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Bin J, Tan Q, Wen S, Huang L, Wang H, Imtiaz M, Zhang Z, Guo H, Xie L, Zeng R, Wei Q. Comprehensive Analyses of Four PhNF-YC Genes from Petunia hybrida and Impacts on Flowering Time. PLANTS (BASEL, SWITZERLAND) 2024; 13:742. [PMID: 38475587 DOI: 10.3390/plants13050742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
Nuclear Factor Y (NF-Y) is a class of heterotrimeric transcription factors composed of three subunits: NF-A, NF-YB, and NF-YC. NF-YC family members play crucial roles in various developmental processes, particularly in the regulation of flowering time. However, their functions in petunia remain poorly understood. In this study, we isolated four PhNF-YC genes from petunia and confirmed their subcellular localization in both the nucleus and cytoplasm. We analyzed the transcript abundance of all four PhNF-YC genes and found that PhNF-YC2 and PhNF-YC4 were highly expressed in apical buds and leaves, with their transcript levels decreasing before flower bud differentiation. Silencing PhNF-YC2 using VIGS resulted in a delayed flowering time and reduced chlorophyll content, while PhNF-YC4-silenced plants only exhibited a delayed flowering time. Furthermore, we detected the transcript abundance of flowering-related genes involved in different signaling pathways and found that PhCO, PhGI, PhFBP21, PhGA20ox4, and PhSPL9b were regulated by both PhNF-YC2 and PhNF-YC4. Additionally, the transcript abundance of PhSPL2, PhSPL3, and PhSPL4 increased only in PhNF-YC2-silenced plants. Overall, these results provide evidence that PhNF-YC2 and PhNF-YC4 negatively regulate flowering time in petunia by modulating a series of flowering-related genes.
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Affiliation(s)
- Jing Bin
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Tan
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Shiyun Wen
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Licheng Huang
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Huimin Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Imtiaz
- Department of Horticulture, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Zhisheng Zhang
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Herong Guo
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Li Xie
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Ruizhen Zeng
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Qian Wei
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
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Bobadilla LK, Baek Y, Tranel PJ. Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus. BMC PLANT BIOLOGY 2023; 23:339. [PMID: 37365527 DOI: 10.1186/s12870-023-04286-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species. RESULTS Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes. CONCLUSIONS This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.
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Affiliation(s)
- Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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Käppel S, Rümpler F, Theißen G. Cracking the Floral Quartet Code: How Do Multimers of MIKC C-Type MADS-Domain Transcription Factors Recognize Their Target Genes? Int J Mol Sci 2023; 24:ijms24098253. [PMID: 37175955 PMCID: PMC10178880 DOI: 10.3390/ijms24098253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023] Open
Abstract
MADS-domain transcription factors (MTFs) are involved in the control of many important processes in eukaryotes. They are defined by the presence of a unique and highly conserved DNA-binding domain, the MADS domain. MTFs bind to double-stranded DNA as dimers and recognize specific sequences termed CArG boxes (such as 5'-CC(A/T)6GG-3') and similar sequences that occur hundreds of thousands of times in a typical flowering plant genome. The number of MTF-encoding genes increased by around two orders of magnitude during land plant evolution, resulting in roughly 100 genes in flowering plant genomes. This raises the question as to how dozens of different but highly similar MTFs accurately recognize the cis-regulatory elements of diverse target genes when the core binding sequence (CArG box) occurs at such a high frequency. Besides the usual processes, such as the base and shape readout of individual DNA sequences by dimers of MTFs, an important sublineage of MTFs in plants, termed MIKCC-type MTFs (MC-MTFs), has evolved an additional mechanism to increase the accurate recognition of target genes: the formation of heterotetramers of closely related proteins that bind to two CArG boxes on the same DNA strand involving DNA looping. MC-MTFs control important developmental processes in flowering plants, ranging from root and shoot to flower, fruit and seed development. The way in which MC-MTFs bind to DNA and select their target genes is hence not only of high biological interest, but also of great agronomic and economic importance. In this article, we review the interplay of the different mechanisms of target gene recognition, from the ordinary (base readout) via the extravagant (shape readout) to the idiosyncratic (recognition of the distance and orientation of two CArG boxes by heterotetramers of MC-MTFs). A special focus of our review is on the structural prerequisites of MC-MTFs that enable the specific recognition of target genes.
