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Adriano EA, Zatti SA, Okamura B. How to build single-celled cnidarians with worm-like motility: Lessons from Myxozoa. J Anat 2022; 240:475-488. [PMID: 34643951 PMCID: PMC8819041 DOI: 10.1111/joa.13566] [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: 05/04/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/27/2022] Open
Abstract
Metazoans with worm-like morphologies across diverse and disparate groups typically demonstrate motility generated by hydrostatic skeletons involving tissue layers (muscles and epithelia). Here we present representative morphological, behavioural and molecular data for parasitic cnidarians (myxozoans) that demonstrate unprecedented variation in form and function, developing as cellular hydrostats. Motile elongate plasmodia characterise a remarkable radiation of species in the genus Ceratomyxa. The vermiform plasmodia inhabit gall bladders of a range of South American freshwater fish and exhibit undulatory motility reminiscent of nematodes but achieved at the cellular level. Collective insights from ultrastructure, confocal and light microscopy along with videos depicting movements highlight key features that we propose explain the unique motility of the plasmodia. These features include cytoskeletal elements (net forming microfilaments and microtubules), a large internal vacuole, a relatively rigid outer glycocalyx and peripherally arranged mitochondria. These constituents provide collective evidence for repurposing of the cnidarian epitheliomuscular cell to support worm-like motility at the cellular level. The apparent restriction of vermiform ceratomyxids to South American freshwaters suggests an origination via Cretaceous or Miocene marine transgressions and subsequent radiation.
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Affiliation(s)
- Edson A. Adriano
- Department de Ecology and Evolutionary BiologyFederal University of São PauloDiademaSPBrazil
- Department of Animal BiologyState University of CampinasCampinasSPBrazil
| | - Suellen A. Zatti
- Department of Veterinary MedicineFaculty of Animal Science and Food EngineeringUniversity of São PauloPirassunungaSPBrazil
| | - Beth Okamura
- Department of Life SciencesNatural History MuseumLondonUK
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52
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Kin K, Chen ZH, Forbes G, Schaap P. Evolution of a novel cell type in Dictyostelia required gene duplication of a cudA-like transcription factor. Curr Biol 2022; 32:428-437.e4. [PMID: 34883046 PMCID: PMC8808424 DOI: 10.1016/j.cub.2021.11.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/04/2021] [Accepted: 11/17/2021] [Indexed: 10/31/2022]
Abstract
The evolution of novel cell types has been proposed to result from duplication of gene regulatory networks, but proven examples are rare. In addition to stalk cells and spores that make up the fruiting bodies of three major groups of Dictyostelia, those in group 4 additionally evolved basal disc and cup cells that respectively anchor the stalk to the substratum and the spore mass to the stalk. We noted a putative group-4-specific duplication of a cudA-like transcription factor (TF) in a comparative analysis of group-representative genomes. Using increased taxon sampling, we here confirmed that this TF, cdl1, duplicated into cdl1a and cdl1b in the common ancestor to group 4. cdl1a, but not cdl1b, showed signatures of positive selection, indicative of functional innovation. Deletion of cdl1a in Dictyostelium discoideum resulted in fruiting bodies with sagging spore heads that lacked the supporting cup cells and expression of cup-specific genes. Deletion of cdl1b resulted in thinner fruiting body stalks, while a cdl1b-cdl1a- double knockout showed more severe stalk defects, suggesting an ancestral role of cdl1 in stalk formation. This was confirmed in a closely related non-group 4 species, Polysphondylium violaceum, where cdl1 knockout caused defective stalk formation. These data indicate that the group-specific duplication of cdl1 and subsequent diversification of cdl1a played a pivotal role in the evolution of a novel somatic cell type in group 4 Dictyostelia.
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Affiliation(s)
- Koryu Kin
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK; Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Zhi-Hui Chen
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK
| | - Gillian Forbes
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK
| | - Pauline Schaap
- University of Dundee, School of Life Sciences, Dow Street, Dundee DD1 5EH, UK.
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Atake OJ, Eames BF. Mineralized Cartilage and Bone-Like Tissues in Chondrichthyans Offer Potential Insights Into the Evolution and Development of Mineralized Tissues in the Vertebrate Endoskeleton. Front Genet 2022; 12:762042. [PMID: 35003210 PMCID: PMC8727550 DOI: 10.3389/fgene.2021.762042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
The impregnation of biominerals into the extracellular matrix of living organisms, a process termed biomineralization, gives rise to diverse mineralized (or calcified) tissues in vertebrates. Preservation of mineralized tissues in the fossil record has provided insights into the evolutionary history of vertebrates and their skeletons. However, current understanding of the vertebrate skeleton and of the processes underlying its formation is biased towards biomedical models such as the tetrapods mouse and chick. Chondrichthyans (sharks, skates, rays, and chimaeras) and osteichthyans are the only vertebrate groups with extant (living) representatives that have a mineralized skeleton, but the basal phylogenetic position of chondrichthyans could potentially offer unique insights into skeletal evolution. For example, bone is a vertebrate novelty, but the internal supporting skeleton (endoskeleton) of extant chondrichthyans is commonly described as lacking bone. The molecular and developmental basis for this assertion is yet to be tested. Subperichondral tissues in the endoskeleton of some chondrichthyans display mineralization patterns and histological and molecular features of bone, thereby challenging the notion that extant chondrichthyans lack endoskeletal bone. Additionally, the chondrichthyan endoskeleton demonstrates some unique features and others that are potentially homologous with other vertebrates, including a polygonal mineralization pattern, a trabecular mineralization pattern, and an unconstricted perichordal sheath. Because of the basal phylogenetic position of chondrichthyans among all other extant vertebrates with a mineralized skeleton, developmental and molecular studies of chondrichthyans are critical to flesh out the evolution of vertebrate skeletal tissues, but only a handful of such studies have been carried out to date. This review discusses morphological and molecular features of chondrichthyan endoskeletal tissues and cell types, ultimately emphasizing how comparative embryology and transcriptomics can reveal homology of mineralized skeletal tissues (and their cell types) between chondrichthyans and other vertebrates.
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Affiliation(s)
- Oghenevwogaga J Atake
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
| | - B Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, SK, Canada
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Abstract
The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.
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55
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Arendt D, Urzainqui IQ, Vergara HM. The conserved core of the nereid brain: Circular CNS, apical nervous system and lhx6-arx-dlx neurons. Curr Opin Neurobiol 2021; 71:178-187. [PMID: 34861534 DOI: 10.1016/j.conb.2021.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 11/28/2022]
Abstract
When bilaterian animals first emerged, an enhanced perception of the Precambrian environment was key to their stunning success. This occurred through the acquisition of an anterior brain, as found in most extant bilaterians. What were the core circuits of the first brain, and how do they relate to today's diversity? With two landmark resources - the full connectome and a multimodal cellular atlas combining gene expression and ultrastructure - the young worm of the marine annelid Platynereis dumerilii takes center stage in comparative bilaterian neuroanatomy. The new data suggest a composite structure of the ancestral bilaterian brain, with the anterior end of a circular CNS fused to a sensory-neurosecretory apical system, and with lhx6-arx-dlx chemosensory circuits giving rise to associative centers in the descending bilaterian lineages.
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Affiliation(s)
- Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69012, Heidelberg, Germany.
| | - Idoia Quintana Urzainqui
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69012, Heidelberg, Germany
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56
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Hines JH. Evolutionary Origins of the Oligodendrocyte Cell Type and Adaptive Myelination. Front Neurosci 2021; 15:757360. [PMID: 34924932 PMCID: PMC8672417 DOI: 10.3389/fnins.2021.757360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/29/2021] [Indexed: 12/23/2022] Open
Abstract
Oligodendrocytes are multifunctional central nervous system (CNS) glia that are essential for neural function in gnathostomes. The evolutionary origins and specializations of the oligodendrocyte cell type are among the many remaining mysteries in glial biology and neuroscience. The role of oligodendrocytes as CNS myelinating glia is well established, but recent studies demonstrate that oligodendrocytes also participate in several myelin-independent aspects of CNS development, function, and maintenance. Furthermore, many recent studies have collectively advanced our understanding of myelin plasticity, and it is now clear that experience-dependent adaptations to myelination are an additional form of neural plasticity. These observations beg the questions of when and for which functions the ancestral oligodendrocyte cell type emerged, when primitive oligodendrocytes evolved new functionalities, and the genetic changes responsible for these evolutionary innovations. Here, I review recent findings and propose working models addressing the origins and evolution of the oligodendrocyte cell type and adaptive myelination. The core gene regulatory network (GRN) specifying the oligodendrocyte cell type is also reviewed as a means to probe the existence of oligodendrocytes in basal vertebrates and chordate invertebrates.
