse of the nematode Pristionchus pacificus. The transcriptomes reflect early larval stages, adult worms including late larvae, and growth-arrested dauer larvae and allowed the identification of developmentally regulated gene clusters. Our data reveals similar trends as previous transcriptome profiling of dauer worms and represents the first expression data for early larvae in P. pacificus. Gene expression clusters characterizing early larval stages show most significant enrichments of chaperones, while collagens are most significantly enriched in transcriptomes of late larvae and adult worms. By combining expression data with phylogenetic analysis, we found that developmentally regulated genes are found in paralogous clusters that have arisen through lineage-specific duplications after the split from the Caenorhabditis elegans branch. Conclusions We propose that gene duplications of developmentally regulated genes represent a plausible evolutionary mechanism to increase the dosage of stage-specific expression. Consequently, this may contribute to the substantial divergence in expression profiles that has been observed across larger evolutionary time scales. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0466-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Praveen Baskaran
- Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.
| | - Christian Rödelsperger
- Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.
| | - Neel Prabh
- Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.
| | - Vahan Serobyan
- Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.
| | - Gabriel V Markov
- Max-Planck Institute for Developmental Biology, Spemannstr. 35, Tübingen, 72076, Germany.
| | - Antje Hirsekorn
- Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, Berlin-Buch, 13125, Germany.
| | - Christoph Dieterich
- Max-Planck Institute for Biology of Aging, Joseph-Stelzmann-Str. 9b, Köln, 50866, Germany.
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Szydlowski L, Boschetti C, Crisp A, Barbosa E, Tunnacliffe A. Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae. Gene 2015; 566:125-37. [DOI: 10.1016/j.gene.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
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Abstract
Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals.
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Affiliation(s)
- Luis Boto
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional Ciencias Naturales. CSIC, , C/ José Gutierrez Abascal 2, 28006 Madrid, Spain
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Figueiredo J, Simões MJ, Gomes P, Barroso C, Pinho D, Conceição L, Fonseca L, Abrantes I, Pinheiro M, Egas C. Assessment of the geographic origins of pinewood nematode isolates via single nucleotide polymorphism in effector genes. PLoS One 2013; 8:e83542. [PMID: 24391785 PMCID: PMC3877046 DOI: 10.1371/journal.pone.0083542] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 11/05/2013] [Indexed: 11/18/2022] Open
Abstract
The pinewood nematode, Bursaphelenchus xylophilus, is native to North America but it only causes damaging pine wilt disease in those regions of the world where it has been introduced. The accurate detection of the species and its dispersal routes are thus essential to define effective control measures. The main goals of this study were to analyse the genetic diversity among B. xylophilus isolates from different geographic locations and identify single nucleotide polymorphism (SNPs) markers for geographic origin, through a comparative transcriptomic approach. The transcriptomes of seven B. xylophilus isolates, from Continental Portugal (4), China (1), Japan (1) and USA (1), were sequenced in the next generation platform Roche 454. Analysis of effector gene transcripts revealed inter-isolate nucleotide diversity that was validated by Sanger sequencing in the genomic DNA of the seven isolates and eight additional isolates from different geographic locations: Madeira Island (2), China (1), USA (1), Japan (2) and South Korea (2). The analysis identified 136 polymorphic positions in 10 effector transcripts. Pairwise comparison of the 136 SNPs through Neighbor-Joining and the Maximum Likelihood methods and 5-mer frequency analysis with the alignment-independent bilinear multivariate modelling approach correlated the SNPs with the isolates geographic origin. Furthermore, the SNP analysis indicated a closer proximity of the Portuguese isolates to the Korean and Chinese isolates than to the Japanese or American isolates. Each geographic cluster carried exclusive alleles that can be used as SNP markers for B. xylophilus isolate identification.
