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Broitman-Maduro G, Maduro MF. Evolutionary Change in Gut Specification in Caenorhabditis Centers on the GATA Factor ELT-3 in an Example of Developmental System Drift. J Dev Biol 2023; 11:32. [PMID: 37489333 PMCID: PMC10366740 DOI: 10.3390/jdb11030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Cells in a developing animal embryo become specified by the activation of cell-type-specific gene regulatory networks. The network that specifies the gut in the nematode Caenorhabditis elegans has been the subject of study for more than two decades. In this network, the maternal factors SKN-1/Nrf and POP-1/TCF activate a zygotic GATA factor cascade consisting of the regulators MED-1,2 → END-1,3 → ELT-2,7, leading to the specification of the gut in early embryos. Paradoxically, the MED, END, and ELT-7 regulators are present only in species closely related to C. elegans, raising the question of how the gut can be specified without them. Recent work found that ELT-3, a GATA factor without an endodermal role in C. elegans, acts in a simpler ELT-3 → ELT-2 network to specify gut in more distant species. The simpler ELT-3 → ELT-2 network may thus represent an ancestral pathway. In this review, we describe the elucidation of the gut specification network in C. elegans and related species and propose a model by which the more complex network might have formed. Because the evolution of this network occurred without a change in phenotype, it is an example of the phenomenon of Developmental System Drift.
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Affiliation(s)
- Gina Broitman-Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - Morris F Maduro
- Department of Molecular, Cell, and Systems Biology, University of California-Riverside, Riverside, CA 92521, USA
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2
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Ding Q, Ren X, Li R, Chan L, Ho VWS, Bi Y, Xie D, Zhao Z. Highly efficient transgenesis with miniMos in Caenorhabditis briggsae. G3 (BETHESDA, MD.) 2022; 12:jkac254. [PMID: 36171682 PMCID: PMC9713419 DOI: 10.1093/g3journal/jkac254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Caenorhabditis briggsae as a companion species for Caenorhabditis elegans has played an increasingly important role in study of evolution of development and genome and gene regulation. Aided by the isolation of its sister spices, it has recently been established as a model for speciation study. To take full advantage of the species for comparative study, an effective transgenesis method especially those with single-copy insertion is important for functional comparison. Here, we improved a transposon-based transgenesis methodology that had been originally developed in C. elegans but worked marginally in C. briggsae. By incorporation of a heat shock step, the transgenesis efficiency in C. briggsae with a single-copy insertion is comparable to that in C. elegans. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over the C. briggsae genome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility between C. briggsae and Caenorhabditis nigoni when combined with the GFP tags we generated previously. Finally, we demonstrated that C. briggsae tolerates the C. elegans toxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array.
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Affiliation(s)
- Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Luyan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Vincy W S Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Bi
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
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3
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Broitman-Maduro G, Sun S, Kikuchi T, Maduro MF. The GATA factor ELT-3 specifies endoderm in Caenorhabditis angaria in an ancestral gene network. Development 2022; 149:277064. [PMID: 36196618 PMCID: PMC9720673 DOI: 10.1242/dev.200984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Endoderm specification in Caenorhabditis elegans occurs through a network in which maternally provided SKN-1/Nrf, with additional input from POP-1/TCF, activates the GATA factor cascade MED-1,2→END-1,3→ELT-2,7. Orthologues of the MED, END and ELT-7 factors are found only among nematodes closely related to C. elegans, raising the question of how gut is specified in their absence in more distant species in the genus. We find that the C. angaria, C. portoensis and C. monodelphis orthologues of the GATA factor gene elt-3 are expressed in the early E lineage, just before their elt-2 orthologues. In C. angaria, Can-pop-1(RNAi), Can-elt-3(RNAi) and a Can-elt-3 null mutation result in a penetrant ‘gutless’ phenotype. Can-pop-1 is necessary for Can-elt-3 activation, showing that it acts upstream. Forced early E lineage expression of Can-elt-3 in C. elegans can direct the expression of a Can-elt-2 transgene and rescue an elt-7 end-1 end-3; elt-2 quadruple mutant strain to viability. Our results demonstrate an ancestral mechanism for gut specification and differentiation in Caenorhabditis involving a simpler POP-1→ELT-3→ELT-2 gene network.
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Affiliation(s)
- Gina Broitman-Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki 2 Department of Infectious Diseases , , 5200 Kihara, Miyazaki 889-1692 , Japan
- Graduate School of Frontier Sciences, The University of Tokyo 3 Department of Integrated Biosciences , , Chiba 277-8562 , Japan
| | - Morris F. Maduro
- University of California 1 Department of Molecular, Cell and Systems Biology , , Riverside, CA 92521 , USA
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Wong MK, Ho VWS, Huang X, Chan LY, Xie D, Li R, Ren X, Guan G, Ma Y, Hu B, Yan H, Zhao Z. Initial characterization of gap phase introduction in every cell cycle of C. elegans embryogenesis. Front Cell Dev Biol 2022; 10:978962. [PMID: 36393848 PMCID: PMC9641140 DOI: 10.3389/fcell.2022.978962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Early embryonic cell cycles usually alternate between S and M phases without any gap phase. When the gap phases are developmentally introduced in various cell types remains poorly defined especially during embryogenesis. To establish the cell-specific introduction of gap phases in embryo, we generate multiple fluorescence ubiquitin cell cycle indicators (FUCCI) in C. elegans. Time-lapse 3D imaging followed by lineal expression profiling reveals sharp and differential accumulation of the FUCCI reporters, allowing the systematic demarcation of cell cycle phases throughout embryogenesis. Accumulation of the reporters reliably identifies both G1 and G2 phases only in two embryonic cells with an extended cell cycle length, suggesting that the remaining cells divide either without a G1 phase, or with a brief G1 phase that is too short to be picked up by our reporters. In summary, we provide an initial picture of gap phase introduction in a metazoan embryo. The newly developed FUCCI reporters pave the way for further characterization of developmental control of cell cycle progression.
