1
|
Li J, Li M, Shen T, Guo Q, Zhang R, Chen Y, Zhang Y, Luo K. Molecular characterization of cassava zinc finger-homeodomain (ZF-HD) transcription factors reveals their role in disease resistance. Int J Biol Macromol 2024; 279:134846. [PMID: 39179062 DOI: 10.1016/j.ijbiomac.2024.134846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024]
Abstract
The production of cassava (Manihot esculenta Crantz) is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas phaseoli pv. manihotis (Xpm). Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes widely implicated in various developmental and physiological processes in plants. Despite their importance, a comprehensive analysis of ZF-HD genes, particularly those involved in disease resistance, has not been performed for cassava. In the present study, we utilized bioinformatics methods to identify 21 ZF-HD genes distributed across 11 chromosomes of cassava genome, with the majority exhibiting gene structure without introns. Phylogenetic analysis categorized these genes into two major groups (MIF and ZHD) with five subgroups. We observed fourteen pairs of duplicated genes, suggesting that segmental duplication has likely facilitated the expansion of the cassava ZF-HD gene family. Comparative orthologous analyses between cassava and other plant species shed light on the evolutionary trajectory of this gene family. Promoter analyses revealed multiple hormone- and stress-related elements, indicative of a functional role in stress responses. Expression profiling through RNA-seq and quantitative real-time PCR (qRT-PCR) demonstrated that certain cassava ZF-HD genes are up-regulated in response to Xpm infection, suggesting their involvement in defense mechanisms. Notably, MeZHD7 gene was identified via virus induced gene silencing (VIGS) as potentially crucial in conferring resistance against CBB. Results from subcellular localization experiments indicated that MeZHD7 was localized in the nucleus. The Luciferase reporter assay demonstrated an interaction between MeZHD7 and MeMIF5. These findings may lay the foundation for further cloning and functional analyses of cassava ZF-HD genes, particularly those associated with pathogen resistance.
Collapse
Affiliation(s)
- Junyi Li
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Mingchao Li
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Tiantian Shen
- School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Qiying Guo
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Rui Zhang
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yinhua Chen
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yindong Zhang
- Key Laboratory of Plant Disease and Pest Control of Hainan Province/Institute of Plant Protection, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Kai Luo
- School of Breeding and Multiplication (Sanya institute of Breeding and Multiplication), Hainan University, Sanya 572025, China; School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| |
Collapse
|
2
|
Li S, Xu J, Cao Y, Wu J, Liu Q, Zhang D. Genome-Wide Analyses of CCHC Family Genes and Their Expression Profiles under Drought Stress in Rose ( Rosa chinensis). Int J Mol Sci 2024; 25:8983. [PMID: 39201669 PMCID: PMC11354476 DOI: 10.3390/ijms25168983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
CCHC-type zinc finger proteins (CCHC-ZFPs), ubiquitous across plant species, are integral to their growth, development, hormonal regulation, and stress adaptation. Roses (Rosa sp.), as one of the most significant and extensively cultivated ornamentals, account for more than 30% of the global cut-flower market. Despite its significance, the CCHC gene family in roses (Rosa sp.) remains unexplored. This investigation identified and categorized 41 CCHC gene members located on seven chromosomes of rose into 14 subfamilies through motif distribution and phylogenetic analyses involving ten additional plant species, including Ginkgo biloba, Ostreococcus lucimarinus, Arabidopsis thaliana, and others. This study revealed that dispersed duplication likely plays a crucial role in the diversification of the CCHC genes, with the Ka/Ks ratio suggesting a history of strong purifying selection. Promoter analysis highlighted a rich presence of cis-acting regulatory elements linked to both abiotic and biotic stress responses. Differential expression analysis under drought conditions grouped the 41 CCHC gene members into five distinct clusters, with those in group 4 exhibiting pronounced regulation in roots and leaves under severe drought. Furthermore, virus-induced gene silencing (VIGS) of the RcCCHC25 member from group 4 compromised drought resilience in rose foliage. This comprehensive analysis lays the groundwork for further investigations into the functional dynamics of the CCHC gene family in rose physiology and stress responses.
Collapse
Affiliation(s)
- Shijie Li
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Jun Xu
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Yong Cao
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Jie Wu
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| | - Qing Liu
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT 2601, Australia;
| | - Deqiang Zhang
- School of Landscape Architecture, Beijing University of Agriculture, Beinong Road 7, Huilongguan, Changping District, Beijing 102206, China; (S.L.); (J.X.); (Y.C.); (J.W.)
| |
Collapse
|
3
|
Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
Collapse
Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| |
Collapse
|
4
|
Liu MD, Liu H, Liu WY, Ni SF, Wang ZY, Geng ZH, Zhu KY, Wang YF, Zhao YH. Systematic Analysis of Zinc Finger-Homeodomain Transcription Factors (ZF-HDs) in Barley ( Hordeum vulgare L.). Genes (Basel) 2024; 15:578. [PMID: 38790207 PMCID: PMC11120690 DOI: 10.3390/genes15050578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
Zinc finger-homeodomain transcription factors (ZF-HDs) are pivotal in regulating plant growth, development, and diverse stress responses. In this study, we found 8 ZF-HD genes in barley genome. Theses eight HvZF-HD genes were located on five chromosomes, and classified into ZHD and MIF subfamily. The collinearity, gene structure, conserved motif, and cis-elements of HvZF-HD genes were also analyzed. Real-time PCR results suggested that the expression of HvZF-HD4, HvZF-HD6, HvZF-HD7 and HvZF-HD8 were up-regulated after hormones (ABA, GA3 and MeJA) or PEG treatments, especially HvZF-HD6 was significantly induced. These results provide useful information of ZF-HD genes to future study aimed at barley breeding.
Collapse
Affiliation(s)
- Meng-Di Liu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Hao Liu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Wen-Yan Liu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Shou-Fei Ni
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Zi-Yi Wang
- College of Life Science, Ludong University, Yantai 264000, China
| | - Zi-Han Geng
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Kong-Yao Zhu
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| | - Yan-Fang Wang
- College of Life Science, Ludong University, Yantai 264000, China
| | - Yan-Hong Zhao
- College of Agriculture, Ludong University, Yantai 264000, China (H.L.)
| |
Collapse
|
5
|
Thiaw MRN, Gantet P. The emerging functions of mini zinc finger (MIF) microproteins in seed plants: A minireview. Biochimie 2024; 218:69-75. [PMID: 37722501 DOI: 10.1016/j.biochi.2023.09.016] [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: 04/18/2023] [Revised: 07/20/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Mini zinc fingers constitute a class of microproteins that appeared early in evolution and expanded in seeds plants. In this review, the phylogenetic history, the functions and the mode of action of Mini zinc fingers in plants are reported and discussed. It appears that mini zinc fingers play an important role in the control of plant development. They are involved in the control of cell division and expansion, in the switch between the determinate/indeterminate state of the meristems and in the regulation of vegetative growth and floral organ development. Their biochemical mode of action seems to be diverse. In some studies, it has been reported that mini zinc fingers can directly bind to DNA and activate target gene expression, whereas other studies have shown that they can interact with and inhibit the activity of specific zinc finger homeodomain transcription factors or act as adaptor proteins necessary to aggregate polymeric protein complexes corresponding to chromatin remodelling factors negatively regulating the expression of specific genes. The diversity of mode of action for mini zinc finger microproteins suggests a wider range of biological functions than what has been that described in the literature thus far, and their involvement in the response to biotic and abiotic stresses should be further investigated in future studies.
Collapse
Affiliation(s)
- Marie Rose Ndella Thiaw
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394, cedex 5, Montpellier, France.
| | - Pascal Gantet
- UMR DIADE, Université de Montpellier, IRD, 911 Avenue Agropolis, 34394, cedex 5, Montpellier, France.
| |
Collapse
|
6
|
Jang MJ, Hong WJ, Park YS, Jung KH, Kim S. Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes. Nucleic Acids Res 2023; 51:7424-7437. [PMID: 37394281 PMCID: PMC10415114 DOI: 10.1093/nar/gkad489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.
Collapse
Affiliation(s)
- Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Young-Soo Park
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul 02504, Republic of Korea
| |
Collapse
|
7
|
Sahara A, Roberdi R, Wiendi NMA, Liwang T. Transcriptome profiling of high and low somatic embryogenesis rate of oil palm ( Elaeis guineensis Jacq. var. Tenera). FRONTIERS IN PLANT SCIENCE 2023; 14:1142868. [PMID: 37251752 PMCID: PMC10213556 DOI: 10.3389/fpls.2023.1142868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023]
Abstract
Oil palm micropropagation through tissue culture is a technique to provide elite oil palms to meet the desired traits. This technique is commonly carried out through somatic embryogenesis. However, the oil palm's somatic embryogenesis rate is quite low. Several approaches have been made to overcome this problem, including transcriptome profiling through RNA-seq to identify key genes involved in oil palm somatic embryogenesis. RNA sequencing was applied in high- and low-embryogenic ortets of Tenera varieties based on the somatic embryoid rate at the callus, globular, scutellar, and coleoptilar embryoid stages. Cellular analysis of embryoid inductions and proliferations showed that high-embryogenic ortets resulted in higher embryoid proliferation and germinations than low-embryogenic ortets. Transcriptome profiling showed that there are a total of 1,911 differentially expressed genes (DEGs) between high- and low-embryogenic ortets. ABA signaling-related genes such as LEA, DDX28, and vicilin-like protein are upregulated in high-embryogenic ortets. Furthermore, DEGs associated with other hormone signaling, such as HD-ZIP associated with brassinosteroids and NPF associated with auxin, are upregulated in high-embryogenic ortets. This result suggests a physiological difference between high- and low-embryogenic ortets that is connected to their capacity for somatic embryogenesis. These DEGs will be used as potential biomarkers for high-embryogenic ortets and will be validated in further studies.
