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Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2024:gkae585. [PMID: 38966997 DOI: 10.1093/nar/gkae585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.
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Affiliation(s)
- Victoria A Bonnell
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Yuning Zhang
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan S Brown
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - John Horton
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Kamat A, Tran NT, Sharda M, Sontakke N, Le TBK, Badrinarayanan A. Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria. PLoS Biol 2024; 22:e3002540. [PMID: 38466718 PMCID: PMC10957082 DOI: 10.1371/journal.pbio.3002540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/21/2024] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.
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Affiliation(s)
- Aditya Kamat
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Ngat T. Tran
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
| | - Mohak Sharda
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Neha Sontakke
- National Centre for Biological Sciences (TIFR), Bengaluru, India
| | - Tung B. K. Le
- John Innes Centre, Department of Molecular Microbiology, Colney Lane, Norwich, United Kingdom
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Contriciani RE, Grade CVC, Buzzatto-Leite I, da Veiga FC, Ledur MC, Reverter A, Alexandre PA, Cesar ASM, Coutinho LL, Alvares LE. Phenotypic divergence between broiler and layer chicken lines is regulated at the molecular level during development. BMC Genomics 2024; 25:168. [PMID: 38347479 PMCID: PMC10863267 DOI: 10.1186/s12864-024-10083-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/02/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Understanding the molecular underpinnings of phenotypic variations is critical for enhancing poultry breeding programs. The Brazilian broiler (TT) and laying hen (CC) lines exhibit striking differences in body weight, growth potential, and muscle mass. Our work aimed to compare the global transcriptome of wing and pectoral tissues during the early development (days 2.5 to 3.5) of these chicken lines, unveiling disparities in gene expression and regulation. RESULTS Different and bona-fide transcriptomic profiles were identified for the compared lines. A similar number of up- and downregulated differentially expressed genes (DEGs) were identified, considering the broiler line as a reference. Upregulated DEGs displayed an enrichment of protease-encoding genes, whereas downregulated DEGs exhibited a prevalence of receptors and ligands. Gene Ontology analysis revealed that upregulated DEGs were mainly associated with hormone response, mitotic cell cycle, and different metabolic and biosynthetic processes. In contrast, downregulated DEGs were primarily linked to communication, signal transduction, cell differentiation, and nervous system development. Regulatory networks were constructed for the mitotic cell cycle and cell differentiation biological processes, as their contrasting roles may impact the development of distinct postnatal traits. Within the mitotic cell cycle network, key upregulated DEGs included CCND1 and HSP90, with central regulators being NF-κB subunits (RELA and REL) and NFATC2. The cell differentiation network comprises numerous DEGs encoding transcription factors (e.g., HOX genes), receptors, ligands, and histones, while the main regulatory hubs are CREB, AR and epigenetic modifiers. Clustering analyses highlighted PIK3CD as a central player within the differentiation network. CONCLUSIONS Our study revealed distinct developmental transcriptomes between Brazilian broiler and layer lines. The gene expression profile of broiler embryos seems to favour increased cell proliferation and delayed differentiation, which may contribute to the subsequent enlargement of pectoral tissues during foetal and postnatal development. Our findings pave the way for future functional studies and improvement of targeted traits of economic interest in poultry.
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Affiliation(s)
- Renata Erbert Contriciani
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Vermeulen Carvalho Grade
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino-Americana (UNILA), Foz do Iguaçu, Brazil
| | - Igor Buzzatto-Leite
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Cristina da Veiga
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | | | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Brisbane, QLD, Australia
| | - Pamela Almeida Alexandre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Brisbane, QLD, Australia
| | - Aline Silva Mello Cesar
- Department of Agri-Food Industry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, Brazil.
| | - Lúcia Elvira Alvares
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
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4
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Li P, Zhang Y, Zhao C, Jiang M. Evolution of the Tóxicos en Levadura 63 (TL63) gene family in plants and functional characterization of Arabidopsis thaliana TL63 under oxidative stress. PLANTA 2023; 258:87. [PMID: 37750983 DOI: 10.1007/s00425-023-04243-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
MAIN CONCLUSION TL63 orthologs were angiosperm specific and had undergone motifs loss and gain, and increased purifying selection. AtTL63 was involved in the response of yeast and Arabidopsis plants to oxidative stress. The Tóxicos en Levadura (TL) family, a class of E3 ubiquitin ligases with typical RING-H2 type zinc finger structure, plays a pivotal role in mediating physiological processes and responding to stress in plants. However, the evolution and function of TL63 remain unclear. In this study, TL63 homologs were dated roughly back to the origin of land plants and confirmed to have subjected to the gain and loss of motifs and increased purifying selection. Phylogenetic analysis displayed that 279 TL63s could be divided into four main clades (Clade A-D). Notably, the ancestral tandem TL40/41 cluster contributed to the expansion of modern Brassicaceae TL40/41. The substitution rate tests revealed that the TL63 lineage was evidently different from other lineages. The codon usage index exhibited that monocotyledons preferred to use not A3s and T3s, but C3s, G3s, CAI, CBI and Fop. Sequence analysis showed that the TL63 homologs had conserved TM and GLD motifs and RING-H2 domain whose key amino acid residues accounted for the high average abundance. Particularly, Arabidopsis thaliana TL63 (AtTL63) was located in the nuclei, cell membranes and peroxisomes and expressed universally and significantly throughout A. thaliana development. Under H2O2 treatment, low or moderate expression of the AtTL63 held beneficial effects on the growth and viability of yeast cells and the mutation or overexpression of the AtTL63 positively affected the growth of A. thaliana plants. In brief, this study could supply useful insight into the evolution of the plant TL63s and the AtTL63 functions under oxidative stress.
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Affiliation(s)
- Peng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuxin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Changling Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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5
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Husbands AY, Feller A, Aggarwal V, Dresden CE, Holub AS, Ha T, Timmermans MCP. The START domain potentiates HD-ZIPIII transcriptional activity. THE PLANT CELL 2023; 35:2332-2348. [PMID: 36861320 DOI: 10.1093/plcell/koad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
The CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIPIII) transcription factors (TFs) were repeatedly deployed over 725 million years of evolution to regulate central developmental innovations. The START domain of this pivotal class of developmental regulators was recognized over 20 years ago, but its putative ligands and functional contributions remain unknown. Here, we demonstrate that the START domain promotes HD-ZIPIII TF homodimerization and increases transcriptional potency. Effects on transcriptional output can be ported onto heterologous TFs, consistent with principles of evolution via domain capture. We also show the START domain binds several species of phospholipids, and that mutations in conserved residues perturbing ligand binding and/or its downstream conformational readout abolish HD-ZIPIII DNA-binding competence. Our data present a model in which the START domain potentiates transcriptional activity and uses ligand-induced conformational change to render HD-ZIPIII dimers competent to bind DNA. These findings resolve a long-standing mystery in plant development and highlight the flexible and diverse regulatory potential coded within this widely distributed evolutionary module.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
| | - Antje Feller
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Vasudha Aggarwal
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Courtney E Dresden
- Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104, USA
- Molecular, Cellular, and Developmental Biology (MCDB), The Ohio State University, Columbus, OH 43215, USA
| | - Ashton S Holub
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
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6
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Del Frate F, Garber ME, Johnson AD. Evolution of a new form of haploid-specific gene regulation appearing in a limited clade of ascomycete yeast species. Genetics 2023; 224:iyad053. [PMID: 37119800 PMCID: PMC10484167 DOI: 10.1093/genetics/iyad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/09/2023] [Accepted: 03/13/2023] [Indexed: 05/01/2023] Open
Abstract
Over evolutionary timescales, the logic and pattern of cell-type specific gene expression can remain constant, yet the molecular mechanisms underlying such regulation can drift between alternative forms. Here, we document a new example of this principle in the regulation of the haploid-specific genes in a small clade of fungal species. For most ascomycete fungal species, transcription of these genes is repressed in the a/α cell type by a heterodimer of two homeodomain proteins, Mata1 and Matα2. We show that in the species Lachancea kluyveri, most of the haploid-specific genes are regulated in this way, but repression of one haploid-specific gene (GPA1) requires, in addition to Mata1 and Matα2, a third regulatory protein, Mcm1. Model building, based on x-ray crystal structures of the three proteins, rationalizes the requirement for all three proteins: no single pair of the proteins is optimally arranged, and we show that no single pair can bring about repression. This case study exemplifies the idea that the energy of DNA binding can be "shared out" in different ways and can result in different DNA-binding solutions across different genes-while maintaining the same overall pattern of gene expression.
