1
|
Cao S, Zhao X, Li Z, Yu R, Li Y, Zhou X, Yan W, Chen D, He C. Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification. PLANT DIVERSITY 2024; 46:372-385. [PMID: 38798726 PMCID: PMC11119547 DOI: 10.1016/j.pld.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks in a cell-type specific manner. Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings. This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets, addressing batch effects and conserving biological variance. This integration spans a broad spectrum of tissues, including both below- and above-ground parts. Utilizing a rigorous approach for cell type annotation, we identified 47 distinct cell types or states, largely expanding our current view of plant cell compositions. We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression. Taken together, our study not only offers extensive plant cell atlas exploration that serves as a valuable resource, but also provides molecular insights into gene-regulatory programs that varies from different cell types.
Collapse
Affiliation(s)
- Shanni Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhuojin Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
2
|
Li Q, Duncan S, Li Y, Huang S, Luo M. Decoding plant specialized metabolism: new mechanistic insights. TRENDS IN PLANT SCIENCE 2024; 29:535-545. [PMID: 38072690 DOI: 10.1016/j.tplants.2023.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 11/02/2023] [Accepted: 11/17/2023] [Indexed: 05/04/2024]
Abstract
Secondary metabolite (SM) production provides biotic and abiotic stress resistance and enables plants to adapt to the environment. Biosynthesis of these metabolites involves a complex interplay between transcription factors (TFs) and regulatory elements, with emerging evidence suggesting an integral role for chromatin dynamics. Here we review key TFs and epigenetic regulators that govern SM biosynthesis in different contexts. We summarize relevant emerging technologies and results from the model species arabidopsis (Arabidopsis thaliana) and outline aspects of regulation that may also function in food, feed, fiber, oil, or industrial crop plants. Finally, we highlight how effective translation of fundamental knowledge from model to non-model species can benefit understanding of SM production in a variety of ecological, agricultural, and pharmaceutical contexts.
Collapse
Affiliation(s)
- Qianqian Li
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Susan Duncan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yuping Li
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shuxian Huang
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ming Luo
- Guangdong Provincial Key Laboratory of Applied Botany and Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
3
|
Rocher F, Dou S, Philippe G, Martin ML, Label P, Langin T, Bonhomme L. Integrative systems biology of wheat susceptibility to Fusarium graminearum uncovers a conserved gene regulatory network and identifies master regulators targeted by fungal core effectors. BMC Biol 2024; 22:53. [PMID: 38443953 PMCID: PMC10916188 DOI: 10.1186/s12915-024-01852-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Plant diseases are driven by an intricate set of defense mechanisms counterbalanced by the expression of host susceptibility factors promoted through the action of pathogen effectors. In spite of their central role in the establishment of the pathology, the primary components of plant susceptibility are still poorly understood and challenging to trace especially in plant-fungal interactions such as in Fusarium head blight (FHB) of bread wheat. Designing a system-level transcriptomics approach, we leveraged the analysis of wheat responses from a susceptible cultivar facing Fusarium graminearum strains of different aggressiveness and examined their constancy in four other wheat cultivars also developing FHB. RESULTS In this study, we describe unexpected differential expression of a conserved set of transcription factors and an original subset of master regulators were evidenced using a regulation network approach. The dual-integration with the expression data of pathogen effector genes combined with database mining, demonstrated robust connections with the plant molecular regulators and identified relevant candidate genes involved in plant susceptibility, mostly able to suppress plant defense mechanisms. Furthermore, taking advantage of wheat cultivars of contrasting susceptibility levels, a refined list of 142 conserved susceptibility gene candidates was proposed to be necessary host's determinants for the establishment of a compatible interaction. CONCLUSIONS Our findings emphasized major FHB determinants potentially controlling a set of conserved responses associated with susceptibility in bread wheat. They provide new clues for improving FHB control in wheat and also could conceivably leverage further original researches dealing with a broader spectrum of plant pathogens.
Collapse
Affiliation(s)
- Florian Rocher
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Samir Dou
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Géraldine Philippe
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Marie-Laure Martin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif Sur Yvette, 91190, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Gif Sur Yvette, 91190, France
- UMR MIA Paris-Saclay, AgroParisTech, INRAE, Université Paris-Saclay, Gif Sur Yvette, France
| | - Philippe Label
- Physique Et Physiologie Intégratives de L'Arbre en Environnement Fluctuant, Université Clermont Auvergne, INRAE, UMR 547, Aubière, Cedex, France
| | - Thierry Langin
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France
| | - Ludovic Bonhomme
- UMR 1095 Génétique Diversité Ecophysiologie Des Céréales, Université Clermont Auvergne, INRAE, Clermont-Ferrand, France.
| |
Collapse
|
4
|
Kadelka C, Butrie TM, Hilton E, Kinseth J, Schmidt A, Serdarevic H. A meta-analysis of Boolean network models reveals design principles of gene regulatory networks. SCIENCE ADVANCES 2024; 10:eadj0822. [PMID: 38215198 PMCID: PMC10786419 DOI: 10.1126/sciadv.adj0822] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean networks, which are intuitive, simple to describe, and can yield qualitative results even when data are sparse. We assembled the largest repository of expert-curated Boolean GRN models. A meta-analysis of this diverse set of models reveals several design principles. GRNs exhibit more canalization, redundancy, and stable dynamics than expected. Moreover, they are enriched for certain recurring network motifs. This raises the important question why evolution favors these design mechanisms.
Collapse
Affiliation(s)
- Claus Kadelka
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| | | | - Evan Hilton
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
| | - Jack Kinseth
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| | - Addison Schmidt
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Haris Serdarevic
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
5
|
Zhu Y, Liu Y, Wang W, Li H, Liu C, Dou L, Wei L, Cheng W, Bao M, Yi Q, He Y. Identification and characterization of CYC2-like genes related to floral symmetric development in Tagetes erecta (Asteraceae). Gene 2023; 889:147804. [PMID: 37716585 DOI: 10.1016/j.gene.2023.147804] [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: 07/19/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
Marigold (Tagetes erecta) is an annual herbaceous flower belonging to Asteraceae, whose capitulum is composed of bilateral symmetry ray florets on the outer periphery and radial symmetry disk florets on the inside. The flower symmetry evolution from radial symmetry to bilateral symmetry has changed the morphology, inflorescence architecture and function of florets among several lineages in Asteraceae. Several studies have identified that CYC2 genes in TCP transcription factor family are the key genes regulating the flower morphogenesis, such as corolla symmetry and stamen development. Here, seven TeCYC2 genes were cloned and phylogenetically grouped into the CYC2 branch of TCP transcription family. TeCYC2c and TeCYC2d were found to be expressed specifically in ray florets, TeCYC2b was strongly expressed in both ray and disk florets, TeCYC2g was significantly higher expressed in ray florets than in disk florets, while TeCYC2a, TeCYC2e1 and TeCYC2e2 were significantly expressed in disk florets, according to an examination of the expression profile. Among the ectopic expression lines of seven TeCYC2 genes in Arabidopsis thaliana, the flower symmetry of all transgenic lines was changed from radial symmetry to bilateral symmetry, and only the reproductive growth of TeCYC2c lines was affected. In TeCYC2c transgenic Arabidopsis, the pollen sac was difficult to crack, and the filaments were shorter than the pistils, resulting in a significant decrease in the seed setting rate. All TeCYC2 proteins were localized in the nucleus. Eight pairs of interactions between TeCYC2 proteins were validated by Y2H and BiFC assays, indicating the possibility of TeCYC2 proteins forming homodimers or heterodimers to improve functional specificity. Our findings verified the main regulatory role of TeCYC2c on the development of corollas and stamen in marigold, and analyzed the interaction network of the formation mechanism of floral symmetry in two florets, which provided more insights into the expansion of CYC2 genes in the evolution of Asteraceae inflorescence and contributed to elucidate the complex regulatory network, as well as the molecular breeding concerning flower form diversity in marigold.
Collapse
Affiliation(s)
- Yu Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuhan Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenjing Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Hang Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuicui Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Linlin Dou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ludan Wei
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhan Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingping Yi
- Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen 448000, Hubei, China.
| | - Yanhong He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
6
|
Lim ARQ, Kong Q, Noor A, Song YQ, Pattanaik S, Yuan L, Ma W. B-BOX-DOMAIN PROTEIN32 modulates seed oil biosynthesis in Arabidopsis by interacting with WRINKLED1. PLANT PHYSIOLOGY 2023; 193:919-922. [PMID: 37467048 DOI: 10.1093/plphys/kiad419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/22/2023] [Accepted: 07/02/2023] [Indexed: 07/21/2023]
Affiliation(s)
- Audrey R Q Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Aqilah Noor
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yu Qing Song
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| |
Collapse
|
7
|
Godbole RC, Kadam SB, Pable AA, Singh S, Barvkar VT. Phylogenomics of transcriptionally active AP2/ERF and bHLH transcription factors and study of their promoter regions in Nothapodytes nimmoniana (J.Graham) Mabb. Genome 2023; 66:235-250. [PMID: 37163758 DOI: 10.1139/gen-2023-0009] [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: 05/12/2023]
Abstract
Nothapodytes nimmoniana is a medicinally important plant producing anticancer monoterpene indole alkaloid (MIA), camptothecin (CPT). The CPT is synthesised through the strictosidine intermediate following the MIA pathway; however, transcriptional regulation of CPT pathway is still elusive in N. nimmoniana. Biosynthesis of MIA is regulated by various transcription factors (TFs) belonging to AP2/ERF, bHLH, MYB, and WRKY families. The present study identified transcriptionally active full-length 105 AP2/ERF and 68 bHLH family TFs from the N. nimmoniana. AP2/ERF TFs were divided into three subfamilies along with a soloist, while bHLH TFs were divided into 10 subfamilies according to their phylogenetic similarities. Three group IXa ERFs, Nn-ERF22, Nn-ERF29, and Nn-ERF41, one subfamily IVa TF Nn-bHLH7, and three subfamilies IIIe Nn-bHLH33, Nn-bHLH51, and Nn-bHLH52 clustered with the TFs regulating alkaloid biosynthesis in Catharanthus roseus, tomato, tobacco, and Artemisia annua. Expression of these TFs in N. nimmoniana was higher in roots, which is a primary CPT accumulating tissue. Moreover, genome skimming approach was used to reconstruct the promoter regions of candidate ERF genes to identify the cis-regulatory elements. The presence of G-boxes and other jasmonic acid-responsive elements in the promoter suggests the regulation of ERFs by bHLHs. The present study effectively generated and used genomics resource for characterisation of regulatory TFs from non-model medicinal plant.
