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Lenuzzi M, Witte H, Riebesell M, Rödelsperger C, Hong RL, Sommer RJ. Influence of environmental temperature on mouth-form plasticity in Pristionchus pacificus acts through daf-11-dependent cGMP signaling. J Exp Zool B Mol Dev Evol 2023; 340:214-224. [PMID: 34379868 DOI: 10.1002/jez.b.23094] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/14/2021] [Accepted: 07/30/2021] [Indexed: 12/16/2022]
Abstract
Mouth-form plasticity in the nematode Pristionchus pacificus has become a powerful system to identify the genetic and molecular mechanisms associated with developmental (phenotypic) plasticity. In particular, the identification of developmental switch genes that can sense environmental stimuli and reprogram developmental processes has confirmed long-standing evolutionary theory. However, how these genes are involved in the direct sensing of the environment, or if the switch genes act downstream of another, primary environmental sensing mechanism, remains currently unknown. Here, we study the influence of environmental temperature on mouth-form plasticity. We find that environmental temperature does influence mouth-form plasticity in most of the 10 wild isolates of P. pacificus tested in this study. We used one of these strains, P. pacificus RSA635, for detailed molecular analysis. Using forward and reverse genetic technology including CRISPR/Cas9, we show that mutations in the guanylyl cyclase Ppa-daf-11, the Ppa-daf-25/AnkMy2, and the cyclic nucleotide-gated channel Ppa-tax-2 eliminate the response to elevated temperatures. Together, our study indicates that DAF-11, DAF-25, and TAX-2 have been co-opted for environmental sensing during mouth-form plasticity regulation in P. pacificus.
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Affiliation(s)
- Maša Lenuzzi
- 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
| | - Metta Riebesell
- 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
| | - Ray L Hong
- Department of Biology, California State University, Northridge, California, USA
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Moreno E, Lightfoot JW, Lenuzzi M, Sommer RJ. Cilia drive developmental plasticity and are essential for efficient prey detection in predatory nematodes. Proc Biol Sci 2019; 286:20191089. [PMID: 31575374 DOI: 10.1098/rspb.2019.1089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cilia are complex organelles involved in a broad array of functions in eukaryotic organisms. Nematodes employ cilia for environmental sensing, which shapes developmental decisions and influences morphologically plastic traits and adaptive behaviours. Here, we assess the role of cilia in the nematode Pristionchus pacificus, and determine their importance in regulating the developmentally plastic mouth-form decision in addition to predatory feeding and self-recognition behaviours, all of which are not present in Caenorhabditis elegans. An analysis of a multitude of cilia-related mutants including representatives of the six protein subcomplexes required in intraflagellar transport (IFT) plus the regulatory factor X transcription factor daf-19 revealed that cilia are essential for processing the external cues influencing the mouth-form decision and for the efficient detection of prey. Surprisingly, we observed that loss-of-function mutations in the different IFT components resulted in contrasting mouth-form phenotypes and different degrees of predation deficiencies. This observation supports the idea that perturbing different IFT subcomplexes has different effects on signalling downstream of the cilium. Finally, self-recognition was maintained in the cilia deficient mutants tested, indicating that the mechanisms triggering self-recognition in P. pacificus may not require the presence of fully functional cilia.
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Affiliation(s)
- Eduardo Moreno
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - James W Lightfoot
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Maša Lenuzzi
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
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Moreno E, Lenuzzi M, Rödelsperger C, Prabh N, Witte H, Roeseler W, Riebesell M, Sommer RJ. DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in
Pristionchus pacificus. Evol Dev 2018; 20:233-243. [DOI: 10.1111/ede.12271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eduardo Moreno
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Maša Lenuzzi
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Neel Prabh
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Hanh Witte
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Waltraud Roeseler
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Metta Riebesell
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
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