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Tate HM, Barone V, Schrankel CS, Hamdoun A, Lyons DC. Localization and origins of juvenile skeletogenic cells in the sea urchin Lytechinuspictus. Dev Biol 2024; 514:12-27. [PMID: 38862087 DOI: 10.1016/j.ydbio.2024.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024]
Abstract
The development of the sea urchin larval body plan is well understood from extensive studies of embryonic patterning. However, fewer studies have investigated the late larval stages during which the unique pentaradial adult body plan develops. Previous work on late larval development highlights major tissue changes leading up to metamorphosis, but the location of specific cell types during juvenile development is less understood. Here, we improve on technical limitations by applying highly sensitive hybridization chain reaction fluorescent in situ hybridization (HCR-FISH) to the fast-developing and transparent sea urchin Lytechinus pictus, with a focus on skeletogenic cells. First, we show that HCR-FISH can be used in L. pictus to precisely localize skeletogenic cells in the rudiment. In doing so, we provide a detailed staging scheme for the appearance of skeletogenic cells around the rudiment prior to and during biomineralization and show that many skeletogenic cells unassociated with larval rods localize outside of the rudiment prior to localizing inside. Second, we show that downstream biomineralization genes have similar expression patterns during larval and juvenile skeletogenesis, suggesting some conservation of skeletogenic mechanisms during development between stages. Third, we find co-expression of blastocoelar and skeletogenic cell markers around juvenile skeleton located outside of the rudiment, which is consistent with data showing that cells from the non-skeletogenic mesoderm embryonic lineage contribute to the juvenile skeletogenic cell lineage. This work sets the foundation for subsequent studies of other cell types in the late larva of L. pictus to better understand juvenile body plan development, patterning, and evolution.
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Affiliation(s)
- Heidi M Tate
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Vanessa Barone
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Catherine S Schrankel
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA; San Diego State University, San Diego, CA, USA
| | - Amro Hamdoun
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA.
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2
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Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR. An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients. Dev Biol 2024; 516:59-70. [PMID: 39098630 DOI: 10.1016/j.ydbio.2024.08.002] [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: 04/07/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/06/2024]
Abstract
Dicer substrate interfering RNAs (DsiRNAs) destroy targeted transcripts using the RNA-Induced Silencing Complex (RISC) through a process called RNA interference (RNAi). This process is ubiquitous among eukaryotes. Here we report the utility of DsiRNA in embryos of the sea urchin Lytechinus variegatus (Lv). Specific knockdowns phenocopy known morpholino and inhibitor knockdowns, and DsiRNA offers a useful alternative to morpholinos. Methods are described for the design of specific DsiRNAs that lead to destruction of targeted mRNA. DsiRNAs directed against pks1, an enzyme necessary for pigment production, show how successful DsiRNA perturbations are monitored by RNA in situ analysis and by qPCR to determine relative destruction of targeted mRNA. DsiRNA-based knockdowns phenocopy morpholino- and drug-based inhibition of nodal and lefty. Other knockdowns demonstrate that the RISC operates early in development as well as on genes that are first transcribed hours after gastrulation is completed. Thus, DsiRNAs effectively mediate destruction of targeted mRNA in the sea urchin embryo. The approach offers significant advantages over other widely used methods in the urchin in terms of cost, and ease of procurement, and offers sizeable experimental advantages in terms of ease of handling, injection, and knockdown validation.
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Affiliation(s)
- Keen Wilson
- University of Cincinnati, Blue Ash College, Biology Dept. 9555 Plainfield Rd., Blue Ash, Ohio; Department of Biology, Duke University, Durham, NC, USA
| | - Carl Manner
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | | | - David R McClay
- Department of Biology, Duke University, Durham, NC, USA.
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3
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Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR. An RNA interference approach for functional studies in the sea urchin and its use in analysis of Nodal signaling gradients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599930. [PMID: 38979202 PMCID: PMC11230266 DOI: 10.1101/2024.06.20.599930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Dicer substrate interfering RNAs (DsiRNAs) destroy targeted transcripts using the RNA-Induced Silencing Complex (RISC) through a process called RNA interference (RNAi). This process is ubiquitous among eukaryotes. Here we report the utility of DsiRNA in embryos of the sea urchin Lytechinus variagatus (Lv). Specific knockdowns phenocopy known morpholino and inhibitor knockdowns, and DsiRNA offers a useful alternative to morpholinos. Methods for designing and obtaining specific DsiRNAs that lead to destruction of targeted mRNA are described. DsiRNAs directed against pks1, an enzyme necessary for pigment production, show how successful DsiRNA perturbations are monitored by RNA in situ analysis and by qPCR to determine relative destruction of targeted mRNA. DsiRNA-based knockdowns phenocopy morpholino- and drug-based inhibition of nodal and lefty. Other knockdowns demonstrate that the RISC operates early in development as well as on genes that are first transcribed hours after gastrulation is completed. Thus, DsiRNAs effectively mediate destruction of targeted mRNA in the sea urchin embryo. The approach offers significant advantages over other widely used methods in the urchin in terms of cost, and ease of procurement, and offers sizeable experimental advantages in terms of ease of handling, injection, and knockdown validation.
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4
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Wessel GM, Xing L, Oulhen N. More than a colour; how pigment influences colourblind microbes. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230077. [PMID: 38497266 PMCID: PMC10945406 DOI: 10.1098/rstb.2023.0077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 03/19/2024] Open
Abstract
Many animals have pigments when they themselves cannot see colour. Perhaps those pigments enable the animal to avoid predators, or to attract mates. Maybe even those pigmented surfaces are hosts for microbes, even when the microbes do not see colour. Do some pigments then serve as a chemical signal for a good or bad microbial substrate? Maybe pigments attract or repel various microbe types? Echinoderms serve as an important model to test the mechanisms of pigment-based microbial interactions. Echinoderms are marine benthic organisms, ranging from intertidal habitats to depths of thousands of metres and are exposed to large varieties of microbes. They are also highly pigmented, with a diverse variety of colours between and even within species. Here we focus on one type of pigment (naphthoquinones) made by polyketide synthase, modified by flavin-dependent monoxygenases, and on one type of function, microbial interaction. Recent successes in targeted gene inactivation by CRISPR/Cas9 in sea urchins supports the contention that colour is more than it seems. Here we dissect the players, and their interactions to better understand how such host factors influence a microbial colonization. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Gary M. Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Nathalie Oulhen
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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5
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Lin Z, Li F, Krug PJ, Schmidt EW. The polyketide to fatty acid transition in the evolution of animal lipid metabolism. Nat Commun 2024; 15:236. [PMID: 38172109 PMCID: PMC10764717 DOI: 10.1038/s41467-023-44497-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Animals synthesize simple lipids using a distinct fatty acid synthase (FAS) related to the type I polyketide synthase (PKS) enzymes that produce complex specialized metabolites. The evolutionary origin of the animal FAS and its relationship to the diversity of PKSs remain unclear despite the critical role of lipid synthesis in cellular metabolism. Recently, an animal FAS-like PKS (AFPK) was identified in sacoglossan molluscs. Here, we explore the phylogenetic distribution of AFPKs and other PKS and FAS enzymes across the tree of life. We found AFPKs widely distributed in arthropods and molluscs (>6300 newly described AFPK sequences). The AFPKs form a clade with the animal FAS, providing an evolutionary link bridging the type I PKSs and the animal FAS. We found molluscan AFPK diversification correlated with shell loss, suggesting AFPKs provide a chemical defense. Arthropods have few or no PKSs, but our results indicate AFPKs contributed to their ecological and evolutionary success by facilitating branched hydrocarbon and pheromone biosynthesis. Although animal metabolism is well studied, surprising new metabolic enzyme classes such as AFPKs await discovery.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Feng Li
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA.
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Xing L, Wang L, Liu S, Sun L, Wessel GM, Yang H. Single-Cell Transcriptome and Pigment Biochemistry Analysis Reveals the Potential for the High Nutritional and Medicinal Value of Purple Sea Cucumbers. Int J Mol Sci 2023; 24:12213. [PMID: 37569587 PMCID: PMC10419132 DOI: 10.3390/ijms241512213] [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: 07/12/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The sea cucumber Apostichopus japonicus has important nutritional and medicinal value. Unfortunately, we know little of the source of active chemicals in this animal, but the plentiful pigments of these animals are thought to function in intriguing ways for translation into clinical and food chemistry usage. Here, we found key cell groups with the gene activity predicted for the color morphology of sea cucumber body using single-cell RNA-seq. We refer to these cell populations as melanocytes and quinocytes, which are responsible for the synthesis of melanin and quinone pigments, respectively. We integrated analysis of pigment biochemistry with the transcript profiles to illuminate the molecular mechanisms regulating distinct pigment formation in echinoderms. In concert with the correlated pigment analysis from each color morph, this study expands our understanding of medically important pigment production, as well as the genetic mechanisms for color morphs, and provides deep datasets for exploring advancements in the fields of bioactives and nutraceuticals.
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Affiliation(s)
- Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (L.X.); (S.L.); (H.Y.)
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lingyu Wang
- Department of Biology, Duke University, Durham, NC 27708, USA;
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (L.X.); (S.L.); (H.Y.)
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (L.X.); (S.L.); (H.Y.)
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gary M. Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (L.X.); (S.L.); (H.Y.)