Collapse
Affiliation(s)
- Rucha C Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Swapnil B Kadam
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Sudhir Singh
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai, 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| |
Collapse
|
8
|
Yang Y, Kong Q, Tee WT, Li Y, Low PM, Patra B, Guo L, Yuan L, Ma W. Transcription factor bZIP52 modulates Arabidopsis seed oil biosynthesis through interaction with WRINKLED1. PLANT PHYSIOLOGY 2023; 192:2628-2639. [PMID: 37148285 DOI: 10.1093/plphys/kiad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
Transcriptional regulation mediated by combinatorial interaction of transcription factors (TFs) is a key molecular mechanism modulating plant development and metabolism. Basic leucine zipper (bZIP) TFs play important roles in various plant developmental and physiological processes. However, their involvement in fatty acid biosynthesis is largely unknown. Arabidopsis (Arabidopsis thaliana) WRINKLED1 (WRI1) is a pivotal TF in regulation of plant oil biosynthesis and interacts with other positive and negative regulators. In this study, we identified two bZIP TFs, bZIP21 and bZIP52, as interacting partners of AtWRI1 by yeast-two-hybrid (Y2H)-based screening of an Arabidopsis TF library. We found that coexpression of bZIP52, but not bZIP21, with AtWRI1 reduced AtWRI1-mediated oil biosynthesis in Nicotiana benthamiana leaves. The AtWRI1-bZIP52 interaction was further verified by Y2H, in vitro pull-down, and bimolecular fluorescence complementation assays. Transgenic Arabidopsis plants overexpressing bZIP52 showed reduced seed oil accumulation, while the CRISPR/Cas9-edited bzip52 knockout mutant exhibited increased seed oil accumulation. Further analysis revealed that bZIP52 represses the transcriptional activity of AtWRI1 on the fatty acid biosynthetic gene promoters. Together, our findings suggest that bZIP52 represses fatty acid biosynthesis genes through interaction with AtWRI1, resulting in a reduction of oil production. Our work reports a previously uncharacterized regulatory mechanism that enables fine-tuning of seed oil biosynthesis.
Collapse
Affiliation(s)
- Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Wan Ting Tee
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Yuqing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Pui Man Low
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Barunava Patra
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| |
Collapse
|
9
|
Yang H, Zhang P, Guo D, Wang N, Lin H, Wang X, Niu L. Transcriptional repressor AGL79 positively regulates flowering time in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2023; 285:153985. [PMID: 37148653 DOI: 10.1016/j.jplph.2023.153985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 05/08/2023]
Abstract
The MADS-box gene family is widely distributed in higher plants and the members of the angiosperm-specific APETALA1/FRUITFULL (AP1/FUL) subfamily plays important roles in the regulation of plant reproductive development. Recent studies revealed that the AP1/FUL subfamily member Dt2, VEGETATIVE1/PsFRUITFULc (VEG1/PsFULc) and MtFRUITFULc (MtFULc) are essential for the stem growth, branching and inflorescence development in legume species soybean (Glycine max), pea (Pisum sativum) and Medicago truncatula. However, the biological function of their homologue in Arabidopsis thaliana, AGAMOUS-LIKE 79 (AGL79), has not been well elucidated. In this study, we investigated the developmental roles of Arabidopsis AGL79 by CRISPR/Cas9-mutagenesis and molecular and physiological analyses. We found that AGL79 mainly acts as a transcriptional repressor and positively regulates Arabidopsis flowering time. We further revealed that AGL79 interacts with SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) and represses the expression of TERMINAL FLOWER 1 (TFL1). Our results demonstrated the AGL79-mediated flowering regulation in Arabidopsis and added an additional layer of complexity to the understanding of flowering time regulation in dicot plants.
Collapse
Affiliation(s)
- Haibo Yang
- College of Life Sciences, Shanxi Agriculture University, Taigu, 030801, China; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pengcheng Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Diandian Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Na Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingchun Wang
- College of Life Sciences, Shanxi Agriculture University, Taigu, 030801, China.
| | - Lifang Niu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
10
|
Liu X, Bulley SM, Varkonyi-Gasic E, Zhong C, Li D. Kiwifruit bZIP transcription factor AcePosF21 elicits ascorbic acid biosynthesis during cold stress. PLANT PHYSIOLOGY 2023; 192:982-999. [PMID: 36823691 PMCID: PMC10231468 DOI: 10.1093/plphys/kiad121] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 06/01/2023]
Abstract
Cold stress seriously affects plant development, resulting in heavy agricultural losses. L-ascorbic acid (AsA, vitamin C) is an antioxidant implicated in abiotic stress tolerance and metabolism of reactive oxygen species (ROS). Understanding whether and how cold stress elicits AsA biosynthesis to reduce oxidative damage is important for developing cold-resistant plants. Here, we show that the accumulation of AsA in response to cold stress is a common mechanism conserved across the plant kingdom, from single-cell algae to angiosperms. We identified a basic leucine zipper domain (bZIP) transcription factor (TF) of kiwifruit (Actinidia eriantha Benth.), AcePosF21, which was triggered by cold and is involved in the regulation of kiwifruit AsA biosynthesis and defense responses against cold stress. AcePosF21 interacted with the R2R3-MYB TF AceMYB102 and directly bound to the promoter of the gene encoding GDP-L-galactose phosphorylase 3 (AceGGP3), a key conduit for regulating AsA biosynthesis, to up-regulate AceGGP3 expression and produce more AsA, which neutralized the excess ROS induced by cold stress. On the contrary, VIGS or CRISPR-Cas9-mediated editing of AcePosF21 decreased AsA content and increased the generation of ROS in kiwifruit under cold stress. Taken together, we illustrated a model for the regulatory mechanism of AcePosF21-mediated regulation of AceGGP3 expression and AsA biosynthesis to reduce oxidative damage by cold stress, which provides valuable clues for manipulating the cold resistance of kiwifruit.
Collapse
Affiliation(s)
- Xiaoying Liu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Jiufeng 1 Road, Wuhan 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Sean M Bulley
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Erika Varkonyi-Gasic
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Caihong Zhong
- Wuhan Botanical Garden, Chinese Academy of Sciences, Jiufeng 1 Road, Wuhan 430074, Hubei, China
| | - Dawei Li
- Wuhan Botanical Garden, Chinese Academy of Sciences, Jiufeng 1 Road, Wuhan 430074, Hubei, China
| |
Collapse
|
11
|
Martínez-Rivas FJ, Blanco-Portales R, Serratosa MP, Ric-Varas P, Guerrero-Sánchez V, Medina-Puche L, Moyano L, Mercado JA, Alseekh S, Caballero JL, Fernie AR, Muñoz-Blanco J, Molina-Hidalgo FJ. FaMYB123 interacts with FabHLH3 to regulate the late steps of anthocyanin and flavonol biosynthesis during ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:683-698. [PMID: 36840368 DOI: 10.1111/tpj.16166] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 02/17/2023] [Indexed: 05/10/2023]
Abstract
In this work, we identified and functionally characterized the strawberry (Fragaria × ananassa) R2R3 MYB transcription factor FaMYB123. As in most genes associated with organoleptic properties of ripe fruit, FaMYB123 expression is ripening-related, receptacle-specific, and antagonistically regulated by ABA and auxin. Knockdown of FaMYB123 expression by RNAi in ripe strawberry fruit receptacles downregulated the expression of enzymes involved in the late steps of anthocyanin/flavonoid biosynthesis. Transgenic fruits showed a parallel decrease in the contents of total anthocyanin and flavonoid, especially malonyl derivatives of pelargonidin and cyanidins. The decrease was concomitant with accumulation of proanthocyanin, propelargonidins, and other condensed tannins associated mainly with green receptacles. Potential coregulation between FaMYB123 and FaMYB10, which may act on different sets of genes for the enzymes involved in anthocyanin production, was explored. FaMYB123 and FabHLH3 were found to interact and to be involved in the transcriptional activation of FaMT1, a gene responsible for the malonylation of anthocyanin components during ripening. Taken together, these results demonstrate that FaMYB123 regulates the late steps of the flavonoid pathway in a specific manner. In this study, a new function for an R2R3 MYB transcription factor, regulating the expression of a gene that encodes a malonyltransferase, has been elucidated.
Collapse
Affiliation(s)
- Félix J Martínez-Rivas
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rosario Blanco-Portales
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - María P Serratosa
- Department of Agricultural Chemistry, University of Cordoba, Edificio Marie Curie, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Pablo Ric-Varas
- Department of Plant Biology, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, University of Málaga, Campus de Teatinos, E-29071, Málaga, Spain
| | - Víctor Guerrero-Sánchez
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Laura Medina-Puche
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
- Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Lourdes Moyano
- Department of Agricultural Chemistry, University of Cordoba, Edificio Marie Curie, Campus de Rabanales, E-14014, Córdoba, Spain
| | - José A Mercado
- Department of Plant Biology, Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, University of Málaga, Campus de Teatinos, E-29071, Málaga, Spain
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria
| | - José L Caballero
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria
| | - Juan Muñoz-Blanco
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Francisco J Molina-Hidalgo
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| |
Collapse
|
12
|
Herrera-Ubaldo H, Campos SE, López-Gómez P, Luna-García V, Zúñiga-Mayo VM, Armas-Caballero GE, González-Aguilera KL, DeLuna A, Marsch-Martínez N, Espinosa-Soto C, de Folter S. The protein-protein interaction landscape of transcription factors during gynoecium development in Arabidopsis. MOLECULAR PLANT 2023; 16:260-278. [PMID: 36088536 DOI: 10.1016/j.molp.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors (TFs). The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development. The gynoecium is the flower's female reproductive part, crucial for fruit and seed production and, hence, for reproductive success. After the establishment of carpel identity, many tissues arise to form a mature gynoecium. TFs have been described as regulators of gynoecium development, and some interactions and complexes have been identified. However, broad knowledge about the interactions among these TFs and their participation during development remains scarce. In this study, we used a systems biology approach to understand the formation of a complex reproductive unit-as the gynoecium-by mapping binary interactions between well-characterized TFs. We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions (PPIs), resulting in a process-specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. In addition, we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs. Furthermore, we analyzed the network by combining PPI data, expression, and genetic data, which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes. Finally, we generated an extended PPI network that predicts new players in gynoecium development. Taken together, all these results serve as a valuable resource for the plant community.