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Affiliation(s)
- Jacob H. Hines
- Biology Department, Winona State University, Winona, MN, United States
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57
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Paganos P, Voronov D, Musser JM, Arendt D, Arnone MI. Single-cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. eLife 2021; 10:70416. [PMID: 34821556 PMCID: PMC8683087 DOI: 10.7554/elife.70416] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying the molecular fingerprint of organismal cell types is key for understanding their function and evolution. Here, we use single-cell RNA sequencing (scRNA-seq) to survey the cell types of the sea urchin early pluteus larva, representing an important developmental transition from non-feeding to feeding larva. We identify 21 distinct cell clusters, representing cells of the digestive, skeletal, immune, and nervous systems. Further subclustering of these reveal a highly detailed portrait of cell diversity across the larva, including the identification of neuronal cell types. We then validate important gene regulatory networks driving sea urchin development and reveal new domains of activity within the larval body. Focusing on neurons that co-express Pdx-1 and Brn1/2/4, we identify an unprecedented number of genes shared by this population of neurons in sea urchin and vertebrate endocrine pancreatic cells. Using differential expression results from Pdx-1 knockdown experiments, we show that Pdx1 is necessary for the acquisition of the neuronal identity of these cells. We hypothesize that a network similar to the one orchestrated by Pdx1 in the sea urchin neurons was active in an ancestral cell type and then inherited by neuronal and pancreatic developmental lineages in sea urchins and vertebrates.
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Affiliation(s)
- Periklis Paganos
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Danila Voronov
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
| | - Jacob M Musser
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Heidelberg, Germany
| | - Maria Ina Arnone
- Stazione Zoologica Anton Dohrn, Department of Biology and Evolution of Marine Organisms, Naples, Italy
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58
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Padilla S, Nurden AT, Prado R, Nurden P, Anitua E. Healing through the lens of immunothrombosis: Biology-inspired, evolution-tailored, and human-engineered biomimetic therapies. Biomaterials 2021; 279:121205. [PMID: 34710794 DOI: 10.1016/j.biomaterials.2021.121205] [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: 06/17/2021] [Revised: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022]
Abstract
Evolution, from invertebrates to mammals, has yielded and shaped immunoclotting as a defense and repair response against trauma and infection. This mosaic of immediate and local wound-sealing and pathogen-killing mechanisms results in survival, restoration of homeostasis, and tissue repair. In mammals, immunoclotting has been complemented with the neuroendocrine system, platelets, and contact system among other embellishments, adding layers of complexity through interconnecting blood-born proteolytic cascades, blood cells, and the neuroendocrine system. In doing so, immunothrombosis endows humans with survival advantages, but entails vulnerabilities in the current unprecedented and increasingly challenging environment. Immunothrombosis and tissue repair appear to go hand in hand with common mechanisms mediating both processes, a fact that is underlined by recent advances that are deciphering the mechanisms of the repair process and of the biochemical pathways that underpins coagulation, hemostasis and thrombosis. This review is intended to frame both the universal aspects of tissue repair and the therapeutic use of autologous fibrin matrix as a biology-as-a-drug approach in the context of the evolutionary changes in coagulation and hemostasis. In addition, we will try to shed some light on the molecular mechanisms underlying the use of the autologous fibrin matrix as a biology-inspired, evolution-tailored, and human-engineered biomimetic therapy.
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Affiliation(s)
- Sabino Padilla
- Eduardo Anitua Foundation for Biomedical Research, Vitoria, Spain; BTI-Biotechnology Institute ImasD, Vitoria, Spain; University Institute for Regenerative Medicine & Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, Spain.
| | - Alan T Nurden
- Institut Hospitalo-Universitaire LIRYC, Hôpital Xavier Arnozan, Pessac, France
| | - Roberto Prado
- Eduardo Anitua Foundation for Biomedical Research, Vitoria, Spain; BTI-Biotechnology Institute ImasD, Vitoria, Spain; University Institute for Regenerative Medicine & Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, Spain
| | - Paquita Nurden
- Institut Hospitalo-Universitaire LIRYC, Hôpital Xavier Arnozan, Pessac, France
| | - Eduardo Anitua
- Eduardo Anitua Foundation for Biomedical Research, Vitoria, Spain; BTI-Biotechnology Institute ImasD, Vitoria, Spain; University Institute for Regenerative Medicine & Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, Spain.
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59
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Abstract
Neurons are highly specialized cells equipped with a sophisticated molecular machinery for the reception, integration, conduction and distribution of information. The evolutionary origin of neurons remains unsolved. How did novel and pre-existing proteins assemble into the complex machinery of the synapse and of the apparatus conducting current along the neuron? In this review, the step-wise assembly of functional modules in neuron evolution serves as a paradigm for the emergence and modification of molecular machinery in the evolution of cell types in multicellular organisms. The pre-synaptic machinery emerged through modification of calcium-regulated large vesicle release, while the postsynaptic machinery has different origins: the glutamatergic postsynapse originated through the fusion of a sensory signaling module and a module for filopodial outgrowth, while the GABAergic postsynapse incorporated an ancient actin regulatory module. The synaptic junction, in turn, is built around two adhesion modules controlled by phosphorylation, which resemble septate and adherens junctions. Finally, neuronal action potentials emerged via a series of duplications and modifications of voltage-gated ion channels. Based on these origins, key molecular innovations are identified that led to the birth of the first neuron in animal evolution.
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60
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Revilla-i-Domingo R, Rajan VBV, Waldherr M, Prohaczka G, Musset H, Orel L, Gerrard E, Smolka M, Stockinger A, Farlik M, Lucas RJ, Raible F, Tessmar-Raible K. Characterization of cephalic and non-cephalic sensory cell types provides insight into joint photo- and mechanoreceptor evolution. eLife 2021; 10:e66144. [PMID: 34350831 PMCID: PMC8367381 DOI: 10.7554/elife.66144] [Citation(s) in RCA: 9] [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: 12/30/2020] [Accepted: 08/04/2021] [Indexed: 12/11/2022] Open
Abstract
Rhabdomeric opsins (r-opsins) are light sensors in cephalic eye photoreceptors, but also function in additional sensory organs. This has prompted questions on the evolutionary relationship of these cell types, and if ancient r-opsins were non-photosensory. A molecular profiling approach in the marine bristleworm Platynereis dumerilii revealed shared and distinct features of cephalic and non-cephalic r-opsin1-expressing cells. Non-cephalic cells possess a full set of phototransduction components, but also a mechanosensory signature. Prompted by the latter, we investigated Platynereis putative mechanotransducer and found that nompc and pkd2.1 co-expressed with r-opsin1 in TRE cells by HCR RNA-FISH. To further assess the role of r-Opsin1 in these cells, we studied its signaling properties and unraveled that r-Opsin1 is a Gαq-coupled blue light receptor. Profiling of cells from r-opsin1 mutants versus wild-types, and a comparison under different light conditions reveals that in the non-cephalic cells light - mediated by r-Opsin1 - adjusts the expression level of a calcium transporter relevant for auditory mechanosensation in vertebrates. We establish a deep-learning-based quantitative behavioral analysis for animal trunk movements and identify a light- and r-Opsin-1-dependent fine-tuning of the worm's undulatory movements in headless trunks, which are known to require mechanosensory feedback. Our results provide new data on peripheral cell types of likely light sensory/mechanosensory nature. These results point towards a concept in which such a multisensory cell type evolved to allow for fine-tuning of mechanosensation by light. This implies that light-independent mechanosensory roles of r-opsins may have evolved secondarily.
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Affiliation(s)
- Roger Revilla-i-Domingo
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Vinoth Babu Veedin Rajan
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Monika Waldherr
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Günther Prohaczka
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Hugo Musset
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Lukas Orel
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
| | - Elliot Gerrard
- Division of Neuroscience & Experimental Psychology, University of ManchesterManchesterUnited Kingdom
| | - Moritz Smolka
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of ViennaViennaAustria
| | - Alexander Stockinger
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Department of Dermatology, Medical University of ViennaViennaAustria
| | - Robert J Lucas
- Division of Neuroscience & Experimental Psychology, University of ManchesterManchesterUnited Kingdom
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform "Single-Cell Regulation of Stem Cells", University of Vienna, Vienna BioCenterViennaAustria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenterViennaAustria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenterViennaAustria
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61
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Moroz LL. Multiple Origins of Neurons From Secretory Cells. Front Cell Dev Biol 2021; 9:669087. [PMID: 34307354 PMCID: PMC8293673 DOI: 10.3389/fcell.2021.669087] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Affiliation(s)
- Leonid L. Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, United States
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
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62
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Zhang Y, Mao F, Mu H, Huang M, Bao Y, Wang L, Wong NK, Xiao S, Dai H, Xiang Z, Ma M, Xiong Y, Zhang Z, Zhang L, Song X, Wang F, Mu X, Li J, Ma H, Zhang Y, Zheng H, Simakov O, Yu Z. The genome of Nautilus pompilius illuminates eye evolution and biomineralization. Nat Ecol Evol 2021; 5:927-938. [PMID: 33972735 PMCID: PMC8257504 DOI: 10.1038/s41559-021-01448-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Nautilus is the sole surviving externally shelled cephalopod from the Palaeozoic. It is unique within cephalopod genealogy and critical to understanding the evolutionary novelties of cephalopods. Here, we present a complete Nautilus pompilius genome as a fundamental genomic reference on cephalopod innovations, such as the pinhole eye and biomineralization. Nautilus shows a compact, minimalist genome with few encoding genes and slow evolutionary rates in both non-coding and coding regions among known cephalopods. Importantly, multiple genomic innovations including gene losses, independent contraction and expansion of specific gene families and their associated regulatory networks likely moulded the evolution of the nautilus pinhole eye. The conserved molluscan biomineralization toolkit and lineage-specific repetitive low-complexity domains are essential to the construction of the nautilus shell. The nautilus genome constitutes a valuable resource for reconstructing the evolutionary scenarios and genomic innovations that shape the extant cephalopods.