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Yamakawa S, Yamazaki A, Morino Y, Wada H. Early expression onset of tissue-specific effector genes during the specification process in sea urchin embryos. EvoDevo 2023; 14:7. [PMID: 37101206 PMCID: PMC10131483 DOI: 10.1186/s13227-023-00210-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND In the course of animal developmental processes, various tissues are differentiated through complex interactions within the gene regulatory network. As a general concept, differentiation has been considered to be the endpoint of specification processes. Previous works followed this view and provided a genetic control scheme of differentiation in sea urchin embryos: early specification genes generate distinct regulatory territories in an embryo to express a small set of differentiation driver genes; these genes eventually stimulate the expression of tissue-specific effector genes, which provide biological identity to differentiated cells, in each region. However, some tissue-specific effector genes begin to be expressed in parallel with the expression onset of early specification genes, raising questions about the simplistic regulatory scheme of tissue-specific effector gene expression and the current concept of differentiation itself. RESULTS Here, we examined the dynamics of effector gene expression patterns during sea urchin embryogenesis. Our transcriptome-based analysis indicated that many tissue-specific effector genes begin to be expressed and accumulated along with the advancing specification GRN in the distinct cell lineages of embryos. Moreover, we found that the expression of some of the tissue-specific effector genes commences before cell lineage segregation occurs. CONCLUSIONS Based on this finding, we propose that the expression onset of tissue-specific effector genes is controlled more dynamically than suggested in the previously proposed simplistic regulation scheme. Thus, we suggest that differentiation should be conceptualized as a seamless process of accumulation of effector expression along with the advancing specification GRN. This pattern of effector gene expression may have interesting implications for the evolution of novel cell types.
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Affiliation(s)
- Shumpei Yamakawa
- Institute of Zoology and Evolutionary Research, Friedrich-Shiller University Jena, Erbertstraße 1, 07747, Jena, Germany.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Atsuko Yamazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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8
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Spurrell M, Oulhen N, Foster S, Perillo M, Wessel G. Gene regulatory divergence amongst echinoderms underlies appearance of pigment cells in sea urchin development. Dev Biol 2023; 494:13-25. [PMID: 36519720 PMCID: PMC9870932 DOI: 10.1016/j.ydbio.2022.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/14/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Larvae of the sea urchin, Strongylocentrotus purpuratus, have pigmented migratory cells implicated in immune defense and gut patterning. The transcription factor SpGcm activates the expression of many pigment cell-specific genes, including those involved in pigment biosynthesis (SpPks1 and SpFmo3) and immune related genes (e.g. SpMif5). Despite the importance of this cell type in sea urchins, pigmented cells are absent in larvae of the sea star, Patiria miniata. In this study, we tested the premises that sea stars lack genes to synthesize echinochrome pigment, that the genes are present but are not expressed in the larvae, or rather that the homologous gene expression does not contribute to echinochrome synthesis. Our results show that orthologs of sea urchin pigment cell-specific genes (PmPks1, PmFmo3-1 and PmMifL1-2) are present in the sea star genome and expressed in the larvae. Although no cell lineage homologous to migratory sea urchin pigment cells is present, dynamic gene activation accomplishes a similar spatial and temporal expression profile. The mechanisms regulating the expression of these genes, though, is highly divergent. In sea stars, PmGcm lacks the central role in pigment gene expression since it is not expressed in PmPks1 and PmFmo3-1-positive cells, and knockdown of Gcm does not abrogate pigment gene expression. Pigment genes are instead expressed in the coelomic mesoderm early in development before later being expressed in the ectoderm. These findings were supported by in situ RNA hybridization and comparative scRNA-seq analyses. We conclude that simply the coexpression of Pks1 and Fmo3 orthologs in cells of the sea star is not sufficient to underlie the emergence of the larval pigment cell in the sea urchin.
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Affiliation(s)
- Maxwell Spurrell
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Nathalie Oulhen
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Stephany Foster
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Margherita Perillo
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA
| | - Gary Wessel
- Brown University, Department of Molecular Biology, Cell Biology & Biochemistry, Providence, RI, USA.
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9
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Oulhen N, Morita S, Warner JF, Wessel G. CRISPR/Cas9 knockin methodology for the sea urchin embryo. Mol Reprod Dev 2023; 90:69-72. [PMID: 36719060 PMCID: PMC9979971 DOI: 10.1002/mrd.23672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Affiliation(s)
- Nathalie Oulhen
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Shumpei Morita
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
- Present Address: Asamushi Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, Aomori, Aomori, 039-3501, Japan
| | - Jacob F. Warner
- Department of Biology and Marine Biology. University of North Carolina Wilmington, Wilmington, NC 28403
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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10
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Foster S, Oulhen N, Fresques T, Zaki H, Wessel G. Single-cell RNA-sequencing analysis of early sea star development. Development 2022; 149:dev200982. [PMID: 36399063 PMCID: PMC9845752 DOI: 10.1242/dev.200982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022]
Abstract
Echinoderms represent a broad phylum with many tractable features to test evolutionary changes and constraints. Here, we present a single-cell RNA-sequencing analysis of early development in the sea star Patiria miniata, to complement the recent analysis of two sea urchin species. We identified 20 cell states across six developmental stages from 8 hpf to mid-gastrula stage, using the analysis of 25,703 cells. The clusters were assigned cell states based on known marker gene expression and by in situ RNA hybridization. We found that early (morula, 8-14 hpf) and late (blastula-to-mid-gastrula) cell states are transcriptionally distinct. Cells surrounding the blastopore undergo rapid cell state changes that include endomesoderm diversification. Of particular import to understanding germ cell specification is that we never see Nodal pathway members within Nanos/Vasa-positive cells in the region known to give rise to the primordial germ cells (PGCs). The results from this work contrast the results of PGC specification in the sea urchin, and the dataset presented here enables deeper comparative studies in tractable developmental models for testing a variety of developmental mechanisms.
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Affiliation(s)
- Stephany Foster
- Department of Molecular Biology, Cellular Biology & Biochemistry Division of BioMedicine, Brown University,Providence, RI 02912, USA
| | - Nathalie Oulhen
- Department of Molecular Biology, Cellular Biology & Biochemistry Division of BioMedicine, Brown University,Providence, RI 02912, USA
| | - Tara Fresques
- Department of Molecular Biology, Cellular Biology & Biochemistry Division of BioMedicine, Brown University,Providence, RI 02912, USA
| | - Hossam Zaki
- Department of Molecular Biology, Cellular Biology & Biochemistry Division of BioMedicine, Brown University,Providence, RI 02912, USA
| | - Gary Wessel
- Department of Molecular Biology, Cellular Biology & Biochemistry Division of BioMedicine, Brown University,Providence, RI 02912, USA
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11
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Ageenko NV, Kiselev KV, Odintsova NA. Quinoid Pigments of Sea Urchins Scaphechinus mirabilis and Strongylocentrotus intermedius: Biological Activity and Potential Applications. Mar Drugs 2022; 20:611. [PMID: 36286435 PMCID: PMC9605347 DOI: 10.3390/md20100611] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/18/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
This review presents literature data: the history of the discovery of quinoid compounds, their biosynthesis and biological activity. Special attention is paid to the description of the quinoid pigments of the sea urchins Scaphechinus mirabilis (from the family Scutellidae) and Strongylocentrotus intermedius (from the family Strongylocentrotidae). The marine environment is considered one of the most important sources of natural bioactive compounds with extremely rich biodiversity. Primary- and some secondary-mouthed animals contain very high concentrations of new biologically active substances, many of which are of significant potential interest for medical purposes. The quinone pigments are products of the secondary metabolism of marine animals, can have complex structures and become the basis for the development of new natural products in echinoids that are modulators of chemical interactions and possible active ingredients in medicinal preparations. More than 5000 chemical compounds with high pharmacological potential have been isolated and described from marine organisms. There are three well known ways of naphthoquinone biosynthesis-polyketide, shikimate and mevalonate. The polyketide pathway is the biosynthesis pathway of various quinones. The shikimate pathway is the main pathway in the biosynthesis of naphthoquinones. It should be noted that all quinoid compounds in plants and animals can be synthesized by various ways of biosynthesis.
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Affiliation(s)
- Natalya V. Ageenko
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Federal State Budgetary Institution of Science, The Far Eastern Branch of the Russian Academy of Sciences (FEB RAS), 690041 Vladivostok, Russia
| | - Konstantin V. Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Federal State Budgetary Institution of Science, FEB RAS, 690022 Vladivostok, Russia
| | - Nelly A. Odintsova
- Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Federal State Budgetary Institution of Science, The Far Eastern Branch of the Russian Academy of Sciences (FEB RAS), 690041 Vladivostok, Russia
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12
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Wound repair in sea urchin larvae involves pigment cells and blastocoelar cells. Dev Biol 2022; 491:56-65. [PMID: 36067837 DOI: 10.1016/j.ydbio.2022.08.005] [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: 04/21/2022] [Revised: 08/02/2022] [Accepted: 08/21/2022] [Indexed: 11/21/2022]
Abstract
Sea urchin larvae spend weeks to months feeding on plankton prior to metamorphosis. When handled in the laboratory they are easily injured, suggesting that in the plankton they are injured with some frequency. Fortunately, larval wounds are repaired through an efficient wound response with mesenchymal pigment cells and blastocoelar cells assisting as the epithelium closes. An injury to the epithelium leads to an immediate calcium transient that rapidly spreads around the entire larva and is necessary for activating pigment cell migration toward the wound. If calcium transport is blocked, the pigment cells fail to activate and remain in place. When activated, pigment cells initiate directed migration to the wound site from distances of at least 85 μm. Upon arrival at the wound site they participate in an innate immune response. Blastocoelar cells are recruited to the injury site as well, though the calcium transient is unnecessary for activating these cells. At the wound site, blastocoelar cells participate in several functions including remodeling the skeleton if it protrudes through the epithelium.