Collapse
Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Sergio E Campos
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Pablo López-Gómez
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Valentín Luna-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Víctor M Zúñiga-Mayo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Gerardo E Armas-Caballero
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Karla L González-Aguilera
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato 36824, México
| | - Carlos Espinosa-Soto
- Instituto de Física, Universidad de San Luis Potosí, San Luis Potosí, SLP 78290, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, México.
| |
Collapse
|
13
|
Expression patterns and correlation analyses of muscle-specific genes in the process of sheep myoblast differentiation. In Vitro Cell Dev Biol Anim 2022; 58:798-809. [PMID: 36178582 DOI: 10.1007/s11626-022-00721-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/05/2022] [Indexed: 11/05/2022]
Abstract
The purpose of this study was to establish a system for the isolation, culture, and differentiation of sheep myoblasts, and to explore the expression patterns as well as mutual relationships of muscle-specific genes. Sheep fetal myoblasts (SFMs) were isolated by two-step enzymatic digestion, purified by differential adhesion and identified using immunofluorescence techniques. Two percent horse serum was used to induce differentiation in SFMs. Real-time quantitative and Western blot analyses were respectively used to detect the mRNA and protein expressions of muscle-specific genes including MyoD, MyoG, Myf5, Myf6, PAX3, PAX7, myomaker, desmin, MYH1, MYH2, MYH4, MYH7, and MSTN during the differentiation of SFMs. Finally, the correlation between muscle-specific genes was analyzed by the Pearson correlation coefficient method. The results showed that the isolated and purified SFMs could form myotubes after the induction for differentiation. The marker factors including MyoD, MyoG, myomaker, desmin, and MyHC were positively stained in SFMs. The mRNA expressions of MyoD, MyoG, and myomaker increased and then decreased, while Myf5, PAX3, and PAX7 decreased; Myf6, desmin, MYH1, MYH2, MYH4, and MYH7 increased; and MSTN fluctuated up and down during the differentiation of SFMs. The expression patterns of protein were basically consistent with those of mRNA except MSTN. There existed significant or highly significant correlations at mRNA or protein level among some genes. Some transcription factor proteins (MyoD, Myf5, Myf6, PAX3, PAX7) showed significant or highly significant correlations with the mRNA level of some other genes and/or themselves. In conclusion, SFMs with good myogenic differentiation ability were successfully isolated, and the expression patterns and correlations of muscle-specific genes during SFM differentiation were revealed, which laid an important foundation for elucidating the gene regulation mechanism of sheep myogenesis.
Collapse
|
14
|
Yang Y, Kong Q, Lim ARQ, Lu S, Zhao H, Guo L, Yuan L, Ma W. Transcriptional regulation of oil biosynthesis in seed plants: Current understanding, applications, and perspectives. PLANT COMMUNICATIONS 2022; 3:100328. [PMID: 35605194 PMCID: PMC9482985 DOI: 10.1016/j.xplc.2022.100328] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/28/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Plants produce and accumulate triacylglycerol (TAG) in their seeds as an energy reservoir to support the processes of seed germination and seedling development. Plant seed oils are vital not only for the human diet but also as renewable feedstocks for industrial use. TAG biosynthesis consists of two major steps: de novo fatty acid biosynthesis in the plastids and TAG assembly in the endoplasmic reticulum. The latest advances in unraveling transcriptional regulation have shed light on the molecular mechanisms of plant oil biosynthesis. We summarize recent progress in understanding the regulatory mechanisms of well-characterized and newly discovered transcription factors and other types of regulators that control plant fatty acid biosynthesis. The emerging picture shows that plant oil biosynthesis responds to developmental and environmental cues that stimulate a network of interacting transcriptional activators and repressors, which in turn fine-tune the spatiotemporal regulation of the pathway genes.
Collapse
Affiliation(s)
- Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Audrey R Q Lim
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| |
Collapse
|
15
|
de Souza Moraes T, van Es SW, Hernández-Pinzón I, Kirschner GK, van der Wal F, da Silveira SR, Busscher-Lange J, Angenent GC, Moscou M, Immink RGH, van Esse GW. The TCP transcription factor HvTB2 heterodimerizes with VRS5 and controls spike architecture in barley. PLANT REPRODUCTION 2022; 35:205-220. [PMID: 35254529 PMCID: PMC9352630 DOI: 10.1007/s00497-022-00441-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Understanding the molecular network, including protein-protein interactions, of VRS5 provide new routes towards the identification of other key regulators of plant architecture in barley. The TCP transcriptional regulator TEOSINTE BRANCHED 1 (TB1) is a key regulator of plant architecture. In barley, an important cereal crop, HvTB1 (also referred to as VULGARE SIX-ROWED spike (VRS) 5), inhibits the outgrowth of side shoots, or tillers, and grains. Despite its key role in barley development, there is limited knowledge on the molecular network that is utilized by VRS5. In this work, we performed protein-protein interaction studies of VRS5. Our analysis shows that VRS5 potentially interacts with a diverse set of proteins, including other class II TCP's, NF-Y TF, but also chromatin remodelers. Zooming in on the interaction capacity of VRS5 with other TCP TFs shows that VRS5 preferably interacts with other class II TCP TFs in the TB1 clade. Induced mutagenesis through CRISPR-Cas of one of the putative VRS5 interactors, HvTB2 (also referred to as COMPOSITUM 1 and BRANCHED AND INDETERMINATE SPIKELET 1), resulted in plants that have lost their characteristic unbranched spike architecture. More specifically, hvtb2 mutants exhibited branches arising at the main spike, suggesting that HvTB2 acts as inhibitor of branching. Our protein-protein interaction studies of VRS5 resulted in the identification of HvTB2 as putative interactor of VRS5, another key regulator of spike architecture in barley. The study presented here provides a first step to underpin the protein-protein interactome of VRS5 and to identify other, yet unknown, key regulators of barley plant architecture.
Collapse
Affiliation(s)
- Tatiana de Souza Moraes
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, CEP 13416-000, Brazil
| | - Sam W van Es
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | | | - Gwendolyn K Kirschner
- Institute of Crop Functional Genomics, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Froukje van der Wal
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sylvia Rodrigues da Silveira
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, CEP 13416-000, Brazil
| | - Jacqueline Busscher-Lange
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Gerco C Angenent
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Matthew Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Richard G H Immink
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
| | - G Wilma van Esse
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands.
| |
Collapse
|
16
|
Teng J, Wang D, Wang W, Ning C, Zhang Q, Tang H. Transcriptional Regulation of the Chicken ASMT Gene- A Preliminary Analysis. Br Poult Sci 2022; 63:833-839. [PMID: 35702898 DOI: 10.1080/00071668.2022.2090230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Melatonin is an indole hormone that, among its myriad biological functions, regulates circadian and seasonal rhythms in animals. The ASMT gene plays an essential role in melatonin synthesis. However, in chickens, little is known about the regulatory elements governing its transcription.2. The following study identified the transcription start site of the chicken ASMT gene by 5'-RACE. Then, the proximal minimal promoter was identified using a series of 5' truncations of the ASMT promoter (e.g., -3502/+17, -2698/+17, -2003/+17, -1378/+17, and -254/+17). Site-directed mutagenesis, overexpression, and electrophoretic mobility shift assay (EMSA) were applied to show that the transcription factor Oct-1 binds to the promoter region of ASMT.3. The translation start site was located 19 bp upstream from the translational start site. The luciferase reporter assay confirmed that the core promoter of chicken ASMT gene was in the -254/+17 region. Using site-directed mutagenesis, overexpression, and EMSA, Oct-1 bound the promoter of ASMT.4. Overall, Oct1 plays an important role in the transcriptional regulation of chicken ASMT gene.
Collapse
Affiliation(s)
- Jun Teng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Dan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Wenwen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Chao Ning
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, 271018, China
| | | |
Collapse
|
17
|
Alem AL, Ariel FD, Cho Y, Hong JC, Gonzalez DH, Viola IL. TCP15 interacts with GOLDEN2-LIKE 1 to control cotyledon opening in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:748-763. [PMID: 35132717 DOI: 10.1111/tpj.15701] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/23/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
After germination, exposure to light promotes the opening and expansion of the cotyledons and the development of the photosynthetic apparatus in a process called de-etiolation. This process is crucial for seedling establishment and photoautotrophic growth. TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTORS (TCP) transcription factors are important developmental regulators of plant responses to internal and external signals that are grouped into two main classes. In this study, we identified GOLDEN2-LIKE 1 (GLK1), a key transcriptional regulator of photomorphogenesis, as a protein partner of class I TCPs during light-induced cotyledon opening and expansion in Arabidopsis. The class I TCP TCP15 and GLK1 are mutually required for cotyledon opening and the induction of SAUR and EXPANSIN genes, involved in cell expansion. TCP15 also participates in the expression of photosynthesis-associated genes regulated by GLK1, like LHCB1.4 and LHCB2.2. Furthermore, GLK1 and TCP15 bind to the same promoter regions of different target genes containing either GLK or TCP binding motifs and binding of TCP15 is affected in a GLK1-deficient background, suggesting that a complex between TCP15 and GLK1 participates in the induction of these genes. We postulate that GLK1 helps to recruit TCP15 for the modulation of cell expansion genes in cotyledons and that the functional interaction between these transcription factors may serve to coordinate the expression of cell expansion genes with that of genes involved in the development of the photosynthetic apparatus.