Collapse
Affiliation(s)
- Asri Sahara
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk, Bogor, Indonesia
| | - Roberdi Roberdi
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk, Bogor, Indonesia
| | - Ni Made Armini Wiendi
- Agronomy and Horticulture Department, Agriculture Faculty, Bogor Agricultural University, Bogor, Indonesia
| | - Tony Liwang
- Biotechnology Department, Plant Production and Biotechnology Division, PT SMART Tbk, Bogor, Indonesia
| |
Collapse
|
8
|
Wang W, Liu H, Xie Y, King GJ, White PJ, Zou J, Xu F, Shi L. Rapid identification of a major locus qPRL-C06 affecting primary root length in Brassica napus by QTL-seq. ANNALS OF BOTANY 2023; 131:569-583. [PMID: 36181516 PMCID: PMC10147330 DOI: 10.1093/aob/mcac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/30/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Brassica napus is one of the most important oilseed crops worldwide. Seed yield of B. napus significantly correlates with the primary root length (PRL). The aims of this study were to identify quantitative trait loci (QTLs) for PRL in B. napus. METHODS QTL-seq and conventional QTL mapping were jointly used to detect QTLs associated with PRL in a B. napus double haploid (DH) population derived from a cross between 'Tapidor' and 'Ningyou 7'. The identified major locus was confirmed and resolved by an association panel of B. napus and an advanced backcross population. RNA-seq analysis of two long-PRL lines (Tapidor and TN20) and two short-PRL lines (Ningyou 7 and TN77) was performed to identify differentially expressed genes in the primary root underlying the target QTLs. KEY RESULTS A total of 20 QTLs impacting PRL in B. napus grown at a low phosphorus (P) supply were found by QTL-seq. Eight out of ten QTLs affecting PRL at a low P supply discovered by conventional QTL mapping could be detected by QTL-seq. The locus qPRL-C06 identified by QTL-seq was repeatedly detected at both an optimal P supply and a low P supply by conventional QTL mapping. This major constitutive QTL was further confirmed by regional association mapping. qPRL-C06 was delimited to a 0.77 Mb genomic region on chromosome C06 using an advanced backcross population. A total of 36 candidate genes within qPRL-C06 were identified that showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in primary root between the long-PRL and short-PRL lines, including five genes involved in phytohormone biosynthesis and signaling. CONCLUSIONS These results both demonstrate the power of the QTL-seq in rapid QTL detection for root traits and will contribute to marker-assisted selective breeding of B. napus cultivars with increased PRL.
Collapse
Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijiang Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Graham John King
- Southern Cross Plant Science, Southern Cross University, Lismore NSW 2480, Australia
| | - Philip John White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
9
|
Bi Y, Shrestha R, Zhang Z, Hsu CC, Reyes AV, Karunadasa S, Baker PR, Maynard JC, Liu Y, Hakimi A, Lopez-Ferrer D, Hassan T, Chalkley RJ, Xu SL, Wang ZY. SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis. THE PLANT CELL 2023; 35:1318-1333. [PMID: 36739885 PMCID: PMC10118272 DOI: 10.1093/plcell/koad023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
The recent discovery of SPINDLY (SPY)-catalyzed protein O-fucosylation revealed a novel mechanism for regulating nucleocytoplasmic protein functions in plants. Genetic evidence indicates the important roles of SPY in diverse developmental and physiological processes. However, the upstream signal controlling SPY activity and the downstream substrate proteins O-fucosylated by SPY remain largely unknown. Here, we demonstrated that SPY mediates sugar-dependent growth in Arabidopsis (Arabidopsis thaliana). We further identified hundreds of O-fucosylated proteins using lectin affinity chromatography followed by mass spectrometry. All the O-fucosylation events quantified in our proteomic analyses were undetectable or dramatically decreased in the spy mutants, and thus likely catalyzed by SPY. The O-fucosylome includes mostly nuclear and cytosolic proteins. Many O-fucosylated proteins function in essential cellular processes, phytohormone signaling, and developmental programs, consistent with the genetic functions of SPY. The O-fucosylome also includes many proteins modified by O-linked N-acetylglucosamine (O-GlcNAc) and by phosphorylation downstream of the target of rapamycin (TOR) kinase, revealing the convergence of these nutrient signaling pathways on key regulatory functions such as post-transcriptional/translational regulation and phytohormone responses. Our study identified numerous targets of SPY/O-fucosylation and potential nodes of crosstalk among sugar/nutrient signaling pathways, enabling future dissection of the signaling network that mediates sugar regulation of plant growth and development.
Collapse
Affiliation(s)
| | | | | | - Chuan-Chih Hsu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Andres V Reyes
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Sumudu Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Peter R Baker
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jason C Maynard
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
| | - Yang Liu
- ThermoFisher Scientific, San Jose, California 95134, USA
| | | | | | - Tahmid Hassan
- ThermoFisher Scientific, Somerset, New Jersey 08873, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143, USA
| | | | | |
Collapse
|
10
|
Ferela A, Debernardi JM, Rosatti S, Liebsch D, Schommer C, Palatnik JF. Interplay among ZF-HD and GRF transcription factors during Arabidopsis leaf development. PLANT PHYSIOLOGY 2023; 191:1789-1802. [PMID: 36652435 PMCID: PMC10022616 DOI: 10.1093/plphys/kiad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The growth-regulating factor (GRF) family of transcriptional factors are involved in the control of leaf size and senescence, inflorescence and root growth, grain size, and plant regeneration. However, there is limited information about the genes regulated by these transcriptional factors, which are in turn responsible for their functions. Using a meta-analysis approach, we identified genes encoding Arabidopsis (Arabidopsis thaliana) zinc-finger homeodomain (ZF-HD) transcriptional factors, as potential targets of the GRFs. We further showed that GRF3 binds to the promoter of one of the members of the ZF-HD family, HOMEOBOX PROTEIN 33 (HB33), and activates its transcription. Increased levels of HB33 led to different modifications in leaf cell number and size that were dependent on its expression levels. Furthermore, we found that expression of HB33 for an extended period during leaf development increased leaf longevity. To cope with the functional redundancy among ZF-HD family members, we generated a dominant repressor version of HB33, HB33-SRDX. Expression of HB33-SRDX from HB33 regulatory regions was seedling-lethal, revealing the importance of the ZF-HD family in plant development. Misexpression of HB33-SRDX in early leaf development caused a reduction in both cell size and number. Interestingly, the loss-of-function of HB33 in lines carrying a GRF3 allele insensitive to miR396 reverted the delay in leaf senescence characteristic of these plants. Our results revealed functions for ZF-HDs in leaf development and linked them to the GRF pathway.
Collapse
Affiliation(s)
- Antonella Ferela
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Juan Manuel Debernardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Santiago Rosatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Daniela Liebsch
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Carla Schommer
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | | |
Collapse
|
11
|
Li M, Dong H, Li J, Dai X, Lin J, Li S, Zhou C, Chiang VL, Li W. PtrVCS2 Regulates Drought Resistance by Changing Vessel Morphology and Stomatal Closure in Populus trichocarpa. Int J Mol Sci 2023; 24:ijms24054458. [PMID: 36901889 PMCID: PMC10003473 DOI: 10.3390/ijms24054458] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
Drought has severe effects on plant growth, forest productivity, and survival throughout the world. Understanding the molecular regulation of drought resistance in forest trees can enable effective strategic engineering of novel drought-resistant genotypes of tree species. In this study, we identified a gene, PtrVCS2, encoding a zinc finger (ZF) protein of the ZF-homeodomain transcription factor in Populus trichocarpa (Black Cottonwood) Torr. & A. Gray. ex Hook. Overexpression of PtrVCS2 (OE-PtrVCS2) in P. trichocarpa resulted in reduced growth, a higher proportion of smaller stem vessels, and strong drought-resistance phenotypes. Stomatal movement experiments revealed that the OE-PtrVCS2 transgenics showed lower stomata apertures than wild-type plants under drought conditions. RNA-seq analysis of the OE-PtrVCS2 transgenics showed that PtrVCS2 regulates the expression of multiple genes involved in regulation of stomatal opening and closing, particularly the PtrSULTR3;1-1 gene, and several genes related to cell wall biosynthesis, such as PtrFLA11-12 and PtrPR3-3. Moreover, we found that the water use efficiency of the OE-PtrVCS2 transgenic plants was consistently higher than that of wild type plants when subjected to chronic drought stress. Taken together, our results suggest that PtrVCS2 plays a positive role in improving drought adaptability and resistance in P. trichocarpa.
Collapse
Affiliation(s)
- Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Hao Dong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jiaojiao Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Correspondence:
| |
Collapse
|
12
|
Healey AL, Piatkowski B, Lovell JT, Sreedasyam A, Carey SB, Mamidi S, Shu S, Plott C, Jenkins J, Lawrence T, Aguero B, Carrell AA, Nieto-Lugilde M, Talag J, Duffy A, Jawdy S, Carter KR, Boston LB, Jones T, Jaramillo-Chico J, Harkess A, Barry K, Keymanesh K, Bauer D, Grimwood J, Gunter L, Schmutz J, Weston DJ, Shaw AJ. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. NATURE PLANTS 2023; 9:238-254. [PMID: 36747050 PMCID: PMC9946827 DOI: 10.1038/s41477-022-01333-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/13/2022] [Indexed: 06/18/2023]
Abstract
Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates. Sphagnum (peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of two Sphagnum species: S. divinum and S. angustifolium. Sphagnum genomes show no gene colinearity with any other reference genome to date, demonstrating that Sphagnum represents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability of Sphagnum to sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment.
Collapse
Affiliation(s)
- Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sarah B Carey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Travis Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jayson Talag
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kelsey R Carter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Lori-Beth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Teresa Jones
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Keykhosrow Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Diane Bauer
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Lee Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | | |
Collapse
|
13
|
Shi B, Haq IU, Fiaz S, Alharthi B, Xu ML, Wang JL, Hou WH, Feng XB. Genome-wide identification and expression analysis of the ZF-HD gene family in pea ( Pisum sativum L.). Front Genet 2023; 13:1089375. [PMID: 36685917 PMCID: PMC9849798 DOI: 10.3389/fgene.2022.1089375] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.
Collapse
Affiliation(s)
- Bowen Shi
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, Saudi Arabia
| | - Ming-Long Xu
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Jian-Lin Wang
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Wei-Hai Hou
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
| | - Xi-Bo Feng
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
| |
Collapse
|
14
|
Dai X, Zhai R, Lin J, Wang Z, Meng D, Li M, Mao Y, Gao B, Ma H, Zhang B, Sun Y, Li S, Zhou C, Lin YCJ, Wang JP, Chiang VL, Li W. Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa. NATURE PLANTS 2023; 9:96-111. [PMID: 36624255 PMCID: PMC9873556 DOI: 10.1038/s41477-022-01315-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 11/17/2022] [Indexed: 05/20/2023]
Abstract
Stem vascular cambium cells in forest trees produce wood for materials and energy. WOX4 affects the proliferation of such cells in Populus. Here we show that PtrWOX4a is the most highly expressed stem vascular-cambium-specific (VCS) gene in P. trichocarpa, and its expression is controlled by the product of the second most highly expressed VCS gene, PtrVCS2, encoding a zinc finger protein. PtrVCS2 binds to the PtrWOX4a promoter as part of a PtrWOX13a-PtrVCS2-PtrGCN5-1-PtrADA2b-3 protein tetramer. PtrVCS2 prevented the interaction between PtrGCN5-1 and PtrADA2b-3, resulting in H3K9, H3K14 and H3K27 hypoacetylation at the PtrWOX4a promoter, which led to fewer cambium cell layers. These effects on cambium cell proliferation were consistent across more than 20 sets of transgenic lines overexpressing individual genes, gene-edited mutants and RNA interference lines in P. trichocarpa. We propose that the tetramer-PtrWOX4a system may coordinate genetic and epigenetic regulation to maintain normal vascular cambium development for wood formation.