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13
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Li F, Lin Z, Torres JP, Hill EA, Li D, Townsend CA, Schmidt EW. Sea Urchin Polyketide Synthase SpPks1 Produces the Naphthalene Precursor to Echinoderm Pigments. J Am Chem Soc 2022; 144:9363-9371. [PMID: 35588530 DOI: 10.1021/jacs.2c01416] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly every animal species on Earth contains a unique polyketide synthase (PKS) encoded in its genome, yet no animal-clade PKS has been biochemically characterized, and even the chemical products of these ubiquitous enzymes are known in only a few cases. The earliest animal genome-encoded PKS gene to be identified was SpPks1 from sea urchins. Previous genetic knockdown experiments implicated SpPks1 in synthesis of the sea urchin pigment echinochrome. Here, we express and purify SpPks1, performing biochemical experiments to demonstrate that the sea urchin protein is responsible for the synthesis of 2-acetyl-1,3,6,8-tetrahydroxynaphthalene (ATHN). Since ATHN is a plausible precursor of echinochromes, this result defines a biosynthetic pathway to the ubiquitous echinoderm pigments and rewrites the previous hypothesis for echinochrome biosynthesis. Truncation experiments showed that, unlike other type I iterative PKSs so far characterized, SpPks1 produces the naphthalene core using solely ketoacylsynthase (KS), acyltransferase, and acyl carrier protein domains, delineating a unique class of animal nonreducing aromatic PKSs (aPKSs). A series of amino acids in the KS domain define the family and are likely crucial in cyclization activity. Phylogenetic analyses indicate that SpPks1 and its homologs are widespread in echinoderms and their closest relatives, the acorn worms, reinforcing their fundamental importance to echinoderm biology. While the animal microbiome is known to produce aromatic polyketides, this work provides biochemical evidence that animals themselves also harbor ancient, convergent, dedicated pathways to carbocyclic aromatic polyketides. More fundamentally, biochemical analysis of SpPks1 begins to define the vast and unexplored biosynthetic space of the ubiquitous animal PKS family.
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Affiliation(s)
- Feng Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China.,Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric A Hill
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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14
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Abstract
Larvae of sea urchins have a population of conspicuous pigmented cells embedded in the outer surface epithelium. Pigment cells are a distinct mesodermal lineage that gives rise to a key component of the larval immune system. During cleavage, signaling from adjacent cells influences a small crescent of cells to initiate a network of genetic interactions that prepare the cells for morphogenesis and specializes them as immunocytes. The cells become active during gastrulation, detach from the epithelium, migrate through the blastocoel, and insert into the ectoderm where they complete their differentiation. Studies of pigment cell development have helped establish how cellular signaling controls networks of genetic interactions that bring about morphogenesis and differentiation. This review summarizes studies of pigment cell development and concludes that pigment cells are an excellent experimental model. Pigment cells provide several opportunities to further test and refine our understanding of the molecular basis of cellular development.
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Affiliation(s)
- Robert D Burke
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
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15
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Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling. Genome Res 2021; 31:1680-1692. [PMID: 34330790 PMCID: PMC8415375 DOI: 10.1101/gr.275684.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expression tended to parallel those of nearby genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays was associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are available at Echinobase, the public database of information related to echinoderm genomics.
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16
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Girija A, Vijayanathan M, Sreekumar S, Basheer J, Menon TG, Krishnankutty RE, Soniya EV. Harnessing the natural pool of polyketide and non-ribosomal peptide family: A route map towards novel drug development. Curr Mol Pharmacol 2021; 15:265-291. [PMID: 33745440 DOI: 10.2174/1874467214666210319145816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/10/2020] [Accepted: 12/31/2020] [Indexed: 11/22/2022]
Abstract
Emergence of communicable and non-communicable diseases possess health challenge to millions of people worldwide and is a major threat to the economic and social development in the coming century. The occurrence of recent pandemic, SARS-CoV-2 caused by lethal severe acute respiratory syndrome coronavirus 2 is one such example. Rapid research and development of drugs for the treatment and management of these diseases has been an incredibly challenging task for the pharmaceutical industry. Although, substantial focus has been made in the discovery of therapeutic compounds from natural sources having significant medicinal potential, their synthesis has shown a slow progress. Hence, the discovery of new targets by the application of the latest biotechnological and synthetic biology approaches is very much the need of the hour. Polyketides (PKs) and non-ribosomal peptides (NRPs) found in bacteria, fungi and plants are a large diverse family of natural products synthesized by two classes of enzymes: polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). These enzymes possess immense biomedical potential due to their simple architecture, catalytic capacity, as well as diversity. With the advent of latest in-silico and in-vitro strategies, these enzymes and their related metabolic pathways, if targeted, can contribute highly towards the biosynthesis of an array of potentially natural drug leads that have antagonist effects on biopolymers associated with various human diseases. In the face of the rising threat from the multidrug-resistant pathogens, this will further open new avenues for the discovery of novel and improved drugs by combining the natural and the synthetic approaches. This review discusses the relevance of polyketides and non-ribosomal peptides and the improvement strategies for the development of their derivatives and scaffolds, and how they will be beneficial to the future bioprospecting and drug discovery.
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Affiliation(s)
- Aiswarya Girija
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.,Institute of Biological Environmental Rural Sciences (IBERS), Aberystwyth University, United Kingdom
| | - Mallika Vijayanathan
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.,Biology Centre - Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Sweda Sreekumar
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India.,Research Centre, University of Kerala, India
| | - Jasim Basheer
- School of Biosciences, Mahatma Gandhi University, PD Hills, Kottayam, Kerala, India.,Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Tara G Menon
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
| | | | - Eppurathu Vasudevan Soniya
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, India
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17
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Perillo M, Oulhen N, Foster S, Spurrell M, Calestani C, Wessel G. Regulation of dynamic pigment cell states at single-cell resolution. eLife 2020; 9:e60388. [PMID: 32812865 PMCID: PMC7455242 DOI: 10.7554/elife.60388] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
Cells bearing pigment have diverse roles and are often under strict evolutionary selection. Here, we explore the regulation of pigmented cells in the purple sea urchin Strongylocentrotus purpuratus, an emerging model for diverse pigment function. We took advantage of single cell RNA-seq (scRNAseq) technology and discovered that pigment cells in the embryo segregated into two distinct populations, a mitotic cluster and a post-mitotic cluster. Gcm is essential for expression of several genes important for pigment function, but is only transiently expressed in these cells. We discovered unique genes expressed by pigment cells and test their expression with double fluorescence in situ hybridization. These genes include new members of the fmo family that are expressed selectively in pigment cells of the embryonic and in the coelomic cells of the adult - both cell-types having immune functions. Overall, this study identifies nodes of molecular intersection ripe for change by selective evolutionary pressures.
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Affiliation(s)
- Margherita Perillo
- Department of Molecular and Cellular Biology Division of Biology and Medicine Brown UniversityProvidenceUnited States
| | - Nathalie Oulhen
- Department of Molecular and Cellular Biology Division of Biology and Medicine Brown UniversityProvidenceUnited States
| | - Stephany Foster
- Department of Molecular and Cellular Biology Division of Biology and Medicine Brown UniversityProvidenceUnited States
| | - Maxwell Spurrell
- Department of Molecular and Cellular Biology Division of Biology and Medicine Brown UniversityProvidenceUnited States
| | | | - Gary Wessel
- Department of Molecular and Cellular Biology Division of Biology and Medicine Brown UniversityProvidenceUnited States
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18
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Ettensohn CA. The gene regulatory control of sea urchin gastrulation. Mech Dev 2020; 162:103599. [PMID: 32119908 DOI: 10.1016/j.mod.2020.103599] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
The cell behaviors associated with gastrulation in sea urchins have been well described. More recently, considerable progress has been made in elucidating gene regulatory networks (GRNs) that underlie the specification of early embryonic territories in this experimental model. This review integrates information from these two avenues of work. I discuss the principal cell movements that take place during sea urchin gastrulation, with an emphasis on molecular effectors of the movements, and summarize our current understanding of the gene regulatory circuitry upstream of those effectors. A case is made that GRN biology can provide a causal explanation of gastrulation, although additional analysis is needed at several levels of biological organization in order to provide a deeper understanding of this complex morphogenetic process.
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Affiliation(s)
- Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave., Pittsburgh, PA 15213, USA.