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Affiliation(s)
- Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, Xi’an, China
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Boyi Hu
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Hong Yan
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- *Correspondence: Zhongying Zhao,
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5
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Velazco-Cruz L, Ross JA. Genetic architecture and temporal analysis of Caenorhabditis briggsae hybrid developmental delay. PLoS One 2022; 17:e0272843. [PMID: 35951524 PMCID: PMC9371335 DOI: 10.1371/journal.pone.0272843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/27/2022] [Indexed: 11/18/2022] Open
Abstract
Identifying the alleles that reduce hybrid fitness is a major goal in the study of speciation genetics. It is rare to identify systems in which hybrid incompatibilities with minor phenotypic effects are segregating in genetically diverse populations of the same biological species. Such traits do not themselves cause reproductive isolation but might initiate the process. In the nematode Caenorhabditis briggsae, a small percent of F2 generation hybrids between two natural populations suffer from developmental delay, in which adulthood is reached after approximately 33% more time than their wild-type siblings. Prior efforts to identify the genetic basis for this hybrid incompatibility assessed linkage using one or two genetic markers on chromosome III and suggested that delay is caused by a toxin-antidote element. Here, we have genotyped F2 hybrids using multiple chromosome III markers to refine the developmental delay locus. Also, to better define the developmental delay phenotype, we measured the development rate of 66 F2 hybrids and found that delay is not restricted to a particular larval developmental stage. Deviation of the developmental delay frequency from hypothetical expectations for a toxin-antidote element adds support to the assertion that the epistatic interaction is not fully penetrant. Our mapping and refinement of the delay phenotype motivates future efforts to study the genetic architecture of hybrid dysfunction between genetically distinct populations of one species by identifying the underlying loci.
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Affiliation(s)
- Leonardo Velazco-Cruz
- Department of Biology, California State University, Fresno, California, United States of America
| | - Joseph A. Ross
- Department of Biology, California State University, Fresno, California, United States of America
- * E-mail:
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6
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Xie D, Ye P, Ma Y, Li Y, Liu X, Sarkies P, Zhao Z. Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfing Caenorhabditis nematode. Genome Res 2022; 32:2015-2027. [PMID: 36351773 PMCID: PMC9808620 DOI: 10.1101/gr.277205.122] [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: 08/14/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Different modes of reproduction evolve rapidly, with important consequences for genome composition. Selfing species often occupy a similar niche as their outcrossing sister species with which they are able to mate and produce viable hybrid progeny, raising the question of how they maintain genomic identity. Here, we investigate this issue by using the nematode Caenorhabditis briggsae, which reproduces as a hermaphrodite, and its outcrossing sister species Caenorhabditis nigoni We hypothesize that selfing species might develop some barriers to prevent gene intrusions through gene regulation. We therefore examined gene regulation in the hybrid F2 embryos resulting from reciprocal backcrosses between F1 hybrid progeny and C. nigoni or C. briggsae F2 hybrid embryos with ∼75% of their genome derived from C. briggsae (termed as bB2) were inviable, whereas those with ∼75% of their genome derived from C. nigoni (termed as nB2) were viable. Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of the C. briggsae genome is strongly affected by genetic exchanges with its outcrossing sister species, C. nigoni, whereas regulation of the C. nigoni genome is more robust on genetic exchange with C. briggsae The results provide new insights into how selfing species might maintain their identity despite genetic exchanges with closely related outcrossing species.
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Affiliation(s)
- Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Pohao Ye
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yongbin Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiao Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, OX1 4BH, United Kingdom
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China;,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
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Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade in Caenorhabditis Endoderm Specification. G3-GENES GENOMES GENETICS 2020; 10:333-356. [PMID: 31740453 PMCID: PMC6945043 DOI: 10.1534/g3.119.400724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene regulatory networks and their evolution are important in the study of animal development. In the nematode, Caenorhabditis elegans, the endoderm (gut) is generated from a single embryonic precursor, E. Gut is specified by the maternal factor SKN-1, which activates the MED → END-1,3 → ELT-2,7 cascade of GATA transcription factors. In this work, genome sequences from over two dozen species within the Caenorhabditis genus are used to identify MED and END-1,3 orthologs. Predictions are validated by comparison of gene structure, protein conservation, and putative cis-regulatory sites. All three factors occur together, but only within the Elegans supergroup, suggesting they originated at its base. The MED factors are the most diverse and exhibit an unexpectedly extensive gene amplification. In contrast, the highly conserved END-1 orthologs are unique in nearly all species and share extended regions of conservation. The END-1,3 proteins share a region upstream of their zinc finger and an unusual amino-terminal poly-serine domain exhibiting high codon bias. Compared with END-1, the END-3 proteins are otherwise less conserved as a group and are typically found as paralogous duplicates. Hence, all three factors are under different evolutionary constraints. Promoter comparisons identify motifs that suggest the SKN-1, MED, and END factors function in a similar gut specification network across the Elegans supergroup that has been conserved for tens of millions of years. A model is proposed to account for the rapid origin of this essential kernel in the gut specification network, by the upstream intercalation of duplicate genes into a simpler ancestral network.