Collapse
Affiliation(s)
- Antonela L Alem
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Federico D Ariel
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Yuhan Cho
- Division of Life Science and Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Jong Chan Hong
- Division of Life Science and Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, South Korea
| | - Daniel H Gonzalez
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Ivana L Viola
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| |
Collapse
|
18
|
Wu G, Zhang X, Li S, Wang L, Bai J, Wang H, Shu Q. Silencing ATF4 inhibits JMJD3‐dependent JUNB/ETS1 axis and mitigates cerebral ischemic injury. J Biochem Mol Toxicol 2022; 36:e23070. [PMID: 35403324 DOI: 10.1002/jbt.23070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Gang Wu
- Department of Anesthesiology The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an China
| | - Xi'an Zhang
- Department of Translational Medicine center Ninth Hospital of Xi'an Affiliated to Xi'an Jiaotong University Xi'an China
| | - Shijun Li
- Department of Pharmacy Wuhan Union Hospital Wuhan China
| | - Lina Wang
- Department of Translational Medicine center Ninth Hospital of Xi'an Affiliated to Xi'an Jiaotong University Xi'an China
| | - Jie Bai
- Department of Anesthesiology The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an China
| | - Hanxiang Wang
- Department of Pharmacy Wuhan Union Hospital Wuhan China
| | - Qing Shu
- Department of Translational Medicine center Ninth Hospital of Xi'an Affiliated to Xi'an Jiaotong University Xi'an China
| |
Collapse
|
19
|
Spies FP, Raineri J, Miguel VN, Cho Y, Hong JC, Chan RL. The Arabidopsis transcription factors AtPHL1 and AtHB23 act together promoting carbohydrate transport from pedicel-silique nodes to seeds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111133. [PMID: 35067303 DOI: 10.1016/j.plantsci.2021.111133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/29/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Carbohydrates are produced in green tissues through photosynthesis and then transported to sink tissues. Carbon partitioning is a strategic process, fine regulated, involving specific sucrose transporters in each connecting tissue. Here we report that a screening of an Arabidopsis transcription factor (TF) library using the homeodomain-leucine zipper I member AtHB23 as bait, allowed identifying the TF AtPHL1 interacting with the former. An independent Y2H assay, and in planta by BiFC, confirmed such interaction. AtHB23 and AtPHL1 coexpressed in the pedicel-silique nodes and the funiculus. Mutant plants (phl1, and amiR23) showed a marked reduction of lipid content in seeds, although lipid composition did not change compared to the wild type. While protein and carbohydrate contents were not significantly different between mutants and control mature seeds, we observed a reduced carbohydrate content in mutant plants young siliques (7 days after pollination). Moreover, using a CFDA probe, we revealed an impaired transport to the seeds, and the gene encoding the carbohydrate transporters SWEET10 and SWEET11, usually expressed in connecting tissues, was repressed in the amiR23 and phl1 mutant plants. Altogether, the results indicated that AtHB23 and AtPHL1 act together, promoting sucrose transport, and the lack of any of them provoked a reduction in seeds lipid content.
Collapse
Affiliation(s)
- Fiorella Paola Spies
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| | - Jesica Raineri
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| | - Virginia Natalí Miguel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| | - Yuhan Cho
- Division of Life Science, Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea.
| | - Jong Chan Hong
- Division of Life Science, Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, Republic of Korea; Division of Plant Sciences, University of Missouri, Columbia, MO, 65211-7310, USA.
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000, Santa Fe, Argentina.
| |
Collapse
|
20
|
Monson RK, Trowbridge AM, Lindroth RL, Lerdau MT. Coordinated resource allocation to plant growth-defense tradeoffs. THE NEW PHYTOLOGIST 2022; 233:1051-1066. [PMID: 34614214 DOI: 10.1111/nph.17773] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Plant resource allocation patterns often reveal tradeoffs that favor growth (G) over defense (D), or vice versa. Ecologists most often explain G-D tradeoffs through principles of economic optimality, in which negative trait correlations are attributed to the reconciliation of fitness costs. Recently, researchers in molecular biology have developed 'big data' resources including multi-omic (e.g. transcriptomic, proteomic and metabolomic) studies that describe the cellular processes controlling gene expression in model species. In this synthesis, we bridge ecological theory with discoveries in multi-omics biology to better understand how selection has shaped the mechanisms of G-D tradeoffs. Multi-omic studies reveal strategically coordinated patterns in resource allocation that are enabled by phytohormone crosstalk and transcriptional signal cascades. Coordinated resource allocation justifies the framework of optimality theory, while providing mechanistic insight into the feedbacks and control hubs that calibrate G-D tradeoff commitments. We use the existing literature to describe the coordinated resource allocation hypothesis (CoRAH) that accounts for balanced cellular controls during the expression of G-D tradeoffs, while sustaining stored resource pools to buffer the impacts of future stresses. The integrative mechanisms of the CoRAH unify the supply- and demand-side perspectives of previous G-D tradeoff theories.
Collapse
Affiliation(s)
- Russell K Monson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Amy M Trowbridge
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Richard L Lindroth
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Manuel T Lerdau
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, 22904, USA
| |
Collapse
|
21
|
Schweizer G, Wagner A. Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana. Genome Biol Evol 2021; 13:6459646. [PMID: 34894231 PMCID: PMC8712246 DOI: 10.1093/gbe/evab273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in DNA sequences that bind transcription factors and thus modulate gene expression are a source of adaptive variation in gene expression. To understand how transcription factor binding sequences evolve in natural populations of the thale cress Arabidopsis thaliana, we integrated genomic polymorphism data for loci bound by transcription factors with in vitro data on binding affinity for these transcription factors. Specifically, we studied 19 different transcription factors, and the allele frequencies of 8,333 genomic loci bound in vivo by these transcription factors in 1,135 A. thaliana accessions. We find that transcription factor binding sequences show very low genetic diversity, suggesting that they are subject to purifying selection. High frequency alleles of such binding sequences tend to bind transcription factors strongly. Conversely, alleles that are absent from the population tend to bind them weakly. In addition, alleles with high frequencies also tend to be the endpoints of many accessible evolutionary paths leading to these alleles. We show that both high affinity and high evolutionary accessibility contribute to high allele frequency for at least some transcription factors. Although binding sequences with stronger affinity are more frequent, we did not find them to be associated with higher gene expression levels. Epistatic interactions among individual mutations that alter binding affinity are pervasive and can help explain variation in accessibility among binding sequences. In summary, combining in vitro binding affinity data with in vivo binding sequence data can help understand the forces that affect the evolution of transcription factor binding sequences in natural populations.
Collapse
Affiliation(s)
- Gabriel Schweizer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.,Santa Fe Institute, Santa Fe, New Mexico, USA.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, South Africa
| |
Collapse
|
22
|
Thakur T, Gandass N, Mittal K, Jamwal P, Muthamilarasan M, Salvi P. A rapid, efficient, and low-cost BiFC protocol and its application in studying in vivo interaction of seed-specific transcription factors, RISBZ and RPBF. Funct Integr Genomics 2021; 21:593-603. [PMID: 34436705 DOI: 10.1007/s10142-021-00801-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 10/20/2022]
Abstract
Proteins regulate cellular and biological processes in all living organisms. More than 80% of the proteins interact with one another to perform their respective functions; therefore, studying the protein-protein-interaction has gained attention in functional characterization studies. Bimolecular fluorescence complement (BiFC) assay is widely adopted to determine the physical interaction of two proteins in vivo. Here, we developed a simple, yet effective BiFC assay for protein-protein-interaction using transient Agrobacterium-mediated-transformation of onion epidermal cells by taking case study of Rice-P-box-Binding-Factor (RPBF) and rice-seed-specific-bZIP (RISBZ) in vivo interaction. Our result revealed that both the proteins, i.e., RISBZ and RPBF, interacted in the nucleus and cytosol. These two transcription factors are known for their coordinate/synergistic regulation of seed-protein content via concurrent binding to the promoter region of the seed storage protein (SSP) encoding genes. We further validated our results with BiFC assay in Nicotiana by agroinfiltration method, which exhibited similar results as Agrobacterium-mediated-transformation of onion epidermal cells. We also examined the subcellular localization of RISBZ and RPBF to assess the efficacy of the protocol. The subcellular localization and BiFC assay presented here is quite easy-to-follow, reliable, and reproducible, which can be completed within 2-3 days without using costly instruments and technologies that demand a high skill set.
Collapse
Affiliation(s)
- Tanika Thakur
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Nishu Gandass
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Kajal Mittal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Pallavi Jamwal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India.
- DST-INSPIRE Faculty, Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, India.
| |
Collapse
|
23
|
Wen X, Chen Y, Fang X. Overexpression of HOXD8 inhibits the proliferation, migration and invasion of breast cancer cells by downregulating ILP2 expression. Exp Ther Med 2021; 22:1006. [PMID: 34345288 PMCID: PMC8311240 DOI: 10.3892/etm.2021.10439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/21/2021] [Indexed: 01/20/2023] Open
Abstract
Breast cancer is one of the most common malignant tumors in women. Although a number of homeobox (HOX) genes are known to serve an important role in breast cancer, the role of HOXD8 in breast cancer remains unclear. The aim of the present study was to investigate the role of HOXD8 in the physiological behaviors of breast cancer cells. The Gene Expression Profiling Interactive Analysis database was used to analyze the expression of HOXD8 in patients with breast cancer and in healthy subjects. Western blotting was performed to determine the expression levels of HOXD8 in several breast cancer cell lines; subsequently, HOXD8 expression was knocked down and overexpressed in MCF-7 cells. Cell Counting Kit-8, colony formation, wound healing and Transwell assays were used to evaluate the effects of HOXD8 on breast cancer cell viability, proliferation, migration and invasion, respectively. Chromatin immunoprecipitation and dual-luciferase reporter assays were conducted to identify the binding sites between HOXD8 and inhibitor of apoptosis-like protein-2 (ILP2). In addition, ILP2 expression levels were knocked down in MCF-7 cells. The results demonstrated that the expression levels of HOXD8 were significantly downregulated in breast cancer tissues and cell lines, and that the overexpression of HOXD8 inhibited the proliferation, invasion and migration of cancer cells. HOXD8 was shown to bind to the ILP2 promoter to regulate the expression of ILP2. Furthermore, ILP2 knockdown reversed the effects of HOXD8 knockdown on breast cancer cell proliferation, invasion and migration. In conclusion, the findings of the present study suggested that HOXD8 may inhibit the proliferation, migration and invasion of breast cancer cells by downregulating ILP2 expression.
Collapse
Affiliation(s)
- Xiaoyun Wen
- Department of Clinical Laboratory, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Yu Chen
- Department of Blood Transfusion, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| | - Xiansong Fang
- Department of Blood Transfusion, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, P.R. China
| |
Collapse
|
24
|
Cui D, Zhao S, Xu H, Allan AC, Zhang X, Fan L, Chen L, Su J, Shu Q, Li K. The interaction of MYB, bHLH and WD40 transcription factors in red pear (Pyrus pyrifolia) peel. PLANT MOLECULAR BIOLOGY 2021; 106:407-417. [PMID: 34117570 DOI: 10.1007/s11103-021-01160-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Sunlight enhanced peel color and significantly up-regulated the expression of PyMYB10 and PybHLH genes. MYB-bHLH-WD40 transcriptional complex forms in the light and is involved in regulating anthocyanin accumulation in the peel. Anthocyanin is the major pigment in the peel of Yunnan red pear (Pyrus pyrifolia (Burm.) Nak.). A transcriptional activation protein complex, involving members of the transcription factor classes of MYB, bHLH and WD40, regulates anthocyanin biosynthesis. This complex was examined in the peel of red pear. In order to clarify the interaction of PyMYB10, PybHLH and PyWD40, fruit were bagged then peel samples collected 0, 3, 5, and 7 days after bag removal. Samples were used for Western blotting and protein interaction analysis. The results showed that sunlight enhanced peel color and significantly up-regulated the expression of both PyMYB10 and PybHLH genes. Co-immunoprecipitation (Co-IP) analysis showed that PybHLH interacted with PyMYB10 or PyWD40, and PyMYB10 interacted with PyWD40. Using onion cells as a model system, bimolecular fluorescence complementation (BiFC) confirmed these interactions and showed that the interaction localized to the nuclei. GST Pull down and Far-Western blotting assays demonstrated that PybHLH interacted with PyMYB10 or PyWD40, respectively, and PyMYB10 interacted with PyWD40 in vitro. In addition, EMSA assay showed that PyMYB10 can directly bind to the promoter of the gene encoding the anthocyanin biosynthesis enzyme anthocyanidin synthase (PyANS). Taken together, these results showed that the ternary complex of PyMYB10, PybHLH and PyWD40 transcription factors forms to regulate anthocyanin biosynthesis and accumulation in Yunnan red pear.