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Affiliation(s)
- Francesca Del Frate
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94102, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94102, USA
| | - Megan E Garber
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94102, USA
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94102, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94102, USA
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7
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Zhang Y, Li P, Niu Y, Zhang Y, Wen G, Zhao C, Jiang M. Evolution of the WRKY66 Gene Family and Its Mutations Generated by the CRISPR/Cas9 System Increase the Sensitivity to Salt Stress in Arabidopsis. Int J Mol Sci 2023; 24:3071. [PMID: 36834483 PMCID: PMC9959582 DOI: 10.3390/ijms24043071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Group Ⅲ WRKY transcription factors (TFs) play pivotal roles in responding to the diverse abiotic stress and secondary metabolism of plants. However, the evolution and function of WRKY66 remains unclear. Here, WRKY66 homologs were traced back to the origin of terrestrial plants and found to have been subjected to both motifs' gain and loss, and purifying selection. A phylogenetic analysis showed that 145 WRKY66 genes could be divided into three main clades (Clade A-C). The substitution rate tests indicated that the WRKY66 lineage was significantly different from others. A sequence analysis displayed that the WRKY66 homologs had conserved WRKY and C2HC motifs with higher proportions of crucial amino acid residues in the average abundance. The AtWRKY66 is a nuclear protein, salt- and ABA- inducible transcription activator. Simultaneously, under salt stress and ABA treatments, the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities, as well as the seed germination rates of Atwrky66-knockdown plants generated by the clustered, regularly interspaced, short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) system, were all lower than those of wild type (WT) plants, but the relative electrolyte leakage (REL) was higher, indicating the increased sensitivities of the knockdown plants to the salt stress and ABA treatments. Moreover, RNA-seq and qRT-PCR analyses revealed that several regulatory genes in the ABA-mediated signaling pathway involved in stress response of the knockdown plants were significantly regulated, being evidenced by the more moderate expressions of the genes. Therefore, the AtWRKY66 likely acts as a positive regulator in the salt stress response, which may be involved in an ABA-mediated signaling pathway.
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Affiliation(s)
- Youze Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Yuqian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuxin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Guosong Wen
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Changling Zhao
- Research & Development Center for Heath Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
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8
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Jiang M, Jian J, Zhou C, Li L, Wang Y, Zhang W, Song Z, Yang J. Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development. FRONTIERS IN PLANT SCIENCE 2023; 13:1078248. [PMID: 36714739 PMCID: PMC9880897 DOI: 10.3389/fpls.2022.1078248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
The origin of seeds is one of the key innovations in land plant evolution. Ovules are the developmental precursors of seeds. The integument is the envelope structure surrounding the nucellus within the ovule and developing into the seed coat when ovules mature upon fertilization. The question of whether the integument arise de novo or evolve from elaboration of pre-existing structures has caused much debate. By exploring the origin and evolution of the key regulatory genes controlling integument development and their functions during both individual and historical developmental processes, we showed the widespread presence of the homologs of ANT, CUC, BEL1, SPL, C3HDZ, INO, ATS, and ETT in seedless plant genomes. All of these genes have undergone duplication-divergence events in their evolutionary history, with most of the descendant paralogous suffering motif gain and/or loss in the coding regions. Expression and functional characterization have shown that these genes are key components of the genetic program that patterns leaf-like lateral organs. Serial homology can thus be postulated between integuments and other lateral organs in terms of the shared master regulatory genes. Given that the genetic program patterning leaf-like lateral organs formed in seedless plants, and was reused during seed origin, the integument is unlikely to arise de novo but evolved from the stem segment-specific modification of pre-existing serially homologous structures. The master 'switches' trigging the modification to specify the integument identity remain unclear. We propose a successive transformation model of integument origin.
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Affiliation(s)
- Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jinjing Jian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Chengchuan Zhou
- Institute of Tree Genetics Breeding and Cultivation, Jiangxi Academy of Forestry, Nanchang, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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9
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Huang Y, Shang R, Lu GA, Zeng W, Huang C, Zou C, Tang T. Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila. Mol Biol Evol 2022; 39:6605656. [PMID: 35687719 PMCID: PMC9254010 DOI: 10.1093/molbev/msac127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Due to extensive pleiotropy, trans-acting elements are often thought to be evolutionarily constrained. While the impact of trans-acting elements on gene expression evolution has been extensively studied, relatively little is understood about the contribution of a single trans regulator to interspecific expression and phenotypic divergence. Here, we disentangle the effects of genomic context and miR-983, an adaptively evolving young microRNA, on expression divergence between Drosophila melanogaster and D. simulans. We show miR-983 effects promote interspecific expression divergence in testis despite its antagonism with the often-predominant context effects. Single-cyst RNA-seq reveals that distinct sets of genes gain and lose miR-983 influence under disruptive or diversifying selection at different stages of spermatogenesis, potentially helping minimize antagonistic pleiotropy. At the round spermatid stage, the effects of miR-983 are weak and distributed, coincident with the transcriptome undergoing drastic expression changes. Knocking out miR-983 causes reduced sperm length with increased within-individual variation in D. melanogaster but not in D. simulans, and the D. melanogaster knockout also exhibits compromised sperm defense ability. Our results provide empirical evidence for the resolution of antagonistic pleiotropy and also have broad implications for the function and evolution of new trans regulators.
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Affiliation(s)
- Yumei Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Rui Shang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Guang-An Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Weishun Zeng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Chenglong Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Chuangchao Zou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
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10
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McDonald JMC, Reed RD. Patterns of selection across gene regulatory networks. Semin Cell Dev Biol 2022; 145:60-67. [PMID: 35474149 DOI: 10.1016/j.semcdb.2022.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.
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Affiliation(s)
- Jeanne M C McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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11
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Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution. Cells 2022; 11:cells11030510. [PMID: 35159319 PMCID: PMC8834487 DOI: 10.3390/cells11030510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 12/18/2022] Open
Abstract
A major driving force behind the evolution of species-specific traits and novel structures is alterations in gene regulatory networks (GRNs). Comprehending evolution therefore requires an understanding of the nature of changes in GRN structure and the responsible mechanisms. Here, we review two insect pigmentation GRNs in order to examine common themes in GRN evolution and to reveal some of the challenges associated with investigating changes in GRNs across different evolutionary distances at the molecular level. The pigmentation GRN in Drosophila melanogaster and other drosophilids is a well-defined network for which studies from closely related species illuminate the different ways co-option of regulators can occur. The pigmentation GRN for butterflies of the Heliconius species group is less fully detailed but it is emerging as a useful model for exploring important questions about redundancy and modularity in cis-regulatory systems. Both GRNs serve to highlight the ways in which redeployment of trans-acting factors can lead to GRN rewiring and network co-option. To gain insight into GRN evolution, we discuss the importance of defining GRN architecture at multiple levels both within and between species and of utilizing a range of complementary approaches.
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12
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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13
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Zhang J, Liu B, Song Y, Chen Y, Fu J, Liu J, Ma T, Xi Z, Liu H. Genome-wide (ChIP-seq) identification of target genes regulated by WRKY33 during submergence stress in Arabidopsis. BMC Genom Data 2021; 22:16. [PMID: 34030628 PMCID: PMC8142642 DOI: 10.1186/s12863-021-00972-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/17/2021] [Indexed: 11/30/2022] Open
Abstract
Background Hypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment. Results Using ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as “TC box”). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment. Conclusions Our study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a “TC box”. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00972-5.
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Affiliation(s)
- Junlin Zhang
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Yang Chen
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jiao Fu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Tao Ma
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Science, Sichuan University, Chengdu, 610065, China.
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14
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Cui X, Deng J, Huang C, Tang X, Li X, Li X, Lu J, Zhang Z. Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor. Life (Basel) 2021; 11:113. [PMID: 33540822 PMCID: PMC7912934 DOI: 10.3390/life11020113] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/14/2023] Open
Abstract
Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely-flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid-flavonoid-anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.