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8
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Haag ES, Fitch DHA, Delattre M. From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes. Genetics 2018; 210:397-433. [PMID: 30287515 PMCID: PMC6216592 DOI: 10.1534/genetics.118.300243] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | | | - Marie Delattre
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS, INSERM, Ecole Normale Supérieure de Lyon, 69007, France
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9
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Chen L, Ho VWS, Wong MK, Huang X, Chan LY, Ng HCK, Ren X, Yan H, Zhao Z. Establishment of Signaling Interactions with Cellular Resolution for Every Cell Cycle of Embryogenesis. Genetics 2018; 209:37-49. [PMID: 29567658 PMCID: PMC5937172 DOI: 10.1534/genetics.118.300820] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022] Open
Abstract
Intercellular signaling interactions play a key role in breaking fate symmetry during animal development. Identification of signaling interactions at cellular resolution is technically challenging, especially in a developing embryo. Here, we develop a platform that allows automated inference and validation of signaling interactions for every cell cycle of Caenorhabditis elegans embryogenesis. This is achieved by the generation of a systems-level cell contact map, which consists of 1114 highly confident intercellular contacts, by modeling analysis and is validated through cell membrane labeling coupled with cell lineage analysis. We apply the map to identify cell pairs between which a Notch signaling interaction takes place. By generating expression patterns for two ligands and two receptors of the Notch signaling pathway with cellular resolution using the automated expression profiling technique, we are able to refine existing and identify novel Notch interactions during C. elegans embryogenesis. Targeted cell ablation followed by cell lineage analysis demonstrates the roles of signaling interactions during cell division in breaking fate symmetry. Finally, we describe the development of a website that allows online access to the cell-cell contact map for mapping of other signaling interactions by the community. The platform can be adapted to establish cellular interactions from any other signaling pathway.
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Affiliation(s)
- Long Chen
- Department of Electronic Engineering, City University of Hong Kong, China
| | | | - Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, China
| | - Xiaotai Huang
- School of Computer Science and Technology, Xidian University, Xi'an, 710126 China
| | - Lu-Yan Chan
- Department of Biology, Hong Kong Baptist University, China
| | | | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, China
| | - Hong Yan
- Department of Electronic Engineering, City University of Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, China
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10
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Comparative proteome analysis between C . briggsae embryos and larvae reveals a role of chromatin modification proteins in embryonic cell division. Sci Rep 2017; 7:4296. [PMID: 28655887 PMCID: PMC5487359 DOI: 10.1038/s41598-017-04533-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/16/2017] [Indexed: 11/12/2022] Open
Abstract
Caenorhabditis briggsae has emerged as a model for comparative biology against model organism C. elegans. Most of its cell fate specifications are completed during embryogenesis whereas its cell growth is achieved mainly in larval stages. The molecular mechanism underlying the drastic developmental changes is poorly understood. To gain insights into the molecular changes between the two stages, we compared the proteomes between the two stages using iTRAQ. We identified a total of 2,791 proteins in the C. briggsae embryos and larvae, 247 of which undergo up- or down-regulation between the two stages. The proteins that are upregulated in the larval stages are enriched in the Gene Ontology categories of energy production, protein translation, and cytoskeleton; whereas those upregulated in the embryonic stage are enriched in the categories of chromatin dynamics and posttranslational modification, suggesting a more active chromatin modification in the embryos than in the larva. Perturbation of a subset of chromatin modifiers followed by cell lineage analysis suggests their roles in controlling cell division pace. Taken together, we demonstrate a general molecular switch from chromatin modification to metabolism during the transition from C. briggsae embryonic to its larval stages using iTRAQ approach. The switch might be conserved across metazoans.
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11
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Differing roles for sur-2/MED23 in C. elegans and C. briggsae vulval development. Dev Genes Evol 2017; 227:213-218. [PMID: 28220250 DOI: 10.1007/s00427-017-0577-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/08/2017] [Indexed: 10/20/2022]
Abstract
Normal vulval development in the nematode Caenorhabditis briggsae is identical to that in the related Caenorhabditis elegans. However, several experiments suggest that there are differences between the two species with respect to the contribution of EGF/Ras signaling. To investigate these differences genetically, we have characterized a C. briggsae mutant strain that phenocopies the effect observed when C. briggsae animals are treated with U0126, an inhibitor of the EGF pathway component MEK. We identify that the gene affected in the mutant strain is Cbr-sur-2, which encodes a MED23 mediator complex protein that acts downstream of EGF signaling in C. elegans and other organisms, such as mammals. When Cbr-sur-2 and Cel-sur-2 mutants are compared, we find that the production of additional vulval cells from P5.p and P7.p in C. elegans is dependent on proper development of P6.p, while C. briggsae does not have a similar requirement. Combined chemical and genetic interference with the EGF pathway completely eliminates vulval development in C. elegans but not in C. briggsae. Our results provide genetic evidence for the differing requirements for EGF signaling in the two species.