Collapse
Affiliation(s)
- Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Zhai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jiaojiao Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dekai Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Meng Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuli Mao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.
| |
Collapse
|
15
|
Kushwaha AK, Dwivedi S, Mukherjee A, Lingwan M, Dar MA, Bhagavatula L, Datta S. Plant microProteins: Small but powerful modulators of plant development. iScience 2022; 25:105400. [PMID: 36353725 PMCID: PMC9638782 DOI: 10.1016/j.isci.2022.105400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MicroProteins (miPs) are small and single-domain containing proteins of less than 20 kDa. This domain allows microProteins to interact with compatible domains of evolutionary-related proteins and fine-tuning the key physiological pathways in several organisms. Since the first report of a microProtein in mice, numerous microProteins have been identified in plants by computational approaches. However, only a few candidates have been functionally characterized, primarily in Arabidopsis. The recent success of synthetic microProteins in modulating physiological activities in crops makes these proteins interesting candidates for crop engineering. Here, we comprehensively summarise the synthesis, mode of action, and functional roles of microProteins in plants. We also discuss different approaches used to identify plant microProteins. Additionally, we discuss novel approaches to design synthetic microProteins that can be used to target proteins regulating plant growth and development. We finally highlight the prospects and challenges of utilizing microProteins in future crop improvement programs. MicroProteins (miPs) are small-sized proteins with a molecular weight of 5–20 kDa MiPs can be detected through multiomics and computational approaches MiPs are crucial regulators of plant growth and development MiPs as condensates, synthetic miPs, and limitations
Collapse
|
16
|
Agisha V, Ashwin N, Vinodhini R, Nalayeni K, Ramesh Sundar A, Malathi P, Viswanathan R. Transcriptome analysis of sugarcane reveals differential switching of major defense signaling pathways in response to Sporisorium scitamineum isolates with varying virulent attributes. FRONTIERS IN PLANT SCIENCE 2022; 13:969826. [PMID: 36325538 PMCID: PMC9619058 DOI: 10.3389/fpls.2022.969826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
Sugarcane smut caused by the basidiomycetous fungus Sporisorium scitamineum is one of the most devastating diseases that affect sugarcane production, globally. At present, the most practical and effective management strategy for the disease is the cultivation of resistant cultivars. In this connection, a detailed understanding of the host’s defense mechanism in response to smut isolates with varying degrees of virulence at the molecular level would facilitate the development of reliable and durable smut-resistant sugarcane varieties. Hence, in this study, a comparative whole transcriptome analysis was performed employing Illumina RNA-seq in the smut susceptible cultivar Co 97009 inoculated with two distinct S. scitamineum isolates, Ss97009 (high-virulent) and SsV89101 (low-virulent) during the early phases of infection (2 dpi and 5 dpi) and at the phase of sporogenesis (whip emergence) (60 dpi). Though the differential gene expression profiling identified significant transcriptional changes during the early phase of infection in response to both the isolates, the number of differentially expressed genes (DEGs) were more abundant at 60 dpi during interaction with the high virulent isolate Ss97009, as compared to the low virulent isolate SsV89101. Functional analysis of these DEGs revealed that a majority of them were associated with hormone signaling and the synthesis of defense-related metabolites, suggesting a complex network of defense mechanisms is being operated in response to specific isolates of the smut pathogen. For instance, up-regulation of hormone-related genes, transcription factors, and flavonoid biosynthesis pathway genes was observed in response to both the isolates in the early phase of interaction. In comparison to early phases of infection, only a few pathogenesis-related proteins were up-regulated at 60 dpi in response to Ss97009, which might have rendered the host susceptible to infection. Strikingly, few other carbohydrate metabolism-associated genes like invertases were up-regulated in Ss97009 inoculated plants during the whip emergence stage, representing a shift from sucrose storage to smut symptoms. Altogether, this study established the major switching of defense signaling pathways in response to S. scitamineum isolates with different virulence attributes and provided novel insights into the molecular mechanisms of sugarcane-smut interaction.
Collapse
|
17
|
Bollier N, Gonzalez N, Chevalier C, Hernould M. Zinc Finger-Homeodomain and Mini Zinc Finger proteins are key players in plant growth and responses to environmental stresses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4662-4673. [PMID: 35536651 DOI: 10.1093/jxb/erac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
The ZINC FINGER-HOMEODOMAIN (ZHD) protein family is a plant-specific family of transcription factors containing two conserved motifs: a non-canonical C5H3 zinc finger domain (ZF) and a DNA-binding homeodomain (HD). The MINI ZINC FINGER (MIF) proteins belong to this family, but were possibly derived from the ZHDs by losing the HD. Information regarding the function of ZHD and MIF proteins is scarce. However, different studies have shown that ZHD/MIF proteins play important roles not only in plant growth and development, but also in response to environmental stresses, including drought and pathogen attack. Here we review recent advances relative to ZHD/MIF functions in multiple species, to provide new insights into the diverse roles of these transcription factors in plants. Their mechanism of action in relation to their ability to interact with other proteins and DNA is also discussed. We then propose directions for future studies to understand better their important roles and pinpoint strategies for potential applications in crop improvement.
Collapse
Affiliation(s)
- Norbert Bollier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Nathalie Gonzalez
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Christian Chevalier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| | - Michel Hernould
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33882 Villenave d'Ornon, France
| |
Collapse
|
18
|
Lee YK, Kumari S, Olson A, Hauser F, Ware D. Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. Int J Mol Sci 2022; 23:ijms23158665. [PMID: 35955798 PMCID: PMC9369202 DOI: 10.3390/ijms23158665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.
Collapse
Affiliation(s)
- Young Koung Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37, Dongjangsan-ro, Gunsan-si 54004, Korea
- Correspondence: (Y.K.L.); (D.W.)
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Felix Hauser
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA
- Correspondence: (Y.K.L.); (D.W.)
| |
Collapse
|
19
|
Tasaki K, Watanabe A, Nemoto K, Takahashi S, Goto F, Sasaki N, Hikage T, Nishihara M. Identification of Candidate Genes Responsible for Flower Colour Intensity in Gentiana triflora. FRONTIERS IN PLANT SCIENCE 2022; 13:906879. [PMID: 35812931 PMCID: PMC9257217 DOI: 10.3389/fpls.2022.906879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Gentians cultivated in Japan (Gentiana triflora and Gentiana scabra and hybrids) have blue flowers, but flower colour intensity differs among cultivars. The molecular mechanism underlying the variation in flower colour intensity is unclear. Here, we produced F2 progeny derived from an F1 cross of intense- and faint-blue lines and attempted to identify the genes responsible for flower colour intensity using RNA-sequencing analyses. Comparative analysis of flower colour intensity and transcriptome data revealed differentially expressed genes (DEGs), although known flavonoid biosynthesis-related genes showed similar expression patterns. From quantitative RT-PCR (qRT-PCR) analysis, we identified two and four genes with significantly different expression levels in the intense- and faint-blue flower lines, respectively. We conducted further analyses on one of the DEGs, termed GtMIF1, which encodes a putative mini zinc-finger protein homolog, which was most differently expressed in faint-blue individuals. Functional analysis of GtMIF1 was performed by producing stable tobacco transformants. GtMIF1-overexpressing tobacco plants showed reduced flower colour intensity compared with untransformed control plants. DNA-marker analysis also confirmed that the GtMIF1 allele of the faint-blue flower line correlated well with faint flower colour in F2 progeny. These results suggest that GtMIF1 is one of the key genes involved in determining the flower colour intensity of gentian.
Collapse
Affiliation(s)
| | - Aiko Watanabe
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | | | - Fumina Goto
- Iwate Biotechnology Research Center, Kitakami, Japan
| | | | - Takashi Hikage
- Hachimantai City Floricultural Research and Development Center, Hachimantai, Japan
| | | |
Collapse
|
20
|
He K, Li C, Zhang Z, Zhan L, Cong C, Zhang D, Cai H. Genome-wide investigation of the ZF-HD gene family in two varieties of alfalfa (Medicago sativa L.) and its expression pattern under alkaline stress. BMC Genomics 2022; 23:150. [PMID: 35189832 PMCID: PMC8859888 DOI: 10.1186/s12864-022-08309-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/07/2022] [Indexed: 11/11/2022] Open
Abstract
Background Zinc finger homeodomain (ZHD) protein is a plant-specific transcription factor and a potential regulator of phosphoenolpyruvate carboxylase (PEPCase)-coding genes, and it also participates in plant growth regulation and abiotic stress responses. To study the function of MsZF-HD genes in the alkaline stress response, this paper assessed biological information and performed transcriptome analysis of the MsZF-HD gene family by using the genomes of two different varieties of alfalfa (XinJiangDa Ye and Zhongmu No. 1). Results In total, 49 and 11 MsZF-HD genes were identified in the two different varieties respectively, including the alleles of XinJiangDa Ye. According to their phylogenetic relationships, the 60 MsZF-HD genes were divided into 5 ZHD subfamilies and 1 MIF subfamily. A total of 88.3% of MsZF-HD genes do not contain introns and are unevenly distributed among the 6 chromosomes of alfalfa. A collinearity analysis indicated that 26 genes of XinJiangDa Ye have no orthologous genes in Zhongmu No. 1, although these genes (such as ZHD-X1–2, ZHD-X3–2 and ZHD-X4–2) have homologous genes in Arabidopsis thaliana, Medicago truncatula and Glycine max. Through RNA-seq and qRT–PCR verification, it was found that MsZF-HD genes are downregulated to participate in the alkaline stress response. Conclusion The results of this study may lay the foundation for the cloning and functional study of MsZF-HD genes and provide a theoretical basis for revealing the difference between XinJiangDa Ye and Zhongmu No. 1 at the genome level. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08309-x.