Collapse
Affiliation(s)
- Daolei Cui
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China
- School of Ecology and Environment, Institute of Environmental Remediation and Human Health, Southwest Forestry University, Kunming, 650224, China
| | - Shuxin Zhao
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China
| | - Huini Xu
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China
| | - Andrew C Allan
- Plant and Food Research, Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand
| | - Xiaodong Zhang
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China
| | - Lei Fan
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China
| | - Limei Chen
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China
| | - Jun Su
- Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Quan Shu
- Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
| | - Kunzhi Li
- Biotechnology Research Centre, Faculty of Life Science and Biotechnology, Chenggong Campus, Kunming University of Science and Technology, Chenggong, 650500, Kunming, China.
| |
Collapse
|
25
|
de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol Ecol 2021; 96:5904760. [PMID: 32918444 PMCID: PMC7585586 DOI: 10.1093/femsec/fiaa184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
Collapse
Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany.,Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany.,Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.,Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| |
Collapse
|
26
|
Górska AM, Gouveia P, Borba AR, Zimmermann A, Serra TS, Carvalho P, Lourenço TF, Oliveira MM, Peterhänsel C, Saibo NJM. ZmOrphan94 Transcription Factor Downregulates ZmPEPC1 Gene Expression in Maize Bundle Sheath Cells. FRONTIERS IN PLANT SCIENCE 2021; 12:559967. [PMID: 33897718 PMCID: PMC8062929 DOI: 10.3389/fpls.2021.559967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Spatial separation of the photosynthetic reactions is a key feature of C4 metabolism. In most C4 plants, this separation requires compartmentation of photosynthetic enzymes between mesophyll (M) and bundle sheath (BS) cells. The upstream region of the gene encoding the maize PHOSPHOENOLPYRUVATE CARBOXYLASE 1 (ZmPEPC1) has been shown sufficient to drive M-specific ZmPEPC1 gene expression. Although this region has been well characterized, to date, only few trans-factors involved in the ZmPEPC1 gene regulation were identified. Here, using a yeast one-hybrid approach, we have identified three novel maize transcription factors ZmHB87, ZmCPP8, and ZmOrphan94 as binding to the ZmPEPC1 upstream region. Bimolecular fluorescence complementation assays in maize M protoplasts unveiled that ZmOrphan94 forms homodimers and interacts with ZmCPP8 and with two other ZmPEPC1 regulators previously reported, ZmbHLH80 and ZmbHLH90. Trans-activation assays in maize M protoplasts unveiled that ZmHB87 does not have a clear transcriptional activity, whereas ZmCPP8 and ZmOrphan94 act as activator and repressor, respectively. Moreover, we observed that ZmOrphan94 reduces the trans-activation activity of both activators ZmCPP8 and ZmbHLH90. Using the electromobility shift assay, we showed that ZmOrphan94 binds to several cis-elements present in the ZmPEPC1 upstream region and one of these cis-elements overlaps with the ZmbHLH90 binding site. Gene expression analysis revealed that ZmOrphan94 is preferentially expressed in the BS cells, suggesting that ZmOrphan94 is part of a transcriptional regulatory network downregulating ZmPEPC1 transcript level in the BS cells. Based on both this and our previous work, we propose a model underpinning the importance of a regulatory mechanism within BS cells that contributes to the M-specific ZmPEPC1 gene expression.
Collapse
Affiliation(s)
- Alicja M. Górska
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Paulo Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Ana Rita Borba
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Anna Zimmermann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Institut für Botanik, Leibniz Universität Hannover, Hannover, Germany
| | - Tânia S. Serra
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - Pedro Carvalho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Tiago F. Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| | | | - Nelson J. M. Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
| |
Collapse
|
27
|
Yu S, Guo J, Sun Z, Lin C, Tao H, Zhang Q, Cui Y, Zuo H, Lin Y, Chen S, Liu H, Chen Z. BMP2-dependent gene regulatory network analysis reveals Klf4 as a novel transcription factor of osteoblast differentiation. Cell Death Dis 2021; 12:197. [PMID: 33608506 PMCID: PMC7895980 DOI: 10.1038/s41419-021-03480-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Transcription factors (TFs) regulate the expression of target genes, inducing changes in cell morphology or activities needed for cell fate determination and differentiation. The BMP signaling pathway is widely regarded as one of the most important pathways in vertebrate skeletal biology, of which BMP2 is a potent inducer, governing the osteoblast differentiation of bone marrow stromal cells (BMSCs). However, the mechanism by which BMP2 initiates its downstream transcription factor cascade and determines the direction of differentiation remains largely unknown. In this study, we used RNA-seq, ATAC-seq, and animal models to characterize the BMP2-dependent gene regulatory network governing osteoblast lineage commitment. Sp7-Cre; Bmp2fx/fx mice (BMP2-cKO) were generated and exhibited decreased bone density and lower osteoblast number (n > 6). In vitro experiments showed that BMP2-cKO mouse bone marrow stromal cells (mBMSCs) had an impact on osteoblast differentiation and deficient cell proliferation. Osteogenic medium induced mBMSCs from BMP2-cKO mice and control were subjected to RNA-seq and ATAC-seq analysis to reveal differentially expressed TFs, along with their target open chromatin regions. Combined with H3K27Ac CUT&Tag during osteoblast differentiation, we identified 2338 BMP2-dependent osteoblast-specific active enhancers. Motif enrichment assay revealed that over 80% of these elements were directly targeted by RUNX2, DLX5, MEF2C, OASIS, and KLF4. We deactivated Klf4 in the Sp7 + lineage to validate the role of KLF4 in osteoblast differentiation of mBMSCs. Compared to the wild-type, Sp7-Cre; Klf4fx/+ mice (KLF4-Het) were smaller in size and had abnormal incisors resembling BMP2-cKO mice. Additionally, KLF4-Het mice had fewer osteoblasts and decreased osteogenic ability. RNA-seq and ATAC-seq revealed that KLF4 mainly "co-bound" with RUNX2 to regulate downstream genes. Given the significant overlap between KLF4- and BMP2-dependent NFRs and enriched motifs, our findings outline a comprehensive BMP2-dependent gene regulatory network specifically governing osteoblast differentiation of the Sp7 + lineage, in which Klf4 is a novel transcription factor.
Collapse
Affiliation(s)
- Shuaitong Yu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jinqiang Guo
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zheyi Sun
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Chujiao Lin
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Huangheng Tao
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qian Zhang
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yu Cui
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Huanyan Zuo
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yuxiu Lin
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Shuo Chen
- Department of Developmental Dentistry, University of Texas Health Science Center, San Antonio, TX, USA
| | - Huan Liu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China.
- Department of Periodontology, School and Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Zhi Chen
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China.
| |
Collapse
|
28
|
Millard PS, Kragelund BB, Burow M. Evolution of A bHLH Interaction Motif. Int J Mol Sci 2021; 22:E447. [PMID: 33466276 PMCID: PMC7794824 DOI: 10.3390/ijms22010447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 01/05/2023] Open
Abstract
Intrinsically disordered proteins and regions with their associated short linear motifs play key roles in transcriptional regulation. The disordered MYC-interaction motif (MIM) mediates interactions between MYC and MYB transcription factors in Arabidopsis thaliana that are critical for constitutive and induced glucosinolate (GLS) biosynthesis. GLSs comprise a class of plant defense compounds that evolved in the ancestor of the Brassicales order. We used a diverse set of search strategies to discover additional occurrences of the MIM in other proteins and in other organisms and evaluate the findings by means of structural predictions, interaction assays, and biophysical experiments. Our search revealed numerous MIM instances spread throughout the angiosperm lineage. Experiments verify that several of the newly discovered MIM-containing proteins interact with MYC TFs. Only hits found within the same transcription factor family and having similar characteristics could be validated, indicating that structural predictions and sequence similarity are good indicators of whether the presence of a MIM mediates interaction. The experimentally validated MIMs are found in organisms outside the Brassicales order, showing that MIM function is broader than regulating GLS biosynthesis.
Collapse
Affiliation(s)
- Peter S. Millard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; (P.S.M.); (B.B.K.)
- REPIN and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Birthe B. Kragelund
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark; (P.S.M.); (B.B.K.)
- REPIN and Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| |
Collapse
|
29
|
Zaborowski AB, Walther D. Determinants of correlated expression of transcription factors and their target genes. Nucleic Acids Res 2020; 48:11347-11369. [PMID: 33104784 PMCID: PMC7672440 DOI: 10.1093/nar/gkaa927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 11/14/2022] Open
Abstract
While transcription factors (TFs) are known to regulate the expression of their target genes (TGs), only a weak correlation of expression between TFs and their TGs has generally been observed. As lack of correlation could be caused by additional layers of regulation, the overall correlation distribution may hide the presence of a subset of regulatory TF-TG pairs with tight expression coupling. Using reported regulatory pairs in the plant Arabidopsis thaliana along with comprehensive gene expression information and testing a wide array of molecular features, we aimed to discern the molecular determinants of high expression correlation of TFs and their TGs. TF-family assignment, stress-response process involvement, short genomic distances of the TF-binding sites to the transcription start site of their TGs, few required protein-protein-interaction connections to establish physical interactions between the TF and polymerase-II, unambiguous TF-binding motifs, increased numbers of miRNA target-sites in TF-mRNAs, and a young evolutionary age of TGs were found particularly indicative of high TF-TG correlation. The modulating roles of post-transcriptional, post-translational processes, and epigenetic factors have been characterized as well. Our study reveals that regulatory pairs with high expression coupling are associated with specific molecular determinants.