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Affiliation(s)
- Sandra Käppel
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Florian Rümpler
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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Li H, Li Y, Zhang X, Cai K, Li Y, Wang Q, Qu G, Han R, Zhao X. Genome-wide identification and expression analysis of the MADS-box gene family during female and male flower development in Juglans mandshurica. FRONTIERS IN PLANT SCIENCE 2022; 13:1020706. [PMID: 36388573 PMCID: PMC9664150 DOI: 10.3389/fpls.2022.1020706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The MADS-box gene family plays a crucial role in multiple developmental processes of plants, especially in floral organ specification and the regulation of fruit development and ripening. Juglans mandshurica is a precious fruit material whose quality and yield are determined by floral organ development. The molecular mechanism of J. mandshurica female and male flower development depending on MADS-box genes remains unclear. In our study, 67 JmMADS genes were identified and unevenly distributed on 15 of 16 J. mandshurica chromosomes. These genes were divided into two types [type I (Mα, Mγ, Mδ) and type II (MIKC)]. The gene structure and motif analyses showed that most genes belonging to the same type had similar gene structures and conserved motifs. The analysis of syntenic relationships showed that MADS-box genes in J. mandshurica, J. sigillata, and J. regia exhibited the highest homology and great collinearity. Analysis of cis-acting elements showed that JmMADS gene promoter regions contained light, stress and hormone response cis-acting elements. The gene expression patterns demonstrated that 30 and 26 JmMADS genes were specifically expressed in the female and male flowers, respectively. In addition, 12 selected genes common to J. mandshurica female and male flowers were significantly upregulated at the mature stage and were used to validate the reliability of the transcriptome data using quantitative real-time PCR. This comprehensive and systematic analysis of J. mandshurica MADS-box genes lays a foundation for future studies on MADS-box gene family functions.
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Affiliation(s)
- Hanxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Yuxi Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinxin Zhang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kewei Cai
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yan Li
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Qingcheng Wang
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guanzheng Qu
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Rui Han
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- State Key Laboratory of tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
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Li X, Kuang Y, Ye Y, Chen Z, Zhang M. Diverse function of the PISTILLATA, APETALA 3, and AGAMOUS-like MADS-box genes involved in the floral development in Alpinia hainanensis (Zingiberaceae). Gene X 2022; 839:146732. [PMID: 35840006 DOI: 10.1016/j.gene.2022.146732] [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: 11/10/2021] [Revised: 06/23/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Zingiberaceae is the vital clue and key node in the decreased process of fertile stamens in Zingiberales, helping to understand the evolution of the ginger families. This study focuses on Alpinia hainanensis to investigate the function of B- and C-class MADS-box genes in floral development. The introns size of two B-class genes AhPI and AhAP3, and one C-class gene AhAG are quite variable. By contrast, the positions of the corresponding introns are conserved, resulting in a similar exon size in homologs. The typical region 70 bp-CCAATCA element was not found in the second intron of AhAG compared to AG homologs. The subcellular localization showed that AhAP3 was in both intranuclear and extranuclear. The heterodimer was formed between APETALA3 and PISTILLATA but not between the B- and C-class proteins using Y2H and BiFC. The 35S::AhAG heterologous transformed Arabidopsis had curly and smaller rosette leaves with early flowering. Floral organs had no homeotic conversion, albeit sepals and petals reduced in size. Siliques development was affected and displayed wrinkled and shorter. By contrast, 35S::AhAP3 and 35S::AhPI did not show any modified phenotype in transgenic Arabidopsis thaliana. We first proposed the model for Alpinia flower development. MADS-box transcription factor binding at particular genomic locations and interaction with partners may be crucial for the development of the floral organ.
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Affiliation(s)
- Xiumei Li
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Yanfeng Kuang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Yushi Ye
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Zhongjian Chen
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Mingyong Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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Characterization of RIN Isoforms and Their Expression in Tomato Fruit Ripening. Cells 2021; 10:cells10071739. [PMID: 34359909 PMCID: PMC8304285 DOI: 10.3390/cells10071739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022] Open
Abstract
Ripening of tomato fleshy fruit is coordinated by transcription factor RIN, which triggers ethylene and carotenoid biosynthesis, sugar accumulation, and cell wall modifications. In this study, we identified and characterized complete sequences of the RIN chromosomal locus in two tomato Solanum lycopersicum cultivars, its rin/RIN genotype, and three wild green-fruited species differing in fruit color and composition. The results reveal that S. lycopersicum cultivars and some wild species (S. pennellii, S. habrochaites, and S. huaylasense) had a 3′-splicing site enabling the transcription of RIN1i and RIN2i isoforms. The other wild species (S. arcanum, S. chmielewskii, S. neorickii, and S. peruvianum) had a 3′-splicing site only for RIN2i, which was consistent with RIN1i and RIN2i expression patterns. The genotype rin/RIN, which had an extended 3′-terminal deletion in the rin allele, mainly expressed the chimeric RIN–MC transcript, which was also found in cultivars (RIN/RIN). The RIN1, but not RIN2, protein is able to induce the transcription of the reporter gene in the Y2H system, which positively correlated with the transcription profile of RIN1i and RIN target genes. We suggest that during fruit ripening, RIN1 activates ripening-related genes, whereas RIN2 and RIN–MC act as modulators by competing for RIN-binding sites in gene promoters, which should be confirmed by further studies on the association between RIN-splicing mechanisms and tomato fruit ripening.
