1
|
Rétaux S. [The toolbox of developmental evolution or how Mexican cave fishes lost their eyes]. Biol Aujourdhui 2022; 216:49-53. [PMID: 35876521 DOI: 10.1051/jbio/2022011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The fish Astyanax mexicanus comes in two very different forms: a "normal" river morph, and a blind, depigmented cave morph, living in the total and permanent darkness of Mexican caves. This species is on the way to becoming a model of choice in evolutionary and comparative biology, both for the study of the evolution of behavior, physiology or morphology, and for molecular genetics or population genetics. Here, I present the advancement of knowledge in the field of the developmental evolution of the eye of the cave morph. By rewinding back in time its development from the eye of the larva to the retinal field at the end of gastrulation, the cave-dwelling Astyanax embryo reveals mechanisms and processes likely to contribute to evolutionary variations between species, but also to pathological variations in the morphogenesis of the optic region.
Collapse
|
2
|
Zhong X, Feng X, Li Y, Guzmán C, Lin N, Xu Q, Zhang Y, Tang H, Qi P, Deng M, Ma J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. Genome-wide identification of bZIP transcription factor genes related to starch synthesis in barley ( Hordeum vulgare L.). Genome 2021; 64:1067-1080. [PMID: 34058097 DOI: 10.1139/gen-2020-0195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The basic leucine zipper (bZIP) family of genes encode transcription factors that play key roles in plant growth and development. In this study, a total of 92 HvbZIP genes were identified and compared with previous studies using recently released barley genome data. Two novel genes were characterized in this study, and some misannotated and duplicated genes from previous studies have been corrected. Phylogenetic analysis results showed that 92 HvbZIP genes were classified into 10 groups and three unknown groups. The gene structure and motif distribution of the three unknown groups implied that the genes of the three groups may be functionally different. Expression profiling indicated that the HvbZIP genes exhibited different patterns of spatial and temporal expression. Using qRT-PCR, more than 10 HvbZIP genes were identified with expression patterns similar to those of starch synthase genes in barley. Yeast one-hybrid analysis revealed that two of the HvbZIP genes exhibited in vitro binding activity to the promoter of HvAGP-S. The two HvbZIP genes may be candidate genes for further study to explore the mechanism by which they regulate the synthesis of barley starch.
Collapse
Affiliation(s)
- Xiaojuan Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiuqin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yulong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Edificio Gregor Mendel, Campus de Rabanales, Universidad de Córdoba, Cordoba, 14071, Spain
| | - Na Lin
- College of Sichuan Tea, Yibin University, Yibin, Sichuan 644000, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| |
Collapse
|
3
|
Abstract
At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.
Collapse
Affiliation(s)
- Rachel M Price
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Marek A Budzyński
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Shivani Kundra
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| | - Sheila S Teves
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
| |
Collapse
|
4
|
Pan Y, Zhao SW, Tang XL, Wang S, Wang X, Zhang XX, Zhou JJ, Xi JH. Transcriptome analysis of maize reveals potential key genes involved in the response to belowground herbivore Holotrichia parallela larvae feeding. Genome 2019; 63:1-12. [PMID: 31533014 DOI: 10.1139/gen-2019-0043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The larvae of Holotrichia parallela, a destructive belowground herbivore, causes tremendous damages to maize plants. However, little is known if there are any defense mechanisms in maize roots to defend themselves against this herbivore. In the current research, we carried out RNA-sequencing to investigate the changes in gene transcription level in maize roots after H. parallela larvae infestation. A total of 644 up-regulated genes and 474 down-regulated genes was found. In addition, Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Weighted gene co-expression network analysis (WGCNA) indicated that peroxidase genes may be the hub genes that regulate maize defenses to H. parallela larvae attack. We also found 105 transcription factors, 44 hormone-related genes, and 62 secondary metabolism-related genes within differentially expressed genes (DEGs). Furthermore, the expression profiles of 12 DEGs from the transcriptome analysis were confirmed by quantitative real-time PCR experiments. This transcriptome analysis provides insights into the molecular mechanisms of the underground defense in maize roots to H. parallela larvae attack and will help to select target genes of maize for defense against belowground herbivory.
