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Fuertes-Aguilar J, Matilla AJ. Transcriptional Control of Seed Life: New Insights into the Role of the NAC Family. Int J Mol Sci 2024; 25:5369. [PMID: 38791407 PMCID: PMC11121595 DOI: 10.3390/ijms25105369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific sequences on DNA through their DNA-binding domain (DBD), a universal process. This update conveys information about the diverse roles of TFs, focusing on the NACs (NAM-ATAF-CUC), in regulating target-gene expression and influencing various aspects of plant biology. NAC TFs appeared before the emergence of land plants. The NAC family constitutes a diverse group of plant-specific TFs found in mosses, conifers, monocots, and eudicots. This update discusses the evolutionary origins of plant NAC genes/proteins from green algae to their crucial roles in plant development and stress response across various plant species. From mosses and lycophytes to various angiosperms, the number of NAC proteins increases significantly, suggesting a gradual evolution from basal streptophytic green algae. NAC TFs play a critical role in enhancing abiotic stress tolerance, with their function conserved in angiosperms. Furthermore, the modular organization of NACs, their dimeric function, and their localization within cellular compartments contribute to their functional versatility and complexity. While most NAC TFs are nuclear-localized and active, a subset is found in other cellular compartments, indicating inactive forms until specific cues trigger their translocation to the nucleus. Additionally, it highlights their involvement in endoplasmic reticulum (ER) stress-induced programmed cell death (PCD) by activating the vacuolar processing enzyme (VPE) gene. Moreover, this update provides a comprehensive overview of the diverse roles of NAC TFs in plants, including their participation in ER stress responses, leaf senescence (LS), and growth and development. Notably, NACs exhibit correlations with various phytohormones (i.e., ABA, GAs, CK, IAA, JA, and SA), and several NAC genes are inducible by them, influencing a broad spectrum of biological processes. The study of the spatiotemporal expression patterns provides insights into when and where specific NAC genes are active, shedding light on their metabolic contributions. Likewise, this review emphasizes the significance of NAC TFs in transcriptional modules, seed reserve accumulation, and regulation of seed dormancy and germination. Overall, it effectively communicates the intricate and essential functions of NAC TFs in plant biology. Finally, from an evolutionary standpoint, a phylogenetic analysis suggests that it is highly probable that the WRKY family is evolutionarily older than the NAC family.
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Affiliation(s)
| | - Angel J. Matilla
- Departamento de Biología Funcional, Universidad de Santiago de Compostela, 14971 Santiago de Compostela, Spain
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Liu J, Qiao Y, Li C, Hou B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1095967. [PMID: 36909440 PMCID: PMC9996081 DOI: 10.3389/fpls.2023.1095967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fruits are derived from flowers and play an important role in human food, nutrition, and health. In general, flowers determine the crop yield, and ripening affects the fruit quality. Although transcription factors (TFs) only account for a small part of plant transcriptomes, they control the global gene expression and regulation. The plant-specific NAC (NAM, ATAF, and CUC) TFs constitute a large family evolving concurrently with the transition of both aquatic-to-terrestrial plants and vegetative-to-reproductive growth. Thus, NACs play an important role in fruit yield and quality by determining shoot apical meristem (SAM) inflorescence and controlling ripening. The present review focuses on the various properties of NACs together with their function and regulation in flower formation and fruit ripening. Hitherto, we have a better understanding of the molecular mechanisms of NACs in ripening through abscisic acid (ABA) and ethylene (ETH), but how NACs regulate the expression of the inflorescence formation-related genes is largely unknown. In the future, we should focus on the analysis of NAC redundancy and identify the pivotal regulators of flowering and ripening. NACs are potentially vital manipulation targets for improving fruit quantity and quality.
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Affiliation(s)
- Jianfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Qiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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3
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Jiang M, Jian J, Zhou C, Li L, Wang Y, Zhang W, Song Z, Yang J. Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development. FRONTIERS IN PLANT SCIENCE 2023; 13:1078248. [PMID: 36714739 PMCID: PMC9880897 DOI: 10.3389/fpls.2022.1078248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
The origin of seeds is one of the key innovations in land plant evolution. Ovules are the developmental precursors of seeds. The integument is the envelope structure surrounding the nucellus within the ovule and developing into the seed coat when ovules mature upon fertilization. The question of whether the integument arise de novo or evolve from elaboration of pre-existing structures has caused much debate. By exploring the origin and evolution of the key regulatory genes controlling integument development and their functions during both individual and historical developmental processes, we showed the widespread presence of the homologs of ANT, CUC, BEL1, SPL, C3HDZ, INO, ATS, and ETT in seedless plant genomes. All of these genes have undergone duplication-divergence events in their evolutionary history, with most of the descendant paralogous suffering motif gain and/or loss in the coding regions. Expression and functional characterization have shown that these genes are key components of the genetic program that patterns leaf-like lateral organs. Serial homology can thus be postulated between integuments and other lateral organs in terms of the shared master regulatory genes. Given that the genetic program patterning leaf-like lateral organs formed in seedless plants, and was reused during seed origin, the integument is unlikely to arise de novo but evolved from the stem segment-specific modification of pre-existing serially homologous structures. The master 'switches' trigging the modification to specify the integument identity remain unclear. We propose a successive transformation model of integument origin.
