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Trigos AS, Bongiovanni F, Zhang Y, Zethoven M, Tothill R, Pearson R, Papenfuss AT, Goode DL. Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins. Genome Biol 2024; 25:110. [PMID: 38685127 PMCID: PMC11057133 DOI: 10.1186/s13059-024-03247-1] [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: 08/08/2023] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Metazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and protein translation. Multicellularity requires careful control and coordination of these unicellular genes to maintain tissue integrity and homeostasis. Gene regulatory networks (GRNs) that arose during metazoan evolution are frequently altered in cancer, resulting in over-expression of unicellular genes. We propose that an imbalance in co-expression of unicellular (UC) and multicellular (MC) genes is a driving force in cancer. RESULTS We combine gene co-expression analysis to infer changes to GRNs in cancer with protein sequence conservation data to distinguish genes with UC and MC origins. Co-expression networks created using RNA sequencing data from 31 tumor types and normal tissue samples are divided into modules enriched for UC genes, MC genes, or mixed UC-MC modules. The greatest differences between tumor and normal tissue co-expression networks occur within mixed UC-MC modules. MC and UC genes not commonly co-expressed in normal tissues form distinct co-expression modules seen only in tumors. The degree of rewiring of genes within mixed UC-MC modules increases with tumor grade and stage. Mixed UC-MC modules are enriched for somatic mutations in cancer genes, particularly amplifications, suggesting an important driver of the rewiring observed in tumors is copy number changes. CONCLUSIONS Our study shows the greatest changes to gene co-expression patterns during tumor progression occur between genes of MC and UC origins, implicating the breakdown and rewiring of metazoan gene regulatory networks in cancer development and progression.
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Affiliation(s)
- Anna S Trigos
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia.
| | - Felicia Bongiovanni
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yangyi Zhang
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Maia Zethoven
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Richard Tothill
- Centre for Cancer Research, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Richard Pearson
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - David L Goode
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Sukmak R, Suttinun C, Kovitvadhi U, Kovitvadhi A, Vongsangnak W. Uncovering nutrients and energy related gene functions of black soldier fly Hermetia illucens strain KUP. Gene 2024; 896:148045. [PMID: 38042219 DOI: 10.1016/j.gene.2023.148045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 12/04/2023]
Abstract
The black soldier fly (Hermetia illucens) has emerged as a significant insect species in the decomposition of organic waste for sustainable agricultural practices. Due to its remarkable characteristics and performance, H. illucens is increasingly utilised for insect farming, particularly for industrial-scale rearing throughout the world. In this study, we employed whole-genome sequencing to annotate the gene and protein functions of H. illucens and to explore the functional genomics related to nutrients and energy. As a result, a genome size of H. illucens strain KUP 1.68 Gb with a GC content of 42.13 % was achieved. Of the 14,036 coding sequences, we determined the function of 12,046 protein-coding genes. Based on metabolic functional assignment, we classified 4,218 protein-coding genes; the main category was metabolism (32.86 %). Comparative genomic analysis across the other H. illucens strain and insect species revealed that the major metabolic gene functions and pathways related to nutrient and energy sources of H. illucens KUP are involved in key amino acid metabolism (e.g., cysteine and methionine) as well as fatty acid biosynthesis and glycerolipid metabolism. These findings underscore the metabolic capability and versatility of H. illucens, which is regarded as a potential source of proteins and lipids. Our study contributes to the knowledge regarding the feed utilisation of H. illucens and offers insights into transforming waste into valuable products. H. illucens has the potential to create globally sustainable nutrients and environmentally friendly solutions, aligning with the goal of responsible resource utilisation.
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Affiliation(s)
- Rachrapee Sukmak
- Graduate Student in Animal Health and Biomedical Science Program, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Chanaporn Suttinun
- Department of Veterinary Biosciences and Veterinary Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Uthaiwan Kovitvadhi
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Attawit Kovitvadhi
- Department of Physiology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand.
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand; Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand.
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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Liu J, Wu Y, Zhang X, Gill RA, Hu M, Bai Z, Zhao C, Zhang Y, Liu Y, Hu Q, Cheng X, Huang J, Liu L, Yan S, Liu S. Functional and evolutionary study of MLO gene family in the regulation of Sclerotinia stem rot resistance in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:86. [PMID: 37217949 DOI: 10.1186/s13068-023-02325-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Oilseed rape (Brassica napus L.) is known as one of the most important oilseed crops cultivated around the world. However, its production continuously faces a huge challenge of Sclerotinia stem rot (SSR), a destructive disease caused by the fungus Sclerotinia sclerotiorum, resulting in huge yield loss annually. The SSR resistance in B. napus is quantitative and controlled by a set of minor genes. Identification of these genes and pyramiding them into a variety are a major strategy for SSR resistance breeding in B. napus. RESULTS Here, we performed a genome-wide association study (GWAS) using a natural population of B. napus consisting of 222 accessions to identify BnaA08g25340D (BnMLO2_2) as a candidate gene that regulates the SSR resistance. BnMLO2_2 was a member of seven homolog genes of Arabidopsis Mildew Locus O 2 (MLO2) and the significantly SNPs were mainly distributed in the promoter of BnMLO2_2, suggesting a role of BnMLO2_2 expression level in the regulation of SSR resistance. We expressed BnMLO2_2 in Arabidopsis and the transgenic plants displayed an enhanced SSR resistance. Transcriptome profiling of different tissues of B. napus revealed that BnMLO2_2 had the most expression level in leaf and silique tissues among all the 7 BnMLO2 members and also expressed higher in the SSR resistant accession than in the susceptible accession. In Arabidopsis, mlo2 plants displayed reduced resistance to SSR, whereas overexpression of MLO2 conferred plants an enhanced SSR resistance. Moreover, a higher expression level of MLO2 showed a stronger SSR resistance in the transgenic plants. The regulation of MLO2 in SSR resistance may be associated with the cell death. Collinearity and phylogenetic analysis revealed a large expansion of MLO family in Brassica crops. CONCLUSION Our study revealed an important role of BnMLO2 in the regulation of SSR resistance and provided a new gene candidate for future improvement of SSR resistance in B. napus and also new insights into understanding of MLO family evolution in Brassica crops.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yupo Wu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Xiong Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Rafaqat Ali Gill
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zetao Bai
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | | | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
| | - Qiong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Junyan Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
| | - Lijiang Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China.