Collapse
Affiliation(s)
- Kai He
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Chunxin Li
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Zhenyue Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Lifeng Zhan
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Chunlong Cong
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Depeng Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Hua Cai
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
21
|
Zheng XB, Wu Y, Wang H, Song SW, Bai TH, Jiao J, Song CH, Pang HG, Wang MM. Genome-Wide Investigation of the Zinc Finger-Homeodomain Family Genes Reveals Potential Roles in Apple Fruit Ripening. Front Genet 2022; 12:783482. [PMID: 35111199 PMCID: PMC8802310 DOI: 10.3389/fgene.2021.783482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/22/2021] [Indexed: 11/17/2022] Open
Abstract
Zinc finger-homeodomain (ZF-HD) transcription factors play an important role in the regulation of plant growth and development, as well as the regulation of stress responses. Studies on the ZF-HD family genes have been conducted in many plants, however, the characteristics of this family in apple (Malus domestica) fruit remains to be poorly understood. In this study, we identified nineteen ZF-HD family genes in apple at the whole-genome scale, which were unevenly located on ten chromosomes. These MdZF-HD genes were phylogenetically divided into two subfamilies: zinc finger-homeodomain (ZHD) and MINI ZINC FINGER (MIF), and the ZHD subfamily was further classified into five groups (ZHDI–ZHDV). Analysis of the gene structures showed that most MdZF-HD genes lack introns. Gene expression analysis indicated that nine selected MdZF-HD genes were differentially responsive to 1-MCP (1-methylcyclopropene) treatment during the postharvest storage of “Qinguan” apple fruit. Moreover, the transcripts of six genes were further validated in “Golden Delicious” apple fruit, and five genes (MdZHD1/2/6/10/11) were significantly repressed and one gene (MdZHD7) was slightly induced by ethylene treatment. These results indicated that these six MdZF-HD genes may involve in the regulation of ethylene induced ripening process of postharvest apple fruit. These findings provide new clues for further functional investigation of ZF-HD genes, such as their roles in the regulation of fruit ripening.
Collapse
|
22
|
Wang Y, Wang Y, Yang R, Wang F, Fu J, Yang W, Bai T, Wang S, Yin H. Effects of gibberellin priming on seedling emergence and transcripts involved in mesocotyl elongation in rice under deep direct-seeding conditions. J Zhejiang Univ Sci B 2021; 22:1002-1021. [PMID: 34904413 DOI: 10.1631/jzus.b2100174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mesocotyl elongation is a key trait influencing seedling emergence and establishment in direct-seeding rice cultivation. The phytohormone gibberellin (GA) has positive effects on mesocotyl elongation in rice. However, the physiological and molecular basis underlying the regulation of mesocotyl elongation mediated by GA priming under deep-sowing conditions remains largely unclear. In the present study, we performed a physiological and comprehensive transcriptomic analysis of the function of GA priming in mesocotyl elongation and seedling emergence using a direct-seeding japonica rice cultivar ZH10 at a 5-cm sowing depth. Physiological experiments indicated that GA priming significantly improved rice seedling emergence by increasing the activity of starch-metabolizing enzymes and compatible solute content to supply the energy essential for subsequent development. Transcriptomic analysis revealed 7074 differentially expressed genes (false discovery rate of <0.05, |log2(fold change)| of ≥1) after GA priming. Furthermore, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses revealed that genes associated with transcriptional regulation, plant hormone biosynthesis or signaling, and starch and sucrose metabolism were critical for GA-mediated promotion of rice mesocotyl elongation. Further analyses showed that the expression of the transcription factor (TF) genes (v-myb avian myeloblastosis viral oncogene homolog (MYB) alternative splicing 1 (MYBAS1), phytochrome-interacting factors 1 (PIF1), Oryza sativa teosinte branched 1/cycloidea/proliferating cell factor 5 (OsTCP5), slender 1 (SLN1), and mini zinc finger 1 (MIF1)), plant hormone biosynthesis or signaling genes (brassinazole-resistant 1 (BZR1), ent-kaurenoic acid oxidase-like (KAO), GRETCHEN HAGEN 3.2 (GH3.2), and small auxin up RNA 36 (SAUR36)), and starch and sucrose metabolism genes (α-amylases (AMY2A and AMY1.4)) was highly correlated with the mesocotyl elongation and deep-sowing tolerance response. These results enhance our understanding of how nutrient metabolism-related substances and genes regulate rice mesocotyl elongation. This may facilitate future studies on related genes and the development of novel rice varieties tolerant to deep sowing.
Collapse
Affiliation(s)
- Ya Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yuetao Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ruifang Yang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Fuhua Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jing Fu
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenbo Yang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tao Bai
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Shengxuan Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Haiqing Yin
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| |
Collapse
|
23
|
Niu H, Xia P, Hu Y, Zhan C, Li Y, Gong S, Li Y, Ma D. Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis. PLoS One 2021; 16:e0256579. [PMID: 34559835 PMCID: PMC8462724 DOI: 10.1371/journal.pone.0256579] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/11/2021] [Indexed: 12/04/2022] Open
Abstract
ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.
Collapse
Affiliation(s)
- Hongli Niu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Pengliang Xia
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Yifeng Hu
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Chuang Zhan
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yiting Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Shuangjun Gong
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
| | - Yan Li
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- * E-mail: (YL); (DM)
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture/Hubei Province Key Laboratory for Control of Crop Diseases, Pest and Weeds/Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (YL); (DM)
| |
Collapse
|
24
|
Vannozzi A, Palumbo F, Magon G, Lucchin M, Barcaccia G. The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases. HORTICULTURE RESEARCH 2021; 8:200. [PMID: 34465729 PMCID: PMC8408131 DOI: 10.1038/s41438-021-00635-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The comprehension of molecular processes underlying the development and progression of flowering in plants is a hot topic, not only because that often the products of interest for human and animal nutrition are linked to the development of fruits or seeds, but also because the processes of gametes formation occurring in sexual organs are at the basis of recombination and genetic variability which constitutes the matter on which evolution acts, whether understood as natural or human driven. In the present study, we used an NGS approach to produce a grapevine flower transcriptome snapshot in different whorls and tissues including calyx, calyptra, filament, anther, stigma, ovary, and embryo in both pre- and post-anthesis phases. Our investigation aimed at identifying hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development. To this end we have used different analytical approaches, some now consolidated in transcriptomic studies on plants, such as pairwise comparison and weighted-gene coexpression network analysis, others used mainly in studies on animals or human's genomics, such as the tau (τ) analysis aimed at isolating highly and absolutely tissue-specific genes. The intersection of data obtained by these analyses allowed us to gradually narrow the field, providing evidence about the molecular mechanisms occurring in those whorls directly involved in reproductive processes, such as anther and stigma, and giving insights into the role of other whorls not directly related to reproduction, such as calyptra and calyx. We believe this work could represent an important genomic resource for functional analyses of grapevine floral organ growth and fruit development shading light on molecular networks underlying grapevine reproductive organ determination.
Collapse
Affiliation(s)
- Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Campus of Agripolis, V. le dell'Università 16, 35020, Legnaro, Padova, Italy.
| |
Collapse
|
25
|
Arrey-Salas O, Caris-Maldonado JC, Hernández-Rojas B, Gonzalez E. Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine ( Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation. Genes (Basel) 2021; 12:302. [PMID: 33672655 PMCID: PMC7924211 DOI: 10.3390/genes12020302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/02/2023] Open
Abstract
Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte development, we performed a genome-wide identification and characterization of genes encoding ZFP (VviZFP family). A total of 98 genes were identified and renamed based on the gene distribution into grapevine genome. The analysis performed indicate significant changes throughout VviZFP genes evolution explained by high heterogeneity in sequence, length, number of ZF and presence of another conserved domains. Moreover, segmental duplication participated in the gene family expansion in grapevine. The VviZFPs were classified based on domain and phylogenetic analysis into three sets and different groups. Heat-map demonstrated differential and tissue-specific expression patterns of these genes and k-means clustering allowed to identify a group of putative orthologs to some ZFPs related to pollen development. In transgenic plants carrying the promVviZFP13::GUS and promVviZFP68::GUS constructs, GUS signals were detectable in the anther and mature pollen grains. Expression profiling of selected VviZFP genes showed differential expression pattern during flower development and provides a basis for deepening in the understanding of VviZFPs role on grapevine reproductive development.
Collapse
Affiliation(s)
- Oscar Arrey-Salas
- Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
| | | | - Bairon Hernández-Rojas
- Ph.D Program in Sciences Mention in Modeling of Chemical and Biological Systems, Faculty of Engineering, University of Talca, Calle 1 Poniente, 1141, 3462227 Talca, Chile;
| | - Enrique Gonzalez
- Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile;
| |
Collapse
|
26
|
Li L, Zhang Y, Zheng T, Zhuo X, Li P, Qiu L, Liu W, Wang J, Cheng T, Zhang Q. Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume. Sci Rep 2021; 11:2675. [PMID: 33514804 PMCID: PMC7846751 DOI: 10.1038/s41598-021-81892-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 01/13/2021] [Indexed: 11/23/2022] Open
Abstract
Prunus mume (also known as Mei) is an important ornamental plant that is popular with Asians. The weeping trait in P. mume has attracted the attention of researchers for its high ornamental value. However, the formation of the weeping trait of woody plants is a complex process and the molecular basis of weeping stem development is unclear. Here, the morphological and histochemical characteristics and transcriptome profiles of upright and weeping stems from P. mume were studied. Significant alterations in the histochemical characteristics of upright and weeping stems were observed, and the absence of phloem fibres and less xylem in weeping stems might be responsible for their inability to resist gravity and to grow downward. Transcriptome analysis showed that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and phytohormone signal transduction pathways. To investigate the differential responses to hormones, upright and weeping stems were treated with IAA (auxin) and GA3 (gibberellin A3), respectively, and the results revealed that weeping stems had a weaker IAA response ability and reduced upward bending angles than upright stems. On the contrary, weeping stems had increased upward bending angles than upright stems with GA3 treatment. Compared to upright stems, interestingly, DEGs associated with diterpenoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched after being treated with IAA, and expression levels of genes associated with phenylpropanoid biosynthesis, ABC transporters, glycosylphosphatidylinositol (GPI)—anchor biosynthesis were altered after being treated with GA3 in weeping stems. Those results reveal that multiple molecular mechanisms regulate the formation of weeping trait in P. mume, which lays a theoretical foundation for the cultivation of new varieties.
Collapse
Affiliation(s)
- Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Like Qiu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Weichao Liu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
27
|
Vercruysse J, Baekelandt A, Gonzalez N, Inzé D. Molecular networks regulating cell division during Arabidopsis leaf growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2365-2378. [PMID: 31748815 PMCID: PMC7178401 DOI: 10.1093/jxb/erz522] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 05/02/2023]
Abstract
Leaves are the primary organs for photosynthesis, and as such have a pivotal role for plant growth and development. Leaf development is a multifactorial and dynamic process involving many genes that regulate size, shape, and differentiation. The processes that mainly drive leaf development are cell proliferation and cell expansion, and numerous genes have been identified that, when ectopically expressed or down-regulated, increase cell number and/or cell size during leaf growth. Many of the genes regulating cell proliferation are functionally interconnected and can be grouped into regulatory modules. Here, we review our current understanding of six important gene regulatory modules affecting cell proliferation during Arabidopsis leaf growth: ubiquitin receptor DA1-ENHANCER OF DA1 (EOD1), GROWTH REGULATING FACTOR (GRF)-GRF-INTERACTING FACTOR (GIF), SWITCH/SUCROSE NON-FERMENTING (SWI/SNF), gibberellin (GA)-DELLA, KLU, and PEAPOD (PPD). Furthermore, we discuss how post-mitotic cell expansion and these six modules regulating cell proliferation make up the final leaf size.