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Affiliation(s)
- Joana Figueiredo
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Maria José Simões
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Paula Gomes
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Cristina Barroso
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Diogo Pinho
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Luci Conceição
- IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Luís Fonseca
- IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- IMAR-CMA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Miguel Pinheiro
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Conceição Egas
- Genoinseq, Next Generation Sequencing Unit, Biocant, Cantanhede, Portugal
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Hansen AK, Moran NA. The impact of microbial symbionts on host plant utilization by herbivorous insects. Mol Ecol 2013; 23:1473-1496. [PMID: 23952067 DOI: 10.1111/mec.12421] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/02/2013] [Accepted: 06/12/2013] [Indexed: 01/18/2023]
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Sommer RJ, McGaughran A. The nematode Pristionchus pacificus as a model system for integrative studies in evolutionary biology. Mol Ecol 2013; 22:2380-93. [PMID: 23530614 DOI: 10.1111/mec.12286] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/06/2023]
Abstract
Comprehensive studies of evolution have historically been hampered by the division among disciplines. Now, as biology moves towards an '-omics' era, it is more important than ever to tackle the evolution of function and form by considering all those research areas involved in the regulation of phenotypes. Here, we review recent attempts to establish the nematode Pristionchus pacificus as a model organism that allows integrative studies of development and evo-devo, with ecology and population genetics. Originally developed for comparative study with the nematode Caenorhabditis elegans, P. pacificus provided insight into developmental pathways including dauer formation, vulva and gonad development, chemosensation, innate immunity and neurobiology. Its subsequent discovery across a wide geographic distribution in association with scarab beetles enabled its evaluation in a biogeographic context. Development of an evolutionary field station on La Réunion Island, where P. pacificus is present in high abundance across a number of widespread habitat types, allows examination of the microfacets of evolution - processes of natural selection, adaptation and drift among populations can now be examined in this island setting. The combination of laboratory-based functional studies with fieldwork in P. pacificus has the long-term prospective to provide both proximate (mechanistic) and ultimate (evolutionary and ecological) causation and might therefore help to overcome the long-term divide between major areas in biology.
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Affiliation(s)
- Ralf J Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Tübingen, Germany.
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Rybarczyk-Mydłowska K, Maboreke HR, van Megen H, van den Elsen S, Mooyman P, Smant G, Bakker J, Helder J. Rather than by direct acquisition via lateral gene transfer, GHF5 cellulases were passed on from early Pratylenchidae to root-knot and cyst nematodes. BMC Evol Biol 2012; 12:221. [PMID: 23171084 PMCID: PMC3575306 DOI: 10.1186/1471-2148-12-221] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant parasitic nematodes are unusual Metazoans as they are equipped with genes that allow for symbiont-independent degradation of plant cell walls. Among the cell wall-degrading enzymes, glycoside hydrolase family 5 (GHF5) cellulases are relatively well characterized, especially for high impact parasites such as root-knot and cyst nematodes. Interestingly, ancestors of extant nematodes most likely acquired these GHF5 cellulases from a prokaryote donor by one or multiple lateral gene transfer events. To obtain insight into the origin of GHF5 cellulases among evolutionary advanced members of the order Tylenchida, cellulase biodiversity data from less distal family members were collected and analyzed. RESULTS Single nematodes were used to obtain (partial) genomic sequences of cellulases from representatives of the genera Meloidogyne, Pratylenchus, Hirschmanniella and Globodera. Combined Bayesian analysis of ≈ 100 cellulase sequences revealed three types of catalytic domains (A, B, and C). Represented by 84 sequences, type B is numerically dominant, and the overall topology of the catalytic domain type shows remarkable resemblance with trees based on neutral (= pathogenicity-unrelated) small subunit ribosomal DNA sequences. Bayesian analysis further suggested a sister relationship between the lesion nematode Pratylenchus thornei and all type B cellulases from root-knot nematodes. Yet, the relationship between the three catalytic domain types remained unclear. Superposition of intron data onto the cellulase tree suggests that types B and C are related, and together distinct from type A that is characterized by two unique introns. CONCLUSIONS All Tylenchida members investigated here harbored one or multiple GHF5 cellulases. Three types of catalytic domains are distinguished, and the presence of at least two types is relatively common among plant parasitic Tylenchida. Analysis of coding sequences of cellulases suggests that root-knot and cyst nematodes did not acquire this gene directly by lateral genes transfer. More likely, these genes were passed on by ancestors of a family nowadays known as the Pratylenchidae.
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Affiliation(s)
- Katarzyna Rybarczyk-Mydłowska
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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