| | - Shunping Yan
- College of Life Science and Technology, Center of Integrative Biology, Interdisciplinary Science Research Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, People's Republic of China
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5
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Yang G, Zhang Y, Wei X, Cui L, Nie X. Genetic Diversity of Transcription Factor Genes in Triticum and Mining for Promising Haplotypes for Beneficial Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:899292. [PMID: 35873966 PMCID: PMC9305608 DOI: 10.3389/fpls.2022.899292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
Transcription factor (TF) is a class of the sequence-specific DNA-binding proteins that modulate the transcription of target genes, and thus regulate their expressions. Variations in TF are the crucial determinants for phenotypic traits. Although much progress has been made in the functions of TF genes in wheat, one of the most important staple crops globally, the diversity of TF genes in wheat and its progenitors are not well understood, especially the agronomically promising haplotypes have not yet been characterized. Here, we identified a total of 6,023 TF genes from hexaploid wheat through a genome-search method and classified them into 59 gene families based on the conserved domain. The characteristics and dN/dS values of these genes showed evidently selective effects. Based on re-sequencing data, we found a strong genetic bottleneck among these TF genes on A and D subgenomes while no found in B subgenome during wheat domestication. Combined with selective signals and known QTLs on the whole genome, 21 TF genes were preliminarily found to be associated with yield-related traits. The haplotype frequency of these TF genes was further investigated in bread wheat and its progenitors and 13 major haplotypes were the casual loci related to key traits. Finally, the tissue-specific TF genes were also identified using RNA-seq analysis. This study provided insights into the diversity and evolution of TF genes and the identified TF genes and excellent haplotypes associating with traits will contribute to wheat genetic improvement.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Ying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xinyu Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Licao Cui
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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6
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A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemone Nematostella vectensis. Proc Natl Acad Sci U S A 2022; 119:e2113701119. [PMID: 35500123 PMCID: PMC9172639 DOI: 10.1073/pnas.2113701119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this study, we demonstrate how a new cell type can arise through duplication of an ancestral cell type followed by functional divergence of the new daughter cell. Specifically, we show that stinging cells in a cnidarian (namely, a sea anemone) emerged by duplication of an ancestral neuron followed by inhibition of the RFamide neuropeptide it once secreted. This finding is evidence that stinging cells evolved from a specific subtype of neurons and suggests other neuronal subtypes may have been coopted for other novel secretory functions. Cnidocytes (i.e., stinging cells) are an unequivocally novel cell type used by cnidarians (i.e., corals, jellyfish, and their kin) to immobilize prey. Although they are known to share a common evolutionary origin with neurons, the developmental program that promoted the emergence of cnidocyte fate is not known. Using functional genomics in the sea anemone, Nematostella vectensis, we show that cnidocytes develop by suppression of neural fate in a subset of neurons expressing RFamide. We further show that a single regulatory gene, a C2H2-type zinc finger transcription factor (ZNF845), coordinates both the gain of novel (cnidocyte-specific) traits and the inhibition of ancestral (neural) traits during cnidocyte development and that this gene arose by domain shuffling in the stem cnidarian. Thus, we report a mechanism by which a truly novel regulatory gene (ZNF845) promotes the development of a truly novel cell type (cnidocyte) through duplication of an ancestral cell lineage (neuron) and inhibition of its ancestral identity (RFamide).
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7
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de Oliveira AL, Mitchell J, Girguis P, Bright M. Novel insights on obligate symbiont lifestyle and adaptation to chemosynthetic environment as revealed by the giant tubeworm genome. Mol Biol Evol 2021; 39:6454105. [PMID: 34893862 PMCID: PMC8789280 DOI: 10.1093/molbev/msab347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mutualism between the giant tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has been extensively researched over the past 40 years. However, the lack of the host whole genome information has impeded the full comprehension of the genotype/phenotype interface in Riftia. Here we described the high-quality draft genome of Riftia, its complete mitogenome, and tissue-specific transcriptomic data. The Riftia genome presents signs of reductive evolution, with gene family contractions exceeding expansions. Expanded gene families are related to sulphur metabolism, detoxification, anti-oxidative stress, oxygen transport, immune system, and lysosomal digestion, reflecting evolutionary adaptations to the vent environment and endosymbiosis. Despite the derived body plan, the developmental gene repertoire in the gutless tubeworm is extremely conserved with the presence of a near intact and complete Hox cluster. Gene expression analyses establishes that the trophosome is a multi-functional organ marked by intracellular digestion of endosymbionts, storage of excretory products and haematopoietic functions. Overall, the plume and gonad tissues both in contact to the environment harbour highly expressed genes involved with cell cycle, programmed cell death, and immunity indicating a high cell turnover and defence mechanisms against pathogens. We posit that the innate immune system plays a more prominent role into the establishment of the symbiosis during the infection in the larval stage, rather than maintaining the symbiostasis in the trophosome. This genome bridges four decades of physiological research in Riftia, whilst simultaneously provides new insights into the development, whole organism functions and evolution in the giant tubeworm.