Collapse
Affiliation(s)
- Jasmien Vercruysse
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Alexandra Baekelandt
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, Villenave d’Ornon cedex, France
| | - Dirk Inzé
- Center for Plant Systems Biology, VIB, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- Correspondence:
| |
Collapse
|
28
|
Golicz AA, Steinfort U, Arya H, Singh MB, Bhalla PL. Analysis of the quinoa genome reveals conservation and divergence of the flowering pathways. Funct Integr Genomics 2020; 20:245-258. [PMID: 31515641 PMCID: PMC7018680 DOI: 10.1007/s10142-019-00711-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 01/09/2023]
Abstract
Quinoa (Chenopodium quinoa Willd.) is a grain crop grown in the Andes renowned as a highly nutritious plant exhibiting tolerance to abiotic stress such as drought, cold and high salinity. Quinoa grows across a range of latitudes corresponding to differing day lengths, suggesting regional adaptations of flowering regulation. Improved understanding and subsequent modification of the flowering process, including flowering time, ensuring high yields, is one of the key factors behind expansion of cultivation zones and goals of the crop improvement programs worldwide. However, our understanding of the molecular basis of flower initiation and development in quinoa is limited. Here, we use a computational approach to perform genome-wide identification and analysis of 611 orthologues of the Arabidopsis thaliana flowering genes. Conservation of the genes belonging to the photoperiod, gibberellin and autonomous pathways was observed, while orthologues of the key genes found in the vernalisation pathway (FRI, FLC) were absent from the quinoa genome. Our analysis indicated that on average each Arabidopsis flowering gene has two orthologous copies in quinoa. Several genes including orthologues of MIF1, FT and TSF were identified as homologue-rich genes in quinoa. We also identified 459 quinoa-specific genes uniquely expressed in the flower and/or meristem, with no known orthologues in other species. The genes identified provide a resource and framework for further studies of flowering in quinoa and related species. It will serve as valuable resource for plant biologists, crop physiologists and breeders to facilitate further research and establishment of modern breeding programs for quinoa.
Collapse
Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Ursula Steinfort
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile.
| | - Hina Arya
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia
| |
Collapse
|
29
|
Guillaumie S, Decroocq S, Ollat N, Delrot S, Gomès E, Cookson SJ. Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators. BMC PLANT BIOLOGY 2020; 20:43. [PMID: 31996141 PMCID: PMC6988314 DOI: 10.1186/s12870-020-2258-0] [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: 07/06/2019] [Accepted: 01/20/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Grapevine is a crop of major economic importance, yet little is known about the regulation of shoot development in grapevine or other perennial fruits crops. Here we combine genetic and genomic tools to identify candidate genes regulating shoot development in Vitis spp. RESULTS An F2 population from an interspecific cross between V. vinifera and V. riparia was phenotyped for shoot development traits, and three Quantitative Trait Loci (QTLs) were identified on linkage groups (LGs) 7, 14 and 18. Around 17% of the individuals exhibited a dwarfed phenotype. A transcriptomic study identified four candidate genes that were not expressed in dwarfed individuals and located within the confidence interval of the QTL on LG7. A deletion of 84,482 bp was identified in the genome of dwarfed plants, which included these four not expressed genes. One of these genes was VviCURLY LEAF (VviCLF), an orthologue of CLF, a regulator of shoot development in Arabidopsis thaliana. CONCLUSIONS The phenotype of the dwarfed grapevine plants was similar to that of clf mutants of A. thaliana and orthologues of the known targets of CLF in A. thaliana were differentially expressed in the dwarfed plants. This suggests that CLF, a major developmental regulator in A. thaliana, also controls shoot development in grapevine.
Collapse
Affiliation(s)
- Sabine Guillaumie
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France.
| | - Stéphane Decroocq
- UMR1332 BFP, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Nathalie Ollat
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Serge Delrot
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Eric Gomès
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| | - Sarah J Cookson
- UMR1287 EGFV, Bordeaux Sciences Agro, INRAE, University of Bordeaux, Villenave d'Ornon, France
| |
Collapse
|
30
|
Amini S, Rosli K, Abu-Bakar MF, Alias H, Mat-Isa MN, Juhari MAA, Haji-Adam J, Goh HH, Wan KL. Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development. PLoS One 2019; 14:e0226338. [PMID: 31851702 PMCID: PMC6919626 DOI: 10.1371/journal.pone.0226338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/25/2019] [Indexed: 11/19/2022] Open
Abstract
Rafflesia possesses unique biological features and known primarily for producing the world’s largest and existing as a single flower. However, to date, little is known about key regulators participating in Rafflesia flower development. In order to further understand the molecular mechanism that regulates Rafflesia cantleyi flower development, RNA-seq data from three developmental stages of floral bud, representing the floral organ primordia initiation, floral organ differentiation, and floral bud outgrowth, were analysed. A total of 89,890 transcripts were assembled of which up to 35% could be annotated based on homology search. Advanced transcriptome analysis using K-mean clustering on the differentially expressed genes (DEGs) was able to identify 12 expression clusters that reflect major trends and key transitional states, which correlate to specific developmental stages. Through this, comparative gene expression analysis of different floral bud stages identified various transcription factors related to flower development. The members of WRKY, NAC, bHLH, and MYB families are the most represented among the DEGs, suggesting their important function in flower development. Furthermore, pathway enrichment analysis also revealed DEGs that are involved in various phytohormone signal transduction events such as auxin and auxin transport, cytokinin and gibberellin biosynthesis. Results of this study imply that transcription factors and phytohormone signalling pathways play major role in Rafflesia floral bud development. This study provides an invaluable resource for molecular studies of the flower development process in Rafflesia and other plant species.
Collapse
Affiliation(s)
- Safoora Amini
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Khadijah Rosli
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | | | - Halimah Alias
- Malaysia Genome Institute, Jalan Bangi, Kajang, Selangor, Malaysia
| | | | - Mohd-Afiq-Aizat Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Jumaat Haji-Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- * E-mail:
| |
Collapse
|
31
|
The flowering hormone florigen accelerates secondary cell wall biogenesis to harmonize vascular maturation with reproductive development. Proc Natl Acad Sci U S A 2019; 116:16127-16136. [PMID: 31324744 DOI: 10.1073/pnas.1906405116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Florigen, a proteinaceous hormone, functions as a universal long-range promoter of flowering and concurrently as a generic growth-attenuating hormone across leaf and stem meristems. In flowering plants, the transition from the vegetative phase to the reproductive phase entails the orchestration of new growth coordinates and a global redistribution of resources, signals, and mechanical loads among organs. However, the ultimate cellular processes governing the adaptation of the shoot system to reproduction remain unknown. We hypothesized that if the mechanism for floral induction is universal, then the cellular metabolic mechanisms underlying the conditioning of the shoot system for reproduction would also be universal and may be best regulated by florigen itself. To understand the cellular basis for the vegetative functions of florigen, we explored the radial expansion of tomato stems. RNA-Seq and complementary genetic and histological studies revealed that florigen of endogenous, mobile, or induced origins accelerates the transcription network navigating secondary cell wall biogenesis as a unit, promoting vascular maturation and thereby adapting the shoot system to the developmental needs of the ensuing reproductive phase it had originally set into motion. We then demonstrated that a remarkably stable and broadly distributed florigen promotes MADS and MIF genes, which in turn regulate the rate of vascular maturation and radial expansion of stems irrespective of flowering or florigen level. The dual acceleration of flowering and vascular maturation by florigen provides a paradigm for coordinated regulation of independent global developmental programs.
Collapse
|
32
|
Roodt D, Li Z, Van de Peer Y, Mizrachi E. Loss of Wood Formation Genes in Monocot Genomes. Genome Biol Evol 2019; 11:1986-1996. [PMID: 31173081 PMCID: PMC6644875 DOI: 10.1093/gbe/evz115] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2019] [Indexed: 12/23/2022] Open
Abstract
Woodiness (secondary xylem derived from vascular cambium) has been gained and lost multiple times in the angiosperms, but has been lost ancestrally in all monocots. Here, we investigate the conservation of genes involved in xylogenesis in fully sequenced angiosperm genomes, hypothesizing that monocots have lost some essential orthologs involved in this process. We analyzed the conservation of genes preferentially expressed in the developing secondary xylem of two eudicot trees in the sequenced genomes of 26 eudicot and seven monocot species, and the early diverging angiosperm Amborella trichopoda. We also reconstructed a regulatory model of early vascular cambial cell identity and differentiation and investigated the conservation of orthologs across the angiosperms. Additionally, we analyzed the genome of the aquatic seagrass Zostera marina for additional losses of genes otherwise essential to, especially, secondary cell wall formation. Despite almost complete conservation of orthology within the early cambial differentiation gene network, we show a clear pattern of loss of genes preferentially expressed in secondary xylem in the monocots that are highly conserved across eudicot species. Our study provides candidate genes that may have led to the loss of vascular cambium in the monocots, and, by comparing terrestrial angiosperms to an aquatic monocot, highlights genes essential to vasculature on land.
Collapse
Affiliation(s)
- Danielle Roodt
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
- Genomics Research Institute, University of Pretoria, South Africa
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Belgium
| | - Yves Van de Peer
- Genomics Research Institute, University of Pretoria, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Belgium
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, South Africa
- Genomics Research Institute, University of Pretoria, South Africa
| |
Collapse
|
33
|
Noman A, Aqeel M, Khalid N, Islam W, Sanaullah T, Anwar M, Khan S, Ye W, Lou Y. Zinc finger protein transcription factors: Integrated line of action for plant antimicrobial activity. Microb Pathog 2019; 132:141-149. [PMID: 31051192 DOI: 10.1016/j.micpath.2019.04.042] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 03/11/2019] [Accepted: 04/29/2019] [Indexed: 11/17/2022]
Abstract
The plants resist/tolerate unfavorable conditions in their natural habitats by using different but aligned and integrated defense mechanisms. Such defense responses include not only morphological and physiological adaptations but also the genomic and transcriptomic reconfiguration. Microbial attack on plants activates multiple pro-survival pathways such as transcriptional reprogramming, hypersensitive response (HR), antioxidant defense system and metabolic remodeling. Up-regulation of these processes during biotic stress conditions directly relates with plant survival. Over the years, hundreds of plant transcription factors (TFs) belonging to diverse families have been identified. Zinc finger protein (ZFP) TFs have crucial role in phytohormone response, plant growth and development, stress tolerance, transcriptional regulation, RNA binding and protein-protein interactions. Recent research progress has revealed regulatory and biological functions of ZFPs in incrementing plant resistance to pathogens. Integration of transcriptional activity with metabolic modulations has miniaturized plant innate immunity. However, the precise roles of different zinc finger TFs in plant immunity to pathogens have not been thoroughly analyzed. This review consolidates the pivotal functioning of zinc finger TFs and proposes the integrative understanding as foundation for the plant growth and development including the stress responses.