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19
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Wessel GM, Kiyomoto M, Shen TL, Yajima M. Genetic manipulation of the pigment pathway in a sea urchin reveals distinct lineage commitment prior to metamorphosis in the bilateral to radial body plan transition. Sci Rep 2020; 10:1973. [PMID: 32029769 PMCID: PMC7005274 DOI: 10.1038/s41598-020-58584-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 12/26/2022] Open
Abstract
Echinoderms display a vast array of pigmentation and patterning in larval and adult life stages. This coloration is thought to be important for immune defense and camouflage. However, neither the cellular nor molecular mechanism that regulates this complex coloration in the adult is known. Here we knocked out three different genes thought to be involved in the pigmentation pathway(s) of larvae and grew the embryos to adulthood. The genes tested were polyketide synthase (PKS), Flavin-dependent monooxygenase family 3 (FMO3) and glial cells missing (GCM). We found that disabling of the PKS gene at fertilization resulted in albinism throughout all life stages and throughout all cells and tissues of this animal, including the immune cells of the coelomocytes. We also learned that FMO3 is an essential modifier of the polyketide. FMO3 activity is essential for larval pigmentation, but in juveniles and adults, loss of FMO3 activity resulted in the animal becoming pastel purple. Linking the LC-MS analysis of this modified pigment to a naturally purple animal suggested a conserved echinochrome profile yielding a pastel purple. We interpret this result as FMO3 modifies the parent polyketide to contribute to the normal brown/green color of the animal, and that in its absence, other biochemical modifications are revealed, perhaps by other members of the large FMO family in this animal. The FMO modularity revealed here may be important in the evolutionary changes between species and for different immune challenges. We also learned that glial cells missing (GCM), a key transcription factor of the endomesoderm gene regulatory network of embryos in the sea urchin, is required for pigmentation throughout the life stages of this sea urchin, but surprisingly, is not essential for larval development, metamorphosis, or maintenance of adulthood. Mosaic knockout of either PKS or GCM revealed spatial lineage commitment in the transition from bilaterality of the larva to a pentaradial body plan of the adult. The cellular lineages identified by pigment presence or absence (wild-type or knock-out lineages, respectively) followed a strict oral/aboral profile. No circumferential segments were seen and instead we observed 10-fold symmetry in the segments of pigment expression. This suggests that the adult lineage commitments in the five outgrowths of the hydropore in the larva are early, complete, fixed, and each bilaterally symmetric. Overall, these results suggest that pigmentation of this animal is genetically determined and dependent on a population of pigment stem cells that are set-aside in a sub-region of each outgrowth of the pentaradial adult rudiment prior to metamorphosis. This study reveals the complex chemistry of pigment applicable to many organisms, and further, provides an insight into the key transitions from bilateral to pentaradial body plans unique to echinoderms.
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Affiliation(s)
- Gary M Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.
| | - Masato Kiyomoto
- Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba, 294-0301, Japan
| | - Tun-Li Shen
- Department of Chemistry, Brown University, Providence, RI, 02912, USA
| | - Mamiko Yajima
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.
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20
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Ganley JG, Derbyshire ER. Linking Genes to Molecules in Eukaryotic Sources: An Endeavor to Expand Our Biosynthetic Repertoire. Molecules 2020; 25:E625. [PMID: 32023950 PMCID: PMC7036892 DOI: 10.3390/molecules25030625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
The discovery of natural products continues to interest chemists and biologists for their utility in medicine as well as facilitating our understanding of signaling, pathogenesis, and evolution. Despite an attenuation in the discovery rate of new molecules, the current genomics and transcriptomics revolution has illuminated the untapped biosynthetic potential of many diverse organisms. Today, natural product discovery can be driven by biosynthetic gene cluster (BGC) analysis, which is capable of predicting enzymes that catalyze novel reactions and organisms that synthesize new chemical structures. This approach has been particularly effective in mining bacterial and fungal genomes where it has facilitated the discovery of new molecules, increased the understanding of metabolite assembly, and in some instances uncovered enzymes with intriguing synthetic utility. While relatively less is known about the biosynthetic potential of non-fungal eukaryotes, there is compelling evidence to suggest many encode biosynthetic enzymes that produce molecules with unique bioactivities. In this review, we highlight how the advances in genomics and transcriptomics have aided natural product discovery in sources from eukaryotic lineages. We summarize work that has successfully connected genes to previously identified molecules and how advancing these techniques can lead to genetics-guided discovery of novel chemical structures and reactions distributed throughout the tree of life. Ultimately, we discuss the advantage of increasing the known biosynthetic space to ease access to complex natural and non-natural small molecules.
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Affiliation(s)
- Jack G Ganley
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
| | - Emily R Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0346, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
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21
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Abstract
Secondary metabolites are often considered within the remit of bacterial or plant research, but animals also contain a plethora of these molecules with important functional roles. Classical feeding studies demonstrate that, whereas some are derived from diet, many of these compounds are made within the animals. In the past 15 years, the genetic and biochemical origin of several animal natural products has been traced to partnerships with symbiotic bacteria. More recently, a number of animal genome-encoded pathways to microbe-like natural products have come to light. These pathways are sometimes horizontally acquired from bacteria, but more commonly they unveil a new and diverse animal biochemistry. In this review, we highlight recent examples of characterized animal biosynthetic enzymes that reveal an unanticipated breadth and intricacy in animal secondary metabolism. The results so far suggest that there may be an immense diversity of animal small molecules and biosynthetic enzymes awaiting discovery. This biosynthetic dark matter is just beginning to be understood, providing a relatively untapped frontier for discovery.
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Affiliation(s)
- Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
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22
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PI3K inhibition highlights new molecular interactions involved in the skeletogenesis of Paracentrotus lividus embryos. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118558. [PMID: 31525406 DOI: 10.1016/j.bbamcr.2019.118558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 02/02/2023]
Abstract
The sea urchin embryo develops a well-defined biomineralized endoskeleton, synthesized exclusively by the skeletogenic cells, supported by ectodermal cues for the correct skeleton patterning. The biomineralization process is tightly regulated via a hierarchical order of gene expression, including transcription and growth factors, biomineralization proteins. Recently, the role of kinases and intracellular signaling pathways in sea urchin skeletogenesis has been addressed, although the downstream components still remain unknown. In this study, we investigated the role of phosphatidylinositide 3-kinase (PI3K)-mediated signaling pathway in Paracentrotus lividus, to identify its genes/proteins targets. The effects of LY294002 (LY), a PI3K-specific inhibitor, were evaluated at morphological and molecular levels. Treatment with 40 μM LY from the blastula stage completely blocked skeleton deposition, which was reversed by wash out experiments. Besides, LY caused a slight delay in the tripartite gut development. Despite the skeleton absence, a few skeleton-specific proteins/mRNAs were regularly expressed and localized in LY-treated embryos, as shown for MSP130 and SM50 by immunofluorescence and in situ hybridization experiments. QPCR analyses showed that LY differently affected the expression of genes coding for other biomineralization proteins, transcription and growth factors. SM30 and carbonic anhydrase expression was severely downregulated, while almost all the transcription factors analyzed were upregulated. Based on the present results and in silico analyses, we propose an "interactomic" model simulating PI3K connections in P. lividus embryos. Our findings define a novel regulatory step in the embryonic skeletogenesis, and provide valuable molecular data for further studies on the role of PI3K signaling in invertebrate biomineralization.
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23
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Fernandez-Nicolas A, Xu D, Yajima M. A tumor suppressor Retinoblastoma1 is essential for embryonic development in the sea urchin. Dev Dyn 2019; 248:1273-1285. [PMID: 31515896 DOI: 10.1002/dvdy.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/19/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Embryonic cells and cancer cells share various cellular characteristics important for their functions. It has been thus proposed that similar mechanisms of regulation may be present in these otherwise disparate cell types. RESULTS To explore how regulative embryonic cells are fundamentally different from cancerous cells, we report here that a fine balance of a tumor suppressor protein Retinoblastoma1 (Rb1) and a germline factor Vasa are important for proper cell proliferation and differentiation of the somatic cells during embryogenesis of the sea urchin. Rb1 knockdown blocked embryonic development and induced Vasa accumulation in the entire embryo, while its overexpression resulted in a smaller-sized embryo with differentiated body structures. These results suggest that a titrated level of Rb1 protein may be essential for a proper balance of cell proliferation and differentiation during development. Vasa knockdown or overexpression, on the other hand, reduced or increased Rb1 protein expression, respectively. CONCLUSIONS Taken together, it appears that Vasa protein positively regulates Rb1 protein while Rb1 protein negatively regulates Vasa protein, balancing the act of these two antagonistic molecules in somatic cells. This mechanism may provide a fine control of cell proliferation and differentiation, which is essential for regulative embryonic development.
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Affiliation(s)
| | - Derek Xu
- MCB Department, Brown University, Providence, Rhode Island
| | - Mamiko Yajima
- MCB Department, Brown University, Providence, Rhode Island
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24
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Liu D, Awazu A, Sakuma T, Yamamoto T, Sakamoto N. Establishment of knockout adult sea urchins by using a CRISPR‐Cas9 system. Dev Growth Differ 2019; 61:378-388. [DOI: 10.1111/dgd.12624] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/23/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Daming Liu
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Hiroshima Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Hiroshima Japan
- Division of Integrated Sciences for Life Graduate School of Integrated Sciences for Life Hiroshima University Hiroshima Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Hiroshima Japan
- Division of Integrated Sciences for Life Graduate School of Integrated Sciences for Life Hiroshima University Hiroshima Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Hiroshima Japan
- Division of Integrated Sciences for Life Graduate School of Integrated Sciences for Life Hiroshima University Hiroshima Japan
| | - Naoaki Sakamoto
- Department of Mathematical and Life Sciences Graduate School of Science Hiroshima University Hiroshima Japan
- Division of Integrated Sciences for Life Graduate School of Integrated Sciences for Life Hiroshima University Hiroshima Japan
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25
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Shikonin derivatives for cancer prevention and therapy. Cancer Lett 2019; 459:248-267. [PMID: 31132429 DOI: 10.1016/j.canlet.2019.04.033] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/15/2019] [Accepted: 04/26/2019] [Indexed: 12/25/2022]
Abstract
Phytochemicals gained considerable interest during the past years as source to develop new treatment options for chemoprevention and cancer therapy. Motivated by the fact that a majority of established anticancer drugs are derived in one way or another from natural resources, we focused on shikonin, a naphthoquinone with high potentials to be further developed as preventive or therapeutic drug to fight cancer. Shikonin is the major chemical component of Lithospermum erythrorhizon (Purple Cromwell) roots. Traditionally, the root extract has been applied to cure dermatitis, burns, and wounds. Over the past three decades, the anti-inflammatory and anticancer effects of root extracts, isolated shikonin as well as semi-synthetic and synthetic derivatives and nanoformulations have been described. In vitro and in vivo experiments were conducted to understand the effect of shikonin at cellular and molecular levels. Preliminary clinical trials indicate the potential of shikonin for translation into clinical oncology. Shikonin exerts additive and synergistic interactions in combination with established chemotherapeutics, immunotherapeutic approaches, radiotherapy and other treatment modalities, which further underscores the potential of this phytochemical to be integrated into standard treatment regimens.