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Affiliation(s)
- Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jinjing Jian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Chengchuan Zhou
- Institute of Tree Genetics Breeding and Cultivation, Jiangxi Academy of Forestry, Nanchang, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Khan K, Van Aken O. The colonization of land was a likely driving force for the evolution of mitochondrial retrograde signalling in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7182-7197. [PMID: 36055768 PMCID: PMC9675596 DOI: 10.1093/jxb/erac351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Most retrograde signalling research in plants was performed using Arabidopsis, so an evolutionary perspective on mitochondrial retrograde regulation (MRR) is largely missing. Here, we used phylogenetics to track the evolutionary origins of factors involved in plant MRR. In all cases, the gene families can be traced to ancestral green algae or earlier. However, the specific subfamilies containing factors involved in plant MRR in many cases arose during the transition to land. NAC transcription factors with C-terminal transmembrane domains, as observed in the key regulator ANAC017, can first be observed in non-vascular mosses, and close homologs to ANAC017 can be found in seed plants. Cyclin-dependent kinases (CDKs) are common to eukaryotes, but E-type CDKs that control MRR also diverged in conjunction with plant colonization of land. AtWRKY15 can be traced to the earliest land plants, while AtWRKY40 only arose in angiosperms and AtWRKY63 even more recently in Brassicaceae. Apetala 2 (AP2) transcription factors are traceable to algae, but the ABI4 type again only appeared in seed plants. This strongly suggests that the transition to land was a major driver for developing plant MRR pathways, while additional fine-tuning events have appeared in seed plants or later. Finally, we discuss how MRR may have contributed to meeting the specific challenges that early land plants faced during terrestrialization.
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Affiliation(s)
- Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
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Ke YD, Huang YW, Viswanath KK, Hu CC, Yeh CM, Mitsuda N, Lin NS, Hsu YH. NbNAC42 and NbZFP3 Transcription Factors Regulate the Virus Inducible NbAGO5 Promoter in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2022; 13:924482. [PMID: 35812928 PMCID: PMC9261433 DOI: 10.3389/fpls.2022.924482] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 05/27/2023]
Abstract
Plant argonautes (AGOs) play important roles in the defense responses against viruses. The expression of Nicotiana benthamiana AGO5 gene (NbAGO5) is highly induced by Bamboo mosaic virus (BaMV) infection; however, the underlying mechanisms remain elusive. In this study, we have analyzed the potential promoter activities of NbAGO5 and its interactions with viral proteins by using a 2,000 bp fragment, designated as PN1, upstream to the translation initiation of NbAGO5. PN1 and seven serial 5'-deletion mutants (PN2-PN8) were fused with a β-glucuronidase (GUS) reporter and introduced into the N. benthamiana genome by Agrobacterium-mediated transformation for further characterization. It was found that PN4-GUS transgenic plants were able to drive strong GUS expression in the whole plant. In the virus infection tests, the GUS activity was strongly induced in PN4-GUS transgenic plants after being challenged with potexviruses. Infiltration of the transgenic plants individually with BaMV coat protein (CP) or triple gene block protein 1 (TGBp1) revealed that only TGBp1 was crucial for inducing the NbAGO5 promoter. To identify the factors responsible for controlling the activity of the NbAGO5 promoter, we employed yeast one-hybrid screening on a transcription factor cDNA library. The result showed that NbNAC42 and NbZFP3 could directly bind the 704 bp promoter regions of NbAGO5. By using overexpressing and virus-induced gene silencing techniques, we found that NbNAC42 and NbZFP3 regulated and downregulated, respectively, the expression of the NbAGO5 gene. Upon virus infection, NbNAC42 played an important role in regulating the expression of NbAGO5. Together, these results provide new insights into the modulation of the defense mechanism of N. benthamiana against viruses. This virus inducible promoter could be an ideal candidate to drive the target gene expression that could improve the anti-virus abilities of crops in the future.
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Affiliation(s)
- Yuan-Dun Ke
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | | | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chuan-Ming Yeh
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei City, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Branchereau C, Quero-García J, Zaracho-Echagüe NH, Lambelin L, Fouché M, Wenden B, Donkpegan A, Le Dantec L, Barreneche T, Alletru D, Parmentier J, Dirlewanger E. New insights into flowering date in Prunus: fine mapping of a major QTL in sweet cherry. HORTICULTURE RESEARCH 2022; 9:uhac042. [PMID: 35184200 PMCID: PMC9070640 DOI: 10.1093/hr/uhac042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Flowering date is an important trait in Prunus fruit species, especially for their adaptation in a global warming context. Numerous quantitative trait loci (QTLs) have been identified and a major one was previously located on LG4. The objectives of this study were to fine-map this QTL in sweet cherry, to identify robust candidate genes by using the new sweet cherry genome sequence of the cultivar 'Regina' and to define markers usable in marker-assisted selection (MAS). We performed QTL analyses on two populations derived from crosses using cultivars 'Regina' and 'Garnet' as parents. The first one (n = 117) was phenotyped over ten years, while the second one (n = 1386) was evaluated during three years. Kompetitive allele specific PCR (KASP) markers located within the QTL region on LG4 were developed and mapped within this region, consisting in the first fine mapping in sweet cherry. The QTL interval was narrowed from 380 kb to 68 kb and candidate genes were identified by using the genome sequence of 'Regina'. Their expression was analyzed from bud dormancy period to flowering in cultivars 'Regina' and 'Garnet'. Several genes, such as PavBOI-E3, PavSR45a and PavSAUR71, were differentially expressed in these two cultivars and could be then considered as promising candidate genes. Two KASP markers were validated using a population derived from a cross between cultivars 'Regina' and 'Lapins' and two collections, including landraces and modern cultivars. Thanks to the high synteny within the Prunus genus, these results give new insights into the control of flowering date in Prunus species and pave the way for the development of molecular breeding strategies.
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Affiliation(s)
- Camille Branchereau
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - José Quero-García
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Nathalia Helena Zaracho-Echagüe
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA, Centre de Recerca en Agrigenómica CSIC-IRTAUAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Laurine Lambelin
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Mathieu Fouché
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Bénédicte Wenden
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Armel Donkpegan
- SYSAAF-Centre INRAE Val de Loire, UMR BOA, 37380 Nouzilly France
| | - Loïck Le Dantec
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - Teresa Barreneche
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
| | - David Alletru
- INRAE, UE 0393, Unité Expérimentale Arboricole, F-33210 Toulenne, France
| | - Julien Parmentier
- INRAE, UE 0393, Unité Expérimentale Arboricole, F-33210 Toulenne, France
| | - Elisabeth Dirlewanger
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie, 33882 Villenave d’Ornon, France
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7
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Wang R, Xue Y, Fan J, Yao JL, Qin M, Lin T, Lian Q, Zhang M, Li X, Li J, Sun M, Song B, Zhang J, Zhao K, Chen X, Hu H, Fei Z, Xue C, Wu J. A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit. Genome Biol 2021; 22:313. [PMID: 34776004 PMCID: PMC8590786 DOI: 10.1186/s13059-021-02531-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh. RESULTS We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation. CONCLUSIONS This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.