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Affiliation(s)
| | - Jessica Mitchell
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Monika Bright
- Department of Functional and Evolutionary Ecology, University of Vienna, Austria
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8
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Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress. Sci Rep 2021; 11:13489. [PMID: 34188147 PMCID: PMC8241847 DOI: 10.1038/s41598-021-92938-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/17/2021] [Indexed: 01/10/2023] Open
Abstract
The indica ecotypes, IR64, an elite drought-susceptible variety adapted to irrigated ecosystem, and Apo (IR55423-01 or NSIC RC9), a moderate drought-tolerant upland genotype together with their hybrid (IR64 × Apo) were exposed to non- and water-stress conditions. By sequencing (RNA-seq) these genotypes, we were able to map genes diverging in cis and/or trans factors. Under non-stress condition, cis dominantly explains (11.2%) regulatory differences, followed by trans (8.9%). Further analysis showed that water-limiting condition largely affects trans and cis + trans factors. On the molecular level, cis and/or trans regulatory divergence explains their genotypic differences and differential drought response. Between the two parental genotypes, Apo appears to exhibit more photosynthetic efficiency even under water-limiting condition and is ascribed to trans. Statistical analyses showed that regulatory divergence is significantly influenced by environmental conditions. Likewise, the mode of parental expression inheritance which drives heterosis (HET) is significantly affected by environmental conditions indicating the malleability of heterosis to external factors. Further analysis revealed that the HET class, dominance, was significantly enriched under water-stress condition. We also identified allelic imbalance switching in which several genes prefer IR64- (or Apo-) specific allele under non-stress condition but switched to Apo- (or IR64-) specific allele when exposed to water-stress condition.
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9
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Weng YM, Francoeur CB, Currie CR, Kavanaugh DH, Schoville SD. A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation. Mol Ecol Resour 2021; 21:2145-2165. [PMID: 33938156 DOI: 10.1111/1755-0998.13409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/13/2021] [Accepted: 04/26/2021] [Indexed: 12/13/2022]
Abstract
The hyperdiverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome evolution of beetles, as well as genetic changes associated with specialization to high-elevation alpine habitats. In particular, this genome resource provides a foundation for expanding comparative molecular research into mechanisms of insect cold adaptation. Comparison to other beetles shows a strong signature of genome compaction, with N. riversi possessing a relatively small genome (~147 Mb) compared to other beetles, with associated reductions in repeat element content and intron length. Small genome size is not, however, associated with fewer protein-coding genes, and an analysis of gene family diversity shows significant expansions of genes associated with cellular membranes and membrane transport, as well as protein phosphorylation and muscle filament structure. Finally, our genomic analyses show that these high-elevation beetles have endosymbiotic Spiroplasma, with several metabolic pathways (e.g., propanoate biosynthesis) that might complement N. riversi, although its role as a beneficial symbiont or as a reproductive parasite remains equivocal.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin - Madison, Madison, WI, USA
| | - Charlotte B Francoeur
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, Madison, WI, USA
| | - David H Kavanaugh
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin - Madison, Madison, WI, USA
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10
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Wong ES, Zheng D, Tan SZ, Bower NL, Garside V, Vanwalleghem G, Gaiti F, Scott E, Hogan BM, Kikuchi K, McGlinn E, Francois M, Degnan BM. Deep conservation of the enhancer regulatory code in animals. Science 2020; 370:370/6517/eaax8137. [PMID: 33154111 DOI: 10.1126/science.aax8137] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 04/29/2020] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
Interactions of transcription factors (TFs) with DNA regulatory sequences, known as enhancers, specify cell identity during animal development. Unlike TFs, the origin and evolution of enhancers has been difficult to trace. We drove zebrafish and mouse developmental transcription using enhancers from an evolutionarily distant marine sponge. Some of these sponge enhancers are located in highly conserved microsyntenic regions, including an Islet enhancer in the Islet-Scaper region. We found that Islet enhancers in humans and mice share a suite of TF binding motifs with sponges, and that they drive gene expression patterns similar to those of sponge and endogenous Islet enhancers in zebrafish. Our results suggest the existence of an ancient and conserved, yet flexible, genomic regulatory syntax that has been repeatedly co-opted into cell type-specific gene regulatory networks across the animal kingdom.
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Affiliation(s)
- Emily S Wong
- School of Biological Sciences, University of Queensland, Brisbane, Australia. .,Victor Chang Cardiac Research Institute, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
| | - Dawei Zheng
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Siew Z Tan
- Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Neil L Bower
- Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia
| | - Victoria Garside
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Australia
| | | | - Federico Gaiti
- School of Biological Sciences, University of Queensland, Brisbane, Australia
| | - Ethan Scott
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Benjamin M Hogan
- Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia.,Department of Anatomy and Neuroscience and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Kazu Kikuchi
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Edwina McGlinn
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Australia
| | - Mathias Francois
- Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia. .,Centenary Institute, David Richmond Program for Cardio-Vascular Research: Gene Regulation and Editing, School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Australia.