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Affiliation(s)
| | | | | | | | | | | | - Jiashi Lu
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.C.); (J.D.); (C.H.); (X.T.); (X.L.); (X.L.)
| | - Zibin Zhang
- Flower Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (X.C.); (J.D.); (C.H.); (X.T.); (X.L.); (X.L.)
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15
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Grant MK, Bobilev AM, Branch A, Lauderdale JD. Structural and functional consequences of PAX6 mutations in the brain: Implications for aniridia. Brain Res 2021; 1756:147283. [PMID: 33515537 DOI: 10.1016/j.brainres.2021.147283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 12/15/2020] [Accepted: 01/05/2021] [Indexed: 12/27/2022]
Abstract
The paired-box 6 (PAX6) gene encodes a highly conserved transcription factor essential for the proper development of the eye and brain. Heterozygous loss-of-function mutations in PAX6 are causal for a condition known as aniridia in humans and the Small eye phenotype in mice. Aniridia is characterized by iris hypoplasia and other ocular abnormalities, but recent evidence of neuroanatomical, sensory, and cognitive impairments in this population has emerged, indicating brain-related phenotypes as a prevalent feature of the disorder. Determining the neurophysiological origins of brain-related phenotypes in this disorder presents a substantial challenge, as the majority of extra-ocular traits in aniridia demonstrate a high degree of heterogeneity. Here, we summarize and integrate findings from human and rodent model studies, which have focused on neuroanatomical and functional consequences of PAX6 mutations. We highlight novel findings from PAX6 central nervous system studies in adult mammals, and integrate these findings into what we know about PAX6's role in development of the central nervous system. This review presents the current literature in the field in order to inform clinical application, discusses what is needed in future studies, and highlights PAX6 as a lens through which to understand genetic disorders affecting the human nervous system.
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Affiliation(s)
- Madison K Grant
- Department of Cellular Biology, The University of Georgia, Athens, GA 30602, USA.
| | - Anastasia M Bobilev
- Neuroscience Division of the Biomedical and Health Sciences Institute, The University of Georgia, Athens, GA 30602, USA; Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Audrey Branch
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - James D Lauderdale
- Department of Cellular Biology, The University of Georgia, Athens, GA 30602, USA; Neuroscience Division of the Biomedical and Health Sciences Institute, The University of Georgia, Athens, GA 30602, USA.
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16
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Hornischer K, Khaledi A, Pohl S, Schniederjans M, Pezoldt L, Casilag F, Muthukumarasamy U, Bruchmann S, Thöming J, Kordes A, Häussler S. BACTOME-a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates. Nucleic Acids Res 2020; 47:D716-D720. [PMID: 30272193 PMCID: PMC6324029 DOI: 10.1093/nar/gky895] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022] Open
Abstract
Extensive use of next-generation sequencing (NGS) for pathogen profiling has the potential to transform our understanding of how genomic plasticity contributes to phenotypic versatility. However, the storage of large amounts of NGS data and visualization tools need to evolve to offer the scientific community fast and convenient access to these data. We introduce BACTOME as a database system that links aligned DNA- and RNA-sequencing reads of clinical Pseudomonas aeruginosa isolates with clinically relevant pathogen phenotypes. The database allows data extraction for any single isolate, gene or phenotype as well as data filtering and phenotypic grouping for specific research questions. With the integration of statistical tools we illustrate the usefulness of a relational database structure for the identification of phenotype-genotype correlations as an essential part of the discovery pipeline in genomic research. Furthermore, the database provides a compilation of DNA sequences and gene expression values of a plethora of clinical isolates to give a consensus DNA sequence and consensus gene expression signature. Deviations from the consensus thereby describe the genomic landscape and the transcriptional plasticity of the species P. aeruginosa. The database is available at https://bactome.helmholtz-hzi.de.
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Affiliation(s)
- Klaus Hornischer
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany.,Molecular Health GmbH, D-69115 Heidelberg, Germany
| | - Ariane Khaledi
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Sarah Pohl
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Monika Schniederjans
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Lorena Pezoldt
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Fiordiligie Casilag
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Uthayakumar Muthukumarasamy
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Sebastian Bruchmann
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany.,Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Janne Thöming
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Adrian Kordes
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
| | - Susanne Häussler
- Institute of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.,Institute of Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, D-30625 Hannover, Germany
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17
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Britton CS, Sorrells TR, Johnson AD. Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit. Science 2020; 367:96-100. [PMID: 31896718 DOI: 10.1126/science.aax5217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022]
Abstract
Changes in both the coding sequence of transcriptional regulators and in the cis-regulatory sequences recognized by these regulators have been implicated in the evolution of transcriptional circuits. However, little is known about how they evolved in concert. We describe an evolutionary pathway in fungi where a new transcriptional circuit (a-specific gene repression by the homeodomain protein Matα2) evolved by coding changes in this ancient regulator, followed millions of years later by cis-regulatory sequence changes in the genes of its future regulon. By analyzing a group of species that has acquired the coding changes but not the cis-regulatory sites, we show that the coding changes became necessary for the regulator's deeply conserved function, thereby poising the regulator to jump-start formation of the new circuit.
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Affiliation(s)
- Candace S Britton
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Trevor R Sorrells
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, CA 94158, USA
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA.
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18
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Michalski N, Petit C. Genes Involved in the Development and Physiology of Both the Peripheral and Central Auditory Systems. Annu Rev Neurosci 2019; 42:67-86. [DOI: 10.1146/annurev-neuro-070918-050428] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genetic approach, based on the study of inherited forms of deafness, has proven to be particularly effective for deciphering the molecular mechanisms underlying the development of the peripheral auditory system, the cochlea and its afferent auditory neurons, and how this system extracts the physical parameters of sound. Although this genetic dissection has provided little information about the central auditory system, scattered data suggest that some genes may have a critical role in both the peripheral and central auditory systems. Here, we review the genes controlling the development and function of the peripheral and central auditory systems, focusing on those with demonstrated intrinsic roles in both systems and highlighting the current underappreciation of these genes. Their encoded products are diverse, from transcription factors to ion channels, as are their roles in the central auditory system, mostly evaluated in brainstem nuclei. We examine the ontogenetic and evolutionary mechanisms that may underlie their expression at different sites.
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Affiliation(s)
- Nicolas Michalski
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, 75015 Paris, France;,
- Institut National de la Santé et de la Recherche Médicale, UMRS 1120, 75015 Paris, France
- Sorbonne Universités, 75005 Paris, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, 75015 Paris, France;,
- Institut National de la Santé et de la Recherche Médicale, UMRS 1120, 75015 Paris, France
- Sorbonne Universités, 75005 Paris, France
- Syndrome de Usher et Autres Atteintes Rétino-Cochléaires, Institut de la Vision, 75012 Paris, France
- Collège de France, 75005 Paris, France
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19
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Antonova SV, Boeren J, Timmers HTM, Snel B. Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID. Genes Dev 2019; 33:888-902. [PMID: 31123066 PMCID: PMC6672047 DOI: 10.1101/gad.300475.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this perspective, Antonova et al. determine the evolutionary history of all TFIID subunits and place them in a functional context to understand their diversification. This analysis of TFIID evolution exemplifies how phylogenetic protein interrogation aids in uncovering existing structures, drawing parallels between related complexes and challenges offered by genome expansions that can be countered by exploiting chromatin modifications. The basal transcription factor TFIID is central for RNA polymerase II-dependent transcription. Human TFIID is endowed with chromatin reader and DNA-binding domains and protein interaction surfaces. Fourteen TFIID TATA-binding protein (TBP)-associated factor (TAF) subunits assemble into the holocomplex, which shares subunits with the Spt–Ada–Gcn5–acetyltransferase (SAGA) coactivator. Here, we discuss the structural and functional evolution of TFIID and its divergence from SAGA. Our orthologous tree and domain analyses reveal dynamic gains and losses of epigenetic readers, plant-specific functions of TAF1 and TAF4, the HEAT2-like repeat in TAF2, and, importantly, the pre-LECA origin of TFIID and SAGA. TFIID evolution exemplifies the dynamic plasticity in transcription complexes in the eukaryotic lineage.