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Affiliation(s)
- Runze Wang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongsong Xue
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Fan
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Auckland, 1025, New Zealand
| | - Mengfan Qin
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Lin
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- College of Horticulture, China Agricultural University, Beijing, 100083, China
| | - Qun Lian
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Mingyue Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaolong Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jiaming Li
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Manyi Sun
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bobo Song
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaying Zhang
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kejiao Zhao
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hongju Hu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430072, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Cheng Xue
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Wu
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Kelly OJM, Allan AC. Time to retire? A life-changing decision made by NAC transcription factors. THE NEW PHYTOLOGIST 2021; 231:505-507. [PMID: 34132413 DOI: 10.1111/nph.17451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Olivia J M Kelly
- School of Biological Sciences, University of Auckland, Private Bag 92019, 3 Symonds Street, Auckland, 1025, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, 120 Mt Albert Road, Auckland, 1142, New Zealand
| | - Andrew C Allan
- School of Biological Sciences, University of Auckland, Private Bag 92019, 3 Symonds Street, Auckland, 1025, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, 120 Mt Albert Road, Auckland, 1142, New Zealand
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9
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Bian Z, Gao H, Wang C. NAC Transcription Factors as Positive or Negative Regulators during Ongoing Battle between Pathogens and Our Food Crops. Int J Mol Sci 2020; 22:E81. [PMID: 33374758 PMCID: PMC7795297 DOI: 10.3390/ijms22010081] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/13/2023] Open
Abstract
The NAC (NAM, ATAF1/2, and CUC2) family of proteins is one of the largest plant-specific transcription factor (TF) families and its members play varied roles in plant growth, development, and stress responses. In recent years, NAC TFs have been demonstrated to participate in crop-pathogen interactions, as positive or negative regulators of the downstream defense-related genes. NAC TFs link signaling pathways between plant hormones, including salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA), or other signals, such as reactive oxygen species (ROS), to regulate the resistance against pathogens. Remarkably, NAC TFs can also contribute to hypersensitive response and stomatal immunity or can be hijacked as virulence targets of pathogen effectors. Here, we review recent progress in understanding the structure, biological functions and signaling networks of NAC TFs in response to pathogens in several main food crops, such as rice, wheat, barley, and tomato, and explore the directions needed to further elucidate the function and mechanisms of these key signaling molecules.
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Affiliation(s)
| | | | - Chongying Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (Z.B.); (H.G.)
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10
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Carrillo-Bermejo EA, Gamboa-Tuz SD, Pereira-Santana A, Keb-Llanes MA, Castaño E, Figueroa-Yañez LJ, Rodriguez-Zapata LC. The SoNAP gene from sugarcane (Saccharum officinarum) encodes a senescence-associated NAC transcription factor involved in response to osmotic and salt stress. JOURNAL OF PLANT RESEARCH 2020; 133:897-909. [DOI: https:/doi.org/10.1007/s10265-020-01230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/08/2020] [Indexed: 03/08/2024]
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11
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Carrillo-Bermejo EA, Gamboa-Tuz SD, Pereira-Santana A, Keb-Llanes MA, Castaño E, Figueroa-Yañez LJ, Rodriguez-Zapata LC. The SoNAP gene from sugarcane (Saccharum officinarum) encodes a senescence-associated NAC transcription factor involved in response to osmotic and salt stress. JOURNAL OF PLANT RESEARCH 2020; 133:897-909. [PMID: 33094397 DOI: 10.1007/s10265-020-01230-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
Climate change has caused serious problems related to the productivity of agricultural crops directly affecting human well-being. Plants have evolved to produce molecular mechanisms in response to environmental stresses, such as transcription factors (TFs), to cope with abiotic stress. The NAC proteins constitute a plant-specific family of TFs involved in plant development processes and tolerance to biotic and abiotic stress. Sugarcane is a perennial grass that accumulates a large amount of sucrose and is a crucial agro-industry crop in tropical regions. Our previous transcriptome analyses on sugarcane that were exposed to drought conditions revealed significant increases in the expression of several NAC TFs through all of the time-point stress conditions. In this work, we characterize all previously detected sugarcane NAC genes, utilizing phylogenetics and expression analyses. Furthermore, we characterized a sugarcane NAC gene orthologous to the senescence-associated genes AtNAP and OsNAP via transient expression in tobacco calluses, from Arabidopsis and rice respectively, thus we named it the SoNAP gene. Transient localization assays on onion epidermal cells confirmed the nuclear localization of the SoNAP. Expression analysis showed that the SoNAP gene was induced by high salinity, drought, and abscisic acid treatments. The overexpression of the SoNAP gene in tobacco calluses caused a senescence associated phenotype. Overall, our results indicated that the SoNAP gene from sugarcane is transcriptionally induced under abiotic stress conditions and conserved the predicted senescence-associated functions when it was overexpressed in a heterologous plant model. This work provides key insights about the senescence mechanisms related to abiotic stress and it provides a benchmark for future work on the improvement of this economically important crop.