Collapse
Affiliation(s)
- Adam B Zaborowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| |
Collapse
|
30
|
Processing of coding and non-coding RNAs in plant development and environmental responses. Essays Biochem 2020; 64:931-945. [DOI: 10.1042/ebc20200029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
Abstract
Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.
Collapse
|
31
|
Kong Q, Yang Y, Low PM, Guo L, Yuan L, Ma W. The function of the WRI1-TCP4 regulatory module in lipid biosynthesis. PLANT SIGNALING & BEHAVIOR 2020; 15:1812878. [PMID: 32880205 PMCID: PMC7588184 DOI: 10.1080/15592324.2020.1812878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 05/20/2023]
Abstract
The plant-specific TCP transcription factors play pivotal roles in various processes of plant growth and development. However, little is known regarding the functions of TCPs in plant oil biosynthesis. Our recent work showed that TCP4 mediates oil production via interaction with WRINKLED1 (WRI1), an essential transcription factor governing plant fatty acid biosynthesis. Arabidopsis WRI1 (AtWRI1) physically interacts with multiple TCPs, including TCP4, TCP10, and TCP24. Transient co-expression of AtWRI1 with TCP4, but not TCP10 or TCP24, represses oil accumulation in Nicotiana benthamiana leaves. Increased TCP4 in transgenic plants overexpressing a miR319-resistant TCP4 (rTCP4) decreased the expression of AtWRI1 target genes. The tcp4 knockout mutant, the jaw-D mutant with significant reduction of TCP4 expression, and a tcp2 tcp4 tcp10 triple mutant, display increased seed oil contents compared to the wild-type Arabidopsis. The APETALA2 (AP2) transcription factor WRI1 is characterized by regulating fatty acid biosynthesis through cross-family interactions with multiple transcriptional, post-transcriptional, and post-translational regulators. The interacting regulator modules control the range of AtWRI1 transcriptional activity, allowing spatiotemporal modulation of lipid production. Interaction of TCP4 with AtWRI1, which results in a reduction of AtWRI1 activity, represents a newly discovered mechanism that enables the fine-tuning of plant oil biosynthesis.
Collapse
Affiliation(s)
- Que Kong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuzhou Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pui Man Low
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ling Yuan
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, USA
| | - Wei Ma
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- CONTACT Wei Ma School of Biological Sciences, Nanyang Technological University, Singapore637551, Singapore
| |
Collapse
|
32
|
Bose U, Juhász A, Broadbent JA, Komatsu S, Colgrave ML. Multi-Omics Strategies for Decoding Smoke-Assisted Germination Pathways and Seed Vigour. Int J Mol Sci 2020; 21:E7512. [PMID: 33053786 PMCID: PMC7593932 DOI: 10.3390/ijms21207512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
The success of seed germination and the successful establishment of seedlings across diverse environmental conditions depends on seed vigour, which is of both economic and ecologic importance. The smoke-derived exogenous compound karrikins (KARs) and the endogenous plant hormone strigolactone (SL) are two classes of butanolide-containing molecules that follow highly similar signalling pathways to control diverse biological activities in plants. Unravelling the precise mode-of-action of these two classes of molecules in model species has been a key research objective. However, the specific and dynamic expression of biomolecules upon stimulation by these signalling molecules remains largely unknown. Genomic and post-genomic profiling approaches have enabled mining and association studies across the vast genetic diversity and phenotypic plasticity. Here, we review the background of smoke-assisted germination and vigour and the current knowledge of how plants perceive KAR and SL signalling and initiate the crosstalk with the germination-associated hormone pathways. The recent advancement of 'multi-omics' applications are discussed in the context of KAR signalling and with relevance to their adoption for superior agronomic trait development. The remaining challenges and future opportunities for integrating multi-omics datasets associated with their application in KAR-dependent seed germination and abiotic stress tolerance are also discussed.
Collapse
Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; (U.B.); (J.A.B.)
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia;
| | - James A. Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; (U.B.); (J.A.B.)
| | - Setsuko Komatsu
- Department of Environmental and Food Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Michelle L. Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; (U.B.); (J.A.B.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia;
| |
Collapse
|
33
|
Yuan C, Huang D, Yang Y, Sun M, Cheng T, Wang J, Pan H, Zhang Q. CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in Chrysanthemum morifolium. PLANT MOLECULAR BIOLOGY 2020; 103:159-171. [PMID: 32088830 DOI: 10.1007/s11103-020-00981-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
Abstract
The complex capitulum of Chrysanthemum morifolium is often comprised of bilaterally symmetrical ray florets and radially symmetrical disc florets. The TCP transcription factor clade CYCLOIDEA2 (CYC2) appears to play a vital role in determining floral symmetry and in regulating floral organ development in Asteraceae. Our previous study identified six CmCYC2 genes from chrysanthemum and showed that CmCYC2c participated in the regulation of ray floret identity. However, the functions of other CmCYC2 genes and the underlying molecular mechanism of CmCYC2-mediated floral development regulation in chrysanthemums have not been elucidated. In this study, we analysed the function of CmCYC2 genes by ectopic expression of CmCYC2 in Arabidopsis. Then, we examined the protein-protein interaction using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Finally, we analysed the protein-DNA interaction using yeast one-hybrid (Y1H) and dual-luciferase reporter assays. We found that ectopic expression of CmCYC2 genes in the Arabidopsis tcp1 mutant changed its floral symmetry and flowering time. Y2H and BiFC assays confirmed three pairs of interactions between CmCYC2 proteins, that is, CmCYC2b-CmCYC2d, CmCYC2b-CmCYC2e and CmCYC2c-CmCYC2d, suggesting that heterodimeric complexes may form between CmCYC2 proteins to increase their functional specificity. The results of Y1H and dual-luciferase reporter assays indicate that CmCYC2c can bind to the promoter of ClCYC2f. Our findings provided clues that CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in C. morifolium. KEY MESSAGE: CmCYC2-like transcription factors may interact with each other or bind to the promoter to regulate floral symmetry development in Chrysanthemum morifolium.
Collapse
Affiliation(s)
- Cunquan Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Di Huang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Yi Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Ming Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, No. 35 East Qinghua Road, Haidian District, Beijing, 100083, China.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
34
|
Cheuk A, Ouellet F, Houde M. The barley stripe mosaic virus expression system reveals the wheat C2H2 zinc finger protein TaZFP1B as a key regulator of drought tolerance. BMC PLANT BIOLOGY 2020; 20:144. [PMID: 32264833 PMCID: PMC7140352 DOI: 10.1186/s12870-020-02355-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/23/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Drought stress is one of the major factors limiting wheat production globally. Improving drought tolerance is important for agriculture sustainability. Although various morphological, physiological and biochemical responses associated with drought tolerance have been documented, the molecular mechanisms and regulatory genes that are needed to improve drought tolerance in crops require further investigation. We have used a novel 4-component version (for overexpression) and a 3-component version (for underexpression) of a barley stripe mosaic virus-based (BSMV) system for functional characterization of the C2H2-type zinc finger protein TaZFP1B in wheat. These expression systems avoid the need to produce transgenic plant lines and greatly speed up functional gene characterization. RESULTS We show that overexpression of TaZFP1B stimulates plant growth and up-regulates different oxidative stress-responsive genes under well-watered conditions. Plants that overexpress TaZFP1B are more drought tolerant at critical periods of the plant's life cycle. Furthermore, RNA-Seq analysis revealed that plants overexpressing TaZFP1B reprogram their transcriptome, resulting in physiological and physical modifications that help wheat to grow and survive under drought stress. In contrast, plants transformed to underexpress TaZFP1B are significantly less tolerant to drought and growth is negatively affected. CONCLUSIONS This study clearly shows that the two versions of the BSMV system can be used for fast and efficient functional characterization of genes in crops. The extent of transcriptome reprogramming in plants that overexpress TaZFP1B indicates that the encoded transcription factor is a key regulator of drought tolerance in wheat.
Collapse
Affiliation(s)
- Arnaud Cheuk
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
| | - Francois Ouellet
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada
| | - Mario Houde
- Département des Sciences biologiques, Université du Québec à Montréal, C.P. 8888, Succ. Centre-ville, Montréal, Québec, H3C 3P8, Canada.
| |
Collapse
|
35
|
Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
Collapse
Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
| |
Collapse
|
36
|
Jo L, Pelletier JM, Hsu SW, Baden R, Goldberg RB, Harada JJ. Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development. Proc Natl Acad Sci U S A 2020; 117:1223-1232. [PMID: 31892538 PMCID: PMC6969526 DOI: 10.1073/pnas.1918441117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The LEAFY COTYLEDON1 (LEC1) transcription factor is a central regulator of seed development, because it controls diverse biological programs during seed development, such as embryo morphogenesis, photosynthesis, and seed maturation. To understand how LEC1 regulates different gene sets during development, we explored the possibility that LEC1 acts in combination with other transcription factors. We identified and compared genes that are directly transcriptionally regulated by ABA-RESPONSIVE ELEMENT BINDING PROTEIN3 (AREB3), BASIC LEUCINE ZIPPER67 (bZIP67), and ABA INSENSITIVE3 (ABI3) with those regulated by LEC1. We showed that LEC1 operates with specific sets of transcription factors to regulate different gene sets and, therefore, distinct developmental processes. Thus, LEC1 controls diverse processes through its combinatorial interactions with other transcription factors. DNA binding sites for the transcription factors are closely clustered in genomic regions upstream of target genes, defining cis-regulatory modules that are enriched for DNA sequence motifs that resemble sequences known to be bound by these transcription factors. Moreover, cis-regulatory modules for genes regulated by distinct transcription factor combinations are enriched for different sets of DNA motifs. Expression assays with embryo cells indicate that the enriched DNA motifs are functional cis elements that regulate transcription. Together, the results suggest that combinatorial interactions between LEC1 and other transcription factors are mediated by cis-regulatory modules containing clustered cis elements and by physical interactions that are documented to occur between the transcription factors.