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26
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Golconda P, Buckley KM, Reynolds CR, Romanello JP, Smith LC. The Axial Organ and the Pharynx Are Sites of Hematopoiesis in the Sea Urchin. Front Immunol 2019; 10:870. [PMID: 31105697 PMCID: PMC6494969 DOI: 10.3389/fimmu.2019.00870] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/04/2019] [Indexed: 01/01/2023] Open
Abstract
Background: The location of coelomocyte proliferation in adult sea urchins is unknown and speculations since the early 1800s have been based on microanatomy and tracer uptake studies. In adult sea urchins (Strongylocentrotus purpuratus) with down-regulated immune systems, coelomocyte numbers increase in response to immune challenge, and whether some or all of these cells are newly proliferated is not known. The gene regulatory network that encodes transcription factors that control hematopoiesis in embryonic and larval sea urchins has not been investigated in adults. Hence, to identify the hematopoietic tissue in adult sea urchins, cell proliferation, expression of phagocyte specific genes, and expression of genes encoding transcription factors that function in the conserved regulatory network that controls hematopoiesis in embryonic and larval sea urchins were investigated for several tissues. Results: Cell proliferation was induced in adult sea urchins either by immune challenge through injection of heat-killed Vibrio diazotrophicus or by cell depletion through aspiration of coelomic fluid. In response to either of these stimuli, newly proliferated coelomocytes constitute only about 10% of the cells in the coelomic fluid. In tissues, newly proliferated cells and cells that express SpTransformer proteins (formerly Sp185/333) that are markers for phagocytes are present in the axial organ, gonad, pharynx, esophagus, and gut with no differences among tissues. The expression level of genes encoding transcription factors that regulate hematopoiesis show that both the axial organ and the pharynx have elevated expression compared to coelomocytes, esophagus, gut, and gonad. Similarly, an RNAseq dataset shows similar results for the axial organ and pharynx, but also suggests that the axial organ may be a site for removal and recycling of cells in the coelomic cavity. Conclusions: Results presented here are consistent with previous speculations that the axial organ may be a site of coelomocyte proliferation and that it may also be a center for cellular removal and recycling. A second site, the pharynx, may also have hematopoietic activity, a tissue that has been assumed to function only as part of the intestinal tract.
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Affiliation(s)
| | | | | | | | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC, United States
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27
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Molina MD, Gache C, Lepage T. Expression of exogenous mRNAs to study gene function in echinoderm embryos. Methods Cell Biol 2019; 151:239-282. [PMID: 30948011 DOI: 10.1016/bs.mcb.2018.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
With the completion of the genome sequencing projects, a new challenge for developmental biologists is to assign a function to the thousands of genes identified. Expression of exogenous mRNAs is a powerful, versatile and rapid technique that can be used to study gene function during development of the sea urchin. This chapter describes how this technique can be used to analyze gene function in echinoderm embryos, how it can be combined with cell transplantation to perform mosaic analysis and how it can be applied to identify downstream targets genes of transcription factors and signaling pathways. We describe specific examples of the use of overexpression of mRNA to analyze gene function, mention the benefits and current limitations of the technique and emphasize the importance of using different controls to assess the specificity of the effects observed. Finally, this chapter details the different steps, vectors and protocols for in vitro production of mRNA and phenotypic analysis.
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Affiliation(s)
| | - Christian Gache
- Université Pierre et Marie Curie, Observatoire Océanologique de Villefranche sur Mer, UMR7009 CNRS, Paris, France
| | - Thierry Lepage
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France.
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28
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Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 (CRISPR-associated nuclease 9) technology enables rapid, targeted, and efficient changes in the genomes of various model organisms. The short guide RNAs (gRNAs) of the CRISPR/Cas9 system can be designed to recognize target DNA within coding regions for functional gene knockouts. Several studies have demonstrated that the CRISPR/Cas9 system efficiently and specifically targets sea urchin genes and results in expected mutant phenotypes. In addition to disrupting gene functions, modifications and additions to the Cas9 protein enable alternative activities targeted to specific sites within the genome. This includes a fusion of cytidine deaminase to Cas9 (Cas9-DA) for single nucleotide conversion in targeted sites. In this chapter, we describe detailed methods for the CRISPR/Cas9 application in sea urchin embryos, including gRNA design, in vitro synthesis of single guide RNA (sgRNA), and the usages of the CRISPR/Cas9 technology for gene knockout and single nucleotide editing. Methods for genotyping the resultant embryos are also provided for assessing efficiencies of gene editing.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Gary Wessel
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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29
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Hou Y, Vasileva EA, Carne A, McConnell M, El-Din A Bekhit A, Mishchenko NP. Naphthoquinones of the spinochrome class: occurrence, isolation, biosynthesis and biomedical applications. RSC Adv 2018; 8:32637-32650. [PMID: 35547692 PMCID: PMC9086473 DOI: 10.1039/c8ra04777d] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/17/2018] [Indexed: 01/17/2023] Open
Abstract
Quinones are widespread in nature and have been found in plants, fungi and bacteria, as well as in members of the animal kingdom. More than forty closely related naphthoquinones have been found in echinoderms, mainly in sea urchins but occasionally in brittle stars, sea stars and starfish. This review aims to examine controversial issues on the chemistry, biosynthesis, functions, stability and application aspects of the spinochrome class, a prominent group of secondary metabolites found in sea urchins. The emphasis of this review is on the isolation and structure of these compounds, together with evaluation of their relevant biological activities, source organisms, the location of origin and methods used for isolation and identification. In addition, the studies of their biosynthesis and ecological function, stability and chemical synthesis have been highlighted. This review aims to establish a focus for future spinochrome research and its potential for benefiting human health and well-being.
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Affiliation(s)
- Yakun Hou
- Department of Food Science, University of Otago PO Box 56 Dunedin 9054 New Zealand
| | - Elena A Vasileva
- Laboratory of the Chemistry of Natural Quinonoid Compounds, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences Prospect 100 let Vladivostoku 159/2 690022 Vladivostok Russia
| | - Alan Carne
- Department of Biochemistry, University of Otago PO Box 56 Dunedin 9054 New Zealand
| | - Michelle McConnell
- Department of Microbiology and Immunology, University of Otago PO Box 56 Dunedin 9054 New Zealand
| | - Alaa El-Din A Bekhit
- Department of Food Science, University of Otago PO Box 56 Dunedin 9054 New Zealand
| | - Natalia P Mishchenko
- Laboratory of the Chemistry of Natural Quinonoid Compounds, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences Prospect 100 let Vladivostoku 159/2 690022 Vladivostok Russia
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30
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Bonaventura R, Zito F, Chiaramonte M, Costa C, Russo R. Nickel toxicity in P. lividus embryos: Dose dependent effects and gene expression analysis. MARINE ENVIRONMENTAL RESEARCH 2018; 139:113-121. [PMID: 29773318 DOI: 10.1016/j.marenvres.2018.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/29/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Many industrial activities release Nickel (Ni) in the environment with harmful effects for terrestrial and marine organisms. Despite many studies on the mechanisms of Ni toxicity are available, the understanding about its toxic effects on marine organisms is more limited. We used Paracentrotus lividus as a model to analyze the effects on the stress pathways in embryos continuously exposed to different Ni doses, ranging from 0.03 to 0.5 mM. We deeply examined the altered embryonic morphologies at 24 and 48 h after Ni exposure. Some different phenotypes have been classified, showing alterations at the expenses of the dorso-ventral axis as well as the skeleton and/or the pigment cells. At the lowest dose used, Ni mainly induced a multi-spicule phenotype observed at 24 h after treatment. On the contrary, at the highest dose of Ni (0.5 mM), 90% of embryos showed no skeleton and no pigment cells. Therefore, we focused on this dose to study protein and gene expression patterns at 24 and 48 h after exposure. Among the proteins analyzed, i.e. p38MAPK, Grp78 and Mn-SOD, only p38MAPK was induced by Ni treatment. Moreover, we analyzed the mRNA profiles of a pool of genes that are involved in stress response and in development mechanisms, i.e. the transcription factors Pl-NFkB and Pl-FOXO; a marker of DNA repair, Pl-XPB/ERCC3; a mitogen-activated protein kinase (MAPK), Pl-p38; an ER stress gene, Pl-grp78; an adapter protein, Pl-14-3-3ε; two markers of pigment cells, Pl-PKS1 and Pl-gcm. The spatial expression of mesenchymal marker genes has been evaluated in Ni-treated embryos at both 24 and 48 h after exposure. Our results indicated that Ni acts at several levels in P. lividus sea urchin, by affecting embryo development, influencing the embryonic immune response and activating stress response pathways to counteract the suffered injury and to promote embryos surviving.