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Wang D, Hao Z, Long X, Wang Z, Zheng X, Ye D, Peng Y, Wu W, Hu X, Wang G, Zheng R, Shi J, Chen J. The Transcriptome of Cunninghamia lanceolata male/female cone reveal the association between MIKC MADS-box genes and reproductive organs development. BMC PLANT BIOLOGY 2020; 20:508. [PMID: 33153428 PMCID: PMC7643283 DOI: 10.1186/s12870-020-02634-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 08/30/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Cunninghamia lanceolata (Chinese fir), a member of the conifer family Cupressaceae, is one of the most popular cultivated trees for wood production in China. Continuous research is being performed to improve C. lanceolata breeding values. Given the high rate of seed abortion (one of the reasons being the failure of ovule and pollen development) in C. lanceolata, the proper formation of female/male cones could theoretically increase the number of offspring in future generations. MIKC MADS-box genes are well-known for their roles in the flower/cone development and comprise the typical/atypical floral development model for both angiosperms and gymnosperms. RESULTS We performed a transcriptomic analysis to find genes differentially expressed between female and male cones at a single, carefully determined developmental stage, focusing on the MIKC MADS-box genes. We finally obtained 47 unique MIKC MADS-box genes from C. lanceolata and divided these genes into separate branches. 27 out of the 47 MIKC MADS-box genes showed differential expression between female and male cones, and most of them were not expressed in leaves. Out of these 27 genes, most B-class genes (AP3/PI) were up-regulated in the male cone, while TM8 genes were up-regulated in the female cone. Then, with no obvious overall preference for AG (class C + D) genes in female/male cones, it seems likely that these genes are involved in the development of both cones. Finally, a small number of genes such as GGM7, SVP, AGL15, that were specifically expressed in female/male cones, making them candidate genes for sex-specific cone development. CONCLUSIONS Our study identified a number of MIKC MADS-box genes showing differential expression between female and male cones in C. lanceolata, illustrating a potential link of these genes with C. lanceolata cone development. On the basis of this, we postulated a possible cone development model for C. lanceolata. The gene expression library showing differential expression between female and male cones shown here, can be used to discover unknown regulatory networks related to sex-specific cone development in the future.
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Affiliation(s)
- Dandan Wang
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhaodong Hao
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaofei Long
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhanjun Wang
- College of Life Sciences, Hefei Normal University, Hefei, 230601, China
| | - Xueyan Zheng
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang, 353211, China
| | - Daiquan Ye
- National Germplasm Bank of Chinese fir at Fujian Yangkou Forest Farm, Shunchang, 353211, China
| | - Ye Peng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Weihuang Wu
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangyang Hu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Guibin Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Renhua Zheng
- Fujian Academy of Forestry, Fuzhou, 350012, China
| | - Jisen Shi
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- Key Laboratory of Forestry Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Comparative transcriptomic analysis of the tea plant (Camellia sinensis) reveals key genes involved in pistil deletion. Hereditas 2020; 157:39. [PMID: 32900387 PMCID: PMC7487804 DOI: 10.1186/s41065-020-00153-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/26/2020] [Indexed: 11/22/2022] Open
Abstract
Background The growth process of the tea plant (Camellia sinensis) includes vegetative growth and reproductive growth. The reproductive growth period is relatively long (approximately 1.5 years), during which a large number of nutrients are consumed, resulting in reduced tea yield and quality, accelerated aging, and shortened economic life of the tea plant. The formation of unisexual and sterile flowers can weaken the reproductive growth process of the tea plant. To further clarify the molecular mechanisms of pistil deletion in the tea plant, we investigated the transcriptome profiles in the pistil-deficient tea plant (CRQS), wild tea plant (WT), and cultivated tea plant (CT) by using RNA-Seq. Results A total of 3683 differentially expressed genes were observed between CRQS and WT flower buds, with 2064 upregulated and 1619 downregulated in the CRQS flower buds. These genes were mainly involved in the regulation of molecular function and biological processes. Ethylene synthesis–related ACC synthase genes were significantly upregulated and ACC oxidase genes were significantly downregulated. Further analysis revealed that one of the WIP transcription factors involved in ethylene synthesis was significantly upregulated. Moreover, AP1 and STK, genes related to flower development, were significantly upregulated and downregulated, respectively. Conclusions The transcriptome analysis indicated that the formation of flower buds with pistil deletion is a complex biological process. Our study identified ethylene synthesis, transcription factor WIP, and A and D-class genes, which warrant further investigation to understand the cause of pistil deletion in flower bud formation.