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Affiliation(s)
- Simona V Antonova
- Molecular Cancer Research and Regenerative Medicine, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands
| | - Jeffrey Boeren
- Department of Developmental Biology, Erasmus MC, 3015 CN Rotterdam, The Netherlands
| | - H T Marc Timmers
- Molecular Cancer Research and Regenerative Medicine, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands.,Department of Urology, Medical Centre-University of Freiburg, 79106 Freiburg, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK) Standort Freiburg, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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20
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Ratcliffe LE, Asiedu EK, Pickett CJ, Warburton MA, Izzi SA, Meedel TH. The Ciona myogenic regulatory factor functions as a typical MRF but possesses a novel N-terminus that is essential for activity. Dev Biol 2019; 448:210-225. [PMID: 30365920 PMCID: PMC6478573 DOI: 10.1016/j.ydbio.2018.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/28/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022]
Abstract
Electroporation-based assays were used to test whether the myogenic regulatory factor (MRF) of Ciona intestinalis (CiMRF) interferes with endogenous developmental programs, and to evaluate the importance of its unusual N-terminus for muscle development. We found that CiMRF suppresses both notochord and endoderm development when it is expressed in these tissues by a mechanism that may involve activation of muscle-specific microRNAs. Because these results add to a large body of evidence demonstrating the exceptionally high degree of functional conservation among MRFs, we were surprised to discover that non-ascidian MRFs were not myogenic in Ciona unless they formed part of a chimeric protein containing the CiMRF N-terminus. Equally surprising, we found that despite their widely differing primary sequences, the N-termini of MRFs of other ascidian species could form chimeric MRFs that were also myogenic in Ciona. This domain did not rescue the activity of a Brachyury protein whose transcriptional activation domain had been deleted, and so does not appear to constitute such a domain. Our results indicate that ascidians have previously unrecognized and potentially novel requirements for MRF-directed myogenesis. Moreover, they provide the first example of a domain that is essential to the core function of an important family of gene regulatory proteins, one that, to date, has been found in only a single branch of the family.
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Affiliation(s)
- Lindsay E Ratcliffe
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Emmanuel K Asiedu
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - C J Pickett
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Megan A Warburton
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Stephanie A Izzi
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Thomas H Meedel
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
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21
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Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. Cells 2019; 8:cells8020130. [PMID: 30736359 PMCID: PMC6406739 DOI: 10.3390/cells8020130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Retroelements (REs) are transposable elements occupying ~40% of the human genome that can regulate genes by providing transcription factor binding sites (TFBS). RE-linked TFBS profile can serve as a marker of gene transcriptional regulation evolution. This approach allows for interrogating the regulatory evolution of organisms with RE-rich genomes. We aimed to characterize the evolution of transcriptional regulation for human genes and molecular pathways using RE-linked TFBS accumulation as a metric. Methods: We characterized human genes and molecular pathways either enriched or deficient in RE-linked TFBS regulation. We used ENCODE database with mapped TFBS for 563 transcription factors in 13 human cell lines. For 24,389 genes and 3124 molecular pathways, we calculated the score of RE-linked TFBS regulation reflecting the regulatory evolution rate at the level of individual genes and molecular pathways. Results: The major groups enriched by RE regulation deal with gene regulation by microRNAs, olfaction, color vision, fertilization, cellular immune response, and amino acids and fatty acids metabolism and detoxication. The deficient groups were involved in translation, RNA transcription and processing, chromatin organization, and molecular signaling. Conclusion: We identified genes and molecular processes that have characteristics of especially high or low evolutionary rates at the level of RE-linked TFBS regulation in human lineage.
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22
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Sommerlandt FMJ, Brockmann A, Rössler W, Spaethe J. Immediate early genes in social insects: a tool to identify brain regions involved in complex behaviors and molecular processes underlying neuroplasticity. Cell Mol Life Sci 2019; 76:637-651. [PMID: 30349993 PMCID: PMC6514070 DOI: 10.1007/s00018-018-2948-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/25/2018] [Accepted: 10/15/2018] [Indexed: 01/31/2023]
Abstract
Social insects show complex behaviors and master cognitive tasks. The underlying neuronal mechanisms, however, are in most cases only poorly understood due to challenges in monitoring brain activity in freely moving animals. Immediate early genes (IEGs) that get rapidly and transiently expressed following neuronal stimulation provide a powerful tool for detecting behavior-related neuronal activity in vertebrates. In social insects, like honey bees, and in insects in general, this approach is not yet routinely established, even though these genes are highly conserved. First studies revealed a vast potential of using IEGs as neuronal activity markers to analyze the localization, function, and plasticity of neuronal circuits underlying complex social behaviors. We summarize the current knowledge on IEGs in social insects and provide ideas for future research directions.
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Affiliation(s)
- Frank M J Sommerlandt
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Axel Brockmann
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, 560065, India
| | - Wolfgang Rössler
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Johannes Spaethe
- Behavioral Physiology and Sociobiology (Zoology II), Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
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23
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Huang JH, Kwan RSY, Tsai ZTY, Lin TC, Tsai HK. Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome. Front Genet 2018; 9:571. [PMID: 30524473 PMCID: PMC6261980 DOI: 10.3389/fgene.2018.00571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/06/2018] [Indexed: 11/17/2022] Open
Abstract
Changes in cis-regulatory DNA sequences and transcription factor (TF) repertoires provide major sources of phenotypic diversity that shape the evolution of gene regulation in eukaryotes. The DNA-binding specificities of TFs may be diversified or produce new variants in different eukaryotic species. However, it is currently unclear how various levels of divergence in TF DNA-binding specificities or motifs became introduced into the cis-regulatory DNA regions of the genome over evolutionary time. Here, we first estimated the evolutionary divergence levels of TF binding motifs and quantified their occurrence at DNase I-hypersensitive sites. Results from our in silico motif scan and experimentally derived chromatin immunoprecipitation (TF-ChIP) show that the divergent motifs tend to be introduced in the edges of cis-regulatory regions, which is probably accompanied by the expansion of the accessible core of promoter-associated regulatory elements during evolution. We also find that the genes neighboring the expanded cis-regulatory regions with the most divergent motifs are associated with functions like development and morphogenesis. Accordingly, we propose that the accumulation of divergent motifs in the edges of cis-regulatory regions provides a functional mechanism for the evolution of divergent regulatory circuits.
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Affiliation(s)
- Jia-Hsin Huang
- Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan
| | | | - Zing Tsung-Yeh Tsai
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Tzu-Chieh Lin
- Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan
| | - Huai-Kuang Tsai
- Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan
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24
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Feltes BC, Grisci BI, Poloni JDF, Dorn M. Perspectives and applications of machine learning for evolutionary developmental biology. Mol Omics 2018; 14:289-306. [PMID: 30168572 DOI: 10.1039/c8mo00111a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Evolutionary Developmental Biology (Evo-Devo) is an ever-expanding field that aims to understand how development was modulated by the evolutionary process. In this sense, "omic" studies emerged as a powerful ally to unravel the molecular mechanisms underlying development. In this scenario, bioinformatics tools become necessary to analyze the growing amount of information. Among computational approaches, machine learning stands out as a promising field to generate knowledge and trace new research perspectives for bioinformatics. In this review, we aim to expose the current advances of machine learning applied to evolution and development. We draw clear perspectives and argue how evolution impacted machine learning techniques.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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25
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Barton-Owen TB, Ferrier DEK, Somorjai IML. Pax3/7 duplicated and diverged independently in amphioxus, the basal chordate lineage. Sci Rep 2018; 8:9414. [PMID: 29925900 PMCID: PMC6010424 DOI: 10.1038/s41598-018-27700-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/06/2018] [Indexed: 01/06/2023] Open
Abstract
The Pax3/7 transcription factor family is integral to developmental gene networks contributing to important innovations in vertebrate evolution, including the neural crest. The basal chordate lineage of amphioxus is ideally placed to understand the dynamics of the gene regulatory network evolution that produced these novelties. We report here the discovery that the cephalochordate lineage possesses two Pax3/7 genes, Pax3/7a and Pax3/7b. The tandem duplication is ancestral to all extant amphioxus, occurring in both Asymmetron and Branchiostoma, but originated after the split from the lineage leading to vertebrates. The two paralogues are differentially expressed during embryonic development, particularly in neural and somitic tissues, suggesting distinct regulation. Our results have implications for the study of amphioxus regeneration, neural plate and crest evolution, and differential tandem paralogue evolution.