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12
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Metheetrairut C, Adams BD, Nallur S, Weidhaas JB, Slack FJ. cel-mir-237 and its homologue, hsa-miR-125b, modulate the cellular response to ionizing radiation. Oncogene 2017; 36:512-524. [PMID: 27321180 PMCID: PMC5173455 DOI: 10.1038/onc.2016.222] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/13/2016] [Accepted: 05/13/2016] [Indexed: 02/06/2023]
Abstract
Elucidating the mechanisms involved in sensitizing radioresistant tumors to ionizing radiation (IR) treatments while minimizing injury to surrounding normal tissue is an important clinical goal. Due to their sequence-derived specificity and properties as gene regulators in IR-affected pathways, microRNAs (miRNAs) could serve as adjuvant therapeutic agents that alter cellular sensitivity to radiation treatment. To identify radiosensitizing miRNAs, we initially utilized the Caenorhabditis elegans vulval cell model, an in vivo system developed to study IR-dependent radiosensitivity as a measure of clonogenic cell death. We tested several candidate miRNA-deletion mutants post γ-irradiation and identified cel-mir-237 as a miRNA which when deleted caused animals to be more resistant to IR, whereas cel-mir-237 overexpressing strains were IR sensitive. In addition, wild-type animals downregulated cel-mir-237 levels post IR in a time-dependent manner. We identified jun-1 (JUN transcription factor homolog) as a novel target of cel-mir-237. Specifically, jun-1 transcript levels increased in wild-type animals post γ-irradiation, and loss of cel-mir-237 also resulted in higher jun-1 expression. As expected, loss of jun-1 resulted in IR sensitivity, similar to the phenotype of cel-mir-237 overexpressors. As miR-237 is the homolog of human miR-125, we validated our findings in MCF-7 and MDA-MB-231 breast cancer cell lines, which harbor lower hsa-miR-125b levels than normal human mammary epithelial cells (HMECs). Forced expression of hsa-miR-125b in these cells resulted in radiosensitivity, as seen by reduced clonogenic survival, enhanced apoptotic activity and enhanced senescence post IR. Finally, re-expression of c-JUN in MDA-MB-231 cells promoted radioresistance and abrogated miR-125-mediated radiosensitization. Our findings suggest that overexpression of cel-mir-237 and its homolog, hsa-miR-125b, functions as sensitizers to γ-irradiation in both a nematode in vivo model and breast cancer cells, and could potentially be utilized as an adjuvant therapeutic to enhance radiation sensitivity.
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Affiliation(s)
- Chanatip Metheetrairut
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Brian D. Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Institute for RNA Medicine, Department of Pathology, BIDMC Cancer Center/Harvard Medical School, Boston, MA 02215, USA
| | - Sunitha Nallur
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Joanne B. Weidhaas
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Frank J. Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Institute for RNA Medicine, Department of Pathology, BIDMC Cancer Center/Harvard Medical School, Boston, MA 02215, USA
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13
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Attreed M, Saied-Santiago K, Bülow HE. Conservation of anatomically restricted glycosaminoglycan structures in divergent nematode species. Glycobiology 2016; 26:862-870. [PMID: 26976619 PMCID: PMC5018047 DOI: 10.1093/glycob/cww037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 11/14/2022] Open
Abstract
Heparan sulfates (HS) are glycosaminoglycans of the extracellular matrices and characterized by complex modification patterns owing to sulfations, epimerization, and acetylation. Distinct HS modification patterns have been shown to modulate protein-protein interactions during development in general and of the nervous system in particular. This has led to the heparan sulfate code hypothesis, which posits that specifically modified HS epitopes are distributed in a tissue and cell-specific fashion to orchestrate neural circuit formation. Whether an HS code exists in vivo, how specific or how evolutionarily conserved the anatomical distribution of an HS code may be has remained unknown. Here we conduct a systematic comparison of HS modification patterns in the nematode Caenorhabditis elegans using transgenic expression of 33 different HS-specific single chain variable fragment antibodies. We find that some HS modification patterns are widely distributed in the nervous system. In contrast, other HS modification patterns appear highly cell-specific in both non-neuronal and neuronal cells. Some patterns can be as restricted in their localization as to single neurites or synaptic connections between two neurons. This restricted anatomical localization of specific HS patterns can be evolutionarily conserved over a span of 80-100 million years in the divergent nematode species Caenorhabditis briggsae suggesting structural and, possibly functional conservation of glycosaminoglycan structures similar to proteins. These findings suggest a HS code with subcellularly localized, unique glycan identities in the nervous system.
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Affiliation(s)
| | | | - Hannes E Bülow
- Department of Genetics
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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14
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Wong MK, Guan D, Ng KHC, Ho VWS, An X, Li R, Ren X, Zhao Z. Timing of Tissue-specific Cell Division Requires a Differential Onset of Zygotic Transcription during Metazoan Embryogenesis. J Biol Chem 2016; 291:12501-12513. [PMID: 27056332 DOI: 10.1074/jbc.m115.705426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 12/20/2022] Open
Abstract
Metazoan development demands not only precise cell fate differentiation but also accurate timing of cell division to ensure proper development. How cell divisions are temporally coordinated during development is poorly understood. Caenorhabditis elegans embryogenesis provides an excellent opportunity to study this coordination due to its invariant development and widespread division asynchronies. One of the most pronounced asynchronies is a significant delay of cell division in two endoderm progenitor cells, Ea and Ep, hereafter referred to as E2, relative to its cousins that mainly develop into mesoderm organs and tissues. To unravel the genetic control over the endoderm-specific E2 division timing, a total of 822 essential and conserved genes were knocked down using RNAi followed by quantification of cell cycle lengths using in toto imaging of C. elegans embryogenesis and automated lineage. Intriguingly, knockdown of numerous genes encoding the components of general transcription pathway or its regulatory factors leads to a significant reduction in the E2 cell cycle length but an increase in cell cycle length of the remaining cells, indicating a differential requirement of transcription for division timing between the two. Analysis of lineage-specific RNA-seq data demonstrates an earlier onset of transcription in endoderm than in other germ layers, the timing of which coincides with the birth of E2, supporting the notion that the endoderm-specific delay in E2 division timing demands robust zygotic transcription. The reduction in E2 cell cycle length is frequently associated with cell migration defect and gastrulation failure. The results suggest that a tissue-specific transcriptional activation is required to coordinate fate differentiation, division timing, and cell migration to ensure proper development.