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Qu Y, Bi C, He B, Ye N, Yin T, Xu LA. Genome-wide identification and characterization of the MADS-box gene family in Salix suchowensis. PeerJ 2019; 7:e8019. [PMID: 31720123 PMCID: PMC6842560 DOI: 10.7717/peerj.8019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/09/2019] [Indexed: 01/19/2023] Open
Abstract
MADS-box genes encode transcription factors that participate in various plant growth and development processes, particularly floral organogenesis. To date, MADS-box genes have been reported in many species, the completion of the sequence of the willow genome provides us with the opportunity to conduct a comprehensive analysis of the willow MADS-box gene family. Here, we identified 60 willow MADS-box genes using bioinformatics-based methods and classified them into 22 M-type (11 Mα, seven Mβ and four Mγ) and 38 MIKC-type (32 MIKCc and six MIKC*) genes based on a phylogenetic analysis. Fifty-six of the 60 SsMADS genes were randomly distributed on 19 putative willow chromosomes. By combining gene structure analysis with evolutionary analysis, we found that the MIKC-type genes were more conserved and played a more important role in willow growth. Further study showed that the MIKC* type was a transition between the M-type and MIKC-type. Additionally, the number of MADS-box genes in gymnosperms was notably lower than that in angiosperms. Finally, the expression profiles of these willow MADS-box genes were analysed in five different tissues (root, stem, leave, bud and bark) and validated by RT-qPCR experiments. This study is the first genome-wide analysis of the willow MADS-box gene family, and the results establish a basis for further functional studies of willow MADS-box genes and serve as a reference for related studies of other woody plants.
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Affiliation(s)
- Yanshu Qu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Changwei Bi
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bing He
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Ning Ye
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Li-An Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Wang Y, Zhang J, Hu Z, Guo X, Tian S, Chen G. Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum. Int J Mol Sci 2019; 20:ijms20122961. [PMID: 31216621 PMCID: PMC6627509 DOI: 10.3390/ijms20122961] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 11/16/2022] Open
Abstract
MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family.
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Affiliation(s)
- Yunshu Wang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Jianling Zhang
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Zongli Hu
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Xuhu Guo
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
| | - Shibing Tian
- The Institute of Vegetable Research, Chongqing Academy of Agricultural Sciences, Chongqing 401329, China.
| | - Guoping Chen
- Laboratory of molecular biology of tomato, Bioengineering College, Chongqing University, Chongqing 400044, China.
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Peréz-Mesa P, Suárez-Baron H, Ambrose BA, González F, Pabón-Mora N. Floral MADS-box protein interactions in the early diverging angiosperm Aristolochia fimbriata Cham. (Aristolochiaceae: Piperales). Evol Dev 2019; 21:96-110. [PMID: 30734997 DOI: 10.1111/ede.12282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Floral identity MADS-box A, B, C, D, E, and AGL6 class genes are predominantly single copy in Magnoliids, and predate the whole genome duplication (WGD) events in monocots and eudicots. By comparison with the model species Arabidopsis thaliana, the expression patterns of B-, C-, and D-class genes in stamen, carpel, and ovules are conserved in Aristolochia fimbriata, whereas A-, E-class, and AGL6 genes have different expression patterns. Nevertheless, the interactions of these proteins that act through multimeric complexes remain poorly known in early divergent angiosperms. This study evaluates protein interactions among all floral MADS-box A. fimbriata proteins using the Yeast Two Hybrid System (Y2H). We found no homodimers and less heterodimers formed by AfimFUL when compared to AfimAGL6, which allowed us to suggest AGL6 homodimers in combination with AfimSEP2 as the most likely tetramer in sepal identity. We found AfimAP3-AfimPI obligate heterodimers and AfimAG-AfimSEP2 protein interactions intact suggesting conserved stamen and carpel tetrameric complexes in A. fimbriata. We observed a broader interaction partner set for AfimSEP2 than for its paralog AfimSEP1. We show conserved and exclusive MADS-box protein interactions in A. fimbriata in comparison with other eudicot and monocot model species in order to establish plesiomorphic MADS-box protein floral networks in angiosperms.