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Affiliation(s)
| | - Samuel David Gamboa-Tuz
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatan, Mexico
| | - Alejandro Pereira-Santana
- Industrial Biotechnology Unit, Centro de Investigacion y Asistencia en Tecnologia y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico
- Direccion de Catedras, Consejo Nacional de Ciencia y Tecnologia, Ciudad de Mexico, Mexico
| | - Miguel A Keb-Llanes
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatan, Mexico
| | - Enrique Castaño
- Plant Biochemistry and Molecular Biology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatán, Mexico
| | - Luis Joel Figueroa-Yañez
- Industrial Biotechnology Unit, Centro de Investigacion y Asistencia en Tecnologia y Diseño del Estado de Jalisco, Zapopan, Jalisco, Mexico.
| | - Luis C Rodriguez-Zapata
- Biotechnology Unit, Centro de Investigacion Cientifica de Yucatan, 97205, Mérida, Yucatan, Mexico.
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Mohanta TK, Yadav D, Khan A, Hashem A, Tabassum B, Khan AL, Abd_Allah EF, Al-Harrasi A. Genomics, molecular and evolutionary perspective of NAC transcription factors. PLoS One 2020; 15:e0231425. [PMID: 32275733 PMCID: PMC7147800 DOI: 10.1371/journal.pone.0231425] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/23/2020] [Indexed: 01/05/2023] Open
Abstract
NAC (NAM, ATAF1,2, and CUC2) transcription factors are one of the largest transcription factor families found in the plants and are involved in diverse developmental and signalling events. Despite the availability of comprehensive genomic information from diverse plant species, the basic genomic, biochemical, and evolutionary details of NAC TFs have not been established. Therefore, NAC TFs family proteins from 160 plant species were analyzed in the current study. Study revealed, Brassica napus (410) encodes highest number and Klebsormidium flaccidum (3) encodes the lowest number of TFs. The study further revealed the presence of NAC TF in the Charophyte algae K. flaccidum. On average, the monocot plants encode higher number (141.20) of NAC TFs compared to the eudicots (125.04), gymnosperm (75), and bryophytes (22.66). Furthermore, our analysis revealed that several NAC TFs are membrane bound and contain monopartite, bipartite, and multipartite nuclear localization signals. NAC TFs were also found to encode several novel chimeric proteins and regulate a complex interactome network. In addition to the presence of NAC domain, several NAC proteins were found to encode other functional signature motifs as well. Relative expression analysis of NAC TFs in A. thaliana revealed root tissue treated with urea and ammonia showed higher level of expression and leaf tissues treated with urea showed lower level of expression. The synonymous codon usage is absent in the NAC TFs and it appears that they have evolved from orthologous ancestors and undergone vivid duplications to give rise to paralogous NAC TFs. The presence of novel chimeric NAC TFs are of particular interest and the presence of chimeric NAC domain with other functional signature motifs in the NAC TF might encode novel functional properties in the plants.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Dhananjay Yadav
- Dept. of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Adil Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Baby Tabassum
- Department of Zoology, Toxicology laboratory, Raza P.G. College, Rampur, Uttar Pradesh, India
| | - Abdul Latif Khan
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Al-Harrasi
- Natural and Medicinal Plant Sciences Research Center, University of Nizwa, Nizwa, Oman
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13
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Hennet L, Berger A, Trabanco N, Ricciuti E, Dufayard JF, Bocs S, Bastianelli D, Bonnal L, Roques S, Rossini L, Luquet D, Terrier N, Pot D. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses. FRONTIERS IN PLANT SCIENCE 2020; 11:224. [PMID: 32194601 PMCID: PMC7064007 DOI: 10.3389/fpls.2020.00224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
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Affiliation(s)
- Lauriane Hennet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Angélique Berger
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Noemi Trabanco
- Parco Tecnologico Padano, Lodi, Italy
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Emeline Ricciuti
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Denis Bastianelli
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Laurent Bonnal
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Sandrine Roques
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Laura Rossini
- Parco Tecnologico Padano, Lodi, Italy
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Delphine Luquet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nancy Terrier
- AGAP, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
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Overexpression of a Malus baccata NAC Transcription Factor Gene MbNAC25 Increases Cold and Salinity Tolerance in Arabidopsis. Int J Mol Sci 2020; 21:ijms21041198. [PMID: 32054040 PMCID: PMC7072804 DOI: 10.3390/ijms21041198] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 11/17/2022] Open
Abstract
NAC (no apical meristem (NAM), Arabidopsis thaliana transcription activation factor (ATAF1/2) and cup shaped cotyledon (CUC2)) transcription factors play crucial roles in plant development and stress responses. Nevertheless, to date, only a few reports regarding stress-related NAC genes are available in Malus baccata (L.) Borkh. In this study, the transcription factor MbNAC25 in M. baccata was isolated as a member of the plant-specific NAC family that regulates stress responses. Expression of MbNAC25 was induced by abiotic stresses such as drought, cold, high salinity and heat. The ORF of MbNAC25 is 1122 bp, encodes 373 amino acids and subcellular localization showed that MbNAC25 protein was localized in the nucleus. In addition, MbNAC25 was highly expressed in new leaves and stems using real-time PCR. To analyze the function of MbNAC25 in plants, we generated transgenic Arabidopsis plants that overexpressed MbNAC25. Under low-temperature stress (4 °C) and high-salt stress (200 mM NaCl), plants overexpressing MbNAC25 enhanced tolerance against cold and drought salinity conferring a higher survival rate than that of wild-type (WT). Correspondingly, the chlorophyll content, proline content, the activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were significantly increased, while malondialdehyde (MDA) content was lower. These results indicated that the overexpression of MbNAC25 in Arabidopsis plants improved the tolerance to cold and salinity stress via enhanced scavenging capability of reactive oxygen species (ROS).
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15
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Matias Hurtado FM, Pinto MDS, de Oliveira PN, Riaño-Pachón DM, Inocente LB, Carrer H. Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition. Genes (Basel) 2019; 11:E20. [PMID: 31878092 PMCID: PMC7016782 DOI: 10.3390/genes11010020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.