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Affiliation(s)
- Yang Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Fan Mao
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Huawei Mu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Minwei Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Nai-Kei Wong
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Xiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Zhiming Xiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Mingli Ma
- Biomarker Technologies Corporation, Beijing, China
| | - Yuanyan Xiong
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwei Zhang
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lvping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Xiaoyuan Song
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fan Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Xiyu Mu
- Biomarker Technologies Corporation, Beijing, China
| | - Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Haitao Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | | | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Ziniu Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
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63
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Feregrino C, Tschopp P. Assessing evolutionary and developmental transcriptome dynamics in homologous cell types. Dev Dyn 2021; 251:1472-1489. [PMID: 34114716 PMCID: PMC9545966 DOI: 10.1002/dvdy.384] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background During development, complex organ patterns emerge through the precise temporal and spatial specification of different cell types. On an evolutionary timescale, these patterns can change, resulting in morphological diversification. It is generally believed that homologous anatomical structures are built—largely—by homologous cell types. However, whether a common evolutionary origin of such cell types is always reflected in the conservation of their intrinsic transcriptional specification programs is less clear. Results Here, we developed a user‐friendly bioinformatics workflow to detect gene co‐expression modules and test for their conservation across developmental stages and species boundaries. Using a paradigm of morphological diversification, the tetrapod limb, and single‐cell RNA‐sequencing data from two distantly related species, chicken and mouse, we assessed the transcriptional dynamics of homologous cell types during embryonic patterning. With mouse limb data as reference, we identified 19 gene co‐expression modules with varying tissue or cell type‐restricted activities. Testing for co‐expression conservation revealed modules with high evolutionary turnover, while others seemed maintained—to different degrees, in module make‐up, density or connectivity—over developmental and evolutionary timescales. Conclusions We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data. We present an approach to identify evolutionary and developmental dynamics in gene co‐expression modules during patterning‐relevant stages of homologous cell type specification using single‐cell RNA‐sequencing data.
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Affiliation(s)
- Christian Feregrino
- DUW Zoology, University of Basel, Basel, Switzerland.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany. Hannoversche Str. 28, Berlin, Germany
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64
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Franklin RA. Fibroblasts and macrophages: Collaborators in tissue homeostasis. Immunol Rev 2021; 302:86-103. [PMID: 34101202 DOI: 10.1111/imr.12989] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/12/2021] [Accepted: 05/15/2021] [Indexed: 12/19/2022]
Abstract
Fibroblasts and macrophages are universal cell types across all mammalian tissues. These cells differ in many ways including their cellular origins; dynamics of renewal, recruitment, and motility within tissues; roles in tissue structure and secretion of signaling molecules; and contributions to the activation and progression of immune responses. However, many of the features that make these two cell types unique are not opposing, but instead complementary. This review will present cell-cell communication in this context and discuss how complementarity makes fibroblasts and macrophages highly compatible partners in the maintenance of tissue homeostasis.
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Affiliation(s)
- Ruth A Franklin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Immunology, Harvard Medical School, Boston, MA, USA
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65
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Jaeger J, Monk N. Dynamical modules in metabolism, cell and developmental biology. Interface Focus 2021; 11:20210011. [PMID: 34055307 PMCID: PMC8086940 DOI: 10.1098/rsfs.2021.0011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2021] [Indexed: 02/06/2023] Open
Abstract
Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function, which can vary (quasi-)independently from its context. Since all phenotypic traits are the product of some underlying regulatory dynamics, the generative processes that constitute the genotype-phenotype map must also be functionally modular. Traditionally, modular processes have been identified as structural modules in regulatory networks. However, structure only constrains, but does not determine, the dynamics of a process. Here, we propose an alternative approach that decomposes the behaviour of a complex regulatory system into elementary activity-functions. Modular activities can occur in networks that show no structural modularity, making dynamical modularity more widely applicable than structural decomposition. Furthermore, the behaviour of a regulatory system closely mirrors its functional contribution to the outcome of a process, which makes dynamical modularity particularly suited for functional decomposition. We illustrate our approach with numerous examples from the study of metabolism, cellular processes, as well as development and pattern formation. We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and serve as the foundation for a new account of process homology, which is presented in a separate contribution by DiFrisco and Jaeger to this focus issue.
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Affiliation(s)
- Johannes Jaeger
- Complexity Science Hub (CSH) Vienna, Josefstädter Strasse 39, 1080 Vienna, Austria
| | - Nick Monk
- School of Mathematics and Statistics, University of Sheffield, Hicks Building, Sheffield S3 7RH, UK
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66
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Tanay A, Sebé-Pedrós A. Evolutionary Cell Type Mapping with Single-Cell Genomics. Trends Genet 2021; 37:919-932. [PMID: 34020820 DOI: 10.1016/j.tig.2021.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 12/14/2022]
Abstract
A fundamental characteristic of animal multicellularity is the spatial coexistence of functionally specialized cell types that are all encoded by a single genome sequence. Cell type transcriptional programs are deployed and maintained by regulatory mechanisms that control the asymmetric, differential access to genomic information in each cell. This genome regulation ultimately results in specific cellular phenotypes. However, the emergence, diversity, and evolutionary dynamics of animal cell types remain almost completely unexplored beyond a few species. Single-cell genomics is emerging as a powerful tool to build comprehensive catalogs of cell types and their associated gene regulatory programs in non-traditional model species. We review the current state of sampling efforts across the animal tree of life and challenges ahead for the comparative study of cell type programs. We also discuss how the phylogenetic integration of cell atlases can lead to the development of models of cell type evolution and a phylogenetic taxonomy of cells.
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Affiliation(s)
- Amos Tanay
- Department of Computer Science and Applied Mathematics, and Department of Biological Regulation, Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
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67
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Almeida N, Chung MWH, Drudi EM, Engquist EN, Hamrud E, Isaacson A, Tsang VSK, Watt FM, Spagnoli FM. Employing core regulatory circuits to define cell identity. EMBO J 2021; 40:e106785. [PMID: 33934382 PMCID: PMC8126924 DOI: 10.15252/embj.2020106785] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between extrinsic signaling and downstream gene networks controls the establishment of cell identity during development and its maintenance in adult life. Advances in next-generation sequencing and single-cell technologies have revealed additional layers of complexity in cell identity. Here, we review our current understanding of transcription factor (TF) networks as key determinants of cell identity. We discuss the concept of the core regulatory circuit as a set of TFs and interacting factors that together define the gene expression profile of the cell. We propose the core regulatory circuit as a comprehensive conceptual framework for defining cellular identity and discuss its connections to cell function in different contexts.
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Affiliation(s)
- Nathalia Almeida
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Matthew W H Chung
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Elena M Drudi
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Elise N Engquist
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Eva Hamrud
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Abigail Isaacson
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Victoria S K Tsang
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
| | - Francesca M Spagnoli
- Centre for Stem Cells and Regenerative MedicineGuy’s HospitalKing’s College LondonLondonUK
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68
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Guernsey MW, van Kruistum H, Reznick DN, Pollux BJA, Baker JC. Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles. Mol Biol Evol 2021; 37:2679-2690. [PMID: 32421768 PMCID: PMC7475030 DOI: 10.1093/molbev/msaa121] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Placentation evolved many times independently in vertebrates. Although the core functions of all placentas are similar, we know less about how this similarity extends to the molecular level. Here, we study Poeciliopsis, a unique genus of live-bearing fish that have independently evolved complex placental structures at least three times. The maternal follicle is a key component of these structures. It envelops yolk-rich eggs and is morphologically simple in lecithotrophic species but has elaborate villous structures in matrotrophic species. Through sequencing, the follicle transcriptome of a matrotrophic, Poeciliopsis retropinna, and lecithotrophic, P. turrubarensis, species we found genes known to be critical for placenta function expressed in both species despite their difference in complexity. Additionally, when we compare the transcriptome of different river populations of P. retropinna, known to vary in maternal provisioning, we find differential expression of secretory genes expressed specifically in the top layer of villi cells in the maternal follicle. This provides some of the first evidence that the placental structures of Poeciliopsis function using a secretory mechanism rather than direct contact with maternal circulation. Finally, when we look at the expression of placenta proteins at the maternal–fetal interface of a larger sampling of Poeciliopsis species, we find expression of key maternal and fetal placenta proteins in their cognate tissue types of all species, but follicle expression of prolactin is restricted to only matrotrophic species. Taken together, we suggest that all Poeciliopsis follicles are poised for placenta function but require expression of key genes to form secretory villi.