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Affiliation(s)
- Pablo Peréz-Mesa
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | | | | | - Favio González
- Universidad Nacional de Colombia, Facultad de Ciencias, Instituto de Ciencias Naturales, Sede Bogotá, Colombia
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Yang F, Zhu G, Wei Y, Gao J, Liang G, Peng L, Lu C, Jin J. Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii. BMC Genomics 2019; 20:53. [PMID: 30654752 PMCID: PMC6335714 DOI: 10.1186/s12864-019-5425-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Cymbidium goeringii is one of the most horticulturally important and popular ornamental plants in the orchid family (Orchidaceae). It blooms in winter during January-March and a period of low temperature is necessary for its normal flowering, otherwise there is flower bud abortion, which seriously affects the economic benefits. However, the molecular mechanism underlying winter-blooming behavior in C. goeringii is unclear. RESULTS In this research, we firstly study the flowering physiology of C. goeringii by cytobiology observations and physiological experiments. Using comparative transcriptome analysis, we identified 582 differentially expressed unigenes responding to cold treatment that were involved in metabolic process, flowering time, hormone signaling, stress response, and cell cycle, implying their potential roles in regulating winter-blooming of C. goeringii. Twelve MADS-box genes among them were investigated by full-length cDNA sequence analysis and expression validation, which indicated that three genes within the SHORT VEGETATIVE PHASE (SVP) sub-group had the most significant repressed expression after cold treatment. Further analysis revealed that the SVP genes showed population variation in expression that correlated with cold-regulated flowering and responded to low temperature earlier than the flowering pathway integrators CgAP1, CgSOC1, and CgLFY, suggesting a potential role of CgSVP genes in the early stage of low-temperature-induced blooming of C. goeringii. Moreover, a yeast two-hybrid experiment confirmed that CgSVP proteins interacted with CgAP1 and CgSOC1, suggesting that they may synergistically control the process of C. goeringii flowering in winter. CONCLUSIONS This study represents the first exploration of flowering physiology of C. goeringii and provides gene expression information that could facilitate our understanding of molecular regulation of orchid plant winter-flowering, which could provide new insights and practical guidance for improving their flowering regulation and molecular breeding.
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Affiliation(s)
- Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Gang Liang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Kunming, Yunnan, 650223, People's Republic of China
| | - Lingyuan Peng
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Jianpeng Jin
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
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Schorderet M, Duvvuru Muni RR, Fiebig A, Reinhardt D. Deregulation of MADS-box transcription factor genes in a mutant defective in the WUSCHEL-LIKE HOMEOBOX gene EVERGREEN of Petunia hybrida. PLANT SIGNALING & BEHAVIOR 2018; 13:e1471299. [PMID: 29995575 PMCID: PMC6207418 DOI: 10.1080/15592324.2018.1471299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 05/14/2023]
Abstract
Angiosperm inflorescences develop in two fundamentally different ways. In monopodial plants, for example in Arabidopsis thaliana, the flowers are initiated as lateral appendages of a central indeterminate inflorescence meristem. In sympodial plants, flowers arise by terminal differentiation of the inflorescence meristem, while further inflorescence development proceeds from new sympodial meristems that are generated at the flank of the terminal flower. We have used the sympodial model species Petunia hybrida to investigate inflorescence development. Here, we describe a mutant, bonsai (bns), which is defective in flower formation, inflorescence branching, and control of meristem size. Detailed microscopic analysis revealed that bns meristems retain vegetative charateristics including spiral phyllotaxis. Consistent with a block in flower formation, bns mutants exhibit a deregulated expression of various MADS-box genes. Molecular analysis revealed that the bns mutant carries a transposon insertion in the previously described EVERGREEN (EVG) gene, which belongs to the WUSCHEL-LIKE HOMEOBOX (WOX) transcription factor gene family. EVG falls in the WOX9 subfamily, which has diverse developmental functions in angiosperms. The comparison of WOX9 orthologues in five model species for flowering shows that these genes play functionally divergent roles in monopodial and sympodial plants, indicating that the WOX9 regulatory node may have played an important role in the evolution of shoot architecture.
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Affiliation(s)
- M. Schorderet
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
| | - R. R. Duvvuru Muni
- Dept. of Biology, University of Fribourg, Fribourg, Switzerland
- Monsanto Holdings Private Limited, Mfar Manyata Tech Park, Nagavara, Bangalore, India
| | - A. Fiebig
- Research Group Bioinformatics and Information Technology, Department Breeding Research, Leibniz Institute of Plant Genetics and CropPlant Research (IPK) Gatersleben, Seeland, Germany
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14
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Coenen H, Viaene T, Vandenbussche M, Geuten K. TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms. BMC PLANT BIOLOGY 2018; 18:129. [PMID: 29929474 PMCID: PMC6013966 DOI: 10.1186/s12870-018-1349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants. RESULTS We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events. Through knock-down of NbTM8 by virus induced gene silencing in Nicotiana benthamiana, we show that NbTM8 represses miR172 together with another MADS-box gene, SHORT VEGETATIVE PHASE (NbSVP). In the closely related species Petunia hybrida, PhTM8 is not expressed under the conditions we investigated and consistent with this, a knock-out mutant did not show a phenotype. Finally, we generated transgenic tomato plants in which TM8 was silenced or ectopically expressed, but these plants did not display a clear phenotype. Therefore, no clear function could be confirmed for Solanum lycopersium. CONCLUSIONS While the presence of TM8 is generally conserved, it remains difficult to propose a general function in angiosperms. Based on all the available data to date, supplemented with our own results, TM8 function seems to have diversified quickly throughout angiosperms and acts as repressor of miR172 in Nicotiana benthamiana, together with NbSVP.