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Affiliation(s)
- Fernando Manuel Matias Hurtado
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Maísa de Siqueira Pinto
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Perla Novais de Oliveira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo. Av. Centenário 303, Piracicaba, SP 13416-000, Brazil;
| | - Laura Beatriz Inocente
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
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Bengoa Luoni S, Astigueta FH, Nicosia S, Moschen S, Fernandez P, Heinz R. Transcription Factors Associated with Leaf Senescence in Crops. PLANTS (BASEL, SWITZERLAND) 2019; 8:E411. [PMID: 31614987 PMCID: PMC6843677 DOI: 10.3390/plants8100411] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
Leaf senescence is a complex mechanism controlled by multiple genetic and environmental variables. Different crops present a delay in leaf senescence with an important impact on grain yield trough the maintenance of the photosynthetic leaf area during the reproductive stage. Additionally, because of the temporal gap between the onset and phenotypic detection of the senescence process, candidate genes are key tools to enable the early detection of this process. In this sense and given the importance of some transcription factors as hub genes in senescence pathways, we present a comprehensive review on senescence-associated transcription factors, in model plant species and in agronomic relevant crops. This review will contribute to the knowledge of leaf senescence process in crops, thus providing a valuable tool to assist molecular crop breeding.
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Affiliation(s)
- Sofia Bengoa Luoni
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
| | - Francisco H Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires 1650, Argentina.
| | - Salvador Nicosia
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Universidad Nacional de Lujan, Cruce Rutas Nac. 5 y 7, Lujan, Buenos Aires 6700, Argentina.
| | - Sebastian Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Famaillá, Tucumán 4142, Argentina.
| | - Paula Fernandez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires 1650, Argentina.
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires 1686, Argentina.
| | - Ruth Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires 1425, Argentina.
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires 1686, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1428, Argentina.
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Perochon A, Kahla A, Vranić M, Jia J, Malla KB, Craze M, Wallington E, Doohan FM. A wheat NAC interacts with an orphan protein and enhances resistance to Fusarium head blight disease. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1892-1904. [PMID: 30821405 PMCID: PMC6737021 DOI: 10.1111/pbi.13105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 05/05/2023]
Abstract
Taxonomically-restricted orphan genes play an important role in environmental adaptation, as recently demonstrated by the fact that the Pooideae-specific orphan TaFROG (Triticum aestivum Fusarium Resistance Orphan Gene) enhanced wheat resistance to the economically devastating Fusarium head blight (FHB) disease. Like most orphan genes, little is known about the cellular function of the encoded protein TaFROG, other than it interacts with the central stress regulator TaSnRK1α. Here, we functionally characterized a wheat (T. aestivum) NAC-like transcription factor TaNACL-D1 that interacts with TaFROG and investigated its' role in FHB using studies to assess motif analyses, yeast transactivation, protein-protein interaction, gene expression and the disease response of wheat lines overexpressing TaNACL-D1. TaNACL-D1 is a Poaceae-divergent NAC transcription factor that encodes a Triticeae-specific protein C-terminal region with transcriptional activity and a nuclear localisation signal. The TaNACL-D1/TaFROG interaction was detected in yeast and confirmed in planta, within the nucleus. Analysis of multi-protein interactions indicated that TaFROG could form simultaneously distinct protein complexes with TaNACL-D1 and TaSnRK1α in planta. TaNACL-D1 and TaFROG are co-expressed as an early response to both the causal fungal agent of FHB, Fusarium graminearum and its virulence factor deoxynivalenol (DON). Wheat lines overexpressing TaNACL-D1 were more resistant to FHB disease than wild type plants. Thus, we conclude that the orphan protein TaFROG interacts with TaNACL-D1, a NAC transcription factor that forms part of the disease response evolved within the Triticeae.
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Affiliation(s)
- Alexandre Perochon
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Amal Kahla
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Monika Vranić
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Jianguang Jia
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | - Keshav B. Malla
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
| | | | | | - Fiona M. Doohan
- UCD School of Biology and Environmental Science and Earth InstituteCollege of ScienceUniversity College DublinBelfield, Dublin 4Ireland
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Meisrimler C, Pelgrom AJE, Oud B, Out S, Van den Ackerveken G. Multiple downy mildew effectors target the stress-related NAC transcription factor LsNAC069 in lettuce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1098-1115. [PMID: 31077456 PMCID: PMC9545932 DOI: 10.1111/tpj.14383] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/04/2019] [Accepted: 04/17/2019] [Indexed: 05/22/2023]
Abstract
To cause disease in lettuce, the biotrophic oomycete Bremia lactucae secretes potential RxLR effector proteins. Here we report the discovery of an effector-target hub consisting of four B. lactucae effectors and one lettuce protein target by a yeast-two-hybrid (Y2H) screening. Interaction of the lettuce tail-anchored NAC transcription factor, LsNAC069, with B. lactucae effectors does not require the N-terminal NAC domain but depends on the C-terminal region including the transmembrane domain. Furthermore, in Y2H experiments, B. lactucae effectors interact with Arabidopsis and potato tail-anchored NACs, suggesting that they are conserved effector targets. Transient expression of RxLR effector proteins BLR05 and BLR09 and their target LsNAC069 in planta revealed a predominant localization to the endoplasmic reticulum. Phytophthora capsici culture filtrate and polyethylene glycol treatment induced relocalization to the nucleus of a stabilized LsNAC069 protein, lacking the NAC-domain (LsNAC069ΔNAC ). Relocalization was significantly reduced in the presence of the Ser/Cys-protease inhibitor TPCK indicating proteolytic cleavage of LsNAC069 allows for relocalization. Co-expression of effectors with LsNAC069ΔNAC reduced its nuclear accumulation. Surprisingly, LsNAC069 silenced lettuce lines had decreased LsNAC069 transcript levels but did not show significantly altered susceptibility to B. lactucae. In contrast, LsNAC069 silencing increased resistance to Pseudomonas cichorii bacteria and reduced wilting effects under moderate drought stress, indicating a broad role of LsNAC069 in abiotic and biotic stress responses.