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11
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Zawisza-Álvarez M, Pérez-Calles C, Gattoni G, Garcia-Fernàndez J, Benito-Gutiérrez È, Herrera-Úbeda C. The ADAR Family in Amphioxus: RNA Editing and Conserved Orthologous Site Predictions. Genes (Basel) 2020; 11:genes11121440. [PMID: 33265998 PMCID: PMC7761149 DOI: 10.3390/genes11121440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 01/21/2023] Open
Abstract
RNA editing is a relatively unexplored process in which transcribed RNA is modified at specific nucleotides before translation, adding another level of regulation of gene expression. Cephalopods use it extensively to increase the regulatory complexity of their nervous systems, and mammals use it too, but less prominently. Nevertheless, little is known about the specifics of RNA editing in most of the other clades and the relevance of RNA editing from an evolutionary perspective remains unknown. Here we analyze a key element of the editing machinery, the ADAR (adenosine deaminase acting on RNA) gene family, in an animal with a key phylogenetic position at the root of chordates: the cephalochordate amphioxus. We show, that as in cephalopods, ADAR genes in amphioxus are predominantly expressed in the nervous system; we identify a number of RNA editing events in amphioxus; and we provide a newly developed method to identify RNA editing events in highly polymorphic genomes using orthology as a guide. Overall, our work lays the foundations for future comparative analysis of RNA-editing events across the metazoan tree.
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Affiliation(s)
- Michał Zawisza-Álvarez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08007 Barcelona, Spain; (M.Z.-Á.); (C.P.-C.); (J.G.-F.)
| | - Claudia Pérez-Calles
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08007 Barcelona, Spain; (M.Z.-Á.); (C.P.-C.); (J.G.-F.)
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK;
| | - Giacomo Gattoni
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK;
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08007 Barcelona, Spain; (M.Z.-Á.); (C.P.-C.); (J.G.-F.)
| | - Èlia Benito-Gutiérrez
- Department of Zoology, University of Cambridge, Cambridge CB2 1TN, UK;
- Correspondence: (È.B.-G.); (C.H.-Ú.)
| | - Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08007 Barcelona, Spain; (M.Z.-Á.); (C.P.-C.); (J.G.-F.)
- Correspondence: (È.B.-G.); (C.H.-Ú.)
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12
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Fonseca E, Machado AM, Vilas-Arrondo N, Gomes-Dos-Santos A, Veríssimo A, Esteves P, Almeida T, Themudo G, Ruivo R, Pérez M, da Fonseca R, Santos MM, Froufe E, Román-Marcote E, Venkatesh B, Castro LFC. Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes. Gen Comp Endocrinol 2020; 295:113527. [PMID: 32526329 DOI: 10.1016/j.ygcen.2020.113527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
Nuclear receptors (NRs) are key transcription factors that originated in the common ancestor of metazoans. The vast majority of NRs are triggered by binding to either endogenous (e.g. retinoic acid) or exogenous (e.g. xenobiotics) ligands, and their evolution and expansion is tightly linked to the function of endocrine systems. Importantly, they represent classic targets of physiological exploitation by endocrine disrupting chemicals. The NR gene repertoire in different lineages has been shaped by gene loss, duplication and mutation, denoting a dynamic evolutionary route. As the earliest diverging class of gnathostomes (jawed vertebrates), cartilaginous fishes offer an exceptional opportunity to address the early diversification of NR gene families and the evolution of the endocrine system in jawed vertebrates. Here we provide an exhaustive analysis into the NR gene composition in five elasmobranch (sharks and rays) and two holocephalan (chimaeras) species. For this purpose, we generated also a low coverage draft genome assembly of the chimaera small-eyed rabbitfish, Hydrolagus affinis. We show that cartilaginous fish retain an archetypal NR gene repertoire, similar to that of mammals and coincident with the two rounds of whole genome duplication that occurred in the gnathostome ancestor. Furthermore, novel gene members of the non-canonical NR0B receptors were found in the genomes of this lineage. Our findings provide an essential view into the early diversification of NRs in gnathostomes, paving the way for functional studies.
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Affiliation(s)
- Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - André M Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Nair Vilas-Arrondo
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain; UVIGO, phD Program "Marine Science, Tehchology and Management" (Do *MAR), Faculty of Biology, University of Vigo, 36200 Vigo, Spain
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, U.Porto, 4485-661 Vairão, Portugal
| | - Pedro Esteves
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; UVIGO, phD Program "Marine Science, Tehchology and Management" (Do *MAR), Faculty of Biology, University of Vigo, 36200 Vigo, Spain
| | - Tereza Almeida
- FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal; CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO, Associate Laboratory, U.Porto, 4485-661 Vairão, Portugal
| | - Gonçalo Themudo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Raquel Ruivo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Montse Pérez
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain
| | - Rute da Fonseca
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Denmark
| | - Miguel M Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal
| | - Esther Román-Marcote
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36390 Vigo, Spain
| | - Byrappa Venkatesh
- Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U.Porto, 4450-208 Matosinhos, Portugal; FCUP - Faculty of Sciences, Department of Biology, U.Porto, 4169-007 Porto, Portugal.