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Affiliation(s)
- Thomas B Barton-Owen
- University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK.,University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - David E K Ferrier
- University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK
| | - Ildikó M L Somorjai
- University of St Andrews, Gatty Marine Laboratory, Scottish Oceans Institute, East Sands, St Andrews, Fife, KY16 8LB, UK. .,University of St Andrews, Biomedical Sciences Research Complex, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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26
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Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development. Proc Natl Acad Sci U S A 2018; 114:5854-5861. [PMID: 28584099 DOI: 10.1073/pnas.1610611114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). Although cis-regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low-affinity, secondary binding motif. The primary, high-affinity motif is conserved. To date, however, no genome-wide comparisons have been performed to provide an unbiased assessment of the evolution of GRNs between these taxa, and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology. The study here measures genome-wide binding of Tbrain orthologs by using ChIP-sequencing and associates these orthologs with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although nonoverlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low-affinity binding motifs is significantly depressed in sea urchins compared with sea star, but both motif types are associated with genes from a range of functional categories. Only a small fraction (∼10%) of genes are predicted to be orthologous targets. Collectively, these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms and that the targets and the binding motifs in associated cis-regulatory sequences are dispersed throughout the hierarchy of the GRN, rather than being biased toward terminal process or discrete functional blocks, which suggests extensive evolutionary tinkering.
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27
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Sepúlveda-Ramírez SP, Toledo-Jacobo L, Henson JH, Shuster CB. Cdc42 controls primary mesenchyme cell morphogenesis in the sea urchin embryo. Dev Biol 2018; 437:140-151. [PMID: 29555242 PMCID: PMC5973877 DOI: 10.1016/j.ydbio.2018.03.015] [Citation(s) in RCA: 15] [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: 11/07/2017] [Revised: 03/05/2018] [Accepted: 03/15/2018] [Indexed: 12/15/2022]
Abstract
In the sea urchin embryo, gastrulation is characterized by the ingression and directed cell migration of primary mesenchyme cells (PMCs), as well as the primary invagination and convergent extension of the endomesoderm. Like all cell shape changes, individual and collective cell motility is orchestrated by Rho family GTPases and their modulation of the actomyosin cytoskeleton. And while endomesoderm specification has been intensively studied in echinoids, much less is known about the proximate regulators driving cell motility. Toward these ends, we employed anti-sense morpholinos, mutant alleles and pharmacological inhibitors to assess the role of Cdc42 during sea urchin gastrulation. While inhibition of Cdc42 expression or activity had only mild effects on PMC ingression, PMC migration, alignment and skeletogenesis were disrupted in the absence of Cdc42, as well as elongation of the archenteron. PMC migration and patterning of the larval skeleton relies on the extension of filopodia, and Cdc42 was required for filopodia in vivo as well as in cultured PMCs. Lastly, filopodial extension required both Arp2/3 and formin actin-nucleating factors, supporting models of filopodial nucleation observed in other systems. Together, these results suggest that Cdc42 plays essential roles during PMC cell motility and organogenesis.
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Affiliation(s)
- Silvia P Sepúlveda-Ramírez
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, United States; University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States
| | - Leslie Toledo-Jacobo
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, United States; University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States
| | - John H Henson
- University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States; Department of Biology, Dickinson College, Carlisle, PA 17013, United States
| | - Charles B Shuster
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, United States; University of Washington Friday Harbor Laboratories, Friday Harbor, WA 98250, United States.
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28
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Martin RC, Vining K, Dombrowski JE. Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress. BMC PLANT BIOLOGY 2018; 18:58. [PMID: 29636001 PMCID: PMC5894230 DOI: 10.1186/s12870-018-1275-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 03/29/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND bZIP transcription factors play a significant role in many aspects of plant growth and development and also play critical regulatory roles during plant responses to various stresses. Overexpression of the Brachypodium bZIP10 (Bradi1g30140) transcription factor conferred enhanced oxidative stress tolerance and increased viability when plants or cells were exposed to the herbicide paraquat. To gain a better understanding of genes involved in bZIP10 conferred oxidative stress tolerance, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) was performed on BdbZIP10 overexpressing plants in the presence of oxidative stress. RESULTS We identified a transcription factor binding motif, TGDCGACA, different from most known bZIP TF motifs but with strong homology to the Arabidopsis zinc deficiency response element. Analysis of the immunoprecipitated sequences revealed an enrichment of gene ontology groups with metal ion transmembrane transporter, transferase, catalytic and binding activities. Functional categories including kinases and phosphotransferases, cation/ion transmembrane transporters, transferases (phosphorus-containing and glycosyl groups), and some nucleoside/nucleotide binding activities were also enriched. CONCLUSIONS Brachypodium bZIP10 is involved in zinc homeostasis, as it relates to oxidative stress.
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Affiliation(s)
- Ruth C. Martin
- USDA ARS National Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97330 USA
| | - Kelly Vining
- Department of Horticulture, 4123 Agricultural & Life Sciences, Oregon State University, Corvallis, OR 97330 USA
| | - James E. Dombrowski
- USDA ARS National Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR 97330 USA
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29
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Hoffmann HM, Gong P, Tamrazian A, Mellon PL. Transcriptional interaction between cFOS and the homeodomain-binding transcription factor VAX1 on the GnRH promoter controls Gnrh1 expression levels in a GnRH neuron maturation specific manner. Mol Cell Endocrinol 2018; 461:143-154. [PMID: 28890143 PMCID: PMC5756504 DOI: 10.1016/j.mce.2017.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 08/23/2017] [Accepted: 09/05/2017] [Indexed: 12/18/2022]
Abstract
Gonadotropin-releasing hormone (GnRH) is required for pubertal onset and reproduction, thus the control of GnRH transcription is tightly regulated during development and adulthood. GnRH neuron development depends on transcription factors of the homeodomain family. For example, Ventral anterior homeobox 1 (Vax1) is necessary to maintain GnRH expression after embryonic day 13 in the mouse. To further our understanding of the mechanisms by which VAX1 regulates GnRH gene expression, we asked whether VAX1 interacts with other transcription factors to modify GnRH expression levels. Using the GnRH cell lines, GN11 and GT1-7, we found that activation of PKC enhances expression of the immediate early gene cFos in both GN11, and GT1-7, and represses expression of Vax1 in GT1-7. Further, VAX1 interacts with cFOS while bound to the GnRH promoter. In immature GN11 cells, VAX1 and cFOS enhance GnRH expression, whereas VAX1 and cFOS have a repressive role in the mature GT1-7 cells.