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Affiliation(s)
- Rosa Bonaventura
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy.
| | - Francesca Zito
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Marco Chiaramonte
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Caterina Costa
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
| | - Roberta Russo
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "A. Monroy", Via Ugo La Malfa 153, 90146 Palermo, Italy
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31
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Bazzi W, Cattenoz PB, Delaporte C, Dasari V, Sakr R, Yuasa Y, Giangrande A. Embryonic hematopoiesis modulates the inflammatory response and larval hematopoiesis in Drosophila. eLife 2018; 7:e34890. [PMID: 29992900 PMCID: PMC6040882 DOI: 10.7554/elife.34890] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/18/2018] [Indexed: 11/25/2022] Open
Abstract
Recent lineage tracing analyses have significantly improved our understanding of immune system development and highlighted the importance of the different hematopoietic waves. The current challenge is to understand whether these waves interact and whether this affects the function of the immune system. Here we report a molecular pathway regulating the immune response and involving the communication between embryonic and larval hematopoietic waves in Drosophila. Down-regulating the transcription factor Gcm specific to embryonic hematopoiesis enhances the larval phenotypes induced by over-expressing the pro-inflammatory Jak/Stat pathway or by wasp infestation. Gcm works by modulating the transduction of the Upd cytokines to the site of larval hematopoiesis and hence the response to chronic (Jak/Stat over-expression) and acute (wasp infestation) immune challenges. Thus, homeostatic interactions control the function of the immune system in physiology and pathology. Our data also indicate that a transiently expressed developmental pathway has a long-lasting effect on the immune response.
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Affiliation(s)
- Wael Bazzi
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Pierre B Cattenoz
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Claude Delaporte
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Vasanthi Dasari
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Rosy Sakr
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Yoshihiro Yuasa
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et CellulaireIllkirchFrance
- UMR7104Centre National de la Recherche ScientifiqueIllkirchFrance
- U1258Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
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32
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Calestani C, Wessel GM. These Colors Don't Run: Regulation of Pigment-Biosynthesis in Echinoderms. Results Probl Cell Differ 2018; 65:515-525. [PMID: 30083933 PMCID: PMC6550297 DOI: 10.1007/978-3-319-92486-1_22] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Pigment production is an important biological process throughout the tree of life. Some pigments function for collecting light energy, or for visual identification, while others have dramatic antimicrobial functions, or camouflage capabilities. The functions of these pigments and their biosynthesis are of great interest if only because of their diversity. The biochemistry of echinoderm pigmentation has been intensively studied for many years, and with more recent technologies, the origin and functions of these pigments are being exposed. Here we summarize the major pigment types in biology and emphasize the status of the field in echinoderms, taking full advantage of the new genomic and technologic resources for studying these important animals and their beautiful pigmentation.
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Affiliation(s)
| | - Gary M Wessel
- Department of Molecular and Cellular Biology and Biochemistry, Brown University, Providence, RI, USA.
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Barca A, Vacca F, Vizioli J, Drago F, Vetrugno C, Verri T, Pagliara P. Molecular and expression analysis of the Allograft inflammatory factor 1 (AIF-1) in the coelomocytes of the common sea urchin Paracentrotus lividus. FISH & SHELLFISH IMMUNOLOGY 2017; 71:136-143. [PMID: 28986218 DOI: 10.1016/j.fsi.2017.09.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
Allograft inflammatory factor 1 (AIF-1) is a highly conserved gene involved in inflammation, cloned and characterized in several evolutionary distant animal species. Here, we report the molecular identification, characterization and expression of AIF-1 from the common sea urchin Paracentrotus lividus. In this species, AIF-1 encodes a predicted 151 amino acid protein with high similarity to vertebrate AIF-1 proteins. Immunocytochemical analyses on coelomocytes reveal localization of the AIF-1 protein in amoebocytes (perinuclear cytoplasmic zone) and red sphaerulocytes (inside granules), but not in vibratile cells and colorless sphaerula cells. The significant increase of AIF-1 expression (mRNA and protein) found in the coelomocytes of the sea urchin after Gram + bacterial challenge suggests the involvement of AIF-1 in the inflammatory response. Our analysis on P. lividus AIF-1 contributes to elucidate AIF-1 function along the evolutionary scale and consolidate the key evolutionary position of echinoderms throughout metazoans with respect to the common immune paths.
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Affiliation(s)
- Amilcare Barca
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università Del Salento, Complesso Ecotekne Pal. A, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Francesca Vacca
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università Del Salento, Complesso Ecotekne Pal. A, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Jacopo Vizioli
- Laboratoire PRISM (Protéomique, Réponse Inflammatoire, Spectrométrie de Masse), INSERM U1192 Université Lille 1 Sciences et Technologies, Bât. SN3, Cité Scientifique, 59650 Villeneuve D'Ascq, France.
| | - Francesco Drago
- Laboratoire PRISM (Protéomique, Réponse Inflammatoire, Spectrométrie de Masse), INSERM U1192 Université Lille 1 Sciences et Technologies, Bât. SN3, Cité Scientifique, 59650 Villeneuve D'Ascq, France.
| | - Carla Vetrugno
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università Del Salento, Complesso Ecotekne Pal. A, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Tiziano Verri
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università Del Salento, Complesso Ecotekne Pal. A, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
| | - Patrizia Pagliara
- Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, Università Del Salento, Complesso Ecotekne Pal. A, Via Prov.le Lecce Monteroni, 73100 Lecce, Italy.
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34
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Cooke TF, Fischer CR, Wu P, Jiang TX, Xie KT, Kuo J, Doctorov E, Zehnder A, Khosla C, Chuong CM, Bustamante CD. Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars. Cell 2017; 171:427-439.e21. [PMID: 28985565 PMCID: PMC5951300 DOI: 10.1016/j.cell.2017.08.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/14/2017] [Accepted: 08/08/2017] [Indexed: 12/31/2022]
Abstract
Parrot feathers contain red, orange, and yellow polyene pigments called psittacofulvins. Budgerigars are parrots that have been extensively bred for plumage traits during the last century, but the underlying genes are unknown. Here we use genome-wide association mapping and gene-expression analysis to map the Mendelian blue locus, which abolishes yellow pigmentation in the budgerigar. We find that the blue trait maps to a single amino acid substitution (R644W) in an uncharacterized polyketide synthase (MuPKS). When we expressed MuPKS heterologously in yeast, yellow pigments accumulated. Mass spectrometry confirmed that these yellow pigments match those found in feathers. The R644W substitution abolished MuPKS activity. Furthermore, gene-expression data from feathers of different bird species suggest that parrots acquired their colors through regulatory changes that drive high expression of MuPKS in feather epithelia. Our data also help formulate biochemical models that may explain natural color variation in parrots. VIDEO ABSTRACT.
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Affiliation(s)
- Thomas F Cooke
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Ping Wu
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Ting-Xin Jiang
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Kathleen T Xie
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Kuo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Elizabeth Doctorov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ashley Zehnder
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chaitan Khosla
- ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Departments of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA; Integrative Stem Cell Center, China Medical University, Taichung 404, Taiwan; Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, Taichung 402, Taiwan
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA.
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35
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Minokawa T. Comparative studies on the skeletogenic mesenchyme of echinoids. Dev Biol 2017; 427:212-218. [PMID: 27856261 DOI: 10.1016/j.ydbio.2016.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 10/25/2016] [Accepted: 11/14/2016] [Indexed: 11/16/2022]
Abstract
Skeletogenic mesenchyme cells in echinoids are suitable for studying developmental mechanisms, and have been used extensively. Most of these studies have been performed on species in the order Camarodonta, which are modern echinoids (subclass Euechinoidea) and are considered "model" echinoid species. In contrast, species belonging to other orders are studied less frequently, especially investigations of their molecular developmental biology such as gene regulatory networks. Recent studies on mesenchyme development in non-camarodont species suggest that these species are potential sources of comparative information to elucidate the mechanisms underlying skeletogenic mesenchyme development. In this review, the importance of using comparative data to understand development and evolution is discussed.
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Affiliation(s)
- Takuya Minokawa
- Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, 9 Sakamoto, Asamushi, Aomori, Aomori 039-3501, Japan.
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36
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Xing L, Sun L, Liu S, Li X, Zhang L, Yang H. IBT-based quantitative proteomics identifies potential regulatory proteins involved in pigmentation of purple sea cucumber, Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 23:17-26. [PMID: 28601631 DOI: 10.1016/j.cbd.2017.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/25/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022]
Abstract
Sea cucumbers are an important economic species and exhibit high yield value among aquaculture animals. Purple sea cucumbers are very rare and beautiful and have stable hereditary patterns. In this study, isobaric tags (IBT) were first used to reveal the molecular mechanism of pigmentation in the body wall of the purple sea cucumber. We analyzed the proteomes of purple sea cucumber in early pigmentation stage (Pa), mid pigmentation stage (Pb) and late pigmentation stage (Pc), resulting in the identification of 5580 proteins, including 1099 differentially expressed proteins in Pb: Pa and 339 differentially expressed proteins in Pc: Pb. GO and KEGG analyses revealed possible differentially expressed proteins, including"melanogenesis", "melanosome", "melanoma", "pigment-biosynthetic process", "Epidermis development", "Ras-signaling pathway", "Wnt-signaling pathway", "response to UV light", and "tyrosine metabolism", involved in pigment synthesis and regulation in purple sea cucumbers. The large number of differentially expressed proteins identified here should be highly useful in further elucidating the mechanisms underlying pigmentation in sea cucumbers. Furthermore, these results may also provide the base for further identification of proteins involved in resistance mechanisms against melanoma, albinism, UV damage, and other diseases in sea cucumbers.