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Affiliation(s)
- Ming-Kin Wong
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Daogang Guan
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Kaoru Hon Chun Ng
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Xiaomeng An
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
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15
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Ward JD. Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes. Genetics 2015; 201:1279-94. [PMID: 26644478 PMCID: PMC4676526 DOI: 10.1534/genetics.115.182717] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/20/2015] [Indexed: 12/14/2022] Open
Abstract
Recent and rapid advances in genetic and molecular tools have brought spectacular tractability to Caenorhabditis elegans, a model that was initially prized because of its simple design and ease of imaging. C. elegans has long been a powerful model in biomedical research, and tools such as RNAi and the CRISPR/Cas9 system allow facile knockdown of genes and genome editing, respectively. These developments have created an additional opportunity to tackle one of the most debilitating burdens on global health and food security: parasitic nematodes. I review how development of nonparasitic nematodes as genetic models informs efforts to import tools into parasitic nematodes. Current tools in three commonly studied parasites (Strongyloides spp., Brugia malayi, and Ascaris suum) are described, as are tools from C. elegans that are ripe for adaptation and the benefits and barriers to doing so. These tools will enable dissection of a huge array of questions that have been all but completely impenetrable to date, allowing investigation into host-parasite and parasite-vector interactions, and the genetic basis of parasitism.
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Affiliation(s)
- Jordan D Ward
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158
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16
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Chang CC, Rodriguez J, Ross J. Mitochondrial-Nuclear Epistasis Impacts Fitness and Mitochondrial Physiology of Interpopulation Caenorhabditis briggsae Hybrids. G3 (BETHESDA, MD.) 2015; 6:209-19. [PMID: 26585825 PMCID: PMC4704720 DOI: 10.1534/g3.115.022970] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/16/2015] [Indexed: 12/18/2022]
Abstract
In order to identify the earliest genetic changes that precipitate species formation, it is useful to study genetic incompatibilities that cause only mild dysfunction when incompatible alleles are combined in an interpopulation hybrid. Such hybridization within the nematode species Caenorhabditis briggsae has been suggested to result in selection against certain combinations of nuclear and mitochondrial alleles, raising the possibility that mitochondrial-nuclear (mitonuclear) epistasis reduces hybrid fitness. To test this hypothesis, cytoplasmic-nuclear hybrids (cybrids) were created to purposefully disrupt any epistatic interactions. Experimental analysis of the cybrids suggests that mitonuclear discord can result in decreased fecundity, increased lipid content, and increased mitochondrial reactive oxygen species levels. Many of these effects were asymmetric with respect to cross direction, as expected if cytoplasmic-nuclear Dobzhansky-Muller incompatibilities exist. One such effect is consistent with the interpretation that disrupting coevolved mitochondrial and nuclear loci impacts mitochondrial function and organismal fitness. These findings enhance efforts to study the genesis, identity, and maintenance of genetic incompatibilities that precipitate the speciation process.
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Affiliation(s)
- Chih-Chiun Chang
- Department of Biology, California State University, Fresno, California, 93740
| | - Joel Rodriguez
- Department of Biology, California State University, Fresno, California, 93740
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California, 93740
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17
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Maduro MF. 20 Years of unc-119 as a transgene marker. WORM 2015; 4:e1046031. [PMID: 26430568 PMCID: PMC4588520 DOI: 10.1080/21624054.2015.1046031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/08/2015] [Accepted: 04/23/2015] [Indexed: 01/01/2023]
Abstract
This fall marks 20 years since the cloning of unc-119 was reported. Despite having a strong phenotype that makes animals somewhat difficult to grow and handle, unc-119 mutant rescue has become one of the most frequently-used markers for C. elegans transformation. In this Commentary, I describe the history of how unc-119 rescue traveled through the worm community, contributing to the development of transgene methods in C. elegans.
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Affiliation(s)
- Morris F Maduro
- Biology Department; University of California, Riverside ; Riverside, CA USA
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18
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A Genome-wide hybrid incompatibility landscape between Caenorhabditis briggsae and C. nigoni. PLoS Genet 2015; 11:e1004993. [PMID: 25692300 PMCID: PMC4334894 DOI: 10.1371/journal.pgen.1004993] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/08/2015] [Indexed: 11/19/2022] Open
Abstract
Systematic characterization of ẖybrid incompatibility (HI) between related species remains the key to understanding speciation. The genetic basis of HI has been intensively studied in Drosophila species, but remains largely unknown in other species, including nematodes, which is mainly due to the lack of a sister species with which C. elegans can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has opened up the possibility of dissecting the genetic basis of HI in nematode species. However, the paucity of dominant and visible marker prevents the efficient mapping of HI loci between the two species. To elucidate the genetic basis of speciation in nematode species, we first generated 96 chromosomally integrated GFP markers in the C. briggsae genome and mapped them into the defined locations by PCR and Next-Generation Sequencing (NGS). Aided by the marker, we backcrossed the GFP-associated C. briggsae genomic fragments into C. nigoni for at least 15 generations and produced 111 independent introgressions. The introgression fragments cover most of the C. briggsae genome. We finally dissected the patterns of HI by scoring the embryonic lethality, larval arrest, sex ratio and male sterility for each introgression line, through which we identified pervasive HI loci and produced a genome-wide landscape of HI between the two nematode species, the first of its type for any non-Drosophila species. The HI data not only provided insights into the genetic basis of speciation, but also established a framework for the possible cloning of HI loci between the two nematode species. Furthermore, the data on hybrids confirmed Haldane’s rule and suggested the presence of a large X effect in terms of fertility between the two species. Importantly, this work opens a new avenue for studying speciation genetics between nematode species and allows parallel comparison of the HI with that in Drosophila and other species. Hybrid incompatibility (HI) has been intensively studied among Drosophila species, but remains largely unknown in other species. Model organism is a species of choice for the HI study because these species provide sophisticated molecular and genetic tools for illustrating mechanism underlying a given HI. C. elegans as a model organism contributed little to the field due to the lack of a sister species with which it can mate and produce viable progeny. The recent discovery of a C. briggsae sister species, C. nigoni, has made it possible to study the HI between nematode species. However, the paucity of molecular and genetic tools in both species inhibits their use in such studies. To empower the use of this species pair in HI studies, we first created a collection of fluorescent markers over the C. briggsae genome to facilitate the directional introduction of the marker-associated C. briggsae genomic fragments into the C. nigoni background. We next mapped the marker insertion sites and introduced the markers into C. nigoni by repeated crossings. Finally, we generated a genome-wide HI landscape between the two species by scoring the HI phenotypes of their hybrid progeny. The study not only provides an invaluable resource for the molecular cloning of HI loci between C. briggsae and C. nigoni, but also permits comparative analysis of speciation genetics between nematode and other species.