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Affiliation(s)
- Claudia‐Nicole Meisrimler
- Plant–Microbe InteractionsDepartment of BiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
- University of CanterburyIlamPrivate Bag 4800Christchurch8041New Zealand
| | - Alexandra J. E. Pelgrom
- Plant–Microbe InteractionsDepartment of BiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Bart Oud
- Enza ZadenHaling 1‐EEnkhuizen1602 DBthe Netherlands
| | - Suzan Out
- Enza ZadenHaling 1‐EEnkhuizen1602 DBthe Netherlands
| | - Guido Van den Ackerveken
- Plant–Microbe InteractionsDepartment of BiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
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Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Castaño E, Rodríguez-Zapata LC. Global Dynamics in Protein Disorder during Maize Seed Development. Genes (Basel) 2019; 10:genes10070502. [PMID: 31262071 PMCID: PMC6678312 DOI: 10.3390/genes10070502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco. División de Biotecnología Industrial. Camino Arenero 1227, El Bajío, Zapopan, Jalisco. C.P. 45019
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México.
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20
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Genome wide characterization of barley NAC transcription factors enables the identification of grain-specific transcription factors exclusive for the Poaceae family of monocotyledonous plants. PLoS One 2018; 13:e0209769. [PMID: 30592743 PMCID: PMC6310276 DOI: 10.1371/journal.pone.0209769] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/11/2018] [Indexed: 12/30/2022] Open
Abstract
The plant NAC transcription factors depict one of the largest plant transcription factor families. They regulate a wide range of different developmental processes and most probably played an important role in the evolutionary diversification of plants. This makes comparative studies of the NAC transcription factor family between individual species and genera highly relevant and such studies have in recent years been greatly facilitated by the increasing number of fully sequenced complex plant genomes. This study combines the characterization of the NAC transcription factors in the recently sequenced genome of the cereal crop barley with expression analysis and a comprehensive phylogenetic characterization of the NAC transcription factors in other monocotyledonous plant species. Our results provide evidence for the emergence of a NAC transcription factor subclade that is exclusively expressed in the grains of the Poaceae family of grasses. These notably comprise a number of cereal crops other than barley, such as wheat, rice, maize or millet, which are all cultivated for their starchy edible grains. Apparently, the grain specific subclade emerged from a well described subgroup of NAC transcription factors associated with the senescence process. A promoter exchange subsequently resulted in grain specific expression. We propose to designate this transcription factor subclade Grain-NACs and we discuss their involvement in programmed cell death as well as their potential role in the evolution of the Poaceae grain, which doubtlessly is of central importance for human nutrition.
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Fujimoto M, Sazuka T, Oda Y, Kawahigashi H, Wu J, Takanashi H, Ohnishi T, Yoneda JI, Ishimori M, Kajiya-Kanegae H, Hibara KI, Ishizuna F, Ebine K, Ueda T, Tokunaga T, Iwata H, Matsumoto T, Kasuga S, Yonemaru JI, Tsutsumi N. Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems. Proc Natl Acad Sci U S A 2018; 115:E8783-E8792. [PMID: 30150370 PMCID: PMC6140496 DOI: 10.1073/pnas.1807501115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pith parenchyma cells store water in various plant organs. These cells are especially important for producing sugar and ethanol from the sugar juice of grass stems. In many plants, the death of pith parenchyma cells reduces their stem water content. Previous studies proposed that a hypothetical D gene might be responsible for the death of stem pith parenchyma cells in Sorghum bicolor, a promising energy grass, although its identity and molecular function are unknown. Here, we identify the D gene and note that it is located on chromosome 6 in agreement with previous predictions. Sorghum varieties with a functional D allele had stems enriched with dry, dead pith parenchyma cells, whereas those with each of six independent nonfunctional D alleles had stems enriched with juicy, living pith parenchyma cells. D expression was spatiotemporally coupled with the appearance of dead, air-filled pith parenchyma cells in sorghum stems. Among D homologs that are present in flowering plants, Arabidopsis ANAC074 also is required for the death of stem pith parenchyma cells. D and ANAC074 encode previously uncharacterized NAC transcription factors and are sufficient to ectopically induce programmed death of Arabidopsis culture cells via the activation of autolytic enzymes. Taken together, these results indicate that D and its Arabidopsis ortholog, ANAC074, are master transcriptional switches that induce programmed death of stem pith parenchyma cells. Thus, targeting the D gene will provide an approach to breeding crops for sugar and ethanol production.
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Affiliation(s)
- Masaru Fujimoto
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoshihisa Oda
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Hiroyuki Kawahigashi
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan
| | - Jianzhong Wu
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan
| | - Hideki Takanashi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takayuki Ohnishi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jun-Ichi Yoneda
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Motoyuki Ishimori
- Laboratory of Biometry and Bioinformatics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hiromi Kajiya-Kanegae
- Laboratory of Biometry and Bioinformatics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ken-Ichiro Hibara
- Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Fumiko Ishizuna
- Technology Advancement Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazuo Ebine
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | | | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Matsumoto
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan
| | - Shigemitsu Kasuga
- Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Jun-Ichi Yonemaru
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan;
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
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Cotton Late Embryogenesis Abundant ( LEA2) Genes Promote Root Growth and Confer Drought Stress Tolerance in Transgenic Arabidopsis thaliana. G3-GENES GENOMES GENETICS 2018; 8:2781-2803. [PMID: 29934376 PMCID: PMC6071604 DOI: 10.1534/g3.118.200423] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Late embryogenesis abundant (LEA) proteins play key roles in plant drought tolerance. In this study, 157, 85 and 89 candidate LEA2 proteins were identified in G. hirsutum, G. arboreum and G. raimondii respectively. LEA2 genes were classified into 6 groups, designated as group 1 to 6. Phylogenetic tree analysis revealed orthologous gene pairs within the cotton genome. The cotton specific LEA2 motifs identified were E, R and D in addition to Y, K and S motifs. The genes were distributed on all chromosomes. LEA2s were found to be highly enriched in non-polar, aliphatic amino acid residues, with leucine being the highest, 9.1% in proportion. The miRNA, ghr-miR827a/b/c/d and ghr-miR164 targeted many genes are known to be drought stress responsive. Various stress-responsive regulatory elements, ABA-responsive element (ABRE), Drought-responsive Element (DRE/CRT), MYBS and low-temperature-responsive element (LTRE) were detected. Most genes were highly expressed in leaves and roots, being the primary organs greatly affected by water deficit. The expression levels were much higher in G. tomentosum as opposed to G. hirsutum. The tolerant genotype had higher capacity to induce more of LEA2 genes. Over expression of the transformed gene Cot_AD24498 showed that the LEA2 genes are involved in promoting root growth and in turn confers drought stress tolerance. We therefore infer that Cot_AD24498, CotAD_20020, CotAD_21924 and CotAD_59405 could be the candidate genes with profound functions under drought stress in upland cotton among the LEA2 genes. The transformed Arabidopsis plants showed higher tolerance levels to drought stress compared to the wild types. There was significant increase in antioxidants, catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) accumulation, increased root length and significant reduction in oxidants, Hydrogen peroxide (H2O2) and malondialdehyde (MDA) concentrations in the leaves of transformed lines under drought stress condition. This study provides comprehensive analysis of LEA2 proteins in cotton thus forms primary foundation for breeders to utilize these genes in developing drought tolerant genotypes.