Collapse
Affiliation(s)
- Ali Noman
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China; Department of Botany, Government College University, Faisalabad, Pakistan; College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, PR China.
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Science, Lanzhou University, Lanzhou, Gansu, PR China
| | - Noreen Khalid
- Department of Botany, Government College Women University, Sialkot, Pakistan
| | - Waqar Islam
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, 350007, China; Institute of Geography, Fujian Normal University, Fuzhou, 350007, China
| | - Tayyaba Sanaullah
- Institute of Pure and Applied Biology, Bahaud Din Zakria University, Multan, Pakistan
| | - Muhammad Anwar
- College of Life Science and Oceanology, Shenzhen University, Shenzhen, PR China
| | - Shahbaz Khan
- College of Agriculture, Shangxi Agricultural University, Jinzhong, PR China
| | - Wenfeng Ye
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China
| | - Yonggen Lou
- Institute of Insect Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, PR China.
| |
Collapse
|
34
|
Janková Drdová E, Klejchová M, Janko K, Hála M, Soukupová H, Cvrčková F, Žárský V. Developmental plasticity of Arabidopsis hypocotyl is dependent on exocyst complex function. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1255-1265. [PMID: 30649396 PMCID: PMC6382343 DOI: 10.1093/jxb/erz005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/15/2018] [Accepted: 12/21/2018] [Indexed: 05/08/2023]
Abstract
The collet (root-hypocotyl junction) region is an important plant transition zone between soil and atmospheric environments. Despite its crucial importance for plant development, little is known about how this transition zone is specified. Here we document the involvement of the exocyst complex in this process. The exocyst, an octameric tethering complex, participates in secretion and membrane recycling and is central to numerous cellular and developmental processes, such as growth of root hairs, cell expansion, recycling of PIN auxin efflux carriers and many others. We show that dark-grown Arabidopsis mutants deficient in exocyst subunits can form a hair-bearing ectopic collet-like structure above the true collet, morphologically resembling the true collet but also retaining some characteristics of the hypocotyl. The penetrance of this phenotypic defect is significantly influenced by cultivation temperature and carbon source, and is related to a defect in auxin regulation. These observations provide new insights into the regulation of collet region formation and developmental plasticity of the hypocotyl.
Collapse
Affiliation(s)
- Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague 2, Czech Republic
- Correspondence:
| | - Martina Klejchová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
| | - Michal Hála
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Hana Soukupová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Viktor Žárský
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague 2, Czech Republic
| |
Collapse
|
35
|
Vyacheslavova AO, Abdeeva IA, Piruzian ES, Bruskin SA. Protein interference for regulation of gene expression in plants. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription factors (TFs) play a central role in the gene regulation associated with a plant's development and its response to the environmental factors. The work of TFs is well regulated at each stage of their activities. TFs usually consist of three protein domains required for DNA binding, dimerization, and transcriptional regulation. Alternative splicing (AS) produces multiple proteins with varying composition of domains. Recent studies have shown that AS of some TF genes form small proteins (small interfering peptide/small interfering protein, siPEP/siPRoT), which lack one or more domains and negatively regulate target TFs by the mechanism of protein interference (peptide interference/protein interference, PEPi/PROTi). The presence of an alternative form for the transcription factor CCA1 of Arabidopsis thaliana, has been shown to be involved in the regulation of the response to cold stress. For the PtFLC protein, one of the isoforms was found, which is formed as a result of alternative splicing and acts as a negative repressor, binding to the full-length TF PtFLC and therefore regulating the development of the Poncirus trifoliata. For A. thaliana, a FLM gene was found forming the FLM-б isoform, which acts as a dominant negative regulator and stimulates the development of the flower formation process due to the formation of a heterodimer with SVP TF. Small interfering peptides and proteins can actively participate in the regulation of gene expression, for example, in situations of stress or at different stages of plant development. Moreover, small interfering peptides and proteins can be used as a tool for fundamental research on the function of genes as well as for applied research for permanent or temporary knockout of genes. In this review, we have demonstrated recent studies related to siPEP/siPROT and their involvement in the response to various stresses, as well as possible ways to obtain small proteins.
Collapse
|
36
|
Xia J, Zhao Y, Burks P, Pauly M, Brown PJ. A sorghum NAC gene is associated with variation in biomass properties and yield potential. PLANT DIRECT 2018; 2:e00070. [PMID: 31245734 PMCID: PMC6508854 DOI: 10.1002/pld3.70] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/13/2023]
Abstract
Sorghum bicolor is a C4 grass widely cultivated for grain, forage, sugar, and biomass. The sorghum Dry Stalk (D) locus controls a qualitative difference between juicy green (dd) and dry white (D-) stalks and midribs, and co-localizes with a quantitative trait locus for sugar yield. Here, we apply fine-mapping and genome-wide association study (GWAS) to identify a candidate gene underlying D, and use nearly isogenic lines (NILs) to characterize the transcriptional, compositional, and agronomic effects of variation at the D locus. The D locus was fine-mapped to a 36 kb interval containing four genes. One of these genes is a NAC transcription factor that contains a stop codon in the NAC domain in the recessive (dd) parent. Allelic variation at D affects grain yield, sugar yield, and biomass composition in NILs. Green midrib (dd) NILs show reductions in lignin in stalk tissue and produce higher sugar and grain yields under well-watered field conditions. Increased yield potential in dd NILs is associated with increased stalk mass and moisture, higher biomass digestibility, and an extended period of grain filling. Transcriptome profiling of midrib tissue at the 4-6 leaf stages, when NILs first become phenotypically distinct, reveals that dd NILs have increased expression of a miniature zinc finger (MIF) gene. MIF genes dimerize with and suppress zinc finger homeodomain (ZF-HD) transcription factors, and a ZF-HD gene is associated with midrib color variation in a GWAS analysis across 1,694 diverse sorghum inbreds. A premature stop codon in a NAC gene is the most likely candidate polymorphism underlying the sorghum D locus. More detailed understanding of the sorghum D locus could help improve agronomic potential in cereals.
Collapse
Affiliation(s)
- Jingnu Xia
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Yunjun Zhao
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Brookhaven National LabUptonNew York
| | - Payne Burks
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Chromatin Inc.LubbockTexas
| | - Markus Pauly
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Heinrich‐Heine UniversityDuesseldorfGermany
| | - Patrick J. Brown
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
University of California, DavisDavisCalifornia
| |
Collapse
|
37
|
Bhati KK, Blaakmeer A, Paredes EB, Dolde U, Eguen T, Hong SY, Rodrigues V, Straub D, Sun B, Wenkel S. Approaches to identify and characterize microProteins and their potential uses in biotechnology. Cell Mol Life Sci 2018; 75:2529-2536. [PMID: 29670998 PMCID: PMC6003976 DOI: 10.1007/s00018-018-2818-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/05/2018] [Accepted: 04/13/2018] [Indexed: 01/29/2023]
Abstract
MicroProteins are small proteins that contain a single protein domain and are related to larger, often multi-domain proteins. At the molecular level, microProteins act by interfering with the formation of higher order protein complexes. In the past years, several microProteins have been identified in plants and animals that strongly influence biological processes. Due to their ability to act as dominant regulators in a targeted manner, microProteins have a high potential for biotechnological use. In this review, we present different ways in which microProteins are generated and we elaborate on techniques used to identify and characterize them. Finally, we give an outlook on possible applications in biotechnology.
Collapse
Affiliation(s)
- Kaushal Kumar Bhati
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Anko Blaakmeer
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Esther Botterweg Paredes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Ulla Dolde
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Tenai Eguen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Shin-Young Hong
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Vandasue Rodrigues
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Daniel Straub
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Bin Sun
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| |
Collapse
|
38
|
Bollier N, Sicard A, Gonzalez N, Chevalier C, Hernould M, Delmas F. Induced ovule-to-flower switch by interfering with SlIMA activity in tomato. PLANT SIGNALING & BEHAVIOR 2018; 13:e1473687. [PMID: 29944450 PMCID: PMC6110368 DOI: 10.1080/15592324.2018.1473687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 05/29/2023]
Abstract
The INHIBITOR OF MERISTEM ACTIVITY in tomato (SlIMA) and MINI ZINC FINGER 2 in Arabidopsis (AtMIF2), two members of the MINI ZINC FINGER family (MIF), are involved in the regulation of flower and ovule development. MIF proteins possess a unique non-canonical zinc-finger domain that confers the capacity to interact with other protein partners. The characterization of SlIMA and AtMIF2 gain- and loss-of-function transgenic lines in Solanum lycopersicum and Arabidopsis thaliana respectively, allowed the demonstration of their conserved functional role in the termination of floral stem cell maintenance. During early floral development, the expression of SlIMA and AtMIF2 is induced by the MADS-Box transcription factor AGAMOUS (AG). Then, SlIMA or AtMIF2 protein recruits the C2H2 zinc finger KNUCKLES (KNU), in a transcriptional repressor complex together with TOPLESS (TPL) and HISTONE DEACETYLASE19 (HDA19). This complex binds to the WUSCHEL (WUS) locus leading to its repression. To further characterize the role of these interactions in flower development, we have investigated the effects of a dominant negative form of SlIMA, SlIMAch that leads to spectacular phenotypes, including ovule conversion into a floral meristem.