Collapse
Affiliation(s)
- Yu Pan
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Shi-Wen Zhao
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xin-Long Tang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Shang Wang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xiao Wang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Xin-Xin Zhang
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Jing-Jiang Zhou
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| | - Jing-Hui Xi
- College of Plant Science, Jilin University, Changchun 130062, P.R. China.,College of Plant Science, Jilin University, Changchun 130062, P.R. China
| |
Collapse
|
5
|
Abstract
Cardiac fibrosis, characterized by excessive accumulation of extracellular matrix, abolishes cardiac contractility, impairs cardiac function, and ultimately leads to heart failure. In recent years, significant evidence has emerged that supports the highly dynamic and responsive nature of the cardiac extracellular matrix. Although our knowledge of cardiac fibrosis has advanced tremendously over the past decade, there is still a lack of specific therapies owing to an incomplete understanding of the disease etiology and process. In this review, we attempt to highlight some of the recently investigated molecular determinants of ischemic and non-ischemic fibrotic remodeling of the myocardium that present as promising avenues for development of anti-fibrotic therapies.
Collapse
Affiliation(s)
- Ryan Wang
- a Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Justin Lin
- b Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Rushita A Bagchi
- c Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| |
Collapse
|
6
|
Abstract
Regulation of cardiac fatty acid metabolism is central to the development of cardiac hypertrophy and heart failure. We investigated the effects of select fatty acids on the expression of genes involved in immediate early as well as inflammatory and hypertrophic responses in adult rat cardiomyocytes. Cardiac remodeling begins with upregulation of immediate early genes for c-fos and c-jun, followed by upregulation of inflammatory genes for nuclear factor kappa B (NF-κB) and nuclear factor of activated T-cells (NFAT). At later stages, genes involved in hypertrophic responses, such as atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), are upregulated. Adult rat cardiomyocytes were treated with palmitic acid, a saturated fatty acid; oleic acid, a monounsaturated fatty acid; linoleic acid, a polyunsaturated fatty acid belonging to the n-6 class; and docosahexaenoic acid, a polyunsaturated fatty acid belonging to the n-3 class. Linoleic acid produced a greater increase in the mRNA expression of c-fos, c-jun, NF-κB, NFAT3, ANP, and BNP relative to palmitic acid and oleic acid. In contrast, docosahexaenoic acid caused a decrease in the expression of genes involved in cardiac hypertrophy. Our findings suggest that linoleic acid may be a potent inducer of genes involved in cardiac hypertrophy, whereas docosahexaenoic acid may be protective against the cardiomyocyte hypertrophic response.
Collapse
Affiliation(s)
- Sukhinder K Cheema
- a Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Paramjit S Tappia
- b Asper Clinical Research Institute, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada
| | - Naranjan S Dhalla
- c Institute of Cardiovascular Sciences, University of Manitoba, St. Boniface Hospital, Albrechtsen Research Centre, Winnipeg, MB R2H 2A6, Canada
| |
Collapse
|
7
|
Cai X, Lin L, Wang X, Xu C, Wang Q. Higher anthocyanin accumulation associated with higher transcription levels of anthocyanin biosynthesis genes in spinach. Genome 2018; 61:487-496. [PMID: 29787681 DOI: 10.1139/gen-2017-0261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Spinach (Spinacia oleracea L.) is widely cultivated as an economically important green leafy vegetable crop for fresh and processing consumption. The red-purple spinach shows abundant anthocyanin accumulation in the leaf and leaf petiole. However, the molecular mechanisms of anthocyanin synthesis in this species are still undetermined. In the present study, we investigated pigment formation and identified anthocyanin biosynthetic genes in spinach. We also analyzed the expression of these genes in purple and green cultivars by quantitative PCR. The accumulation of anthocyanin showed that it was the dominant pigment resulting in the red coloration in spinach. In total, 22 biosynthesis genes and 25 regulatory genes were identified in spinach, based on the spinach genomic and transcriptomic database. Furthermore, the expression patterns of genes encoding enzymes indicated that SoPAL, SoUFGT3, and SoUFGT4 were possible candidate genes for anthocyanin biosynthesis in red-purple spinach. The expression patterns of transcription factors indicated that two SoMYB genes, three SobHLH genes, and one SoWD40 gene were drastically up-regulated and co-expression in red-purple spinach, suggesting an essential role of regulatory genes in the anthocyanin biosynthesis of spinach. These results will enhance our understanding of the molecular mechanisms of anthocyanin biosynthesis in purple spinach.
Collapse
Affiliation(s)
- Xiaofeng Cai
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China.,Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China
| | - Lihao Lin
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China.,Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaoli Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China.,Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China
| | - Chenxi Xu
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China.,Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China
| | - Quanhua Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China.,Development and Collaborative Innovation Center of Plant Germplasm Resources, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life and Environment Science, Shanghai Normal University, Shanghai, 200234, China
| |
Collapse
|