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19
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Sharanya D, Fillis CJ, Kim J, Zitnik EM, Ward KA, Gallagher ME, Chamberlin HM, Gupta BP. Mutations in Caenorhabditis briggsae identify new genes important for limiting the response to EGF signaling during vulval development. Evol Dev 2015; 17:34-48. [PMID: 25627712 DOI: 10.1111/ede.12105] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Studies of vulval development in the nematode C. elegans have identified many genes that are involved in cell division and differentiation processes. Some of these encode components of conserved signal transduction pathways mediated by EGF, Notch, and Wnt. To understand how developmental mechanisms change during evolution, we are doing a comparative analysis of vulva formation in C. briggsae, a species that is closely related to C. elegans. Here, we report 14 mutations in 7 Multivulva (Muv) genes in C. briggsae that inhibit inappropriate division of vulval precursors. We have developed a new efficient and cost-effective gene mapping method to localize Muv mutations to small genetic intervals on chromosomes, thus facilitating cloning and functional studies. We demonstrate the utility of our method by determining molecular identities of three of the Muv genes that include orthologs of Cel-lin-1 (ETS) and Cel-lin-31 (Winged-Helix) of the EGF-Ras pathway and Cel-pry-1 (Axin), of the Wnt pathway. The remaining four genes reside in regions that lack orthologs of known C. elegans Muv genes. Inhibitor studies demonstrate that the Muv phenotype of all four new genes is dependent on the activity of the EGF pathway kinase, MEK. One of these, Cbr-lin(gu167), shows modest increase in the expression of Cbr-lin-3/EGF compared to wild type. These results argue that while Cbr-lin(gu167) may act upstream of Cbr-lin-3/EGF, the other three genes influence the EGF pathway downstream or in parallel to Cbr-lin-3. Overall, our findings demonstrate that the genetic program underlying a conserved developmental process includes both conserved and divergent functional contributions.
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Affiliation(s)
- Devika Sharanya
- Department of Biology, McMaster University, Hamilton, ON, Canada
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20
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Frokjaer-Jensen C, Davis MW, Sarov M, Taylor J, Flibotte S, LaBella M, Pozniakovski A, Moerman DG, Jorgensen EM. Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon. Nat Methods 2014; 11:529-34. [PMID: 24820376 PMCID: PMC4126194 DOI: 10.1038/nmeth.2889] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/29/2014] [Indexed: 12/22/2022]
Abstract
We have generated a recombinant Mos1 transposon that can insert up to 45-kb transgenes into the Caenorhabditis elegans genome. The minimal Mos1 transposon (miniMos) is 550 bp long and inserts DNA into the genome at high frequency (~60% of injected animals). Genetic and antibiotic markers can be used for selection, and the transposon is active in C. elegans isolates and Caenorhabditis briggsae. We used the miniMos transposon to generate six universal Mos1-mediated single-copy insertion (mosSCI) landing sites that allow targeted transgene insertion with a single targeting vector into permissive expression sites on all autosomes. We also generated two collections of strains: a set of bright fluorescent insertions that are useful as dominant, genetic balancers and a set of lacO insertions to track genome position.
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Affiliation(s)
- Christian Frokjaer-Jensen
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
- Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, Copenhagen, Denmark
| | - M Wayne Davis
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
| | - Mihail Sarov
- TransgeneOmics, Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Jon Taylor
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew LaBella
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
| | - Andrei Pozniakovski
- TransgeneOmics, Max Planck Institute of Molecular Cell Biology and Genetics, D-01307 Dresden, Germany
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erik M Jorgensen
- Howard Hughes Medical Institute, University of Utah, Salt Lake City, Utah, USA
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
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21
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Verster AJ, Ramani AK, McKay SJ, Fraser AG. Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function. PLoS Genet 2014; 10:e1004077. [PMID: 24516395 PMCID: PMC3916228 DOI: 10.1371/journal.pgen.1004077] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/18/2013] [Indexed: 01/27/2023] Open
Abstract
Although two related species may have extremely similar phenotypes, the genetic networks underpinning this conserved biology may have diverged substantially since they last shared a common ancestor. This is termed Developmental System Drift (DSD) and reflects the plasticity of genetic networks. One consequence of DSD is that some orthologous genes will have evolved different in vivo functions in two such phenotypically similar, related species and will therefore have different loss of function phenotypes. Here we report an RNAi screen in C. elegans and C. briggsae to identify such cases. We screened 1333 genes in both species and identified 91 orthologues that have different RNAi phenotypes. Intriguingly, we find that recently evolved genes of unknown function have the fastest evolving in vivo functions and, in several cases, we identify the molecular events driving these changes. We thus find that DSD has a major impact on the evolution of gene function and we anticipate that the C. briggsae RNAi library reported here will drive future studies on comparative functional genomics screens in these nematodes.