Collapse
Affiliation(s)
- Leonardo Jo
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Julie M Pelletier
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Ssu-Wei Hsu
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Russell Baden
- Department of Plant Biology, University of California, Davis, CA 95616
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - John J Harada
- Department of Plant Biology, University of California, Davis, CA 95616;
| |
Collapse
|
37
|
Millard PS, Bugge K, Marabini R, Boomsma W, Burow M, Kragelund BB. IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors. Protein Sci 2020; 29:169-183. [PMID: 31642121 PMCID: PMC6933863 DOI: 10.1002/pro.3754] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022]
Abstract
Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence-based approach to assess and visualize domain organization in long intrinsically disordered regions based on compositional sequence biases. An online tool to find putative intrinsically disordered domains (IDDomainSpotter) in any protein sequence or sequence alignment using any particular sequence trait is available at http://www.bio.ku.dk/sbinlab/IDDomainSpotter. Using this tool, we have identified a putative domain enriched in hydrophilic and disorder-promoting residues (Pro, Ser, and Thr) and depleted in positive charges (Arg and Lys) bordering the folded DNA-binding domains of several transcription factors (p53, GCR, NAC46, MYB28, and MYB29). This domain, from two different MYB transcription factors, was characterized biophysically to determine its properties. Our analyses show the domain to be extended, dynamic and highly disordered. It connects the DNA-binding domain to other disordered domains and is present and conserved in several transcription factors from different families and domains of life. This example illustrates the potential of IDDomainSpotter to predict, from sequence alone, putative domains of functional interest in otherwise uncharacterized disordered proteins.
Collapse
Affiliation(s)
- Peter S. Millard
- DynaMo Center, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
38
|
Millard PS, Weber K, Kragelund BB, Burow M. Specificity of MYB interactions relies on motifs in ordered and disordered contexts. Nucleic Acids Res 2019; 47:9592-9608. [PMID: 31400117 PMCID: PMC6765112 DOI: 10.1093/nar/gkz691] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/18/2019] [Accepted: 08/08/2019] [Indexed: 02/05/2023] Open
Abstract
Physical interactions between members of the MYB and bHLH transcription factor (TF) families regulate many important biological processes in plants. Not all reported MYB-bHLH interactions can be explained by the known binding sites in the R3 repeat of the MYB DNA-binding domain. Noteworthy, most of the sequence diversity of MYB TFs lies in their non-MYB regions, which contain orphan small subgroup-defining motifs not yet linked to molecular functions. Here, we identified the motif mediating interaction between MYB TFs from subgroup 12 and their bHLH partners. Unlike other known MYB-bHLH interactions, the motif locates to the centre of the predicted disordered non-MYB region. We characterised the core motif, which enabled accurate prediction of previously unknown bHLH-interacting MYB TFs in Arabidopsis thaliana, and we confirmed its functional importance in planta. Our results indicate a correlation between the MYB-bHLH interaction affinity and the phenotypic output controlled by the TF complex. The identification of an interaction motif outside R3 indicates that MYB-bHLH interactions must have arisen multiple times, independently and suggests many more motifs of functional relevance to be harvested from subgroup-specific studies.
Collapse
Affiliation(s)
- Peter S Millard
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Konrad Weber
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| |
Collapse
|
39
|
Millard PS, Kragelund BB, Burow M. R2R3 MYB Transcription Factors - Functions outside the DNA-Binding Domain. TRENDS IN PLANT SCIENCE 2019; 24:934-946. [PMID: 31358471 DOI: 10.1016/j.tplants.2019.07.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 05/20/2023]
Abstract
Several transcription factor (TF) families, including the MYB family, regulate a wide array of biological processes. TFs contain DNA-binding domains (DBDs) and regulatory regions; although information on protein structure is scarce for plant MYB TFs, various in silico methods suggest that the non-MYB regions contain extensive intrinsically disordered regions (IDRs). Although IDRs do not fold into stable globular structures, they comprise functional regions including interaction motifs, and recent research has shown that IDRs perform crucial biological roles. We map here domain organization, disorder predictions, and functional regions across the entire Arabidopsis thaliana R2R3 MYB TF family, and highlight where an increased research focus will be necessary to shape a new understanding of structure-function relationships in plant TFs.
Collapse
Affiliation(s)
- Peter S Millard
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark; Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
40
|
Perez M, Guerringue Y, Ranty B, Pouzet C, Jauneau A, Robe E, Mazars C, Galaud JP, Aldon D. Specific TCP transcription factors interact with and stabilize PRR2 within different nuclear sub-domains. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110197. [PMID: 31481190 DOI: 10.1016/j.plantsci.2019.110197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/12/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
Plants possess a large set of transcription factors both involved in the control of plant development or in plant stress responses coordination. We previously identified PRR2, a Pseudo-Response Regulator, as a plant-specific CML-interacting partner. We reported that PRR2 acts as a positive actor of plant defense by regulating the production of antimicrobial compounds. Here, we report new data on the interaction between PRR2 and transcription factors belonging to the Teosinte branched Cycloidea and PCF (TCP) family. TCPs have been described to be involved in plant development and immunity. We evaluated the ability of PRR2 to interact with seven TCPs representative of the different subclades of the family. PRR2 is able to interact with TCP13, TCP15, TCP19 and TCP20 in yeast two-hybrid system and in planta interactions were validated for TCP19 and TCP20. Transient expression in tobacco highlighted that PRR2 protein is more easily detected when co-expressed with TCP19 or TC20. This stabilization is associated with a specific sub-nuclear localization of the complex in Cajal bodies or in nuclear speckles according to the interaction of PRR2 with TCP19 or TCP20 respectively. The interaction between PRR2 and TCP19 or TCP20 would contribute to the biological function in specific nuclear compartments.
Collapse
Affiliation(s)
- M Perez
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France; Toulouse NeuroImaging Center, INSERM, UPS, Pavillon Baudot, CHU Purpan, Place du Dr Baylac, 31024 Toulouse, France.
| | - Y Guerringue
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.
| | - B Ranty
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France.
| | - C Pouzet
- Fédération de Recherche FR3450 (Agrobiosciences, Interactions et Biodiversité), Plateforme Imagerie-Microscopie, CNRS, Université Toulouse, 31326, Castanet-Tolosan, France.
| | - A Jauneau
- Fédération de Recherche FR3450 (Agrobiosciences, Interactions et Biodiversité), Plateforme Imagerie-Microscopie, CNRS, Université Toulouse, 31326, Castanet-Tolosan, France.
| | - E Robe
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France.
| | - C Mazars
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France.
| | - J P Galaud
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France.
| | - D Aldon
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet-Tolosan, France.
| |
Collapse
|
41
|
Wang L, Wang Y. Transcription factor VqERF114 regulates stilbene synthesis in Chinese wild Vitis quinquangularis by interacting with VqMYB35. PLANT CELL REPORTS 2019; 38:1347-1360. [PMID: 31414199 DOI: 10.1007/s00299-019-02456-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/05/2019] [Indexed: 05/03/2023]
Abstract
VqERF114 regulates stilbene synthesis by interacting with VqMYB35. Resveratrol is a stilbene, an important class of secondary metabolites that accumulates in some plant species, including grapevine. In the plant, these are involved in the response to attack by plant pathogens and, as a component of the human diet, they offer a range of significant health benefits. Stilbene synthase (STS), the key enzyme responsible for resveratrol synthesis, has been characterised in a small number of plant species. However, the regulatory mechanisms for stilbene synthesis are uncertain. Here, an ERF family transcription factor from Chinese wild Vitis quinquangularis, VqERF114, was characterised as an indirect regulator of stilbene synthesis. A transient overexpression assay of VqERF114 in grapevine leaves led to increased STS expression and stilbene accumulation. However, VqERF114 did not bind to the promoters of VqSTSs but the MYB transcription factor, VqMYB35, did interact with VqERF114. This interaction was confirmed by a yeast two-hybrid assay and bimolecular fluorescence complementation. Furthermore, VqMYB35 showed activation effects on the expressions of VqSTS15, VqSTS28, VqSTS42 and VqSTS46 by binding directly to the MBS elements in their promoters. Co-overexpression of VqERF114 and VqMYB35 resulted in higher VqSTSs expression and more stilbene synthesis. These results demonstrate that VqERF114 regulates stilbene synthesis by interacting with VqMYB35.
Collapse
Affiliation(s)
- Lan Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yuejin Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
42
|
Swinnen G, Goossens A, Colinas M. Metabolic editing: small measures, great impact. Curr Opin Biotechnol 2019; 59:16-23. [DOI: 10.1016/j.copbio.2019.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 12/23/2022]
|
43
|
Kulkarni SR, Vaneechoutte D, Van de Velde J, Vandepoele K. TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Nucleic Acids Res 2019; 46:e31. [PMID: 29272447 PMCID: PMC5888541 DOI: 10.1093/nar/gkx1279] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022] Open
Abstract
A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidopsis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75–92% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response.
Collapse
Affiliation(s)
- Shubhada R Kulkarni
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dries Vaneechoutte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Jan Van de Velde
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 927, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- To whom correspondence should be addressed. Tel: +32 9 3313822; Fax: +32 9 3313809;
| |
Collapse
|
44
|
Niu SH, Liu SW, Ma JJ, Han FX, Li Y, Li W. The transcriptional activity of a temperature-sensitive transcription factor module is associated with pollen shedding time in pine. TREE PHYSIOLOGY 2019; 39:1173-1186. [PMID: 31073594 DOI: 10.1093/treephys/tpz023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/07/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
It has long been known that the pollen shedding time in pine trees is correlated with temperature, but the molecular basis for this has remained largely unknown. To better understand the mechanisms driving temperature response and to identify the hub regulators of pollen shedding time regulation in Pinus tabuliformis Carr., we identified a set of temperature-sensitive genes by carrying out a comparative transcriptome analysis using six early pollen shedding trees (EPs) and six late pollen shedding trees (LPs) during mid-winter and at three consecutive time points in early spring. We carried out a weighted gene co-expression network analysis and constructed a transcription factor (TF) collaborative network, merging the common but differentially expressed TFs of the EPs and LPs into a joint network. We found five hub genes in the core TF module whose expression was rapidly induced by low temperatures. The transcriptional activity of this TF module was strongly associated with pollen shedding time, and likely to produce the fine balance between cold hardiness and growth activity in early spring. We confirmed the key role of temperature in regulating flowering time and identified a transcription factor module associated with pollen shedding time in P. tabuliformis. This suggests that repression of growth activity by repressors is the main mechanism balancing growth and cold hardiness in pine trees in early spring. Our results provide new insights into the molecular mechanisms regulating seasonal flowering time in pines.