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13
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Mohanta TK, Yadav D, Khan A, Hashem A, Tabassum B, Khan AL, Abd_Allah EF, Al-Harrasi A. Genomics, molecular and evolutionary perspective of NAC transcription factors. PLoS One 2020; 15:e0231425. [PMID: 32275733 PMCID: PMC7147800 DOI: 10.1371/journal.pone.0231425] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/23/2020] [Indexed: 01/05/2023] Open
Abstract
NAC (NAM, ATAF1,2, and CUC2) transcription factors are one of the largest transcription factor families found in the plants and are involved in diverse developmental and signalling events. Despite the availability of comprehensive genomic information from diverse plant species, the basic genomic, biochemical, and evolutionary details of NAC TFs have not been established. Therefore, NAC TFs family proteins from 160 plant species were analyzed in the current study. Study revealed, Brassica napus (410) encodes highest number and Klebsormidium flaccidum (3) encodes the lowest number of TFs. The study further revealed the presence of NAC TF in the Charophyte algae K. flaccidum. On average, the monocot plants encode higher number (141.20) of NAC TFs compared to the eudicots (125.04), gymnosperm (75), and bryophytes (22.66). Furthermore, our analysis revealed that several NAC TFs are membrane bound and contain monopartite, bipartite, and multipartite nuclear localization signals. NAC TFs were also found to encode several novel chimeric proteins and regulate a complex interactome network. In addition to the presence of NAC domain, several NAC proteins were found to encode other functional signature motifs as well. Relative expression analysis of NAC TFs in A. thaliana revealed root tissue treated with urea and ammonia showed higher level of expression and leaf tissues treated with urea showed lower level of expression. The synonymous codon usage is absent in the NAC TFs and it appears that they have evolved from orthologous ancestors and undergone vivid duplications to give rise to paralogous NAC TFs. The presence of novel chimeric NAC TFs are of particular interest and the presence of chimeric NAC domain with other functional signature motifs in the NAC TF might encode novel functional properties in the plants.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Dhananjay Yadav
- Dept. of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Adil Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Baby Tabassum
- Department of Zoology, Toxicology laboratory, Raza P.G. College, Rampur, Uttar Pradesh, India
| | - Abdul Latif Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
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14
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Lai X, Chahtane H, Martin-Arevalillo R, Zubieta C, Parcy F. Contrasted evolutionary trajectories of plant transcription factors. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:101-107. [PMID: 32417720 DOI: 10.1016/j.pbi.2020.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Because of their prominent roles in plant development, transcription factors (TF) play central roles as drivers of innovation in the evolution of the green lineage (viridiplantae). The advent of massive sequencing combined with comparative genetics/genomics allows a rigorous investigation of how TF families have contributed to plant diversification from charophyte algae to bryophytes to angiosperms. Here, we review recent progress on TF family reconstruction and the identification of distantly related TFs present throughout the evolutionary timeline from algae to angiosperms. These data provide examples of contrasting evolutionary trajectories of TF families and illustrate how conserved TFs adopt diverse roles over the course of evolution.
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Affiliation(s)
- Xuelei Lai
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - Raquel Martin-Arevalillo
- Laboratoire de Reproduction et de Développement des Plantes, INRAE, CNRS, ENS de Lyon, UCB Lyon 1, Université de Lyon, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-LPCV, 38000 Grenoble, France.
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15
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Williams LM, Inge MM, Mansfield KM, Rasmussen A, Afghani J, Agrba M, Albert C, Andersson C, Babaei M, Babaei M, Bagdasaryants A, Bonilla A, Browne A, Carpenter S, Chen T, Christie B, Cyr A, Dam K, Dulock N, Erdene G, Esau L, Esonwune S, Hanchate A, Huang X, Jennings T, Kasabwala A, Kehoe L, Kobayashi R, Lee M, LeVan A, Liu Y, Murphy E, Nambiar A, Olive M, Patel D, Pavesi F, Petty CA, Samofalova Y, Sanchez S, Stejskal C, Tang Y, Yapo A, Cleary JP, Yunes SA, Siggers T, Gilmore TD. Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 104:103559. [PMID: 31751628 DOI: 10.1016/j.dci.2019.103559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/15/2019] [Accepted: 11/17/2019] [Indexed: 06/10/2023]
Abstract
Herein, we characterize transcription factor NF-κB from the demosponge Amphimedon queenslandica (Aq). Aq-NF-κB is most similar to NF-κB p100/p105 among vertebrate proteins, with an N-terminal DNA-binding domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile akin to human NF-κB proteins. Like mammalian NF-κB p100, C-terminal truncation allows nuclear translocation of Aq-NF-κB and increases its transcriptional activation activity. Expression of IκB kinases (IKKs) induces proteasome-dependent C-terminal processing of Aq-NF-κB in human cells, and processing requires C-terminal serines in Aq-NF-κB. Unlike NF-κB p100, C-terminal sequences of Aq-NF-κB do not inhibit its DNA-binding activity. Tissue of a black encrusting demosponge contains NF-κB site DNA-binding activity, as well as nuclear and processed NF-κB. Treatment of sponge tissue with LPS increases both DNA-binding activity and processing of NF-κB. A. queenslandica transcriptomes contain homologs to upstream NF-κB pathway components. This is first functional characterization of NF-κB in sponge, the most basal multicellular animal.
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Affiliation(s)
- Leah M Williams
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Melissa M Inge
- Department of Biology, Boston University, Boston, MA, 02215, USA; Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | | | - Anna Rasmussen
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Jamie Afghani
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Mikhail Agrba
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Colleen Albert
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Cecilia Andersson
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Milad Babaei
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Mohammad Babaei
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Abigail Bagdasaryants
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Arianna Bonilla
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Amanda Browne
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Sheldon Carpenter
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Tiffany Chen
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Blake Christie
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Andrew Cyr
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Katie Dam
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Nicholas Dulock
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Galbadrakh Erdene
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Lindsie Esau
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Stephanie Esonwune
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Anvita Hanchate
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Xinli Huang
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Timothy Jennings
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Aarti Kasabwala
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Leanne Kehoe
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Ryan Kobayashi
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Migi Lee
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Andre LeVan
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yuekun Liu
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Emily Murphy
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Avanti Nambiar
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Meagan Olive
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Devansh Patel
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Flaminio Pavesi
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Christopher A Petty
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yelena Samofalova
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Selma Sanchez
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Camilla Stejskal
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Yinian Tang
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Alia Yapo
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - John P Cleary
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Sarah A Yunes
- Molecular Biology Laboratory (BB522), Program in Biochemistry & Molecular Biology, Boston University, Boston, MA, 02215, USA
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Thomas D Gilmore
- Department of Biology, Boston University, Boston, MA, 02215, USA.