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Affiliation(s)
- Michael W Guernsey
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Henri van Kruistum
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - David N Reznick
- Department of Biology, University of California Riverside, Riverside, CA
| | - Bart J A Pollux
- Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
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69
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Parisi C, Vashisht S, Winata CL. Fish-Ing for Enhancers in the Heart. Int J Mol Sci 2021; 22:3914. [PMID: 33920121 PMCID: PMC8069060 DOI: 10.3390/ijms22083914] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precise control of gene expression is crucial to ensure proper development and biological functioning of an organism. Enhancers are non-coding DNA elements which play an essential role in regulating gene expression. They contain specific sequence motifs serving as binding sites for transcription factors which interact with the basal transcription machinery at their target genes. Heart development is regulated by intricate gene regulatory network ensuring precise spatiotemporal gene expression program. Mutations affecting enhancers have been shown to result in devastating forms of congenital heart defect. Therefore, identifying enhancers implicated in heart biology and understanding their mechanism is key to improve diagnosis and therapeutic options. Despite their crucial role, enhancers are poorly studied, mainly due to a lack of reliable way to identify them and determine their function. Nevertheless, recent technological advances have allowed rapid progress in enhancer discovery. Model organisms such as the zebrafish have contributed significant insights into the genetics of heart development through enabling functional analyses of genes and their regulatory elements in vivo. Here, we summarize the current state of knowledge on heart enhancers gained through studies in model organisms, discuss various approaches to discover and study their function, and finally suggest methods that could further advance research in this field.
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Affiliation(s)
- Costantino Parisi
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Shikha Vashisht
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
| | - Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland; (C.P.); (S.V.)
- Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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70
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Kishi Y, Parker J. Cell type innovation at the tips of the animal tree. Curr Opin Genet Dev 2021; 69:112-121. [PMID: 33784538 DOI: 10.1016/j.gde.2021.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022]
Abstract
Understanding how organs originate is challenging due to the twin problems of explaining how new cell types evolve and how collective interactions between cell types arise and become selectively advantageous. Animals are assemblages of organs and cell types of different antiquities, and among the most rapidly and convergently evolving are exocrine glands and their constituent secretory cell types. Such structures have arisen independently thousands of times across the Metazoa, impacting how animals chemically interact with their environments. The recurrent evolution of exocrine systems provides a paradigm for examining how qualitative phenotypic novelties arise from variation at the cellular level. Here, we take a hierarchical perspective, focusing on the evolutionary assembly of novel biosynthetic pathways and secretory cell types, and how both selection and non-adaptive molecular processes may combine to build the complex, modular architectures of many animal glands.
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Affiliation(s)
- Yuriko Kishi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125, United States.
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71
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Abstract
The evolutionary origin of the nervous system has been a matter of long-standing debate. This is due to the different perspectives taken. Earlier studies addressed nervous system origins at the cellular level. They focused on the selective advantage of the first neuron in its local context, and considered vertical sensory-motor reflex arcs the first nervous system. Later studies emphasized the value of the nervous system at the tissue level. Rather than acting locally, early neurons were seen as part of an elementary nerve net that enabled the horizontal coordination of tissue movements. Opinions have also differed on the nature of effector cells. While most authors have favoured contractile systems, others see the key output of the incipient nervous system in the coordination of motile cilia, or the secretion of antimicrobial peptides. I will discuss these divergent views and explore how they can be validated by molecular and single-cell data. From this survey, possible consensus emerges: (i) the first manifestation of the nervous system likely was a nerve net, whereas specialized local circuits evolved later; (ii) different nerve nets may have evolved for the coordination of contractile or cilia-driven movements; (iii) all evolving nerve nets facilitated new forms of animal behaviour with increasing body size. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Detlev Arendt
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
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72
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Jékely G. The chemical brain hypothesis for the origin of nervous systems. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190761. [PMID: 33550946 PMCID: PMC7935135 DOI: 10.1098/rstb.2019.0761] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
In nervous systems, there are two main modes of transmission for the propagation of activity between cells. Synaptic transmission relies on close contact at chemical or electrical synapses while volume transmission is mediated by diffusible chemical signals and does not require direct contact. It is possible to wire complex neuronal networks by both chemical and synaptic transmission. Both types of networks are ubiquitous in nervous systems, leading to the question which of the two appeared first in evolution. This paper explores a scenario where chemically organized cellular networks appeared before synapses in evolution, a possibility supported by the presence of complex peptidergic signalling in all animals except sponges. Small peptides are ideally suited to link up cells into chemical networks. They have unlimited diversity, high diffusivity and high copy numbers derived from repetitive precursors. But chemical signalling is diffusion limited and becomes inefficient in larger bodies. To overcome this, peptidergic cells may have developed projections and formed synaptically connected networks tiling body surfaces and displaying synchronized activity with pulsatile peptide release. The advent of circulatory systems and neurohemal organs further reduced the constraint imposed on chemical signalling by diffusion. This could have contributed to the explosive radiation of peptidergic signalling systems in stem bilaterians. Neurosecretory centres in extant nervous systems are still predominantly chemically wired and coexist with the synaptic brain. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
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73
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Kin K, Schaap P. Evolution of Multicellular Complexity in The Dictyostelid Social Amoebas. Genes (Basel) 2021; 12:487. [PMID: 33801615 PMCID: PMC8067170 DOI: 10.3390/genes12040487] [Citation(s) in RCA: 9] [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: 02/11/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/14/2022] Open
Abstract
Multicellularity evolved repeatedly in the history of life, but how it unfolded varies greatly between different lineages. Dictyostelid social amoebas offer a good system to study the evolution of multicellular complexity, with a well-resolved phylogeny and molecular genetic tools being available. We compare the life cycles of the Dictyostelids with closely related amoebozoans to show that complex life cycles were already present in the unicellular common ancestor of Dictyostelids. We propose frost resistance as an early driver of multicellular evolution in Dictyostelids and show that the cell signalling pathways for differentiating spore and stalk cells evolved from that for encystation. The stalk cell differentiation program was further modified, possibly through gene duplication, to evolve a new cell type, cup cells, in Group 4 Dictyostelids. Studies in various multicellular organisms, including Dictyostelids, volvocine algae, and metazoans, suggest as a common principle in the evolution of multicellular complexity that unicellular regulatory programs for adapting to environmental change serve as "proto-cell types" for subsequent evolution of multicellular organisms. Later, new cell types could further evolve by duplicating and diversifying the "proto-cell type" gene regulatory networks.
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Affiliation(s)
- Koryu Kin
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, 08003 Barcelona, Spain
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
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74
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Anastasia I, Ilacqua N, Raimondi A, Lemieux P, Ghandehari-Alavijeh R, Faure G, Mekhedov SL, Williams KJ, Caicci F, Valle G, Giacomello M, Quiroga AD, Lehner R, Miksis MJ, Toth K, de Aguiar Vallim TQ, Koonin EV, Scorrano L, Pellegrini L. Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis. Cell Rep 2021; 34:108873. [PMID: 33730569 DOI: 10.1016/j.celrep.2021.108873] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Contacts between organelles create microdomains that play major roles in regulating key intracellular activities and signaling pathways, but whether they also regulate systemic functions remains unknown. Here, we report the ultrastructural organization and dynamics of the inter-organellar contact established by sheets of curved rough endoplasmic reticulum closely wrapped around the mitochondria (wrappER). To elucidate the in vivo function of this contact, mouse liver fractions enriched in wrappER-associated mitochondria are analyzed by transcriptomics, proteomics, and lipidomics. The biochemical signature of the wrappER points to a role in the biogenesis of very-low-density lipoproteins (VLDL). Altering wrappER-mitochondria contacts curtails VLDL secretion and increases hepatic fatty acids, lipid droplets, and neutral lipid content. Conversely, acute liver-specific ablation of Mttp, the most upstream regulator of VLDL biogenesis, recapitulates this hepatic dyslipidemia phenotype and promotes remodeling of the wrappER-mitochondria contact. The discovery that liver wrappER-mitochondria contacts participate in VLDL biology suggests an involvement of inter-organelle contacts in systemic lipid homeostasis.
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Affiliation(s)
- Irene Anastasia
- Graduate Program in Neuroscience, Faculty of Medicine, Laval University, Quebec, QC, Canada; Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | - Nicolò Ilacqua
- Graduate Program in Neuroscience, Faculty of Medicine, Laval University, Quebec, QC, Canada; Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | - Andrea Raimondi
- Experimental Imaging Center, San Raffaele Scientific Institute, Milan, Italy
| | - Philippe Lemieux
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada
| | | | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Sergei L Mekhedov
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Kevin J Williams
- Department of Biological Chemistry, Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Giorgio Valle
- Department of Biology, University of Padua, Padua, Italy
| | | | - Ariel D Quiroga
- Instituto de Fisiología Experimental, CONICET, UNR, Rosario, Argentina; Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Richard Lehner
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Michael J Miksis
- Department of Engineering Science and Applied Mathematics, Northwestern University, Evanston, IL, USA
| | - Katalin Toth
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Thomas Q de Aguiar Vallim
- Department of Biological Chemistry, Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Medicine, Division of Cardiology, UCLA, Los Angeles, CA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA
| | - Luca Scorrano
- Department of Biology, University of Padua, Padua, Italy
| | - Luca Pellegrini
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, QC, Canada.