Collapse
Affiliation(s)
- N. Bollier
- UMR1332 BFP, INRA, University of Bordeaux, Bordeaux, France
| | - A. Sicard
- UMR1332 BFP, INRA, University of Bordeaux, Bordeaux, France
| | - N. Gonzalez
- UMR1332 BFP, INRA, University of Bordeaux, Bordeaux, France
| | - C. Chevalier
- UMR1332 BFP, INRA, University of Bordeaux, Bordeaux, France
| | - M. Hernould
- UMR1332 BFP, INRA, University of Bordeaux, Bordeaux, France
| | - F. Delmas
- UMR1332 BFP, INRA, University of Bordeaux, Bordeaux, France
| |
Collapse
|
39
|
Yang H, Xue Q, Zhang Z, Du J, Yu D, Huang F. GmMYB181, a Soybean R2R3-MYB Protein, Increases Branch Number in Transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:1027. [PMID: 30065741 PMCID: PMC6056663 DOI: 10.3389/fpls.2018.01027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/25/2018] [Indexed: 05/11/2023]
Abstract
Soybean (Glycine max) is an important economic crop that provides abundant oil and high quality protein for human beings. As the process of reproductive growth directly determines the crop seed yield and quality, we initiated studies to identify genes that regulate soybean floral organ development. One R2R3-MYB transcription factor gene, designated as GmMYB181, was found to be enriched in flowers based on microarray analysis and was further functionally investigated in transgenic Arabidopsis. GmMYB181 protein contains two MYB domains, which localized to the nucleus and displayed transcriptional activation in yeast hybrid system. Real-time quantitative PCR (qRT-PCR) results suggested GmMYB181 exclusively expressed in flower tissue. In Arabidopsis, overexpression of GmMYB181 altered the morphology of floral organs, fruit size and plant architecture, including outward curly sepals, smaller siliques, increased lateral branches and reduced plant height, indicating that GmMYB181 is involved in the development of reproductive organs and plays an important role in controlling plant architecture. Further, microarray analysis revealed that overexpressing GmMYB181 in Arabidopsis affected the expression of 3450 genes in mature flowers, including those involved in floral organ, seed/fruit development, and responded to different hormone signals.
Collapse
|
40
|
Straub D, Wenkel S. Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins. Genome Biol Evol 2017; 9:777-789. [PMID: 28338802 PMCID: PMC5381583 DOI: 10.1093/gbe/evx041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/30/2022] Open
Abstract
MicroProteins are small single-domain proteins that act by engaging their targets into different, sometimes nonproductive protein complexes. In order to identify novel microProteins in any sequenced genome of interest, we have developed miPFinder, a program that identifies and classifies potential microProteins. In the past years, several microProteins have been discovered in plants where they are mainly involved in the regulation of development by fine-tuning transcription factor activities. The miPFinder algorithm identifies all up to date known plant microProteins and extends the microProtein concept beyond transcription factors to other protein families. Here, we reveal potential microProtein candidates in several plant and animal reference genomes. A large number of these microProteins are species-specific while others evolved early and are evolutionary highly conserved. Most known microProtein genes originated from large ancestral genes by gene duplication, mutation and subsequent degradation. Gene ontology analysis shows that putative microProtein ancestors are often located in the nucleus, and involved in DNA binding and formation of protein complexes. Additionally, microProtein candidates act in plant transcriptional regulation, signal transduction and anatomical structure development. MiPFinder is freely available to find microProteins in any genome and will aid in the identification of novel microProteins in plants and animals.
Collapse
Affiliation(s)
- Daniel Straub
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg C, Denmark
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg C, Denmark
| |
Collapse
|
41
|
Khatun K, Nath UK, Robin AHK, Park JI, Lee DJ, Kim MB, Kim CK, Lim KB, Nou IS, Chung MY. Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. BMC Genomics 2017; 18:695. [PMID: 28874115 PMCID: PMC5585987 DOI: 10.1186/s12864-017-4082-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 01/23/2023] Open
Abstract
Background Zinc finger homeodomain proteins (ZHD) constitute a plant-specific transcription factor family with a conserved DNA binding homeodomain and a zinc finger motif. Members of the ZHD protein family play important roles in plant growth, development, and stress responses. Genome-wide characterization of ZHD genes has been carried out in several model plants, including Arabidopsis thaliana and Oryza sativa, but not yet in tomato (Solanum lycopersicum). Results In this study, we performed the first comprehensive genome-wide characterization and expression profiling of the ZHD gene family in tomato (Solanum lycopersicum). We identified 22 SlZHD genes and classified them into six subfamilies based on phylogeny. The SlZHD genes were generally conserved in each subfamily, with minor variations in gene structure and motif distribution. The 22 SlZHD genes were distributed on six of the 12 tomato chromosomes, with segmental duplication detected in four genes. Analysis of Ka/Ks ratios revealed that the duplicated genes are under negative or purifying selection. Comprehensive expression analysis revealed that the SlZHD genes are widely expressed in various tissues, with most genes preferentially expressed in flower buds compared to other tissues. Moreover, many of the genes are responsive to abiotic stress and phytohormone treatment. Conclusion Systematic analysis revealed structural diversity among tomato ZHD proteins, which indicates the possibility for diverse roles of SlZHD genes in different developmental stages as well as in response to abiotic stresses. Our expression analysis of SlZHD genes in various tissues/organs and under various abiotic stress and phytohormone treatments sheds light on their functional divergence. Our findings represent a valuable resource for further analysis to explore the biological functions of tomato ZHD genes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4082-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Khadiza Khatun
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Do-Jin Lee
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.,Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Min-Bae Kim
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.,Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Chang Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea
| | - Mi-Young Chung
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea. .,Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam, 57922, South Korea.
| |
Collapse
|
42
|
Wang H, Li S, Teng S, Liang H, Xin H, Gao H, Huang D, Lang Z. Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid. PLoS One 2017; 12:e0177739. [PMID: 28520800 PMCID: PMC5433750 DOI: 10.1371/journal.pone.0177739] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/02/2017] [Indexed: 12/12/2022] Open
Abstract
Chewing insects cause severe yield losses in crop production worldwide. Crop plants counteract chewing insects by transcriptionally promoting a repertoire of defense gene products that are either toxic to, or attractive to the natural enemies of, pest insects. However, the complexity of the transcriptional reprogramming in plant defense response against chewing insects is still not well understood. In this study, the genome-wide early responses in maize seedlings to Asian corn borer (ACB, Ostrinia furnacalis) and also to jasmonic acid(JA), the pivotal phytohormone controlling plant defense response against herbivory, were transcriptionally profiled by RNA-Seq. Clustering of differentially expressed genes (DEGs) along with functional enrichment analysis revealed important biological processes regulated in response to ACB infestation and/or jasmonic acid. Moreover, DEGs with distinct expression patterns were differentially enriched with diverse families of cis-elements on their promoters. Multiple inventories of differentially expressed transcription factors (DETFs) in each DEG group were also analyzed. A transient expression assay using transfected maize protoplastswas established to examine the potential roles of DETFs in maize defense response and JA signaling, and this was used to show that ZmNAC60, an ACB- and JA-inducible DETF, represented a novel positive regulator of JA and defense pathway genes. This study provided a comprehensive transcriptional picture for the early dynamics of maize defense responses and JA signaling, and the identification of DETFs offered potential targets for further functional genomics investigation of master regulators in maize defense responses against herbivory.
Collapse
Affiliation(s)
- Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Shengyan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Shouzhen Teng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Haisheng Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Hongjia Xin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Hongjiang Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Dafang Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhihong Lang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| |
Collapse
|
43
|
Han M, Jin X, Yao W, Kong L, Huang G, Tao Y, Li L, Wang X, Wang Y. A Mini Zinc-Finger Protein (MIF) from Gerbera hybrida Activates the GASA Protein Family Gene, GEG, to Inhibit Ray Petal Elongation. FRONTIERS IN PLANT SCIENCE 2017; 8:1649. [PMID: 29018462 PMCID: PMC5615213 DOI: 10.3389/fpls.2017.01649] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/08/2017] [Indexed: 05/19/2023]
Abstract
Petal appearance is an important horticultural trail that is generally used to evaluate the ornamental value of plants. However, knowledge of the molecular regulation of petal growth is mostly derived from analyses of Arabidopsis thaliana, and relatively little is known about this process in ornamental plants. Previously, GEG (Gerbera hybrida homolog of the gibberellin [GA]-stimulated transcript 1 [GAST1] from tomato), a gene from the GA stimulated Arabidopsis (GASA) family, was reported to be an inhibitor of ray petal growth in the ornamental species, G. hybrida. To explore the molecular regulatory mechanism of GEG in petal growth inhibition, a mini zinc-finger protein (MIF) was identified using yeast one-hybrid (Y1H) screen. The direct binding of GhMIF to the GEG promoter was verified by using an electrophoretic mobility shift assay and a dual-luciferase assay. A yeast two-hybrid (Y2H) revealed that GhMIF acts as a transcriptional activator. Transient transformation assay indicated that GhMIF is involved in inhibiting ray petal elongation by activating the expression of GEG. Spatiotemporal expression analyses and hormone treatment assay showed that the expression of GhMIF and GEG is coordinated during petal development. Taken together, these results suggest that GhMIF acts as a direct transcriptional activator of GEG, a gene from the GASA protein family to regulate the petal elongation.
Collapse
Affiliation(s)
- Meixiang Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Xuefeng Jin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Wei Yao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Lingjie Kong
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Gan Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Yujin Tao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Lingfei Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of SciencesShenzhen, China
| | - Xiaojing Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
| | - Yaqin Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal UniversityGuangzhou, China
- *Correspondence: Yaqin Wang,
| |
Collapse
|
44
|
Phung NTP, Mai CD, Hoang GT, Truong HTM, Lavarenne J, Gonin M, Nguyen KL, Ha TT, Do VN, Gantet P, Courtois B. Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam. BMC PLANT BIOLOGY 2016; 16:64. [PMID: 26964867 PMCID: PMC4785749 DOI: 10.1186/s12870-016-0747-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/26/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. RESULTS The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. CONCLUSIONS Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.
Collapse
Affiliation(s)
- Nhung Thi Phuong Phung
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Chung Duc Mai
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Giang Thi Hoang
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Hue Thi Minh Truong
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
| | - Jeremy Lavarenne
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
| | | | - Khanh Le Nguyen
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
| | - Thuy Thi Ha
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Vinh Nang Do
- />Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000 Hanoi, Vietnam
| | - Pascal Gantet
- />University of Science and Technology of Hanoi, LMI RICE, 00000 Hanoi, Vietnam
- />IRD, LMI RICE, 00000 Hanoi, Vietnam
- />Université de Montpellier, UMR DIADE, 34095 Montpellier, France
| | | |
Collapse
|
45
|
Wang W, Wu P, Li Y, Hou X. Genome-wide analysis and expression patterns of ZF-HD transcription factors under different developmental tissues and abiotic stresses in Chinese cabbage. Mol Genet Genomics 2015; 291:1451-64. [PMID: 26546019 DOI: 10.1007/s00438-015-1136-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/16/2015] [Indexed: 01/28/2023]
Abstract
The ZF-HD gene family plays an important role in plant developmental processes and stress responses. However, the function of the ZF-HD genes in Chinese cabbage remains largely unknown. Chinese cabbage (Brassica rapa ssp. pekinensis) is a member of one of the most important leaf vegetables grown worldwide. The entire Chinese cabbage genome sequence has been determined, and more than forty thousand proteins have been identified to date. In this study, 31 ZF-HD genes were identified in Chinese cabbage. We show here that the BraZF-HD genes could be categorized into ZHD and MIF subfamilies. Among them, ZHD genes are plant-specific, nearly all intronless, and related to MINI ZINC FINGER genes that possess only the zinc finger. Phylogenetic analysis suggested that ZHDs have expanded considerably during angiosperm evolution. In addition, the ZHD group has 24 members, which is twice as much as the Arabidopsis ZHD group, indicating that the Chinese cabbage ZHD genes have been retained more frequently than other group genes. Real-time PCR analysis showed that most of BraZF-HD genes are preferentially expressed in flower. Furthermore, most of these genes are significantly induced under photoperiod or vernalization conditions, as well as abiotic stresses. Thereby implying that they may play important roles in these processes. This study provides insight into the evolution of ZF-HD genes in Chinese cabbage genome and may aid efforts to further characterize the function of these predicted ZF-HD genes in flowering and resistance.