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16
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Simkin A, Geissler R, McIntyre ABR, Grimson A. Evolutionary dynamics of microRNA target sites across vertebrate evolution. PLoS Genet 2020; 16:e1008285. [PMID: 32012152 PMCID: PMC7018135 DOI: 10.1371/journal.pgen.1008285] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 02/13/2020] [Accepted: 01/02/2020] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3' untranslated regions (3'UTRs) of mRNAs, and are amongst the most highly conserved motifs within 3'UTRs. However, little is known regarding the evolutionary pressures that lead to loss and gain of such target sites. Here, we quantify the selective pressures that act upon miRNA target sites. Notably, selective pressure extends beyond deeply conserved binding sites to those that have undergone recent substitutions. Our approach reveals that even amongst ancient animal miRNAs, which exert the strongest selective pressures on 3'UTR sequences, there are striking differences in patterns of target site evolution between miRNAs. Considering only ancient animal miRNAs, we find three distinct miRNA groups, each exhibiting characteristic rates of target site gain and loss during mammalian evolution. The first group both loses and gains sites rarely. The second group shows selection only against site loss, with site gains occurring at a neutral rate, whereas the third loses and gains sites at neutral or above expected rates. Furthermore, mutations that alter the strength of existing target sites are disfavored. Applying our approach to individual transcripts reveals variation in the distribution of selective pressure across the transcriptome and between miRNAs, ranging from strong selection acting on a small subset of targets of some miRNAs, to weak selection on many targets for other miRNAs. miR-20 and miR-30, and many other miRNAs, exhibit broad, deeply conserved targeting, while several other comparably ancient miRNAs show a lack of selective constraint, and a small number, including mir-146, exhibit evidence of rapidly evolving target sites. Our approach adds valuable perspective on the evolution of miRNAs and their targets, and can also be applied to characterize other 3'UTR regulatory motifs.
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Affiliation(s)
- Alfred Simkin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Elon University, Elon, North Carolina, United States of America
| | - Rene Geissler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Alexa B. R. McIntyre
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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17
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18
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Tempos and modes of collectivity in the history of life. Theory Biosci 2019; 140:343-351. [PMID: 31529373 DOI: 10.1007/s12064-019-00303-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/04/2019] [Indexed: 10/26/2022]
Abstract
Collective integration and processing of information have increased through the history of life, through both the formation of aggregates in which the entities may have very different properties and which jointly coarse-grained environmental variables (ranging from widely varying metabolism in microbial consortia to the ecological diversity of species on reefs) and through collectives of similar entities (such as cells within an organism or social groups). Such increases have been implicated in significant transitions in the history of life, including aspects of the origin of life, the generation of pangenomes among microbes and microbial communities such as stromatolites, multicellularity and social insects. This contribution provides a preliminary overview of the dominant modes of collective information processing in the history of life, their phylogenetic distribution and extent of convergence, and the effects of new modes for integrating and acting upon information on the tempo of evolutionary change.
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19
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Karakostis K, Fåhraeus R. Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures. BMC Cancer 2019; 19:915. [PMID: 31519161 PMCID: PMC6743176 DOI: 10.1186/s12885-019-6118-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Structured RNA regulatory motifs exist from the prebiotic stages of the RNA world to the more complex eukaryotic systems. In cases where a functional RNA structure is within the coding sequence a selective pressure drives a parallel co-evolution of the RNA structure and the encoded peptide domain. The p53-MDM2 axis, describing the interactions between the p53 tumor suppressor and the MDM2 E3 ubiquitin ligase, serves as particularly useful model revealing how secondary RNA structures have co-evolved along with corresponding interacting protein motifs, thus having an impact on protein - RNA and protein - protein interactions; and how such structures developed signal-dependent regulation in mammalian systems. The p53(BOX-I) RNA sequence binds the C-terminus of MDM2 and controls p53 synthesis while the encoded peptide domain binds MDM2 and controls p53 degradation. The BOX-I peptide domain is also located within p53 transcription activation domain. The folding of the p53 mRNA structure has evolved from temperature-regulated in pre-vertebrates to an ATM kinase signal-dependent pathway in mammalian cells. The protein - protein interaction evolved in vertebrates and became regulated by the same signaling pathway. At the same time the protein - RNA and protein - protein interactions evolved, the p53 trans-activation domain progressed to become integrated into a range of cellular pathways. We discuss how a single synonymous mutation in the BOX-1, the p53(L22 L), observed in a chronic lymphocyte leukaemia patient, prevents the activation of p53 following DNA damage. The concepts analysed and discussed in this review may serve as a conceptual mechanistic paradigm of the co-evolution and function of molecules having roles in cellular regulation, or the aetiology of genetic diseases and how synonymous mutations can affect the encoded protein.
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Affiliation(s)
| | - Robin Fåhraeus
- Université Paris 7, INSERM UMR 1131, 27 Rue Juliette Dodu, 75010 Paris, France
- Department of Medical Biosciences, Umea University, SE-90185 Umea, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
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20
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Herrera-Úbeda C, Marín-Barba M, Navas-Pérez E, Gravemeyer J, Albuixech-Crespo B, Wheeler GN, Garcia-Fernàndez J. Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation. BIOLOGY 2019; 8:biology8030061. [PMID: 31450588 PMCID: PMC6784235 DOI: 10.3390/biology8030061] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 01/10/2023]
Abstract
Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.