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75
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Wang J, Sun H, Jiang M, Li J, Zhang P, Chen H, Mei Y, Fei L, Lai S, Han X, Song X, Xu S, Chen M, Ouyang H, Zhang D, Yuan GC, Guo G. Tracing cell-type evolution by cross-species comparison of cell atlases. Cell Rep 2021; 34:108803. [PMID: 33657376 DOI: 10.1016/j.celrep.2021.108803] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/13/2020] [Accepted: 02/08/2021] [Indexed: 01/11/2023] Open
Abstract
Cell types are the basic building units of multicellular life, with extensive diversities. The evolution of cell types is a crucial layer of comparative cell biology but is thus far not comprehensively studied. We define a compendium of cell atlases using single-cell RNA-seq (scRNA-seq) data from seven animal species and construct a cross-species cell-type evolutionary hierarchy. We present a roadmap for the origin and diversity of major cell categories and find that muscle and neuron cells are conserved cell types. Furthermore, we identify a cross-species transcription factor (TF) repertoire that specifies major cell categories. Overall, our study reveals conservation and divergence of cell types during animal evolution, which will further expand the landscape of comparative genomics.
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Affiliation(s)
- Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China
| | - Yuqing Mei
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shujing Lai
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China
| | - Xinhui Song
- Core Facilities, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Suhong Xu
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongwei Ouyang
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China
| | - Dan Zhang
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Guo-Cheng Yuan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou 310058, China; Stem Cell Institute, Zhejiang University, Hangzhou 310058, China.
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76
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Colquitt BM, Merullo DP, Konopka G, Roberts TF, Brainard MS. Cellular transcriptomics reveals evolutionary identities of songbird vocal circuits. Science 2021; 371:371/6530/eabd9704. [PMID: 33574185 DOI: 10.1126/science.abd9704] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Birds display advanced behaviors, including vocal learning and problem-solving, yet lack a layered neocortex, a structure associated with complex behavior in mammals. To determine whether these behavioral similarities result from shared or distinct neural circuits, we used single-cell RNA sequencing to characterize the neuronal repertoire of the songbird song motor pathway. Glutamatergic vocal neurons had considerable transcriptional similarity to neocortical projection neurons; however, they displayed regulatory gene expression patterns more closely related to neurons in the ventral pallium. Moreover, while γ-aminobutyric acid-releasing neurons in this pathway appeared homologous to those in mammals and other amniotes, the most abundant avian class is largely absent in the neocortex. These data suggest that songbird vocal circuits and the mammalian neocortex have distinct developmental origins yet contain transcriptionally similar neurons.
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Affiliation(s)
- Bradley M Colquitt
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Departments of Physiology and Psychiatry, University of California-San Francisco, San Francisco, CA 94158, USA
| | - Devin P Merullo
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Todd F Roberts
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael S Brainard
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. .,Departments of Physiology and Psychiatry, University of California-San Francisco, San Francisco, CA 94158, USA
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77
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Porto DS, Almeida EAB, Pennell MW. Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees. Syst Biol 2021; 70:295-306. [PMID: 32722788 PMCID: PMC7882150 DOI: 10.1093/sysbio/syaa059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022] Open
Abstract
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here, we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is a useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes. [Apidae; entropy; morphological modules; phenotypic integration; phylogenetic information.].
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Affiliation(s)
- Diego S Porto
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 926 West Campus Drive, Blacksburg, VA 24061 USA
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA), Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo, 14040-901 Ribeirão Preto, SP, Brazil
| | - Matthew W Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver BC V6T 1Z4, Canada
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78
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Stundl J, Bertucci PY, Lauri A, Arendt D, Bronner ME. Evolution of new cell types at the lateral neural border. Curr Top Dev Biol 2021; 141:173-205. [PMID: 33602488 DOI: 10.1016/bs.ctdb.2020.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
During the course of evolution, animals have become increasingly complex by the addition of novel cell types and regulatory mechanisms. A prime example is represented by the lateral neural border, known as the neural plate border in vertebrates, a region of the developing ectoderm where presumptive neural and non-neural tissue meet. This region has been intensively studied as the source of two important embryonic cell types unique to vertebrates-the neural crest and the ectodermal placodes-which contribute to diverse differentiated cell types including the peripheral nervous system, pigment cells, bone, and cartilage. How did these multipotent progenitors originate in animal evolution? What triggered the elaboration of the border during the course of chordate evolution? How is the lateral neural border patterned in various bilaterians and what is its fate? Here, we review and compare the development and fate of the lateral neural border in vertebrates and invertebrates and we speculate about its evolutionary origin. Taken together, the data suggest that the lateral neural border existed in bilaterian ancestors prior to the origin of vertebrates and became a developmental source of exquisite evolutionary change that frequently enabled the acquisition of new cell types.
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Affiliation(s)
- Jan Stundl
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | | | | | - Detlev Arendt
- European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
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79
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Hussein AAA, Bloem E, Fodor I, Baz ES, Tadros MM, Soliman MFM, El-Shenawy NS, Koene JM. Slowly seeing the light: an integrative review on ecological light pollution as a potential threat for mollusks. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:5036-5048. [PMID: 33341922 PMCID: PMC7838132 DOI: 10.1007/s11356-020-11824-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Seasonal changes in the natural light condition play a pivotal role in the regulation of many biological processes in organisms. Disruption of this natural condition via the growing loss of darkness as a result of anthropogenic light pollution has been linked to species-wide shifts in behavioral and physiological traits. This review starts with a brief overview of the definition of light pollution and the most recent insights into the perception of light. We then go on to review the evidence for some adverse effects of ecological light pollution on different groups of animals and will focus on mollusks. Taken together, the available evidence suggests a critical role for light pollution as a recent, growing threat to the regulation of various biological processes in these animals, with the potential to disrupt ecosystem stability. The latter indicates that ecological light pollution is an environmental threat that needs to be taken seriously and requires further research attention.
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Affiliation(s)
- Ahmed A A Hussein
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt.
- Theodor Bilharz Research Institute (TBRI), Giza, Egypt.
- Department of Ecological Science, Faculty of Science, Vrije University, De Boelelaan 1085, 1081, Amsterdam, Netherlands.
| | - Erik Bloem
- Department of Ecological Science, Faculty of Science, Vrije University, De Boelelaan 1085, 1081, Amsterdam, Netherlands
| | - István Fodor
- NAP Adaptive Neuroethology, Department of Experimental Zoology, Balaton Limnological Institute, Centre for Ecological Research, 8237, Tihany, Hungary
| | - El-Sayed Baz
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | | | - Maha F M Soliman
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Nahla S El-Shenawy
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Joris M Koene
- Department of Ecological Science, Faculty of Science, Vrije University, De Boelelaan 1085, 1081, Amsterdam, Netherlands
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80
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Abstract
Large amounts of effort have been invested in trying to understand how a single genome is able to specify the identity of hundreds of cell types. Inspired by some aspects of Caenorhabditis elegans biology, we implemented an in silico evolutionary strategy to produce gene regulatory networks (GRNs) that drive cell-specific gene expression patterns, mimicking the process of terminal cell differentiation. Dynamics of the gene regulatory networks are governed by a thermodynamic model of gene expression, which uses DNA sequences and transcription factor degenerate position weight matrixes as input. In a version of the model, we included chromatin accessibility. Experimentally, it has been determined that cell-specific and broadly expressed genes are regulated differently. In our in silico evolved GRNs, broadly expressed genes are regulated very redundantly and the architecture of their cis-regulatory modules is different, in accordance to what has been found in C. elegans and also in other systems. Finally, we found differences in topological positions in GRNs between these two classes of genes, which help to explain why broadly expressed genes are so resilient to mutations. Overall, our results offer an explanatory hypothesis on why broadly expressed genes are regulated so redundantly compared to cell-specific genes, which can be extrapolated to phenomena such as ChIP-seq HOT regions.
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Affiliation(s)
- Carlos Mora-Martinez
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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81
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Kuratani S, Uesaka M, Irie N. How can recapitulation be reconciled with modern concepts of evolution? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 338:28-35. [PMID: 33382203 DOI: 10.1002/jez.b.23020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
To understand Haeckel's idea of recapitulation with modern evolutionary biology, one has to realize how evolutionarily conserved embryonic stages appear sequentially in developmental processes as chains of causality. Whether the idea of evolution was accepted or not, Haeckel and von Baer commonly saw an importance of a particularly conserved mid-embryonic stage in biphasic development of metazoans, the phylotype, that defines an animal phylum as the developmental source of a basic body plan. In an evolutionary context, the phylotypic stage was once understood by Haeckel to reflect the common ancestor of animal phyla, which went through hypermorphosis independently into various phyla. Recent comprehensive molecular studies, however, accumulated data to refute this idea. The conserved embryonic pattern does not reflect an ancestral adult morphology but appears to have arisen primarily as an embodiment of developmental constraints established through evolutionary processes. How the developmental burden results in a nested series of constraints will solve the recapitulative tendency of developmental programs.