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Affiliation(s)
- Heleen Coenen
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Tom Viaene
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes, University Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Koen Geuten
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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15
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Sobral R, Costa MMR. Role of floral organ identity genes in the development of unisexual flowers of Quercus suber L. Sci Rep 2017; 7:10368. [PMID: 28871195 PMCID: PMC5583232 DOI: 10.1038/s41598-017-10732-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/04/2017] [Indexed: 11/29/2022] Open
Abstract
Monoecious species provide an excellent system to study the specific determinants that underlie male and female flower development. Quercus suber is a monoecious species with unisexual flowers at inception. Despite the overall importance of this and other tree species with a similar reproductive habit, little is known regarding the mechanisms involved in the development of their male and female flowers. Here, we have characterised members of the ABCDE MADS-box gene family of Q. suber. The temporal expression of these genes was found to be sex-biased. The B-class genes, in particular, are predominantly, or exclusively (in the case of QsPISTILLATA), expressed in the male flowers. Functional analysis in Arabidopsis suggests that the B-class genes have their function conserved. The identification of sex-biased gene expression plus the identification of unusual protein-protein interactions suggest that the floral organ identity of Q. suber may be under control of specific changes in the dynamics of the ABCDE model. This study constitutes a major step towards the characterisation of the mechanisms involved in reproductive organ identity in a monoecious tree with a potential contribution towards the knowledge of conserved developmental mechanisms in other species with a similar sex habit.
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Affiliation(s)
- Rómulo Sobral
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - M Manuela R Costa
- Biosystems and Integrative Sciences Institute (BioISI), Plant Functional Biology Center, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Kitazawa Y, Iwabuchi N, Himeno M, Sasano M, Koinuma H, Nijo T, Tomomitsu T, Yoshida T, Okano Y, Yoshikawa N, Maejima K, Oshima K, Namba S. Phytoplasma-conserved phyllogen proteins induce phyllody across the Plantae by degrading floral MADS domain proteins. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2799-2811. [PMID: 28505304 PMCID: PMC5853863 DOI: 10.1093/jxb/erx158] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/13/2017] [Indexed: 05/21/2023]
Abstract
ABCE-class MADS domain transcription factors (MTFs) are key regulators of floral organ development in angiosperms. Aberrant expression of these genes can result in abnormal floral traits such as phyllody. Phyllogen is a virulence factor conserved in phytoplasmas, plant pathogenic bacteria of the class Mollicutes. It triggers phyllody in Arabidopsis thaliana by inducing degradation of A- and E-class MTFs. However, it is still unknown whether phyllogen can induce phyllody in plants other than A. thaliana, although phytoplasma-associated phyllody symptoms are observed in a broad range of angiosperms. In this study, phyllogen was shown to cause phyllody phenotypes in several eudicot species belonging to three different families. Moreover, phyllogen can interact with MTFs of not only angiosperm species including eudicots and monocots but also gymnosperms and a fern, and induce their degradation. These results suggest that phyllogen induces phyllody in angiosperms and inhibits MTF function in diverse plant species.
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Affiliation(s)
- Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Misako Himeno
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Momoka Sasano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Takamichi Nijo
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Tomomitsu
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Tetsuya Yoshida
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Yukari Okano
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Nobuyuki Yoshikawa
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka-shi, Iwate, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Kenro Oshima
- Faculty of Bioscience, Hosei University, 3-7-2 Kajino-cho, Koganei-shi, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
- Correspondence:
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Preston JC, Jorgensen SA, Orozco R, Hileman LC. Paralogous SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes differentially regulate leaf initiation and reproductive phase change in petunia. PLANTA 2016; 243:429-40. [PMID: 26445769 PMCID: PMC4722060 DOI: 10.1007/s00425-015-2413-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/22/2015] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Duplicated petunia clade-VI SPL genes differentially promote the timing of inflorescence and flower development, and leaf initiation rate. The timing of plant reproduction relative to favorable environmental conditions is a critical component of plant fitness, and is often associated with variation in plant architecture and habit. Recent studies have shown that overexpression of the microRNA miR156 in distantly related annual species results in plants with perennial characteristics, including late flowering, weak apical dominance, and abundant leaf production. These phenotypes are largely mediated through the negative regulation of a subset of genes belonging to the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family of transcription factors. In order to determine how and to what extent paralogous SPL genes have partitioned their roles in plant growth and development, we functionally characterized petunia clade-VI SPL genes under different environmental conditions. Our results demonstrate that PhSBP1and PhSBP2 differentially promote discrete stages of the reproductive transition, and that PhSBP1, and possibly PhCNR, accelerates leaf initiation rate. In contrast to the closest homologs in annual Arabidopsis thaliana and Mimulus guttatus, PhSBP1 and PhSBP2 transcription is not mediated by the gibberellic acid pathway, but is positively correlated with photoperiod and developmental age. The developmental functions of clade-VI SPL genes have, thus, evolved following both gene duplication and speciation within the core eudicots, likely through differential regulation and incomplete sub-functionalization.