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Affiliation(s)
- Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Marta Marín-Barba
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Enrique Navas-Pérez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Jan Gravemeyer
- German Cancer Research Center, 69120 Heidelberg, Germany
| | - Beatriz Albuixech-Crespo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
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21
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Defoort J, Van de Peer Y, Vermeirssen V. Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. Nucleic Acids Res 2019; 46:6480-6503. [PMID: 29873777 PMCID: PMC6061849 DOI: 10.1093/nar/gky468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/14/2018] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein–DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.
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Affiliation(s)
- Jonas Defoort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Vanessa Vermeirssen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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22
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Trigos AS, Pearson RB, Papenfuss AT, Goode DL. Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer. eLife 2019; 8:40947. [PMID: 30803482 DOI: 10.7554/elife.40947.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/06/2019] [Indexed: 05/27/2023] Open
Abstract
Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumors, we show many transcriptional changes in tumors are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach.
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Affiliation(s)
- Anna S Trigos
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Richard B Pearson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Anthony T Papenfuss
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - David L Goode
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
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23
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Trigos AS, Pearson RB, Papenfuss AT, Goode DL. Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer. eLife 2019; 8:40947. [PMID: 30803482 PMCID: PMC6402835 DOI: 10.7554/elife.40947] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/06/2019] [Indexed: 12/11/2022] Open
Abstract
Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumors, we show many transcriptional changes in tumors are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach. Cancers arise when harmful changes happen in the genetic information of certain cells. These ‘mutations’ are different from person to person, but overall, they disrupt healthy cells in similar ways. In particular, cancer cells tend to lose features that help cells work together in the body. Researchers have suggested that cancers may emerge when cells stop being able to cooperate with each other as part of an organism. Our bodies still rely on old genes that were present in our earliest, single-cell ancestors. However, we also have newer genes that evolved when the organisms in our lineage started to have more than one cell. A complex network of signals exists to ensure that both sets of genes work together smoothly, and previous studies have suggested that cancers may appear when this delicate balance is disrupted. To address this question, Trigos et al. have now used a computational approach to analyse different types of tumours from over 9,000 patients. This showed that, in cancer, many mutations disrupt the genes that coordinate old and new genes. These mutations were usually small, punctual changes in the genetic sequence. However, large modifications, such as an entire gene being deleted or repeated, took place more often in the old or the new genes themselves. Therefore, different classes of mutations have specific roles when disrupting how old and new genes work in cancer. While certain genes highlighted during this analysis were already known to be associated with cancer, others were not – including genes present during the evolution of the earliest animals on Earth. Looking more closely into how these genes can cause disease may help us better understand and fight cancer.
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Affiliation(s)
- Anna S Trigos
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
| | - Richard B Pearson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Anthony T Papenfuss
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia.,Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - David L Goode
- Computational Cancer Biology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia
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24
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Kurafeiski JD, Pinto P, Bornberg-Bauer E. Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding. Genome Biol Evol 2019; 11:406-414. [PMID: 30597011 PMCID: PMC6370388 DOI: 10.1093/gbe/evy269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2018] [Indexed: 01/25/2023] Open
Abstract
Transcriptional regulation is crucial for all biological processes and well investigated at the molecular level for a wide range of organisms. However, it is quite unclear how innovations, such as the activity of a novel regulatory element, evolve. In the case of transcription factor (TF) binding, both a novel TF and a novel-binding site would need to evolve concertedly. Since promiscuous functions have recently been identified as important intermediate steps in creating novel specific functions in many areas such as enzyme evolution and protein-protein interactions, we ask here how promiscuous binding of TFs to TF-binding sites (TFBSs) affects the robustness and evolvability of this tightly regulated system. Specifically, we investigate the binding behavior of several hundred TFs from different species at unprecedented breadth. Our results illustrate multiple aspects of TF-binding interactions, ranging from correlations between the strength of the interaction bond and specificity, to preferences regarding TFBS nucleotide composition in relation to both domains and binding specificity. We identified a subset of high A/T binding motifs. Motifs in this subset had many functionally neutral one-error mutants, and were bound by multiple different binding domains. Our results indicate that, especially for some TF-TFBS associations, low binding specificity confers high degrees of evolvability, that is that few mutations facilitate rapid changes in transcriptional regulation, in particular for large and old TF families. In this study we identify binding motifs exhibiting behavior indicating high evolutionary potential for innovations in transcriptional regulation.
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Affiliation(s)
| | - Paulo Pinto
- Molecular Evolution and Bioinformatics, University of Muenster, Germany
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25
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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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26
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de Souza MM, Zerlotini A, Geistlinger L, Tizioto PC, Taylor JF, Rocha MIP, Diniz WJS, Coutinho LL, Regitano LCA. A comprehensive manually-curated compendium of bovine transcription factors. Sci Rep 2018; 8:13747. [PMID: 30213987 PMCID: PMC6137171 DOI: 10.1038/s41598-018-32146-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/29/2018] [Indexed: 01/28/2023] Open
Abstract
Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a context-dependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an improved comprehension of regulatory mechanisms that are specific to the species.