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Affiliation(s)
- Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Cluster for Pioneering Research, Kobe, Japan.,Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Naoki Irie
- Department of Biological Sciences and Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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82
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Mondanelli G, Volpi C. The double life of serotonin metabolites: in the mood for joining neuronal and immune systems. Curr Opin Immunol 2020; 70:1-6. [PMID: 33360496 DOI: 10.1016/j.coi.2020.11.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
Abstract
Neuroimmune system is nowadays considered as one complex, but unique example of coordination between cellular and molecular networks, only apparently segregated, but strictly collaborating for the maintenance of body integrity. Too often, serotonin and its metabolites have been considered merely as neurotransmitters, when they have multiple effects spreading from the modulation of mood and behavioral processes to the regulation of a wide range of physiologic and pathophysiologic processes in most human organs, not least the immune response. The purpose of this review is to highlight the importance of metabolites generated along the serotonin pathway in the constant dialogue between neuroendocrine and immune systems; moreover, we would like to point out that the molecules produced in the two main routes of tryptophan metabolism are involved in a loop of self-regulation aimed at maintaining the equilibrium between these two metabolic pathways in the neuroimmune system, in both physiologic and pathologic conditions.
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Affiliation(s)
- Giada Mondanelli
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Claudia Volpi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy.
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83
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Cook SJ, Crouse CM, Yemini E, Hall DH, Emmons SW, Hobert O. The connectome of the Caenorhabditis elegans pharynx. J Comp Neurol 2020; 528:2767-2784. [PMID: 32352566 PMCID: PMC7601127 DOI: 10.1002/cne.24932] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/06/2020] [Accepted: 04/17/2020] [Indexed: 12/31/2022]
Abstract
Detailed anatomical maps of individual organs and entire animals have served as invaluable entry points for ensuing dissection of their evolution, development, and function. The pharynx of the nematode Caenorhabditis elegans is a simple neuromuscular organ with a self-contained, autonomously acting nervous system, composed of 20 neurons that fall into 14 anatomically distinct types. Using serial electron micrograph (EM) reconstruction, we re-evaluate here the connectome of the pharyngeal nervous system, providing a novel and more detailed view of its structure and predicted function. Contrasting the previous classification of pharyngeal neurons into distinct inter- and motor neuron classes, we provide evidence that most pharyngeal neurons are also likely sensory neurons and most, if not all, pharyngeal neurons also classify as motor neurons. Together with the extensive cross-connectivity among pharyngeal neurons, which is more widespread than previously realized, the sensory-motor characteristics of most neurons define a shallow network architecture of the pharyngeal connectome. Network analysis reveals that the patterns of neuronal connections are organized into putative computational modules that reflect the known functional domains of the pharynx. Compared with the somatic nervous system, pharyngeal neurons both physically associate with a larger fraction of their neighbors and create synapses with a greater proportion of their neighbors. We speculate that the overall architecture of the pharyngeal nervous system may be reminiscent of the architecture of ancestral, primitive nervous systems.
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Affiliation(s)
- Steven J. Cook
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027
| | - Charles M. Crouse
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027
| | - David H. Hall
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Scott W. Emmons
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027
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84
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Sequence heterochrony led to a gain of functionality in an immature stage of the central complex: A fly-beetle insight. PLoS Biol 2020; 18:e3000881. [PMID: 33104689 PMCID: PMC7644108 DOI: 10.1371/journal.pbio.3000881] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 11/05/2020] [Accepted: 09/18/2020] [Indexed: 12/25/2022] Open
Abstract
Animal behavior is guided by the brain. Therefore, adaptations of brain structure and function are essential for animal survival, and each species differs in such adaptations. The brain of one individual may even differ between life stages, for instance, as adaptation to the divergent needs of larval and adult life of holometabolous insects. All such differences emerge during development, but the cellular mechanisms behind the diversification of brains between taxa and life stages remain enigmatic. In this study, we investigated holometabolous insects in which larvae differ dramatically from the adult in both behavior and morphology. As a consequence, the central complex, mainly responsible for spatial orientation, is conserved between species at the adult stage but differs between larvae and adults of one species as well as between larvae of different taxa. We used genome editing and established transgenic lines to visualize cells expressing the conserved transcription factor retinal homeobox, thereby marking homologous genetic neural lineages in both the fly Drosophila melanogaster and the beetle Tribolium castaneum. This approach allowed us for the first time to compare the development of homologous neural cells between taxa from embryo to the adult. We found complex heterochronic changes including shifts of developmental events between embryonic and pupal stages. Further, we provide, to our knowledge, the first example of sequence heterochrony in brain development, where certain developmental steps changed their position within the ontogenetic progression. We show that through this sequence heterochrony, an immature developmental stage of the central complex gains functionality in Tribolium larvae. The central complex, part of the brain responsible for spatial orientation, differs between insect species and life stages. This study marks and compares the development of homologous neurons between a beetle and a fly, revealing that by heterochronic development an immature form of the central complex becomes functional in beetle larvae.
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85
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Döring CC, Kumar S, Tumu SC, Kourtesis I, Hausen H. The visual pigment xenopsin is widespread in protostome eyes and impacts the view on eye evolution. eLife 2020; 9:55193. [PMID: 32880369 PMCID: PMC7529461 DOI: 10.7554/elife.55193] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 09/01/2020] [Indexed: 12/31/2022] Open
Abstract
Photoreceptor cells in the eyes of Bilateria are often classified into microvillar cells with rhabdomeric opsin and ciliary cells with ciliary opsin, each type having specialized molecular components and physiology. First data on the recently discovered xenopsin point towards a more complex situation in protostomes. In this study, we provide clear evidence that xenopsin enters cilia in the eye of the larval bryozoan Tricellaria inopinata and triggers phototaxis. As reported from a mollusc, we find xenopsin coexpressed with rhabdomeric-opsin in eye photoreceptor cells bearing both microvilli and cilia in larva of the annelid Malacoceros fuliginosus. This is the first organism known to have both xenopsin and ciliary opsin, showing that these opsins are not necessarily mutually exclusive. Compiling existing data, we propose that xenopsin may play an important role in many protostome eyes and provides new insights into the function, evolution, and possible plasticity of animal eye photoreceptor cells.
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Affiliation(s)
| | - Suman Kumar
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Sharat Chandra Tumu
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Ioannis Kourtesis
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Harald Hausen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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86
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Lavergne A, Tarifeño-Saldivia E, Pirson J, Reuter AS, Flasse L, Manfroid I, Voz ML, Peers B. Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes. BMC Biol 2020; 18:109. [PMID: 32867764 PMCID: PMC7457809 DOI: 10.1186/s12915-020-00840-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 08/04/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Endocrine cells of the zebrafish digestive system play an important role in regulating metabolism and include pancreatic endocrine cells (PECs) clustered in the islets of Langerhans and the enteroendocrine cells (EECs) scattered in the intestinal epithelium. Despite EECs and PECs are being located in distinct organs, their differentiation involves shared molecular mechanisms and transcription factors. However, their degree of relatedness remains unexplored. In this study, we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory programmes controlled by Pax6b, a key player in both EEC and PEC differentiations. RESULTS RNA sequencing was performed on EECs and PECs isolated from wild-type and pax6b mutant zebrafish. Data mining of wild-type zebrafish EEC data confirmed the expression of orthologues for most known mammalian EEC hormones, but also revealed the expression of three additional neuropeptide hormones (Proenkephalin-a, Calcitonin-a and Adcyap1a) not previously reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs, PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs, with more than 70% of genes being expressed in both endocrine cell types. Comparison of Pax6b-regulated genes in EECs and PECs revealed a significant overlap. pax6b loss-of-function does not affect the total number of EECs and PECs but instead disrupts the balance between endocrine cell subtypes, leading to an increase of ghrelin- and motilin-like-expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb-expressing cells in the intestine. Finally, we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. CONCLUSION We have analysed the transcriptomic landscape of wild-type and pax6b mutant zebrafish EECs and PECs. Our study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels, supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as type 2 diabetes.
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Affiliation(s)
- Arnaud Lavergne
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium
| | - Estefania Tarifeño-Saldivia
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium.,Present Address: Gene Expression and Regulation Laboratory, Department of Biochemistry and Molecular Biology, University of Concepción, Concepción, Chile
| | - Justine Pirson
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium
| | - Anne-Sophie Reuter
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium
| | - Lydie Flasse
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium
| | - Isabelle Manfroid
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium
| | - Marianne L Voz
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium.
| | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l'Hôpital 1, B34, Sart Tilman, 4000, Liège, Belgium.