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Mathew IE, Agarwal P. May the Fittest Protein Evolve: Favoring the Plant-Specific Origin and Expansion of NAC Transcription Factors. Bioessays 2018; 40:e1800018. [PMID: 29938806 DOI: 10.1002/bies.201800018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/26/2018] [Indexed: 12/12/2022]
Abstract
Plant-specific NAC transcription factors (TFs) evolve during the transition from aquatic to terrestrial plant life and are amplified to become one of the biggest TF families. This is because they regulate genes involved in water conductance and cell support. They also control flower and fruit formation. The review presented here focuses on various properties, regulatory intricacies, and developmental roles of NAC family members. Processes controlled by NACs depend majorly on their transcriptional properties. NACs can function as both activators and/or repressors. Additionally, their homo/hetero dimerization abilities can also affect DNA binding and activation properties. The active protein levels are dependent on the regulatory cascades. Because NACs regulate both development and stress responses in plants, in-depth knowledge about them has the potential to help guide future crop improvement studies.
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Affiliation(s)
- Iny Elizebeth Mathew
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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24
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Sablok G, Hayward RJ, Davey PA, Santos RP, Schliep M, Larkum A, Pernice M, Dolferus R, Ralph PJ. SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants. Sci Rep 2018; 8:2749. [PMID: 29426939 PMCID: PMC5807536 DOI: 10.1038/s41598-017-18782-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/11/2017] [Indexed: 12/04/2022] Open
Abstract
Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php.
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Affiliation(s)
- Gaurav Sablok
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia.
| | - Regan J Hayward
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Peter A Davey
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Rosiane P Santos
- Laboratório de Recursos Genéticos, Universidade Federal de São João Del-Rei, Campus CTAN, São João Del Rei, Minas Gerais, 36307-352, Brazil
| | - Martin Schliep
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Anthony Larkum
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Rudy Dolferus
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Peter J Ralph
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia.
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Karanja BK, Xu L, Wang Y, Muleke EM, Jabir BM, Xie Y, Zhu X, Cheng W, Liu L. Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish ( Raphanus sativus L.). PeerJ 2017; 5:e4172. [PMID: 29259849 PMCID: PMC5733918 DOI: 10.7717/peerj.4172] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/28/2017] [Indexed: 01/23/2023] Open
Abstract
NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.
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Affiliation(s)
- Bernard Kinuthia Karanja
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Everlyne M'mbone Muleke
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Bashir Mohammed Jabir
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yang Xie
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Wanwan Cheng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of Horticulture, Nanjing Agricultural University, Nanjing, China
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26
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Zhao C, Lasses T, Bako L, Kong D, Zhao B, Chanda B, Bombarely A, Cruz-Ramírez A, Scheres B, Brunner AM, Beers EP. XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED. THE NEW PHYTOLOGIST 2017; 216:76-89. [PMID: 28742236 DOI: 10.1111/nph.14704] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 (XND1) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly conserved C-terminal region containing linear motifs (CKII-acidic, LXCXE, E2FTD -like and LXCXE-mimic) predicted to interact with the cell cycle and differentiation regulator RETINOBLASTOMA-RELATED (RBR). Protein-protein interaction and functional analyses of XND1 deletion mutants were used to test the importance of RBR-interaction motifs. Deletion of either the LXCXE or the LXCXE-mimic motif reduced both the XND1-RBR interaction and XND1 efficacy as a repressor of differentiation, with loss of the LXCXE motif having the strongest negative impacts. The function of the XND1 C-terminal domain could be partially replaced by RBR fused to the N-terminal domain of XND1. XND1 also transactivated gene expression in yeast and plants. The properties of XND1, a transactivator that depends on multiple linear RBR-interaction motifs to inhibit differentiation, have not previously been described for a plant protein. XND1 harbors an apparently angiosperm-specific combination of interaction motifs potentially linking the general differentiation regulator RBR with a xylem-specific pathway for inhibition of differentiation.