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Affiliation(s)
- Hanne M Hoffmann
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ping Gong
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Anika Tamrazian
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pamela L Mellon
- Department of Reproductive Medicine, Center for Reproductive Science and Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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30
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Khadka A, Martínez-Bartolomé M, Burr SD, Range RC. A novel gene's role in an ancient mechanism: secreted Frizzled-related protein 1 is a critical component in the anterior-posterior Wnt signaling network that governs the establishment of the anterior neuroectoderm in sea urchin embryos. EvoDevo 2018; 9:1. [PMID: 29387332 PMCID: PMC5778778 DOI: 10.1186/s13227-017-0089-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/18/2017] [Indexed: 01/20/2023] Open
Abstract
The anterior neuroectoderm (ANE) in many deuterostome embryos (echinoderms, hemichordates, urochordates, cephalochordates, and vertebrates) is progressively restricted along the anterior-posterior axis to a domain around the anterior pole. In the sea urchin embryo, three integrated Wnt signaling branches (Wnt/β-catenin, Wnt/JNK, and Wnt/PKC) govern this progressive restriction process, which begins around the 32- to 60-cell stage and terminates by the early gastrula stage. We previously have established that several secreted Wnt modulators of the Dickkopf and secreted Frizzled-related protein families (Dkk1, Dkk3, and sFRP-1/5) are expressed within the ANE and play important roles in modulating the Wnt signaling network during this process. In this study, we use morpholino and dominant-negative interference approaches to characterize the function of a novel Frizzled-related protein, secreted Frizzled-related protein 1 (sFRP-1), during ANE restriction. sFRP-1 appears to be related to a secreted Wnt modulator, sFRP3/4, that is essential to block Wnt signaling and establish the ANE in vertebrates. Here, we show that the sea urchin sFRP3/4 orthologue is not expressed during ANE restriction in the sea urchin embryo. Instead, our results indicate that ubiquitously expressed maternal sFRP-1 and Fzl1/2/7 signaling act together as early as the 32- to 60-cell stage to antagonize the ANE restriction mechanism mediated by Wnt/β-catenin and Wnt/JNK signaling. Then, starting from the blastula stage, Fzl5/8 signaling activates zygotic sFRP-1 within the ANE territory, where it works with the secreted Wnt antagonist Dkk1 (also activated by Fzl5/8 signaling) to antagonize Wnt1/Wnt8-Fzl5/8-JNK signaling in a negative feedback mechanism that defines the outer ANE territory boundary. Together, these data indicate that maternal and zygotic sFRP-1 protects the ANE territory by antagonizing the Wnt1/Wnt8-Fzl5/8-JNK signaling pathway throughout ANE restriction, providing precise spatiotemporal control of the mechanism responsible for the establishment of the ANE territory around the anterior pole of the sea urchin embryo.
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Affiliation(s)
- Anita Khadka
- 1Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 USA
| | | | - Stephanie D Burr
- 1Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 USA.,2School of Pharmacy, University of Mississippi, Oxford, MS USA
| | - Ryan C Range
- 1Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 USA
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31
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Mäkinen H, Sävilammi T, Papakostas S, Leder E, Vøllestad LA, Primmer CR. Modularity Facilitates Flexible Tuning of Plastic and Evolutionary Gene Expression Responses during Early Divergence. Genome Biol Evol 2018; 10:77-93. [PMID: 29293993 PMCID: PMC5758911 DOI: 10.1093/gbe/evx278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2017] [Indexed: 12/14/2022] Open
Abstract
Gene expression changes have been recognized as important drivers of adaptation to changing environmental conditions. Little is known about the relative roles of plastic and evolutionary responses in complex gene expression networks during the early stages of divergence. Large gene expression data sets coupled with in silico methods for identifying coexpressed modules now enable systems genetics approaches also in nonmodel species for better understanding of gene expression responses during early divergence. Here, we combined gene coexpression analyses with population genetics to separate plastic and population (evolutionary) effects in expression networks using small salmonid populations as a model system. We show that plastic and population effects were highly variable among the six identified modules and that the plastic effects explained larger proportion of the total eigengene expression than population effects. A more detailed analysis of the population effects using a QST - FST comparison across 16,622 annotated transcripts revealed that gene expression followed neutral expectations within modules and at the global level. Furthermore, two modules showed enrichment for genes coding for early developmental traits that have been previously identified as important phenotypic traits in thermal responses in the same model system indicating that coexpression analysis can capture expression patterns underlying ecologically important traits. We suggest that module-specific responses may facilitate the flexible tuning of expression levels to local thermal conditions. Overall, our study indicates that plasticity and neutral evolution are the main drivers of gene expression variance in the early stages of thermal adaptation in this system.
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Affiliation(s)
| | | | | | - Erica Leder
- Department of Biology, University of Turku, Finland
- Natural History Museum, University of Oslo, Norway
| | - Leif A Vøllestad
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Craig R Primmer
- Department of Biosciences, University of Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Finland
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32
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Holland PWH, Marlétaz F, Maeso I, Dunwell TL, Paps J. New genes from old: asymmetric divergence of gene duplicates and the evolution of development. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0480. [PMID: 27994121 DOI: 10.1098/rstb.2015.0480] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2016] [Indexed: 01/10/2023] Open
Abstract
Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such 'asymmetric evolution' seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Ferdinand Marlétaz
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Ignacio Maeso
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Thomas L Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Jordi Paps
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.,School of Biological Sciences, University of Essex, Colchester, Essex, UK
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33
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Khor JM, Ettensohn CA. Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms. eLife 2017; 6:e32728. [PMID: 29154754 PMCID: PMC5758115 DOI: 10.7554/elife.32728] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022] Open
Abstract
Alx1 is a pivotal transcription factor in a gene regulatory network that controls skeletogenesis throughout the echinoderm phylum. We performed a structure-function analysis of sea urchin Alx1 using a rescue assay and identified a novel, conserved motif (Domain 2) essential for skeletogenic function. The paralogue of Alx1, Alx4, was not functionally interchangeable with Alx1, but insertion of Domain 2 conferred robust skeletogenic function on Alx4. We used cross-species expression experiments to show that Alx1 proteins from distantly related echinoderms are not interchangeable, although the sequence and function of Domain 2 are highly conserved. We also found that Domain 2 is subject to alternative splicing and provide evidence that this domain was originally gained through exonization. Our findings show that a gene duplication event permitted the functional specialization of a transcription factor through changes in exon-intron organization and thereby supported the evolution of a major morphological novelty.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghUnited States
| | - Charles A Ettensohn
- Department of Biological SciencesCarnegie Mellon UniversityPittsburghUnited States
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34
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miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Romanovskaya EV, Vikhnina MV, Grishina TV, Ivanov MP, Leonova LE, Tsvetkova EV. Transcription factors of the NF1 family: Possible mechanisms of inducible gene expression in the evolutionary lineage of multicellular animals. J EVOL BIOCHEM PHYS+ 2017. [DOI: 10.1134/s123456781702001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Weinberger S, Topping MP, Yan J, Claeys A, Geest ND, Ozbay D, Hassan T, He X, Albert JT, Hassan BA, Ramaekers A. Evolutionary changes in transcription factor coding sequence quantitatively alter sensory organ development and function. eLife 2017; 6. [PMID: 28406397 PMCID: PMC5432213 DOI: 10.7554/elife.26402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/27/2017] [Indexed: 11/16/2022] Open
Abstract
Animals are characterized by a set of highly conserved developmental regulators. Changes in the cis-regulatory elements of these regulators are thought to constitute the major driver of morphological evolution. However, the role of coding sequence evolution remains unresolved. To address this question, we used the Atonal family of proneural transcription factors as a model. Drosophila atonal coding sequence was endogenously replaced with that of atonal homologues (ATHs) at key phylogenetic positions, non-ATH proneural genes, and the closest homologue to ancestral proneural genes. ATHs and the ancestral-like coding sequences rescued sensory organ fate in atonal mutants, in contrast to non-ATHs. Surprisingly, different ATH factors displayed different levels of proneural activity as reflected by the number and functionality of sense organs. This proneural potency gradient correlated directly with ATH protein stability, including in response to Notch signaling, independently of mRNA levels or codon usage. This establishes a distinct and ancient function for ATHs and demonstrates that coding sequence evolution can underlie quantitative variation in sensory development and function. DOI:http://dx.doi.org/10.7554/eLife.26402.001
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Affiliation(s)
- Simon Weinberger
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium.,Program in Molecular and Developmental Genetics, Doctoral School for Biomedical Sciences, University of Leuven School Group Biomedicine, Leuven, Belgium
| | - Matthew P Topping
- Ear Institute, University College London, London, United Kingdom.,Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Jiekun Yan
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Annelies Claeys
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Natalie De Geest
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Duru Ozbay
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium
| | - Talah Hassan
- Ear Institute, University College London, London, United Kingdom
| | - Xiaoli He
- Ear Institute, University College London, London, United Kingdom
| | - Joerg T Albert
- Ear Institute, University College London, London, United Kingdom.,Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom.,Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Bassem A Hassan
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium.,Program in Molecular and Developmental Genetics, Doctoral School for Biomedical Sciences, University of Leuven School Group Biomedicine, Leuven, Belgium.,Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, UPMC, Sorbonne Universités, Inserm, CNRS, Paris, France
| | - Ariane Ramaekers
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium.,Center for Human Genetics, University of Leuven School of Medicine, Leuven, Belgium.,Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, UPMC, Sorbonne Universités, Inserm, CNRS, Paris, France
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37
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Wang X, Kültz D. Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish. Proc Natl Acad Sci U S A 2017; 114:E2729-E2738. [PMID: 28289196 PMCID: PMC5380061 DOI: 10.1073/pnas.1614712114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fish respond to salinity stress by transcriptional induction of many genes, but the mechanism of their osmotic regulation is unknown. We developed a reporter assay using cells derived from the brain of the tilapia Oreochromis mossambicus (OmB cells) to identify osmolality/salinity-responsive enhancers (OSREs) in the genes of Omossambicus Genomic DNA comprising the regulatory regions of two strongly salinity-induced genes, inositol monophosphatase 1 (IMPA1.1) and myo-inositol phosphate synthase (MIPS), was isolated and analyzed with dual luciferase enhancer trap reporter assays. We identified five sequences (two in IMPA1.1 and three in MIPS) that share a common consensus element (DDKGGAAWWDWWYDNRB), which we named "OSRE1." Additional OSREs that were less effective in conferring salinity-induced trans-activation and do not match the OSRE1 consensus also were identified in both MIPS and IMPA1.1 Although OSRE1 shares homology with the mammalian osmotic-response element/tonicity-responsive enhancer (ORE/TonE) enhancer, the latter is insufficient to confer osmotic induction in fish. Like other enhancers, OSRE1 trans-activates genes independent of orientation. We conclude that OSRE1 is a cis-regulatory element (CRE) that enhances the hyperosmotic induction of osmoregulated genes in fish. Our study also shows that tailored reporter assays developed for OmB cells facilitate the identification of CREs in fish genomes. Knowledge of the OSRE1 motif allows affinity-purification of the corresponding transcription factor and computational approaches for enhancer screening of fish genomes. Moreover, our study enables targeted inactivation of OSRE1 enhancers, a method superior to gene knockout for functional characterization because it confines impairment of gene function to a specific context (salinity stress) and eliminates pitfalls of constitutive gene knockouts (embryonic lethality, developmental compensation).