Collapse
Affiliation(s)
- Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Shuang-Wei Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Jing-Jing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Fang-Xu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Forest Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, PR China
| |
Collapse
|
45
|
Joo H, Lim CW, Lee SC. A pepper RING-type E3 ligase, CaASRF1, plays a positive role in drought tolerance via modulation of CaAIBZ1 stability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:5-18. [PMID: 30548716 DOI: 10.1111/tpj.14191] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 05/11/2023]
Abstract
Plants have evolved complex defense mechanisms to adapt and survive under adverse growth conditions. Abscisic acid (ABA) is a phytohormone that plays a pivotal role in the stress response, especially regulation of the stomatal aperture in response to drought. Here, we identified the pepper CaASRF1 (Capsicum annuum ABA Sensitive RING Finger E3 ligase 1) gene, which modulates drought stress tolerance via ABA-mediated signaling. CaASRF1 contains a C3H2C3-type RING finger domain, which functions as an E3 ligase by attaching ubiquitins to the target proteins. CaASRF1 expression was enhanced after exposure to ABA, drought and NaCl. Loss-of-function in pepper plants and gain-of-function in Arabidopsis plants revealed that CaASRF1 positively modulates ABA signaling and the drought stress response. Moreover, CaASRF1 interacted with and was associated with degradation of the bZIP transcription factor CaAIBZ1 (Capsicum annuum ASRF1-Interacting bZIP transcription factor 1). Contrary to CaASRF1 phenotypes, CaAIBZ1-silenced pepper and CaAIBZ1-overexpressing Arabidopsis exhibited drought-tolerant and drought-sensitive phenotypes, respectively. Taken together, our data indicate that CaASRF1 positively modulates ABA signaling and the drought stress response via modulation of CaAIBZ1 stability.
Collapse
Affiliation(s)
- Hyunhee Joo
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, 06974, Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, 06974, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, 06974, Korea
| |
Collapse
|
46
|
Zúñiga-Mayo VM, Gómez-Felipe A, Herrera-Ubaldo H, de Folter S. Gynoecium development: networks in Arabidopsis and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1447-1460. [PMID: 30715461 DOI: 10.1093/jxb/erz026] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 05/27/2023]
Abstract
Life has always found a way to preserve itself. One strategy that has been developed for this purpose is sexual reproduction. In land plants, the gynoecium is considered to be at the top of evolutionary innovation, since it has been a key factor in the success of the angiosperms. The gynoecium is composed of carpels with different tissues that need to develop and differentiate in the correct way. In order to control and guide gynoecium development, plants have adapted elements of pre-existing gene regulatory networks (GRNs) but new ones have also evolved. The GRNs can interact with internal factors (e.g. hormones and other metabolites) and external factors (e.g. mechanical signals and temperature) at different levels, giving robustness and flexibility to gynoecium development. Here, we review recent findings regarding the role of cytokinin-auxin crosstalk and the genes that connect these hormonal pathways during early gynoecium development. We also discuss some examples of internal and external factors that can modify GRNs. Finally, we make a journey through the flowering plant lineage to determine how conserved are these GRNs that regulate gynoecium and fruit development.
Collapse
Affiliation(s)
- Victor M Zúñiga-Mayo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| |
Collapse
|
47
|
Herrera-Ubaldo H, Lozano-Sotomayor P, Ezquer I, Di Marzo M, Chávez Montes RA, Gómez-Felipe A, Pablo-Villa J, Diaz-Ramirez D, Ballester P, Ferrándiz C, Sagasser M, Colombo L, Marsch-Martínez N, de Folter S. New roles of NO TRANSMITTING TRACT and SEEDSTICK during medial domain development in Arabidopsis fruits. Development 2019; 146:dev.172395. [PMID: 30538100 DOI: 10.1242/dev.172395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/03/2018] [Indexed: 01/11/2023]
Abstract
The gynoecium, the female reproductive part of the flower, is key for plant sexual reproduction. During its development, inner tissues such as the septum and the transmitting tract tissue, important for pollen germination and guidance, are formed. In Arabidopsis, several transcription factors are known to be involved in the development of these tissues. One of them is NO TRANSMITTING TRACT (NTT), essential for transmitting tract formation. We found that the NTT protein can interact with several gynoecium-related transcription factors, including several MADS-box proteins, such as SEEDSTICK (STK), known to specify ovule identity. Evidence suggests that NTT and STK control enzyme and transporter-encoding genes involved in cell wall polysaccharide and lipid distribution in gynoecial medial domain cells. The results indicate that the simultaneous loss of NTT and STK activity affects polysaccharide and lipid deposition and septum fusion, and delays entry of septum cells to their normal degradation program. Furthermore, we identified KAWAK, a direct target of NTT and STK, which is required for the correct formation of fruits in Arabidopsis These findings position NTT and STK as important factors in determining reproductive competence.
Collapse
Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Maurizio Di Marzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Ricardo Aarón Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Jeanneth Pablo-Villa
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - David Diaz-Ramirez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Martin Sagasser
- Bielefeld University, Faculty of Biology, Chair of Genetics and Genomics of Plants, Bielefeld 33615, Germany
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| |
Collapse
|
48
|
Wang YY, Lyu YN, Xin HY, Cheng JT, Liu XQ, Wang XW, Peng XC, Xiang Y, Xin VW, Lu CB, Ren BX, Liang YF, Ji JF, Ma Z, Cui SZ, Xin HW. Identification of Putative UL54 (ICP27) Transcription Regulatory Sequences Binding to Oct-1, v-Myb, Pax-6 and Hairy in Herpes Simplex Viruses. J Cancer 2019; 10:430-440. [PMID: 30719137 PMCID: PMC6360293 DOI: 10.7150/jca.29787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/23/2018] [Indexed: 02/03/2023] Open
Abstract
An oncolytic herpes simplex virus (oHSV) has proven amenable in oncolytic virotherapy and was approved to treat melanoma. The immediate-early (IE) protein ICP27 encoded by gene UL54 is essential for HSV infection. Post-transcriptional modification of UL54 would increase tumor targeting of oHSVs. However, UL54 gene transcription regulatory sequences and factors were not reported yet. Here we isolated a new strain LXMW of type 1 HSV (HSV-1-LXMW) in China and found it's closely related to HSV-1 strains Patton and H129 in the US by the first and next generation DNA sequencing viral DNA phylogenetic analysis. Using a weight matrix-based program Match, we found the UL54 transcription regulatory sequences binding to the transcription factors Oct-1, v-Myb and Pax-6 in HSV-1-LXMW, while the sequences binding to Oct-1 and Hairy in a HSV-2 strain. Further validation showed that HSV-1 and HSV-2 shared the common sequence binding to Oct-1, but had unique sequences to bind v-Myb and Pax-6, or Hairy, respectively, by DNA sequence alignment of total 11 HSV strains. The published results howed that the expression of transcription factors is consistent with the tissue tropism of HSV-1 and HSV-2. In the current article a new HSV-1 strain LXMW was isolated and its putative HSV UL54 transcription regulatory sequences and factors were identified for the first time. Our findings highlight the new understanding of the principles of transcriptional regulation in HSV biology and oncolytic virotherapy.
Collapse
Affiliation(s)
- Ying-Ying Wang
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Yan-Ning Lyu
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Center for Diseases Prevention and Control, Beijing, 100013, China
| | - Hong-Yi Xin
- Animal Health Biotechnology, Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - Jun-Ting Cheng
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Xiao-Qin Liu
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Medical Imaging, School of Basic Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Xian-Wang Wang
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Laboratory Medicine, School of Basic Medicine, Yangtze University, 1 Nanhuan Road, Jingzhou, Hubei 434023, China
| | - Xiao-Chun Peng
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Pathophysiology, School of Basic Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Ying Xiang
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Victoria W Xin
- Montgomery Blair High School Magnet Program Class of 2020, Silver Spring, MD 20901-2451, USA
| | - Cheng-Biao Lu
- Laboratory of Neuronal Network and Brain Diseases Modulation, School of Medicine, Yangtze University, Jingzhou, Hubei Province, China
| | - Bo-Xu Ren
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Pathophysiology, School of Basic Medicine, Yangtze University, Jingzhou, Hubei 434023, China
| | - Yan-Fang Liang
- Department of Radiology, Guangzhou Medical University Cancer Hospital, Guangzhou, China
| | - Jia-Fu Ji
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhaowu Ma
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| | - Shu-Zhong Cui
- Department of Theromotherapy, Guangzhou Medical University Cancer Hospital, Guangzhou, China
| | - Hong-Wu Xin
- The First School of Clinical Medicine, Department of Medicine, Yangtze University, Jingzhou, Hubei 434023, China.,Laboratory of Oncology, Center for Molecular Medicine, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, Hubei 434023, China
| |
Collapse
|
49
|
Stortenbeker N, Bemer M. The SAUR gene family: the plant's toolbox for adaptation of growth and development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:17-27. [PMID: 30239806 DOI: 10.1093/jxb/ery332] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/14/2018] [Indexed: 05/20/2023]
Abstract
The family of small auxin up-regulated RNA (SAUR) genes is a family of auxin-responsive genes with ~60-140 members in most higher plant species. Despite the early discovery of their auxin responsiveness, their function and mode of action remained unknown for a long time. In recent years, the importance of SAUR genes in the regulation of dynamic and adaptive growth, and the molecular mechanisms by which SAUR proteins act are increasingly well understood. SAURs play a central role in auxin-induced acid growth, but can also act independently of auxin, tissue specifically regulated by various other hormone pathways and transcription factors. In this review, we summarize recent advances in the characterization of the SAUR genes in Arabidopsis and other plant species. We particularly elaborate on their capacity to fine-tune growth in response to internal and external signals, and discuss the breakthroughs in understanding the mode of action of SAURs in relation to their complex regulation.
Collapse
Affiliation(s)
- Niek Stortenbeker
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology and Business Unit Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
50
|
Flavonoid biosynthetic pathways in plants: Versatile targets for metabolic engineering. Biotechnol Adv 2018; 38:107316. [PMID: 30458225 DOI: 10.1016/j.biotechadv.2018.11.005] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/28/2018] [Accepted: 11/14/2018] [Indexed: 02/08/2023]
Abstract
Plants, fungi, and microorganisms are equipped with biosynthesis machinery for producing thousands of secondary metabolites. These compounds have important functions in nature as a defence against predators or competitors as well as other ecological significances. The full utilization of these compounds for food, medicine, and other purposes requires a thorough understanding of their structures and the distinct biochemical pathways of their production in cellular systems. In this review, flavonoids as classical examples of secondary metabolites are employed to highlight recent advances in understanding how valuable compounds can be regulated at various levels. With extensive diversity in their chemistry and pharmacology, understanding the metabolic engineering of flavonoids now allows us to fine-tune the eliciting of their production, accumulation, and extraction from living systems. More specifically, recent advances in the shikimic acid and acetate biosynthetic pathways of flavonoids production from metabolic engineering point of view, from genes expression to multiple principles of regulation, are addressed. Specific examples of plants and microorganisms as the sources of flavonoids-based compounds with particular emphasis on therapeutic applications are also discussed.
Collapse
|