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Affiliation(s)
- Marcela M de Souza
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, 13560-970, Brazil.,Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, São Paulo, 13560-970, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, 70770-901, Brazil
| | - Ludwig Geistlinger
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, São Paulo, 13560-970, Brazil
| | | | - Jeremy F Taylor
- Division of Animal Science, University of Missouri, Columbia, Missouri, 65211-5300, USA
| | - Marina I P Rocha
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, 13560-970, Brazil
| | - Wellison J S Diniz
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, 13560-970, Brazil
| | - Luiz L Coutinho
- Functional Genomic Center, University of São Paulo, Piracicaba, São Paulo, 13418-900, Brazil
| | - Luciana C A Regitano
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, São Paulo, 13560-970, Brazil.
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27
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Harrison MC, Arning N, Kremer LPM, Ylla G, Belles X, Bornberg‐Bauer E, Huylmans AK, Jongepier E, Piulachs M, Richards S, Schal C. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:254-264. [DOI: 10.1002/jez.b.22824] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Mark C. Harrison
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | - Nicolas Arning
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | - Lukas P. M. Kremer
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | - Guillem Ylla
- Institut de Biologia Evolutiva CSIC‐University Pompeu Fabra Barcelona Spain
| | - Xavier Belles
- Institut de Biologia Evolutiva CSIC‐University Pompeu Fabra Barcelona Spain
| | | | | | - Evelien Jongepier
- Institute for Evolution and Biodiversity University of Münster Münster Germany
| | | | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics Baylor College of Medicine Houston Texas
| | - Coby Schal
- Department of Entomology and Plant Pathology North Carolina State University Raleigh North Carolina
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28
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The remembrance of the things past: Conserved signalling pathways link protozoa to mammalian nervous system. Cell Calcium 2018; 73:25-39. [DOI: 10.1016/j.ceca.2018.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/01/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
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29
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Klasberg S, Bitard-Feildel T, Callebaut I, Bornberg-Bauer E. Origins and structural properties of novel and de novo protein domains during insect evolution. FEBS J 2018; 285:2605-2625. [PMID: 29802682 DOI: 10.1111/febs.14504] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 04/12/2018] [Accepted: 05/11/2018] [Indexed: 12/11/2022]
Abstract
Over long time scales, protein evolution is characterized by modular rearrangements of protein domains. Such rearrangements are mainly caused by gene duplication, fusion and terminal losses. To better understand domain emergence mechanisms we investigated 32 insect genomes covering a speciation gradient ranging from ~ 2 to ~ 390 mya. We use established domain models and foldable domains delineated by hydrophobic cluster analysis (HCA), which does not require homologous sequences, to also identify domains which have likely arisen de novo, that is, from previously noncoding DNA. Our results indicate that most novel domains emerge terminally as they originate from ORF extensions while fewer arise in middle arrangements, resulting from exonization of intronic or intergenic regions. Many novel domains rapidly migrate between terminal or middle positions and single- and multidomain arrangements. Young domains, such as most HCA-defined domains, are under strong selection pressure as they show signals of purifying selection. De novo domains, linked to ancient domains or defined by HCA, have higher degrees of intrinsic disorder and disorder-to-order transition upon binding than ancient domains. However, the corresponding DNA sequences of the novel domains of de novo origins could only rarely be found in sister genomes. We conclude that novel domains are often recruited by other proteins and undergo important structural modifications shortly after their emergence, but evolve too fast to be characterized by cross-species comparisons alone.
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Affiliation(s)
- Steffen Klasberg
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Germany
| | - Tristan Bitard-Feildel
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Germany
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30
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Mittal S, Banduni P, Mallikarjuna MG, Rao AR, Jain PA, Dash PK, Thirunavukkarasu N. Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize. Front Chem 2018; 6:177. [PMID: 29876347 PMCID: PMC5974147 DOI: 10.3389/fchem.2018.00177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/03/2018] [Indexed: 01/22/2023] Open
Abstract
Drought is one of the major threats to the maize yield especially in subtropical production systems. Understanding the genes and regulatory mechanisms of drought tolerance is important to sustain the yield. Transcription factors (TFs) play a major role in gene regulation under drought stress. In the present study, a set of 15 major TF families comprising 1,436 genes was structurally and functionally characterized. The functional annotation indicated that the genes were involved in ABA signaling, ROS scavenging, photosynthesis, stomatal regulation, and sucrose metabolism. Duplication was identified as the primary force in divergence and expansion of TF families. Phylogenetic relationship was developed for individual TF and combined TF families. Phylogenetic analysis clustered the genes into specific and mixed groups. Gene structure analysis revealed that more number of genes were intron-rich as compared to intron-less. Drought-responsive cis-regulatory elements such as ABREA, ABREB, DRE1, and DRECRTCOREAT have been identified. Expression and interaction analyses identified leaf-specific bZIP TF, GRMZM2G140355, as a potential contributor toward drought tolerance in maize. Protein-protein interaction network of 269 drought-responsive genes belonging to different TFs has been provided. The information generated on structural and functional characteristics, expression, and interaction of the drought-related TF families will be useful to decipher the drought tolerance mechanisms and to breed drought-tolerant genotypes in maize.
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Affiliation(s)
- Shikha Mittal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pooja Banduni
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Atmakuri R Rao
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Prashant A Jain
- Department of Computational Biology & Bioinformatics, J.I.B.B., Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, India
| | - Prasanta K Dash
- National Research Centre on Plant Biotechnology, New Delhi, India
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31
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Hemimetabolous genomes reveal molecular basis of termite eusociality. Nat Ecol Evol 2018; 2:557-566. [PMID: 29403074 PMCID: PMC6482461 DOI: 10.1038/s41559-017-0459-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022]
Abstract
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
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33
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Abstract
Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.
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