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Affiliation(s)
- Lili Xing
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xiaoni Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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37
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Oulhen N, Wessel GM. Albinism as a visual, in vivo guide for CRISPR/Cas9 functionality in the sea urchin embryo. Mol Reprod Dev 2016; 83:1046-1047. [PMID: 27859831 DOI: 10.1002/mrd.22757] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 11/10/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Nathalie Oulhen
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Gary M Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
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38
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39
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Ch Ho E, Buckley KM, Schrankel CS, Schuh NW, Hibino T, Solek CM, Bae K, Wang G, Rast JP. Perturbation of gut bacteria induces a coordinated cellular immune response in the purple sea urchin larva. Immunol Cell Biol 2016; 94:861-874. [PMID: 27192936 PMCID: PMC5073156 DOI: 10.1038/icb.2016.51] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 02/07/2023]
Abstract
The purple sea urchin (Strongylocentrotus purpuratus) genome sequence contains a complex repertoire of genes encoding innate immune recognition proteins and homologs of important vertebrate immune regulatory factors. To characterize how this immune system is deployed within an experimentally tractable, intact animal, we investigate the immune capability of the larval stage. Sea urchin embryos and larvae are morphologically simple and transparent, providing an organism-wide model to view immune response at cellular resolution. Here we present evidence for immune function in five mesenchymal cell types based on morphology, behavior and gene expression. Two cell types are phagocytic; the others interact at sites of microbial detection or injury. We characterize immune-associated gene markers for three cell types, including a perforin-like molecule, a scavenger receptor, a complement-like thioester-containing protein and the echinoderm-specific immune response factor 185/333. We elicit larval immune responses by (1) bacterial injection into the blastocoel and (2) seawater exposure to the marine bacterium Vibrio diazotrophicus to perturb immune state in the gut. Exposure at the epithelium induces a strong response in which pigment cells (one type of immune cell) migrate from the ectoderm to interact with the gut epithelium. Bacteria that accumulate in the gut later invade the blastocoel, where they are cleared by phagocytic and granular immune cells. The complexity of this coordinated, dynamic inflammatory program within the simple larval morphology provides a system in which to characterize processes that direct both aspects of the echinoderm-specific immune response as well as those that are shared with other deuterostomes, including vertebrates.
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Affiliation(s)
- Eric Ch Ho
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Katherine M Buckley
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Catherine S Schrankel
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas W Schuh
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Taku Hibino
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Cynthia M Solek
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Koeun Bae
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Guizhi Wang
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Jonathan P Rast
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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40
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Tyunin AP, Ageenko NV, Kiselev KV. Effects of 5-azacytidine-induced DNA demethylation on polyketide synthase gene expression in larvae of sea urchin Strongylocentrotus intermedius. Biotechnol Lett 2016; 38:2035-2041. [DOI: 10.1007/s10529-016-2191-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022]
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41
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Schrankel CS, Solek CM, Buckley KM, Anderson MK, Rast JP. A conserved alternative form of the purple sea urchin HEB/E2-2/E2A transcription factor mediates a switch in E-protein regulatory state in differentiating immune cells. Dev Biol 2016; 416:149-161. [PMID: 27265865 DOI: 10.1016/j.ydbio.2016.05.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 12/11/2022]
Abstract
E-proteins are basic helix-loop-helix (bHLH) transcription factors with essential roles in animal development. In mammals, these are encoded by three loci: E2-2 (ITF-2/ME2/SEF2/TCF4), E2A (TCF3), and HEB (ME1/REB/TCF12). The HEB and E2-2 paralogs are expressed as alternative (Alt) isoforms with distinct N-terminal sequences encoded by unique exons under separate regulatory control. Expression of these alternative transcripts is restricted relative to the longer (Can) forms, suggesting distinct regulatory roles, although the functions of the Alt proteins remain poorly understood. Here, we characterize the single sea urchin E-protein ortholog (SpE-protein). The organization of the SpE-protein gene closely resembles that of the extended HEB/E2-2 vertebrate loci, including a transcript that initiates at a homologous alternative transcription start site (SpE-Alt). The existence of an Alt form in the sea urchin indicates that this feature predates the emergence of the vertebrates. We present additional evidence indicating that this transcript was present in the common bilaterian ancestor. In contrast to the widely expressed canonical form (SpE-Can), SpE-Alt expression is tightly restricted. SpE-Alt is expressed in two phases: first in aboral non-skeletogenic mesenchyme (NSM) cells and then in oral NSM cells preceding their differentiation and ingression into the blastocoel. Derivatives of these cells mediate immune response in the larval stage. Inhibition of SpE-Alt activity interferes with these events. Notably, although the two isoforms are initially co-expressed, as these cells differentiate, SpE-Can is excluded from the SpE-Alt(+) cell population. This mutually exclusive expression is dependent on SpE-Alt function, which reveals a previously undescribed negative regulatory linkage between the two E-protein forms. Collectively, these findings reorient our understanding of the evolution of this transcription factor family and highlight fundamental properties of E-protein biology.
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Affiliation(s)
- Catherine S Schrankel
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Cynthia M Solek
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Katherine M Buckley
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Michele K Anderson
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jonathan P Rast
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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Chang YC, Pai CY, Chen YC, Ting HC, Martinez P, Telford MJ, Yu JK, Su YH. Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning. Dev Biol 2016; 410:108-18. [DOI: 10.1016/j.ydbio.2015.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
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Widhalm JR, Rhodes D. Biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants. HORTICULTURE RESEARCH 2016; 3:16046. [PMID: 27688890 PMCID: PMC5030760 DOI: 10.1038/hortres.2016.46] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/23/2016] [Indexed: 05/20/2023]
Abstract
The 1,4-naphthoquinones (1,4-NQs) are a diverse group of natural products found in every kingdom of life. Plants, including many horticultural species, collectively synthesize hundreds of specialized 1,4-NQs with ecological roles in plant-plant (allelopathy), plant-insect and plant-microbe interactions. Numerous horticultural plants producing 1,4-NQs have also served as sources of traditional medicines for hundreds of years. As a result, horticultural species have been at the forefront of many basic studies conducted to understand the metabolism and function of specialized plant 1,4-NQs. Several 1,4-NQ natural products derived from horticultural plants have also emerged as promising scaffolds for developing new drugs. In this review, the current understanding of the core metabolic pathways leading to plant 1,4-NQs is provided with additional emphasis on downstream natural products originating from horticultural species. An overview on the biochemical mechanisms of action, both from an ecological and pharmacological perspective, of 1,4-NQs derived from horticultural plants is also provided. In addition, future directions for improving basic knowledge about plant 1,4-NQ metabolism are discussed.
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Affiliation(s)
- Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
- ()
| | - David Rhodes
- Department of Horticulture and Landscape Architecture, Purdue University, 625 Agriculture Mall Drive, West Lafayette, IN 47907-2010, USA
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Katow H. Mechanisms of the epithelial-to-mesenchymal transition in sea urchin embryos. Tissue Barriers 2015; 3:e1059004. [PMID: 26716069 PMCID: PMC4681286 DOI: 10.1080/21688370.2015.1059004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 12/30/2022] Open
Abstract
Sea urchin mesenchyme is composed of the large micromere-derived spiculogenetic primary mesenchyme cells (PMC), veg2-tier macromere-derived non-spiculogenetic mesenchyme cells, the small micromere-derived germ cells, and the macro- and mesomere-derived neuronal mesenchyme cells. They are formed through the epithelial-to-mesenchymal transition (EMT) and possess multipotency, except PMCs that solely differentiate larval spicules. The process of EMT is associated with modification of epithelial cell surface property that includes loss of affinity to the apical and basal extracellular matrices, inter-epithelial cell adherens junctions and epithelial cell surface-specific proteins. These cell surface structures and molecules are endocytosed during EMT and utilized as initiators of cytoplasmic signaling pathways that often initiate protein phosphorylation to activate the gene regulatory networks. Acquisition of cell motility after EMT in these mesenchyme cells is associated with the expression of proteins such as Lefty, Snail and Seawi. Structural simplicity and genomic database of this model will further promote detailed EMT research.
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Affiliation(s)
- Hideki Katow
- Research Center for Marine Biology; Tohoku University; Asamushi, Aomori, Japan
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Zito F, Koop D, Byrne M, Matranga V. Carbonic anhydrase inhibition blocks skeletogenesis and echinochrome production in Paracentrotus lividus and Heliocidaris tuberculata embryos and larvae. Dev Growth Differ 2015; 57:507-14. [PMID: 26108341 DOI: 10.1111/dgd.12229] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 11/26/2022]
Abstract
Carbonic anhydrases (CAs) are a family of widely distributed metalloenzymes, involved in diverse physiological processes. These enzymes catalyse the reversible conversion of carbon dioxide to protons and bicarbonate. At least 19 genes encoding for CAs have been identified in the sea urchin genome, with one of these localized to the skeletogenic mesoderm (primary mesenchyme cells, PMCs). We investigated the effects of a specific inhibitor of CA, acetazolamide (AZ), on development of two sea urchin species with contrasting investment in skeleton production, Paracentrotus lividus and Heliocidaris tuberculata, to determine the role of CA on PMC differentiation, skeletogenesis and on non-skeletogenic mesodermal (NSM) cells. Embryos were cultured in the presence of AZ from the blastula stage prior to skeleton formation and development to the larval stage was monitored. At the dose of 8 mmol/L AZ, 98% and 90% of P. lividus and H. tuberculata embryos lacked skeleton, respectively. Nevertheless, an almost normal PMC differentiation was indicated by the expression of msp130, a PMC-specific marker. Strikingly, the AZ-treated embryos also lacked the echinochrome pigment produced by the pigment cells, a subpopulation of NSM cells with immune activities within the larva. Conversely, all ectoderm and endoderm derivatives and other subpopulations of mesoderm developed normally. The inhibitory effects of AZ were completely reversed after removal of the inhibitor from the medium. Our data, together with new information concerning the involvement of CA on skeleton formation, provide evidence for the first time of a possible role of the CAs in larval immune pigment cells.