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87
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Petrucci L, Maranesi M, Verini Supplizi A, Dall’Aglio C, Mandara MT, Quassinti L, Bramucci M, Miano A, Gobbetti A, Catone G, Boiti C, Zerani M. Kisspeptin/GnRH1 system in Leydig cells of horse (Equus caballus): Presence and function. Theriogenology 2020; 152:1-7. [DOI: 10.1016/j.theriogenology.2020.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/25/2022]
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88
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Baldwin MW, Ko MC. Functional evolution of vertebrate sensory receptors. Horm Behav 2020; 124:104771. [PMID: 32437717 DOI: 10.1016/j.yhbeh.2020.104771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.
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Affiliation(s)
| | - Meng-Ching Ko
- Max Planck Institute for Ornithology, Seewiesen, Germany
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89
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Alam T, Agrawal S, Severin J, Young RS, Andersson R, Arner E, Hasegawa A, Lizio M, Ramilowski JA, Abugessaisa I, Ishizu Y, Noma S, Tarui H, Taylor MS, Lassmann T, Itoh M, Kasukawa T, Kawaji H, Marchionni L, Sheng G, R R Forrest A, Khachigian LM, Hayashizaki Y, Carninci P, de Hoon MJL. Comparative transcriptomics of primary cells in vertebrates. Genome Res 2020; 30:951-961. [PMID: 32718981 PMCID: PMC7397866 DOI: 10.1101/gr.255679.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 06/09/2020] [Indexed: 12/18/2022]
Abstract
Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.
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Affiliation(s)
- Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom.,MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | | | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yuri Ishizu
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama 230-0045, Japan
| | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hiroshi Tarui
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Timo Lassmann
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QEII Medical Centre, Perth, WA 6009, Australia
| | - Levon M Khachigian
- Vascular Biology and Translational Research, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052 Australia
| | | | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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90
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van Wijk BCM, Alkemade A, Forstmann BU. Functional segregation and integration within the human subthalamic nucleus from a micro- and meso-level perspective. Cortex 2020; 131:103-113. [PMID: 32823130 DOI: 10.1016/j.cortex.2020.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/20/2020] [Accepted: 07/06/2020] [Indexed: 12/25/2022]
Abstract
The subthalamic nucleus (STN) is a core basal ganglia structure involved in the control of motor, cognitive, motivational and affective functions. The (challenged) tripartite subdivision hypothesis places these functions into distinct sensorimotor, cognitive/associative, and limbic subregions based on the topography of cortical projections. To a large extent, this hypothesis is used to motivate the choice of target coordinates for implantation of deep brain stimulation electrodes for treatment of neurological and psychiatric disorders. Yet, the parallel organization of basal ganglia circuits has been known to allow considerable cross-talk, which might contribute to the occurrence of neuropsychiatric side effects when stimulating the dorsolateral, putative sensorimotor, part of the STN for treatment of Parkinson's disease. Any functional segregation within the STN is expected to be reflected both at micro-level microscopy and meso-level neural population activity. As such, we review the current empirical evidence from anterograde tracing and immunocytochemistry studies and from local field potential recordings for delineating the STN into distinct subregions. The spatial distribution of immunoreactivity presents as a combination of gradients, and although neural activity in distinct frequency bands appears spatially clustered, there is substantial overlap in peak locations. We argue that regional specialization without sharply defined borders is likely most representative of the STN's functional organization.
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Affiliation(s)
- Bernadette C M van Wijk
- Integrative Model-based Cognitive Neuroscience Research Unit, Department of Psychology, University of Amsterdam, the Netherlands.
| | - Anneke Alkemade
- Integrative Model-based Cognitive Neuroscience Research Unit, Department of Psychology, University of Amsterdam, the Netherlands
| | - Birte U Forstmann
- Integrative Model-based Cognitive Neuroscience Research Unit, Department of Psychology, University of Amsterdam, the Netherlands
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91
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Van der Auwera P, Frooninckx L, Buscemi K, Vance RT, Watteyne J, Mirabeau O, Temmerman L, De Haes W, Fancsalszky L, Gottschalk A, Raizen DM, Nelson MD, Schoofs L, Beets I. RPamide neuropeptides NLP-22 and NLP-2 act through GnRH-like receptors to promote sleep and wakefulness in C. elegans. Sci Rep 2020; 10:9929. [PMID: 32555288 PMCID: PMC7303124 DOI: 10.1038/s41598-020-66536-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 05/22/2020] [Indexed: 01/26/2023] Open
Abstract
Sleep and wakefulness are fundamental behavioral states of which the underlying molecular principles are becoming slowly elucidated. Transitions between these states require the coordination of multiple neurochemical and modulatory systems. In Caenorhabditis elegans sleep occurs during a larval transition stage called lethargus and is induced by somnogenic neuropeptides. Here, we identify two opposing neuropeptide/receptor signaling pathways: NLP-22 promotes behavioral quiescence, whereas NLP-2 promotes movement during lethargus, by signaling through gonadotropin-releasing hormone (GnRH) related receptors. Both NLP-2 and NLP-22 belong to the RPamide neuropeptide family and share sequence similarities with neuropeptides of the bilaterian GnRH, adipokinetic hormone (AKH) and corazonin family. RPamide neuropeptides dose-dependently activate the GnRH/AKH-like receptors GNRR-3 and GNRR-6 in a cellular receptor activation assay. In addition, nlp-22-induced locomotion quiescence requires the receptor gnrr-6. By contrast, wakefulness induced by nlp-2 overexpression is diminished by deletion of either gnrr-3 or gnrr-6. nlp-2 is expressed in a pair of olfactory AWA neurons and cycles with larval periodicity, as reported for nlp-22, which is expressed in RIA. Our data suggest that the somnogenic NLP-22 neuropeptide signals through GNRR-6, and that both GNRR-3 and GNRR-6 are required for the wake-promoting action of NLP-2 neuropeptides.
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Affiliation(s)
- Petrus Van der Auwera
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, D-60438, Frankfurt, Germany
| | - Lotte Frooninckx
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Kristen Buscemi
- Department of Biology, Saint Joseph's University, 5600 City Ave, Philadelphia, PA, 19131, USA
| | - Ryan T Vance
- Department of Biology, Saint Joseph's University, 5600 City Ave, Philadelphia, PA, 19131, USA
| | - Jan Watteyne
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | | | - Liesbet Temmerman
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Wouter De Haes
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Luca Fancsalszky
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, D-60438, Frankfurt, Germany
| | - David M Raizen
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Matthew D Nelson
- Department of Biology, Saint Joseph's University, 5600 City Ave, Philadelphia, PA, 19131, USA
| | - Liliane Schoofs
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium.
| | - Isabel Beets
- Department of Biology, KU Leuven, Naamsestraat 59, 3000, Leuven, Belgium.
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92
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Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2020; 47:D309-D314. [PMID: 30418610 PMCID: PMC6324079 DOI: 10.1093/nar/gky1085] [Citation(s) in RCA: 1975] [Impact Index Per Article: 493.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 10/26/2018] [Indexed: 11/25/2022] Open
Abstract
eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de
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Affiliation(s)
- Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Damian Szklarczyk
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Davide Heller
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Ana Hernández-Plaza
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Sofia K Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany
| | - Helen Cook
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education (C-MORE), University of Hawaii, Honolulu, HI 96822, USA
| | - Ivica Letunic
- Biobyte solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany
| | - Thomas Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna 1090, Austria
| | - Lars J Jensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Max Delbrück Centre for Molecular Medicine, Berlin, Germany.,Department of Bioinformatics, Biocenter University of Würzburg, Würzburg, Germany
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93
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Abstract
The cerebellum is a pivotal centre for the integration and processing of motor and sensory information. Its extended development into the postnatal period makes this structure vulnerable to a variety of pathologies, including neoplasia. These properties have prompted intensive investigations that reveal not only developmental mechanisms in common with other regions of the neuraxis but also unique strategies to generate neuronal diversity. How the phenotypically distinct cell types of the cerebellum emerge rests on understanding how gene expression differences arise in a spatially and temporally coordinated manner from initially homogeneous cell populations. Increasingly sophisticated fate mapping approaches, culminating in genetic-induced fate mapping, have furthered the understanding of lineage relationships between early- versus later-born cells. Tracing the developmental histories of cells in this way coupled with analysis of gene expression patterns has provided insight into the developmental genetic programmes that instruct cellular heterogeneity. A limitation to date has been the bulk analysis of cells, which blurs lineage relationships and obscures gene expression differences between cells that underpin the cellular taxonomy of the cerebellum. This review emphasises recent discoveries, focusing mainly on single-cell sequencing in mouse and parallel human studies that elucidate neural progenitor developmental trajectories with unprecedented resolution. Complementary functional studies of neural repair after cerebellar injury are challenging assumptions about the stability of postnatal cellular identities. The result is a wealth of new information about the developmental mechanisms that generate cerebellar neural diversity, with implications for human evolution.