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Affiliation(s)
- Adrian J. Verster
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Arun K. Ramani
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sheldon J. McKay
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Andrew G. Fraser
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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22
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Liu Q, Haag ES. Evolutionarily dynamic roles of a PUF RNA-binding protein in the somatic development of Caenorhabditis briggsae. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:129-41. [PMID: 24254995 DOI: 10.1002/jez.b.22550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/19/2013] [Accepted: 10/18/2013] [Indexed: 11/12/2022]
Abstract
Gene duplication and divergence has emerged as an important aspect of developmental evolution. The genomes of Caenorhabditis nematodes encode an ancient family of PUF RNA-binding proteins. Most have been implicated in germline development, and are often redundant with paralogs of the same sub-family. An exception is Cbr-puf-2 (one of three Caenorhabditis briggsae PUF-2 sub-family paralogs), which is required for development past the second larval stage. Here, we provide a detailed functional characterization of Cbr-puf-2. The larval arrest of Cbr-puf-2 mutant animals is caused by inefficient breakdown of bacterial food, which leads to starvation. Cbr-puf-2 is required for the normal grinding cycle of the muscular terminal bulb during early larval stages, and is transiently expressed in this tissue. In addition, rescue of larval arrest reveals that Cbr-puf-2 also promotes normal vulval development. It is expressed in the anchor cell (which induces vulval fate) and vulval muscles, but not in the vulva precursor cells (VPCs) themselves. This contrasts with the VPC-autonomous repression of vulval development described for the Caenorhabditis elegans homologs fbf-1/2. These different roles for PUF proteins occur even as the vulva and pharynx maintain highly conserved anatomies across Caenorhabditis, indicating pervasive developmental system drift (DSD). Because Cbr-PUF-2 shares RNA-binding specificity with its paralogs and with C. elegans FBF, we suggest that functional novelty of RNA-binding proteins evolves through changes in the site of their expression, perhaps in concert with cis-regulatory evolution in target mRNAs.
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Affiliation(s)
- Qinwen Liu
- Department of Biology, University of Maryland, College Park, Maryland
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23
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Riche S, Zouak M, Argoul F, Arneodo A, Pecreaux J, Delattre M. Evolutionary comparisons reveal a positional switch for spindle pole oscillations in Caenorhabditis embryos. ACTA ACUST UNITED AC 2013; 201:653-62. [PMID: 23690175 PMCID: PMC3664713 DOI: 10.1083/jcb.201210110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In one-cell stage embryos of different worm species, a conserved positional switch controls the onset of mitotic spindle oscillations, whereas the maximum amplitude of oscillations is determined by the time spent in the oscillating phase. During the first embryonic division in Caenorhabditis elegans, the mitotic spindle is pulled toward the posterior pole of the cell and undergoes vigorous transverse oscillations. We identified variations in spindle trajectories by analyzing the outwardly similar one-cell stage embryo of its close relative Caenorhabditis briggsae. Compared with C. elegans, C. briggsae embryos exhibit an anterior shifting of nuclei in prophase and reduced anaphase spindle oscillations. By combining physical perturbations and mutant analysis in both species, we show that differences can be explained by interspecies changes in the regulation of the cortical Gα–GPR–LIN-5 complex. However, we found that in both species (1) a conserved positional switch controls the onset of spindle oscillations, (2) GPR posterior localization may set this positional switch, and (3) the maximum amplitude of spindle oscillations is determined by the time spent in the oscillating phase. By investigating microevolution of a subcellular process, we identify new mechanisms that are instrumental to decipher spindle positioning.
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Affiliation(s)
- Soizic Riche
- Laboratory of Molecular Biology of the Cell, UMR5239, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, 69007 Lyon, France
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24
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Sharanya D, Thillainathan B, Marri S, Bojanala N, Taylor J, Flibotte S, Moerman DG, Waterston RH, Gupta BP. Genetic control of vulval development in Caenorhabditis briggsae. G3 (BETHESDA, MD.) 2012; 2:1625-41. [PMID: 23275885 PMCID: PMC3516484 DOI: 10.1534/g3.112.004598] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/19/2012] [Indexed: 01/23/2023]
Abstract
The nematode Caenorhabditis briggsae is an excellent model organism for the comparative analysis of gene function and developmental mechanisms. To study the evolutionary conservation and divergence of genetic pathways mediating vulva formation, we screened for mutations in C. briggsae that cause the egg-laying defective (Egl) phenotype. Here, we report the characterization of 13 genes, including three that are orthologs of Caenorhabditis elegans unc-84 (SUN domain), lin-39 (Dfd/Scr-related homeobox), and lin-11 (LIM homeobox). Based on the morphology and cell fate changes, the mutants were placed into four different categories. Class 1 animals have normal-looking vulva and vulva-uterine connections, indicating defects in other components of the egg-laying system. Class 2 animals frequently lack some or all of the vulval precursor cells (VPCs) due to defects in the migration of P-cell nuclei into the ventral hypodermal region. Class 3 animals show inappropriate fusion of VPCs to the hypodermal syncytium, leading to a reduced number of vulval progeny. Finally, class 4 animals exhibit abnormal vulval invagination and morphology. Interestingly, we did not find mutations that affect VPC induction and fates. Our work is the first study involving the characterization of genes in C. briggsae vulva formation, and it offers a basis for future investigations of these genes in C. elegans.