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Affiliation(s)
- Jill C Preston
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA.
| | - Stacy A Jorgensen
- Department of Plant Biology, The University of Vermont, 111 Jeffords Hall, 63 Carrigan Drive, Burlington, VT, 05405, USA
| | - Rebecca Orozco
- Ecology and Evolutionary Biology, The University of Kansas, 8009 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Lena C Hileman
- Ecology and Evolutionary Biology, The University of Kansas, 8009 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
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Grimplet J, Martínez-Zapater JM, Carmona MJ. Structural and functional annotation of the MADS-box transcription factor family in grapevine. BMC Genomics 2016; 17:80. [PMID: 26818751 PMCID: PMC4729134 DOI: 10.1186/s12864-016-2398-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/14/2016] [Indexed: 02/02/2023] Open
Abstract
Background MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in eukaryotes. In plants, they are associated to numerous development processes most notably those related to reproductive development: flowering induction, specification of inflorescence and flower meristems, establishment of flower organ identity, as well as regulation of fruit, seed and embryo development. Genomic analyses of MADS-box genes in different plant species are providing new relevant information on the function and evolution of this transcriptional factor family. We have performed a true genome-wide analysis of the complete set of MADS-box genes in grapevine (Vitis vinifera), analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with genes from 16 other plant species. This study was integrated to previous works on the family in grapevine. Results A total of 90 MADS-box genes were detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence similarity. We performed a thorough in-depth curation of all gene models and combined the results with gene expression information including RNAseq data to clarifying the expression of newly identified genes and improve their functional characterization. Curated data were uploaded to the ORCAE database for grapevine in the frame of the grapevine genome curation effort. This approach resulted in the identification of 30 additional MADS box genes. Among them, ten new MIKCC genes were identified, including a potential new group of short proteins similar to the SVP protein subfamily. The MIKC* subgroup contains six genes in grapevine that can be grouped in the S (4 genes) and P (2 genes) clades, showing less redundancy than that observed in Arabidopsis thaliana. Expression pattern of these genes in grapevine is compatible with a role in male gametophyte development. Most of the identified new genes belong to the type I MADS-box genes and were classified as members of the Mα and Mγ subclasses. Ours analyses indicate that only few members of type I genes in grapevine have homology in other species and that species-specific clades appeared both in the Mα and Mγ subclasses. On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for development of central cell, endosperm and embryos seems to be conserved in plants. Conclusions The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic analysis with other plant species allowed the identification of new MADS-box genes not yet described in other plant species as well as basic characterization of their possible role, particularly in the case of type I and MIKC* genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2398-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, 26007, Spain.
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Logroño, 26007, Spain.
| | - María José Carmona
- Departamento de Biotecnología, Escuela Técnica Superior Ingenieros Agrónomos, Universidad Politécnica de Madrid, Madrid, 28040, Spain.