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Affiliation(s)
- Xiaodan Wang
- Biochemical Evolution Laboratory, Department of Animal Science, University of California, Davis, CA, 95616
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dietmar Kültz
- Biochemical Evolution Laboratory, Department of Animal Science, University of California, Davis, CA, 95616;
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Cary GA, Hinman VF. Echinoderm development and evolution in the post-genomic era. Dev Biol 2017; 427:203-211. [PMID: 28185788 DOI: 10.1016/j.ydbio.2017.02.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 01/01/2023]
Abstract
The highly recognizable animals within the phylum Echinodermata encompass an enormous disparity of adult and larval body plans. The extensive knowledge of sea urchin development has culminated in the description of the exquisitely detailed gene regulatory network (GRN) that governs the specification of various embryonic territories. This information provides a unique opportunity for comparative studies in other echinoderm taxa to understand the evolution and developmental mechanisms underlying body plan change. This review focuses on recent work that has utilized new genomic resources and systems-level experiments to address questions of evolutionary developmental biology. In particular, we synthesize the results of several recent studies from various echinoderm classes that have explored the development and evolution of the larval skeleton, which is a major feature that distinguishes the two predominant larval subtypes within the Phylum. We specifically examine the ways in which GRNs can evolve, either through cis regulatory and/or protein-level changes in transcription factors. We also examine recent work comparing evolution across shorter time scales that occur within and between species of sea urchin, and highlight the kinds of questions that can be addressed by these comparisons. The advent of new genomic and transcriptomic datasets in additional species from all classes of echinoderm will continue to empower the use of these taxa for evolutionary developmental studies.
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Affiliation(s)
- Gregory A Cary
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, United States
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, United States.
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Babonis LS, Martindale MQ. Phylogenetic evidence for the modular evolution of metazoan signalling pathways. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150477. [PMID: 27994120 PMCID: PMC5182411 DOI: 10.1098/rstb.2015.0477] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2016] [Indexed: 12/12/2022] Open
Abstract
Communication among cells was paramount to the evolutionary increase in cell type diversity and, ultimately, the origin of large body size. Across the diversity of Metazoa, there are only few conserved cell signalling pathways known to orchestrate the complex cell and tissue interactions regulating development; thus, modification to these few pathways has been responsible for generating diversity during the evolution of animals. Here, we summarize evidence for the origin and putative function of the intracellular, membrane-bound and secreted components of seven metazoan cell signalling pathways with a special focus on early branching metazoans (ctenophores, poriferans, placozoans and cnidarians) and basal unikonts (amoebozoans, fungi, filastereans and choanoflagellates). We highlight the modular incorporation of intra- and extracellular components in each signalling pathway and suggest that increases in the complexity of the extracellular matrix may have further promoted the modulation of cell signalling during metazoan evolution. Most importantly, this updated view of metazoan signalling pathways highlights the need for explicit study of canonical signalling pathway components in taxa that do not operate a complete signalling pathway. Studies like these are critical for developing a deeper understanding of the evolution of cell signalling.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Leslie S Babonis
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
| | - Mark Q Martindale
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA
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40
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Schneider RF, Meyer A. How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations. Mol Ecol 2016; 26:330-350. [PMID: 27747962 DOI: 10.1111/mec.13880] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/30/2016] [Accepted: 10/07/2016] [Indexed: 12/13/2022]
Abstract
There is increasing evidence that phenotypic plasticity can promote population divergence by facilitating phenotypic diversification and, eventually, genetic divergence. When a 'plastic' population colonizes a new habitat, it has the possibility to occupy multiple niches by expressing several distinct phenotypes. These initially reflect the population's plastic range but may later become genetically fixed by selection via the process of 'genetic assimilation' (GA). Through this process multiple specialized sister lineages can arise that share a common plastic ancestor - the 'flexible stem'. Here, we review possible molecular mechanisms through which natural selection could fix an initially plastic trait during GA. These mechanisms could also explain how GA may contribute to cryptic genetic variation that can subsequently be coopted into other phenotypes or traits, but also lead to nonadaptive responses. We outline the predicted patterns of genetic and transcriptional divergence accompanying flexible stem radiations. The analysis of such patterns of (retained) adaptive and nonadaptive plastic responses within and across radiating lineages can inform on the state of ongoing GA. We conclude that, depending on the stability of the environment, the molecular architecture underlying plastic traits can facilitate diversification, followed by fixation and consolidation of an adaptive phenotype and degeneration of nonadaptive ones. Additionally, the process of GA may increase the cryptic genetic variation of populations, which on one hand may serve as substrate for evolution, but on another may be responsible for nonadaptive responses that consolidate local allopatry and thus reproductive isolation.
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Affiliation(s)
- Ralf F Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitaetstrasse 10, 78457, Konstanz, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitaetstrasse 10, 78457, Konstanz, Germany
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A Derived Allosteric Switch Underlies the Evolution of Conditional Cooperativity between HOXA11 and FOXO1. Cell Rep 2016; 15:2097-2108. [DOI: 10.1016/j.celrep.2016.04.088] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 02/23/2016] [Accepted: 04/26/2016] [Indexed: 12/11/2022] Open
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Babonis LS, Martindale MQ, Ryan JF. Do novel genes drive morphological novelty? An investigation of the nematosomes in the sea anemone Nematostella vectensis. BMC Evol Biol 2016; 16:114. [PMID: 27216622 PMCID: PMC4877951 DOI: 10.1186/s12862-016-0683-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The evolution of novel genes is thought to be a critical component of morphological innovation but few studies have explicitly examined the contribution of novel genes to the evolution of novel tissues. Nematosomes, the free-floating cellular masses that circulate through the body cavity of the sea anemone Nematostella vectensis, are the defining apomorphy of the genus Nematostella and are a useful model for understanding the evolution of novel tissues. Although many hypotheses have been proposed, the function of nematosomes is unknown. To gain insight into their putative function and to test hypotheses about the role of lineage-specific genes in the evolution of novel structures, we have re-examined the cellular and molecular biology of nematosomes. RESULTS Using behavioral assays, we demonstrate that nematosomes are capable of immobilizing live brine shrimp (Artemia salina) by discharging their abundant cnidocytes. Additionally, the ability of nematosomes to engulf fluorescently labeled bacteria (E. coli) reveals the presence of phagocytes in this tissue. Using RNA-Seq, we show that the gene expression profile of nematosomes is distinct from that of the tentacles and the mesenteries (their tissue of origin) and, further, that nematosomes (a Nematostella-specific tissue) are enriched in Nematostella-specific genes. CONCLUSIONS Despite the small number of cell types they contain, nematosomes are distinct among tissues, both functionally and molecularly. We provide the first evidence that nematosomes comprise part of the innate immune system in N. vectensis, and suggest that this tissue is potentially an important place to look for genes associated with pathogen stress. Finally, we demonstrate that Nematostella-specific genes comprise a significant proportion of the differentially expressed genes in all three of the tissues we examined and may play an important role in novel cell functions.