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Affiliation(s)
- Chengsong Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Theres Lasses
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, S-901 87, Umeå, Sweden
| | - Laszlo Bako
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, S-901 87, Umeå, Sweden
| | - Danyu Kong
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bidisha Chanda
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
| | | | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada, CINVESTAV, Irapuato, Guanajuato, 36821, México
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University & Research, 6708PB, Wageningen, the Netherlands
| | - Amy M Brunner
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Eric P Beers
- Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA
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Kamiya M, Higashio SY, Isomoto A, Kim JM, Seki M, Miyashima S, Nakajima K. Control of root cap maturation and cell detachment by BEARSKIN transcription factors in Arabidopsis. Development 2017; 143:4063-4072. [PMID: 27803060 DOI: 10.1242/dev.142331] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/19/2016] [Indexed: 01/29/2023]
Abstract
The root cap supports root growth by protecting the root meristem, sensing gravity and interacting with the rhizosphere through metabolite secretion and cell dispersal. Sustained root cap functions therefore rely on balanced proliferation of proximal stem cells and regulated detachment of distal mature cells. Although the gene regulatory network that governs stem cell activity in the root cap has been extensively studied in Arabidopsis, the mechanisms by which root cap cells mature and detach from the root tip are poorly understood. We performed a detailed expression analysis of three regulators of root cap differentiation, SOMBRERO, BEARSKIN1 and BEARSKIN2, and identified their downstream genes. Our results indicate that expression of BEARSKIN1 and BEARSKIN2 is associated with cell positioning on the root surface. We identified a glycosyl hydrolase 28 (GH28) family polygalacturonase (PG) gene as a direct target of BEARSKIN1. Overexpression and loss-of-function analyses demonstrated that the protein encoded by this PG gene facilitates cell detachment. We thus revealed a molecular link between the key regulators of root cap differentiation and the cellular events underlying root cap-specific functions.
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Affiliation(s)
- Masako Kamiya
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Shin-Ya Higashio
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Atsushi Isomoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Jong-Myong Kim
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Miyashima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Keiji Nakajima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Borrill P, Harrington SA, Uauy C. Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat. G3 (BETHESDA, MD.) 2017; 7:3019-3029. [PMID: 28698232 PMCID: PMC5592928 DOI: 10.1534/g3.117.043679] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/07/2017] [Indexed: 11/18/2022]
Abstract
Many important genes in agriculture correspond to transcription factors (TFs) that regulate a wide range of pathways from flowering to responses to disease and abiotic stresses. In this study, we identified 5776 TFs in hexaploid wheat (Triticum aestivum) and classified them into gene families. We further investigated the NAC family exploring the phylogeny, C-terminal domain (CTD) conservation, and expression profiles across 308 RNA-seq samples. Phylogenetic trees of NAC domains indicated that wheat NACs divided into eight groups similar to rice (Oryza sativa) and barley (Hordeum vulgare). CTD motifs were frequently conserved between wheat, rice, and barley within phylogenetic groups; however, this conservation was not maintained across phylogenetic groups. Three homeologous copies were present for 58% of NACs, whereas evidence of single homeolog gene loss was found for 33% of NACs. We explored gene expression patterns across a wide range of developmental stages, tissues, and abiotic stresses. We found that more phylogenetically related NACs shared more similar expression patterns compared to more distant NACs. However, within each phylogenetic group there were clades with diverse expression profiles. We carried out a coexpression analysis on all wheat genes and identified 37 modules of coexpressed genes of which 23 contained NACs. Using gene ontology (GO) term enrichment, we obtained putative functions for NACs within coexpressed modules including responses to heat and abiotic stress and responses to water: these NACs may represent targets for breeding or biotechnological applications. This study provides a framework and data for hypothesis generation for future studies on NAC TFs in wheat.
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Affiliation(s)
- Philippa Borrill
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK
| | | | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK
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29
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Marques DN, Reis SPD, de Souza CR. Plant NAC transcription factors responsive to abiotic stresses. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Bhatia R, Gallagher JA, Gomez LD, Bosch M. Genetic engineering of grass cell wall polysaccharides for biorefining. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1071-1092. [PMID: 28557198 PMCID: PMC5552484 DOI: 10.1111/pbi.12764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/17/2017] [Accepted: 05/24/2017] [Indexed: 05/10/2023]
Abstract
Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.
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Affiliation(s)
- Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Joe A. Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
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Lehti-Shiu MD, Panchy N, Wang P, Uygun S, Shiu SH. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:3-20. [PMID: 27522016 DOI: 10.1016/j.bbagrm.2016.08.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/06/2016] [Indexed: 12/19/2022]
Abstract
Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
| | - Nicholas Panchy
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Peipei Wang
- Department of Plant Biology, East Lansing, MI 48824, USA
| | - Sahra Uygun
- The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA
| | - Shin-Han Shiu
- Department of Plant Biology, East Lansing, MI 48824, USA; The Genetics Graduate Program, Michigan State University, East Lansing, MI 48824, USA.
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Mathew IE, Das S, Mahto A, Agarwal P. Three Rice NAC Transcription Factors Heteromerize and Are Associated with Seed Size. FRONTIERS IN PLANT SCIENCE 2016; 7:1638. [PMID: 27872632 PMCID: PMC5098391 DOI: 10.3389/fpls.2016.01638] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/17/2016] [Indexed: 05/18/2023]
Abstract
NACs are plant-specific transcription factors (TFs) involved in multiple aspects of development and stress. In rice, three NAC TF encoding genes, namely ONAC020, ONAC026, and ONAC023 express specifically during seed development, at extremely high levels. They exhibit significantly strong association with seed size/weight with the sequence variations located in the upstream regulatory region. Concomitantly, their expression pattern/levels during seed development vary amongst different accessions with variation in seed size. The alterations in the promoter sequences of the three genes, amongst the five rice accessions, correlate with the expression levels to a certain extent only. In terms of transcriptional properties, the three NAC TFs can activate and/or suppress downstream genes, though to different extents. Only ONAC026 is localized to the nucleus while ONAC020 and ONAC023 are targeted to the ER and cytoplasm, respectively. Interestingly, these two proteins interact with ONAC026 and the dimers localize in the nucleus. Trans-splicing between ONAC020 and ONAC026 results in three additional forms of ONAC020. The transcriptional properties including activation, repression, subcellular localization and heterodimerization of trans-spliced forms of ONAC020 and ONAC026 are different, indicating toward their role as competitors. The analysis presented in this paper helps to conclude that the three NAC genes, which are associated with seed size, have independent as well as overlapping roles during the process and can be exploited as potential targets for crop improvement.
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