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Affiliation(s)
- Devika Sharanya
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Sujatha Marri
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | | | - Jon Taylor
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephane Flibotte
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Donald G. Moerman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Robert H. Waterston
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065
| | - Bhagwati P. Gupta
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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25
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Yan C, Bi Y, Yin D, Zhao Z. A method for rapid and simultaneous mapping of genetic loci and introgression sizes in nematode species. PLoS One 2012; 7:e43770. [PMID: 22952761 PMCID: PMC3432054 DOI: 10.1371/journal.pone.0043770] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 07/25/2012] [Indexed: 12/24/2022] Open
Abstract
Caenorhabditis briggsae is emerging as an attractive model organism not only in studying comparative biology against C. elegans, but also in developing novel experimentation avenues. In particular, recent identification of a new Caenorhabditis species, C. sp.9 with which it can mate and produce viable progeny provides an opportunity for studying the genetics of hybrid incompatibilities (HI) between the two. Mapping of a specific HI locus demands repeated backcrossing to get hold of the specific genomic region underlying an observed phenotype. To facilitate mapping of HI loci between C. briggsae and C. sp.9, an efficient mapping method and a genetic map ideally consisting of dominant markers are required for systematic introgression of genomic fragments between the two species. We developed a fast and cost-effective method for high throughput mapping of dominant loci with resolution up to 1 million bps in C. briggsae. The method takes advantage of the introgression between C. briggsae and C. sp.9 followed by PCR genotyping using C. briggsae specific primers. Importantly, the mapping results can not only serve as an effective way for estimating the chromosomal position of a genetic locus in C. briggsae, but also provides size information for the introgression fragment in an otherwise C. sp.9 background. In addition, it also helps generate introgression line as a side-product that is invaluable for the subsequent mapping of HI loci. The method will greatly facilitate the construction of a genetic map consisting of dominant markers and pave the way for systematic isolation of HI loci between C. briggsae and C. sp.9 which has so far not been attempted between nematode species. The method is designed for mapping of a dominant allele, but can be easily adapted for mapping of any other type of alleles in any other species if introgression between a sister species pair is feasible.
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Affiliation(s)
| | | | | | - Zhongying Zhao
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
- * E-mail:
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26
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Rutter MT, Cross KV, Van Woert PA. Birth, death and subfunctionalization in the Arabidopsis genome. TRENDS IN PLANT SCIENCE 2012; 17:204-12. [PMID: 22326563 DOI: 10.1016/j.tplants.2012.01.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/12/2012] [Accepted: 01/16/2012] [Indexed: 05/08/2023]
Abstract
Arabidopsis thaliana is now a model system, not just for plant biology but also for comparative genomics. The completion of the sequences of two closely related species, Arabidopsis lyrata and Brassica rapa, is complemented by genomic comparisons among A. thaliana accessions and mutation accumulation lines. Together these genomic data document the birth of new genes via gene duplication, transposon exaptation and de novo formation of new genes from noncoding sequence. Most novel loci exhibit low expression, and are undergoing pseudogenization or subfunctionalization. Comparatively, A. thaliana has lost large amounts of sequence through deletion, particularly of transposable elements. Intraspecific genomic variation indicates high rates of deletion mutations and deletion polymorphisms across accessions, shedding light on the history of Arabidopsis genome architecture.
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Affiliation(s)
- Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, SC 29401, USA.
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27
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Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination. PLoS Genet 2011; 7:e1002174. [PMID: 21779179 PMCID: PMC3136444 DOI: 10.1371/journal.pgen.1002174] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 05/23/2011] [Indexed: 12/16/2022] Open
Abstract
The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.
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Abstract
The ability to manipulate the genome of organisms at will is perhaps the single most useful ability for the study of biological systems. Techniques for the generation of transgenics in the nematode Caenorhabditis elegans became available in the late 1980s. Since then, improvements to the original approach have been made to address specific limitations with transgene expression, expand on the repertoire of the types of biological information that transgenes can provide, and begin to develop methods to target transgenes to defined chromosomal locations. Many recent, detailed protocols have been published, and hence in this chapter, we will review various approaches to making C. elegans transgenics, discuss their applications, and consider their relative advantages and disadvantages. Comments will also be made on anticipated future developments and on the application of these methods to other nematodes.
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Affiliation(s)
- Vida Praitis
- Biology Department, Grinnell College, Grinnell, Iowa, USA
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Jones MR, Lohn Z, Rose AM. Specialized chromosomes and their uses in Caenorhabditis elegans. Methods Cell Biol 2011; 106:23-64. [PMID: 22118273 DOI: 10.1016/b978-0-12-544172-8.00002-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Research on Caenorhabditis elegans involves the use of a wide range of genetic and molecular tools consisting of chromosomal material captured and modified for specific purposes. These "specialized chromosomes" come in many forms ranging from relatively simple gene deletions to complex rearrangements involving endogenous chromosomes as well as transgenic constructs. In this chapter, we describe the specialized chromosomes that are available in C. elegans, their origins, practical considerations, and methods for generation and evaluation. We will summarize their uses for biological studies, and their contribution to our knowledge about chromosome biology.
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Affiliation(s)
- Martin R Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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An antibiotic selection marker for nematode transgenesis. Nat Methods 2010; 7:721-3. [DOI: 10.1038/nmeth.1494] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 06/14/2010] [Indexed: 11/08/2022]
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Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD, Gupta BP. A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics 2010; 11:236. [PMID: 20385026 PMCID: PMC2864247 DOI: 10.1186/1471-2164-11-236] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 04/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers. RESULTS We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3. CONCLUSIONS We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.
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Affiliation(s)
- Daniel C Koboldt
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Julia Staisch
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | - Karen Haines
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Scott E Baird
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA
| | - Helen M Chamberlin
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Eric S Haag
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Raymond D Miller
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Bhagwati P Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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