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Affiliation(s)
- Leslie S Babonis
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA.
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, FL, 32080, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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Short S, Peterkin T, Guille M, Patient R, Sharpe C. Short linear motif acquisition, exon formation and alternative splicing determine a pathway to diversity for NCoR-family co-repressors. Open Biol 2016; 5:rsob.150063. [PMID: 26289800 PMCID: PMC4554918 DOI: 10.1098/rsob.150063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Vertebrate NCoR-family co-repressors play central roles in the timing of embryo and stem cell differentiation by repressing the activity of a range of transcription factors. They interact with nuclear receptors using short linear motifs (SLiMs) termed co-repressor for nuclear receptor (CoRNR) boxes. Here, we identify the pathway leading to increasing co-repressor diversity across the deuterostomes. The final complement of CoRNR boxes arose in an ancestral cephalochordate, and was encoded in one large exon; the urochordates and vertebrates then split this region between 10 and 12 exons. In Xenopus, alternative splicing is prevalent in NCoR2, but absent in NCoR1. We show for one NCoR1 exon that alternative splicing can be recovered by a single point mutation, suggesting NCoR1 lost the capacity for alternative splicing. Analyses in Xenopus and zebrafish identify that cellular context, rather than gene sequence, predominantly determines species differences in alternative splicing. We identify a pathway to diversity for the NCoR family beginning with the addition of a SLiM, followed by gene duplication, the generation of alternatively spliced isoforms and their differential deployment.
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Affiliation(s)
- Stephen Short
- Institute of Marine Sciences, School of Biological Science, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Tessa Peterkin
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Matthew Guille
- Institute of Biomolecular and Biomedical Science, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK European Xenopus Resource Centre, University of Portsmouth, St Michael's Building, Portsmouth PO1 2DT, UK
| | - Roger Patient
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Colin Sharpe
- Institute of Biomolecular and Biomedical Science, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK European Xenopus Resource Centre, University of Portsmouth, St Michael's Building, Portsmouth PO1 2DT, UK
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Rosenfeld JA, Foox J, DeSalle R. Insect genome content phylogeny and functional annotation of core insect genomes. Mol Phylogenet Evol 2016; 97:224-232. [DOI: 10.1016/j.ympev.2015.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/02/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
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Evolution of mammalian sound localization circuits: A developmental perspective. Prog Neurobiol 2016; 141:1-24. [PMID: 27032475 DOI: 10.1016/j.pneurobio.2016.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 02/27/2016] [Accepted: 02/27/2016] [Indexed: 01/06/2023]
Abstract
Localization of sound sources is a central aspect of auditory processing. A unique feature of mammals is the smooth, tonotopically organized extension of the hearing range to high frequencies (HF) above 10kHz, which likely induced positive selection for novel mechanisms of sound localization. How this change in the auditory periphery is accompanied by changes in the central auditory system is unresolved. I will argue that the major VGlut2(+) excitatory projection neurons of sound localization circuits (dorsal cochlear nucleus (DCN), lateral and medial superior olive (LSO and MSO)) represent serial homologs with modifications, thus being paramorphs. This assumption is based on common embryonic origin from an Atoh1(+)/Wnt1(+) cell lineage in the rhombic lip of r5, same cell birth, a fusiform cell morphology, shared genetic components such as Lhx2 and Lhx9 transcription factors, and similar projection patterns. Such a parsimonious evolutionary mechanism likely accelerated the emergence of neurons for sound localization in all three dimensions. Genetic analyses indicate that auditory nuclei in fish, birds, and mammals receive contributions from the same progenitor lineages. Anatomical and physiological differences and the independent evolution of tympanic ears in vertebrate groups, however, argue for convergent evolution of sound localization circuits in tetrapods (amphibians, reptiles, birds, and mammals). These disparate findings are discussed in the context of the genetic architecture of the developing hindbrain, which facilitates convergent evolution. Yet, it will be critical to decipher the gene regulatory networks underlying development of auditory neurons across vertebrates to explore the possibility of homologous neuronal populations.
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Lesoway MP. The future of Evo-Devo: the inaugural meeting of the Pan American Society for evolutionary developmental biology. Evol Dev 2016; 18:71-7. [PMID: 26773456 DOI: 10.1111/ede.12181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
What is the future of evolutionary developmental biology? This question and more were discussed at the inaugural meeting for the Pan American Society for Evolutionary Developmental Biology, held August 5-9, 2015, in Berkeley, California, USA. More than 300 participants attended the first meeting of the new society, representing the current diversity of Evo-Devo. Speakers came from throughout the Americas, presenting work using an impressive range of study systems, techniques, and approaches. Current research draws from themes including the role of gene regulatory networks, plasticity and the role of the environment, novelty, population genetics, and regeneration, using new and emerging techniques as well as traditional tools. Multiple workshops and a discussion session covered subjects both practical and theoretical, providing an opportunity for members to discuss the current challenges and future directions for Evo-Devo. The excitement and discussion generated over the course of the meeting demonstrates the current dynamism of the field, suggesting that the future of Evo-Devo is bright indeed.
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Affiliation(s)
- Maryna P Lesoway
- Department of Biology, McGill University, 1205 Avenue Dr Penfield, Montreal, QC, Canada, H3A-1B1.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa, Ancon, Republic of Panama
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Bionaz M, Osorio J, Loor JJ. TRIENNIAL LACTATION SYMPOSIUM: Nutrigenomics in dairy cows: Nutrients, transcription factors, and techniques1,2. J Anim Sci 2015; 93:5531-53. [DOI: 10.2527/jas.2015-9192] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- M. Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis 97333
| | - J. Osorio
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis 97333
| | - J. J. Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
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Li H, Richardson WD. Evolution of the CNS myelin gene regulatory program. Brain Res 2015; 1641:111-121. [PMID: 26474911 DOI: 10.1016/j.brainres.2015.10.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 01/06/2023]
Abstract
Myelin is a specialized subcellular structure that evolved uniquely in vertebrates. A myelinated axon conducts action potentials many times faster than an unmyelinated axon of the same diameter; for the same conduction speed, the unmyelinated axon would need a much larger diameter and volume than its myelinated counterpart. Hence myelin speeds information transfer and saves space, allowing the evolution of a powerful yet portable brain. Myelination in the central nervous system (CNS) is controlled by a gene regulatory program that features a number of master transcriptional regulators including Olig1, Olig2 and Myrf. Olig family genes evolved from a single ancestral gene in non-chordates. Olig2, which executes multiple functions with regard to oligodendrocyte identity and development in vertebrates, might have evolved functional versatility through post-translational modification, especially phosphorylation, as illustrated by its evolutionarily conserved serine/threonine phospho-acceptor sites and its accumulation of serine residues during more recent stages of vertebrate evolution. Olig1, derived from a duplicated copy of Olig2 in early bony fish, is involved in oligodendrocyte development and is critical to remyelination in bony vertebrates, but is lost in birds. The origin of Myrf orthologs might be the result of DNA integration between an invading phage or bacterium and an early protist, producing a fusion protein capable of self-cleavage and DNA binding. Myrf seems to have adopted new functions in early vertebrates - initiation of the CNS myelination program as well as the maintenance of mature oligodendrocyte identity and myelin structure - by developing new ways to interact with DNA motifs specific to myelin genes. This article is part of a Special Issue entitled SI: Myelin Evolution.
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Affiliation(s)
- Huiliang Li
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - William D Richardson
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK
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