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Affiliation(s)
- Francesca Zito
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, Palermo, 153 - 90146, Italy
| | - Demian Koop
- Schools of Medical and Biological Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Maria Byrne
- Schools of Medical and Biological Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Valeria Matranga
- Institute of Biomedicine and Molecular Immunology "A. Monroy", National Research Council, Via Ugo La Malfa, Palermo, 153 - 90146, Italy
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Odintsova NA, Ageenko NV, Kipryushina YO, Maiorova MA, Boroda AV. Freezing tolerance of sea urchin embryonic cells: Differentiation commitment and cytoskeletal disturbances in culture. Cryobiology 2015; 71:54-63. [PMID: 26049089 DOI: 10.1016/j.cryobiol.2015.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/15/2015] [Accepted: 06/02/2015] [Indexed: 11/29/2022]
Abstract
This study focuses on the freezing tolerance of sea urchin embryonic cells. To significantly reduce the loss of physiological activity of these cells that occurs after cryopreservation and to study the effects of ultra-low temperatures on sea urchin embryonic cells, we tested the ability of the cells to differentiate into spiculogenic or pigment directions in culture, including an evaluation of the expression of some genes involved in pigment differentiation. A morphological analysis of cytoskeletal disturbances after freezing in a combination of penetrating (dimethyl sulfoxide and ethylene glycol) and non-penetrating (trehalose and polyvinylpyrrolidone) cryoprotectants revealed that the distribution pattern of filamentous actin and tubulin was similar to that in the control cultures. In contrast, very rare spreading cells and a small number of cells with filamentous actin and tubulin were detected after freezing in the presence of only non-penetrating cryoprotectants. The largest number of pigment cells was found in cultures frozen with trehalose or trehalose and dimethyl sulfoxide. The ability to induce the spicule formation was lost in the cells frozen only with non-penetrating cryoprotectants, while it was maximal in cultures frozen in a cryoprotective mixture containing both non-penetrating and penetrating cryoprotectants (particularly, when ethylene glycol was present). Using different markers for cell state assessment, an effective cryopreservation protocol for sea urchin cells was developed: three-step freezing with a low cooling rate (1-2°C/min) and a combination of non-penetrating and penetrating cryoprotectants made it possible to obtain a high level of cell viability (up to 65-80%).
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Affiliation(s)
- Nelly A Odintsova
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, 690041, Palchevsky st. 17, Vladivostok, Russia.
| | - Natalya V Ageenko
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, 690041, Palchevsky st. 17, Vladivostok, Russia
| | - Yulia O Kipryushina
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, 690041, Palchevsky st. 17, Vladivostok, Russia
| | - Mariia A Maiorova
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, 690041, Palchevsky st. 17, Vladivostok, Russia
| | - Andrey V Boroda
- Laboratory of Cytotechnology, A.V. Zhirmunsky Institute of Marine Biology, The Far Eastern Branch of the Russian Academy of Sciences, 690041, Palchevsky st. 17, Vladivostok, Russia
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Hojo M, Omi A, Hamanaka G, Shindo K, Shimada A, Kondo M, Narita T, Kiyomoto M, Katsuyama Y, Ohnishi Y, Irie N, Takeda H. Unexpected link between polyketide synthase and calcium carbonate biomineralization. ZOOLOGICAL LETTERS 2015; 1:3. [PMID: 26605048 PMCID: PMC4604110 DOI: 10.1186/s40851-014-0001-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/15/2014] [Indexed: 06/05/2023]
Abstract
INTRODUCTION Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms. RESULTS We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates. CONCLUSION The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.
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Affiliation(s)
- Motoki Hojo
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Department of Pharmaceutical and Environmental Sciences, Tokyo Metropolitan Institute of Public Health, 3-24–1, Hyakunincho, Shinju-ku, Tokyo 169-0073 Japan
| | - Ai Omi
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022 Japan
| | - Gen Hamanaka
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Kazutoshi Shindo
- />Department of Food and Nutrition, Japan Women’s University, 2-8-1, Mejirodai, Bunkyo-ku, Tokyo 112-8681 Japan
| | - Atsuko Shimada
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Mariko Kondo
- />Misaki Marine Biological Station, Graduate School of Science, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225 Japan
| | - Takanori Narita
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
- />Present address: Laboratory of Veterinary Biochemistry, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa, Kanagawa 252-0880 Japan
| | - Masato Kiyomoto
- />Tateyama Marine Laboratory, Marine and Coastal Research Center, Ochanomizu University, Kou-yatsu 11, Tateyama, Chiba 294-0301 Japan
| | - Yohei Katsuyama
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Yasuo Ohnishi
- />Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Naoki Irie
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- />Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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Ageenko NV, Kiselev KV, Dmitrenok PS, Odintsova NA. Pigment cell differentiation in sea urchin blastula-derived primary cell cultures. Mar Drugs 2014; 12:3874-91. [PMID: 24979272 PMCID: PMC4113803 DOI: 10.3390/md12073874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/27/2014] [Accepted: 05/30/2014] [Indexed: 12/03/2022] Open
Abstract
The quinone pigments of sea urchins, specifically echinochrome and spinochromes, are known for their effective antioxidant, antibacterial, antifungal, and antitumor activities. We developed in vitro technology for inducing pigment differentiation in cell culture. The intensification of the pigment differentiation was accompanied by a simultaneous decrease in cell proliferation. The number of pigment cells was two-fold higher in the cells cultivated in the coelomic fluids of injured sea urchins than in those intact. The possible roles of the specific components of the coelomic fluids in the pigment differentiation process and the quantitative measurement of the production of naphthoquinone pigments during cultivation were examined by MALDI and electrospray ionization mass spectrometry. Echinochrome A and spinochrome E were produced by the cultivated cells of the sand dollar Scaphechinus mirabilis in all tested media, while only spinochromes were found in the cultivated cells of another sea urchin, Strongylocentrotus intermedius. The expression of genes associated with the induction of pigment differentiation was increased in cells cultivated in the presence of shikimic acid, a precursor of naphthoquinone pigments. Our results should contribute to the development of new techniques in marine biotechnology, including the generation of cell cultures producing complex bioactive compounds with therapeutic potential.
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Affiliation(s)
- Natalya V Ageenko
- Cytotechnology Laboratory, A.V. Zhirmunsky Institute of Marine Biology, FEB RAS, Vladivostok 690041, Russia.
| | - Konstantin V Kiselev
- Laboratory of Biotechnology, Institute of Biology and Soil Sciences, FEB RAS, Vladivostok 690022, Russia.
| | - Pavel S Dmitrenok
- Laboratory of Instrumental and Radioisotope Methods of Analysis, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, FEB RAS, Vladivostok 690022, Russia.
| | - Nelly A Odintsova
- Cytotechnology Laboratory, A.V. Zhirmunsky Institute of Marine Biology, FEB RAS, Vladivostok 690041, Russia.
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Della Sala G, Hochmuth T, Costantino V, Teta R, Gerwick W, Gerwick L, Piel J, Mangoni A. Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:809-818. [PMID: 24249289 PMCID: PMC3908369 DOI: 10.1111/1758-2229.12081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 06/22/2013] [Indexed: 05/31/2023]
Abstract
Sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. Insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. Screening of the metagenome of the marine sponge Plakortis simplex led to the discovery of the swf family, a new group of mono-modular type I polyketide synthase/fatty acid synthase (PKS/FAS) specifically associated with sponge symbionts. Two different examples of the swf cluster were present in the metagenome of P. simplex. A third example of the cluster is present in the previously sequenced genome of a poribacterium from the sponge Aplysina aerophoba but was formerly considered orthologous to the wcb/rkp cluster. The swf cluster was also found in six additional species of sponges. Therefore, the swf cluster represents the second group of mono-modular PKS, after the supA family, to be widespread in marine sponges. The putative swf operon consists of swfA (type I PKS/FAS), swfB (reductase and sulphotransferase domains) and swfC (radical S-adenosylmethionine, or radical SAM). Activation of the acyl carrier protein (ACP) domain of the SwfA protein to its holo-form by co-expression with Svp is the first functional proof of swf type genes in marine sponges. However, the precise biosynthetic role of the swf clusters remains unknown.
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Affiliation(s)
- Gerardo Della Sala
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Thomas Hochmuth
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Valeria Costantino
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - Roberta Teta
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
| | - William Gerwick
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego9500 Gilman Drive, MC 0212, La Jolla, CA, 92093-0212, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego9500 Gilman Drive, MC 0212, La Jolla, CA, 92093-0212, USA
| | - Jörn Piel
- Institute of Microbiology, Eidgenoessische Technische Hochschule (ETH) ZurichWolfgang-Pauli-Str. 10, 8093, Zurich, Switzerland
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università di Napoli Federico IIVia Domenico Montesano, 49, 80131, Napoli, Italy
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50
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Garfield DA, Runcie DE, Babbitt CC, Haygood R, Nielsen WJ, Wray GA. The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network. PLoS Biol 2013; 11:e1001696. [PMID: 24204211 PMCID: PMC3812118 DOI: 10.1371/journal.pbio.1001696] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/16/2013] [Indexed: 11/18/2022] Open
Abstract
Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear), allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role.
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Affiliation(s)
- David A. Garfield
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Daniel E. Runcie
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Courtney C. Babbitt
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Ralph Haygood
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
| | - William J. Nielsen
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- Center for Systems Biology, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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