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Affiliation(s)
- Max J. van Essen
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Samuel Nayler
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Esther B. E. Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - John Jacob
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- * E-mail:
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94
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Remesal L, Roger-Baynat I, Chirivella L, Maicas M, Brocal-Ruiz R, Pérez-Villalba A, Cucarella C, Casado M, Flames N. PBX1 acts as terminal selector for olfactory bulb dopaminergic neurons. Development 2020; 147:dev.186841. [PMID: 32156753 DOI: 10.1242/dev.186841] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/24/2020] [Indexed: 02/03/2023]
Abstract
Neuronal specification is a protracted process that begins with the commitment of progenitor cells and culminates with the generation of mature neurons. Many transcription factors are continuously expressed during this process but it is presently unclear how these factors modify their targets as cells transition through different stages of specification. In olfactory bulb adult neurogenesis, the transcription factor PBX1 controls neurogenesis in progenitor cells and the survival of migrating neuroblasts. Here, we show that, at later differentiation stages, PBX1 also acts as a terminal selector for the dopaminergic neuron fate. PBX1 is also required for the morphological maturation of dopaminergic neurons and to repress alternative interneuron fates, findings that expand the known repertoire of terminal-selector actions. Finally, we reveal that the temporal diversification of PBX1 functions in neuronal specification is achieved, at least in part, through the dynamic regulation of alternative splicing. In Caenorhabditis elegans, PBX/CEH-20 also acts as a dopaminergic neuron terminal selector, which suggests an ancient role for PBX factors in the regulation of terminal differentiation of dopaminergic neurons.
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Affiliation(s)
- Laura Remesal
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Isabel Roger-Baynat
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Laura Chirivella
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Ana Pérez-Villalba
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), and Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, 46100 Burjassot, Spain
| | - Carme Cucarella
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Metabolic Experimental Pathology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Marta Casado
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III (ISCIII), Metabolic Experimental Pathology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia, IBV-CSIC, 46010 Valencia, Spain
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95
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Callier V. Inner Workings: Understanding the evolution of cell types to explain the roots of animal diversity. Proc Natl Acad Sci U S A 2020; 117:5547-5549. [PMID: 32184373 PMCID: PMC7084151 DOI: 10.1073/pnas.2002403117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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96
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Borriello E, Walker SI, Laubichler MD. Cell phenotypes as macrostates of the GRN dynamics. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:213-224. [DOI: 10.1002/jez.b.22938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Enrico Borriello
- ASU‐SFI Center for Biosocial Complex SystemsArizona State UniversityTempe Arizona
| | - Sara I. Walker
- ASU‐SFI Center for Biosocial Complex SystemsArizona State UniversityTempe Arizona
- Beyond Center for Fundamental Concepts in ScienceArizona State UniversityTempe Arizona
- School of Earth and Space ExplorationArizona State UniversityTempe Arizona
- Blue Marble Space Institute of ScienceSeattle Washington
| | - Manfred D. Laubichler
- ASU‐SFI Center for Biosocial Complex SystemsArizona State UniversityTempe Arizona
- Santa Fe InstituteSanta Fe New Mexico
- Marine Biological LaboratoryWoods Hole Massachusetts
- School of Life SciencesArizona State UniversityTempe Arizona
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97
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Zhao D, Chen S, Horie T, Gao Y, Bao H, Liu X. Comparison of differentiation gene batteries for migratory mechanosensory neurons across bilaterians. Evol Dev 2020; 22:438-450. [PMID: 32078235 DOI: 10.1111/ede.12331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In embryos of distantly related bilaterian phyla, their lateral neural borders give rise to the peripheral nervous system elements, including various mechanosensory cells derived from migratory precursors, such as hair cells and dorsal root ganglion (DRG) neurons in vertebrates, bipolar tail neuron (BTN) in Ciona, chordotonal organ in Drosophila, and AVM/PVM in Caenorhabditis elegans. Developmental genetics studies had revealed a couple of transcription factors (TFs) regulating differentiation of mechanosensory cells shared by vertebrates and arthropods. However, unbiased systematic profiling of regulators is needed to demonstrate conservation of differentiation gene batteries for mechanosensory cells across bilaterians. At first, we observed that in both C. elegans Q neuroblasts and Drosophila lateral neuroectoderm, conserved NPB specifier Msx/vab-15 regulates Atoh1/lin-32, supporting the homology of mechanosensory neuron development in lateral neural border lineage of Ecdysozia. So we used C. elegans as a protostomia model. Single-cell resolution expression profiling of TFs and genetic analysis revealed a differentiation gene battery (Atonh1/lin-32, Drg11/alr-1, Gfi1/pag-3, Lhx5/mec-3, and Pou4/unc-86) for AVM/PVM mechanosensory neurons. The worm-gene battery significantly overlaps with both that of placode-derived Atonh1/lin-32-dependent hair cells and that of NPB-derived Neurogenin-dependent DRG neurons in vertebrates, supporting the homology of molecular mechanisms underlying the differentiation of neural border-derived mechanosensory cells between protostome and deuterostome. At last, Ciona BTN, the homolog of vertebrate DRG, also expresses Atonh1/lin-32, further supporting the homology notion and indicating a common origin of hair cells and DRG in vertebrate lineage.
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Affiliation(s)
- Di Zhao
- School of Life Sciences, Capital Normal University, Beijing, China.,Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siyu Chen
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Takeo Horie
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Yimeng Gao
- School of Life Sciences, Capital Normal University, Beijing, China
| | - Hongcun Bao
- Department of Genetics, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Liu
- School of Life Sciences, Capital Normal University, Beijing, China.,Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
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98
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Erwin DH. The origin of animal body plans: a view from fossil evidence and the regulatory genome. Development 2020; 147:147/4/dev182899. [DOI: 10.1242/dev.182899] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
The origins and the early evolution of multicellular animals required the exploitation of holozoan genomic regulatory elements and the acquisition of new regulatory tools. Comparative studies of metazoans and their relatives now allow reconstruction of the evolution of the metazoan regulatory genome, but the deep conservation of many genes has led to varied hypotheses about the morphology of early animals and the extent of developmental co-option. In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.
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Affiliation(s)
- Douglas H. Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, PO Box 37012, Washington, DC 20013-7012, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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99
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Nguyen JKB, Eames BF. Evolutionary repression of chondrogenic genes in the vertebrate osteoblast. FEBS J 2020; 287:4354-4361. [PMID: 31994313 DOI: 10.1111/febs.15228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/30/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
Gene expression in extant animals might reveal how skeletal cells have evolved over the past 500 million years. The cells that make up cartilage (chondrocytes) and bone (osteoblasts) express many of the same genes, but they also have important molecular differences that allow us to distinguish them as separate cell types. For example, traditional studies of later-diverged vertebrates, such as mouse and chick, defined the genes Col2a1 and sex-determining region Y-box 9 as cartilage-specific. However, recent studies have shown that osteoblasts of earlier-diverged vertebrates, such as frog, gar, and zebrafish, express these 'chondrogenic' markers. In this review, we examine the resulting hypothesis that chondrogenic gene expression became repressed in osteoblasts over evolutionary time. The amphibian is an underexplored skeletal model that is uniquely positioned to address this hypothesis, especially given that it diverged when life transitioned from water to land. Given the relationship between phylogeny and ontogeny, a novel discovery for skeletal cell evolution might bolster our understanding of skeletal cell development.
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Affiliation(s)
- Jason K B Nguyen
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Canada
| | - B Frank Eames
- Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Canada
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100
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Brückner A, Parker J. Molecular evolution of gland cell types and chemical interactions in animals. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb211938. [PMID: 32034048 DOI: 10.1242/jeb.211938] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Across the Metazoa, the emergence of new ecological interactions has been enabled by the repeated evolution of exocrine glands. Specialized glands have arisen recurrently and with great frequency, even in single genera or species, transforming how animals interact with their environment through trophic resource exploitation, pheromonal communication, chemical defense and parental care. The widespread convergent evolution of animal glands implies that exocrine secretory cells are a hotspot of metazoan cell type innovation. Each evolutionary origin of a novel gland involves a process of 'gland cell type assembly': the stitching together of unique biosynthesis pathways; coordinated changes in secretory systems to enable efficient chemical release; and transcriptional deployment of these machineries into cells constituting the gland. This molecular evolutionary process influences what types of compound a given species is capable of secreting, and, consequently, the kinds of ecological interactions that species can display. Here, we discuss what is known about the evolutionary assembly of gland cell types and propose a framework for how it may happen. We posit the existence of 'terminal selector' transcription factors that program gland function via regulatory recruitment of biosynthetic enzymes and secretory proteins. We suggest ancestral enzymes are initially co-opted into the novel gland, fostering pleiotropic conflict that drives enzyme duplication. This process has yielded the observed pattern of modular, gland-specific biosynthesis pathways optimized for manufacturing specific secretions. We anticipate that single-cell technologies and gene editing methods applicable in diverse species will transform the study of animal chemical interactions, revealing how gland cell types are assembled and functionally configured at a molecular level.
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Affiliation(s)
- Adrian Brückner
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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