Collapse
Affiliation(s)
- Wenli Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - XiLin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
46
|
Liu Q, Wang Z, Xu X, Zhang H, Li C. Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). PLoS One 2015; 10:e0134753. [PMID: 26237514 PMCID: PMC4523194 DOI: 10.1371/journal.pone.0134753] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/13/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND C2H2 zinc-finger (C2H2-ZF) proteins are a large gene family in plants that participate in various aspects of normal plant growth and development, as well as in biotic and abiotic stress responses. To date, no overall analysis incorporating evolutionary history and expression profiling of the C2H2-ZF gene family in model tree species poplar (Populus trichocarpa) has been reported. PRINCIPAL FINDINGS Here, we identified 109 full-length C2H2-ZF genes in P. trichocarpa, and classified them into four groups, based on phylogenetic analysis. The 109 C2H2-ZF genes were distributed unequally on 19 P. trichocarpa linkage groups (LGs), with 39 segmental duplication events, indicating that segmental duplication has been important in the expansion of the C2H2-ZF gene family. Promoter cis-element analysis indicated that most of the C2H2-ZF genes contain phytohormone or abiotic stress-related cis-elements. The expression patterns of C2H2-ZF genes, based on heatmap analysis, suggested that C2H2-ZF genes are involved in tissue and organ development, especially root and floral development. Expression analysis based on quantitative real-time reverse transcription polymerase chain reaction indicated that C2H2-ZF genes are significantly involved in drought, heat and salt response, possibly via different mechanisms. CONCLUSIONS This study provides a thorough overview of the P. trichocarpa C2H2-ZF gene family and presents a new perspective on the evolution of this gene family. In particular, some C2H2-ZF genes may be involved in environmental stress tolerance regulation. PtrZFP2, 19 and 95 showed high expression levels in leaves and/or roots under environmental stresses. Additionally, this study provided a solid foundation for studying the biological roles of C2H2-ZF genes in Populus growth and development. These results form the basis for further investigation of the roles of these candidate genes and for future genetic engineering and gene functional studies in Populus.
Collapse
Affiliation(s)
- Quangang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Zhanchao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Xuemei Xu
- Library of Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Haizhen Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, People’s Republic of China
| |
Collapse
|
47
|
Eguen T, Straub D, Graeff M, Wenkel S. MicroProteins: small size-big impact. TRENDS IN PLANT SCIENCE 2015; 20:477-82. [PMID: 26115780 DOI: 10.1016/j.tplants.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/13/2015] [Accepted: 05/23/2015] [Indexed: 05/04/2023]
Abstract
MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect. Recent bioinformatic attempts to identify miPs have resulted in a list of potential miPs, many of which lack the defining characteristics of a miP. In this opinion article, we clearly state the characteristics of a miP as evidenced by known proteins that fit the definition; we explain why modulatory proteins misrepresented as miPs do not qualify as true miPs. We also discuss the evolutionary history of miPs, and how the miP concept can extend beyond transcription factors (TFs) to encompass different non-TF proteins that require dimerization for full function.
Collapse
Affiliation(s)
- Tenai Eguen
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Daniel Straub
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Moritz Graeff
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark
| | - Stephan Wenkel
- Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Copenhagen, Denmark.
| |
Collapse
|
48
|
Graeff M, Wenkel S. Regulation of protein function by interfering protein species. Biomol Concepts 2014; 3:71-8. [PMID: 25436525 DOI: 10.1515/bmc.2011.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 11/02/2011] [Indexed: 11/15/2022] Open
Abstract
Abstract Most proteins do not function alone but act in protein complexes. For several transcriptional regulators, it is known that they have to homo- or heterodimerize prior to DNA binding. These protein interactions occur through defined protein-protein-interaction (PPI) domains. More than two decades ago, inhibitor of DNA binding (ID), a small protein containing a single helix-loop-helix (HLH) motif was identified. ID is able to interact with the larger DNA-binding basic helix-loop-helix (bHLH) transcription factors, but due to the lack of the basic domain required for DNA binding, ID traps bHLH proteins in non-functional complexes. Work in plants has, in the recent years, identified more small proteins acting in analogy to ID. A hallmark of these small negative acting proteins is the presence of a protein-interaction domain and the absence of other functional domains required for transcriptional activation or DNA binding. Because these proteins are often very small and function in analogy to microRNAs (meaning in a dominant-negative manner), we propose to refer to these protein species as 'microProteins' (miPs). miPs can be encoded in the genome as individual transcription units but can also be produced by alternative splicing. Other negatively acting proteins, consisting of more than one domain, have also been identified, and we propose to call these proteins 'interfering proteins' (iPs). The aim of this review is to state more precisely how to discriminate miPs from iPs. Therefore, we will highlight recent findings on both protein species and describe their mode of action. Furthermore, miPs have the ability to regulate proteins of diverse functions, emphasizing their value as biotechnological tools.
Collapse
|
49
|
Tadege M, Mysore KS. Tnt1 retrotransposon tagging of STF in Medicago truncatula reveals tight coordination of metabolic, hormonal and developmental signals during leaf morphogenesis. Mob Genet Elements 2014; 1:301-303. [PMID: 22545243 PMCID: PMC3337141 DOI: 10.4161/mge.18686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Tnt1 (transposable element if Nicotiana tabaccum cell type 1) is one of the very few active LTR retrotransposons used for gene tagging in plants. In the model legume Medicago truncatula, Tnt1 has been effectively used as a gene knock-out tool to generate several very useful mutants. stenofolia (stf) is such a mutant identified by Tnt1 insertion in a WUSCHEL-like homeobox transcription factor. STF is required for blade outgrowth, leaf vascular patterning and female reproductive organ development in barrel medic and woodland tobacco. Using transcript profiling and metabolite analysis, we uncovered that mutant leaves are compromised in steady-state levels of multiple phytohormones, sugar metabolites and derivatives including flavonoids and polyamines. In the lam1 mutant (caused by deletion of the STF ortholog in Nicotiana sylvestris), while glucose, fructose, mannose, galactose, myo-inositol and aromatic aminoacids are dramatically reduced, sucrose is comparable to wild-type levels, and glutamine, proline, putrescine, nicotine and sorbitol are highly increased. We demonstrated that both stf and lam1 mutants accumulate reduced levels of free auxin and ABA in their leaves, and ectopic expression of STF in tobacco leads to auxin and cytokinin overproduction phenotypes including formation of tumors on the roots and crown. These data suggest that STF mediated integration of metabolic and hormonal signals are required for lateral organ morphogenesis and elaboration.
Collapse
|
50
|
Mittal A, Balasubramanian R, Cao J, Singh P, Subramanian S, Hicks G, Nothnagel EA, Abidi N, Janda J, Galbraith DW, Rock CD. TOPOISOMERASE 6B is involved in chromatin remodelling associated with control of carbon partitioning into secondary metabolites and cell walls, and epidermal morphogenesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4217-39. [PMID: 24821950 PMCID: PMC4112631 DOI: 10.1093/jxb/eru198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant growth is continuous and modular, a combination that allows morphogenesis by cell division and elongation and serves to facilitate adaptation to changing environments. The pleiotropic phenotypes of the harlequin (hlq) mutant, isolated on the basis of ectopic expression of the abscisic acid (ABA)- and auxin-inducible proDc3:GUS reporter gene, were previously characterized. Mutants are skotomorphogenic, have deformed and collapsed epidermal cells which accumulate callose and starch, cell walls abundant in pectins and cell wall proteins, and abnormal and reduced root hairs and leaf trichomes. hlq and two additional alleles that vary in their phenotypic severity of starch accumulation in the light and dark have been isolated, and it is shown that they are alleles of bin3/hyp6/rhl3/Topoisomerase6B. Mutants and inhibitors affecting the cell wall phenocopy several of the traits displayed in hlq. A microarray analysis was performed, and coordinated expression of physically adjacent pairs/sets of genes was observed in hlq, suggesting a direct effect on chromatin. Histones, WRKY and IAA/AUX transcription factors, aquaporins, and components of ubiquitin-E3-ligase-mediated proteolysis, and ABA or biotic stress response markers as well as proteins involved in cellular processes affecting carbon partitioning into secondary metabolites were also identified. A comparative analysis was performed of the hlq transcriptome with other previously published TopoVI mutant transcriptomes, namely bin3, bin5, and caa39 mutants, and limited concordance between data sets was found, suggesting indirect or genotype-specific effects. The results shed light on the molecular mechanisms underlying the det/cop/fus-like pleiotropic phenotypes of hlq and support a broader role for TopoVI regulation of chromatin remodelling to mediate development in response to environmental and hormonal signals.
Collapse
Affiliation(s)
- Amandeep Mittal
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Rajagopal Balasubramanian
- Tamil Nadu Agricultural University, Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Madurai-625 104, India
| | - Jin Cao
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Prabhjeet Singh
- Department of Biotechnology, Guru Nanak Dev University, Amritsar-143 005, Punjab, India
| | - Senthil Subramanian
- South Dakota State University, Department of Plant Science, Brookings, SD 57007, USA
| | - Glenn Hicks
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Eugene A Nothnagel
- Department of Botany and Plant Sciences, University of California, Riverside CA 92521-0124, USA
| | - Noureddine Abidi
- Texas Tech University, Department of Plant and Soil Science and Fiber and Biopolymer Research Institute, 1001 East Loop 289, Lubbock, TX 79409-5019, USA
| | - Jaroslav Janda
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - David W Galbraith
- University of Arizona, Department of Plant Sciences and BIO5 Institute, 341 Keating Bldg, Tucson, AZ 85721, USA
| | - Christopher D Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409-3131, USA
| |
Collapse
|