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19
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Wang L, Yin X, Cheng C, Wang H, Guo R, Xu X, Zhao J, Zheng Y, Wang X. Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines. Mol Genet Genomics 2014; 290:825-46. [DOI: 10.1007/s00438-014-0961-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 11/17/2014] [Indexed: 11/28/2022]
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20
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Melzer R, Härter A, Rümpler F, Kim S, Soltis PS, Soltis DE, Theißen G. DEF- and GLO-like proteins may have lost most of their interaction partners during angiosperm evolution. ANNALS OF BOTANY 2014; 114:1431-43. [PMID: 24902716 PMCID: PMC4204782 DOI: 10.1093/aob/mcu094] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS DEFICIENS (DEF)- and GLOBOSA (GLO)-like proteins constitute two sister clades of floral homeotic transcription factors that were already present in the most recent common ancestor (MRCA) of extant angiosperms. Together they specify the identity of petals and stamens in flowering plants. In core eudicots, DEF- and GLO-like proteins are functional in the cell only as heterodimers with each other. There is evidence that this obligate heterodimerization contributed to the canalization of the flower structure of core eudicots during evolution. It remains unknown as to whether this strict heterodimerization is an ancient feature that can be traced back to the MRCA of extant flowering plants or if it evolved later during the evolution of the crown group angiosperms. METHODS The interactions of DEF- and GLO-like proteins of the early-diverging angiosperms Amborella trichopoda and Nuphar advena and of the magnoliid Liriodendron tulipifera were analysed by employing yeast two-hybrid analysis and electrophoretic mobility shift assay (EMSA). Character-state reconstruction, including data from other species as well, was used to infer the ancestral interaction patterns of DEF- and GLO-like proteins. KEY RESULTS The yeast two-hybrid and EMSA data suggest that DEF- and GLO-like proteins from early-diverging angiosperms both homo- and heterodimerize. Character-state reconstruction suggests that the ability to form heterodimeric complexes already existed in the MRCA of extant angiosperms and that this property remained highly conserved throughout angiosperm evolution. Homodimerization of DEF- and GLO-like proteins also existed in the MRCA of all extant angiosperms. DEF-like protein homodimerization was probably lost very early in angiosperm evolution and was not present in the MRCA of eudicots and monocots. GLO-like protein homodimerization might have been lost later during evolution, but very probably was not present in the MRCA of eudicots. CONCLUSIONS The flexibility of DEF- and GLO-like protein interactions in early-diverging angiosperms may be one reason for the highly diverse flower morphologies observed in these species. The results strengthen the hypothesis that a reduction in the number of interaction partners of DEF- and GLO-like proteins, with DEF-GLO heterodimers remaining the only DNA-binding dimers in core eudicots, contributed to developmental robustness, canalization of flower development and the diversification of angiosperms.
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Affiliation(s)
- Rainer Melzer
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany Department of Genetics, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
| | - Andrea Härter
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
| | - Florian Rümpler
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
| | | | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Department of Biology Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
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21
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Sheth BP, Thaker VS. Plant systems biology: insights, advances and challenges. PLANTA 2014; 240:33-54. [PMID: 24671625 DOI: 10.1007/s00425-014-2059-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.
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Affiliation(s)
- Bhavisha P Sheth
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, 360005, Gujarat, India,
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22
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Dhar MK, Sharma R, Koul A, Kaul S. Development of fruit color in Solanaceae: a story of two biosynthetic pathways. Brief Funct Genomics 2014; 14:199-212. [PMID: 24916164 DOI: 10.1093/bfgp/elu018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This review highlights the major differences between the regulation of two important pathways namely anthocyanin and carotenoid pathways, responsible for fruit color generation in Solanaceae mediated by transcription factors (TFs). The anthocyanin pathway is regulated by a common set of TFs (MYB, MYC and WD40) belonging to specific families of DNA-binding proteins. Their regulation is aimed at controlling the type and amount of pigments produced and the physiological conditions (like pH) at which they are finally stored. In the carotenoid pathway, the color diversity depends on the quantity of pigment produced and the point where the pathway is arrested. TFs in the latter case are accordingly found to influence the sequestration and degradation of these pigments, which determines their final concentration in the tissue. TFs (phytochrome interacting factors, MADS-BOX, HB-ZIP and B-ZIP) also regulate important rate-determining steps, which decide the direction in which the pathway proceeds and the point at which it is terminated. In the absence of a clear pattern of TF-mediated regulation, it is suggested that the carotenoid pathway is more significantly influenced by other regulatory methods which need to be explored. It is expected that common factors affecting these pathways are the ones acting much before the initiation of the biosynthesis of respective pigments.
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Preston JC, Jorgensen SA, Jha SG. Functional characterization of duplicated Suppressor of Overexpression of Constans 1-like genes in petunia. PLoS One 2014; 9:e96108. [PMID: 24787903 PMCID: PMC4006870 DOI: 10.1371/journal.pone.0096108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/03/2014] [Indexed: 12/31/2022] Open
Abstract
Flowering time is strictly controlled by a combination of internal and external signals that match seed set with favorable environmental conditions. In the model plant species Arabidopsis thaliana (Brassicaceae), many of the genes underlying development and evolution of flowering have been discovered. However, much remains unknown about how conserved the flowering gene networks are in plants with different growth habits, gene duplication histories, and distributions. Here we functionally characterize three homologs of the flowering gene Suppressor Of Overexpression of Constans 1 (SOC1) in the short-lived perennial Petunia hybrida (petunia, Solanaceae). Similar to A. thaliana soc1 mutants, co-silencing of duplicated petunia SOC1-like genes results in late flowering. This phenotype is most severe when all three SOC1-like genes are silenced. Furthermore, expression levels of the SOC1-like genes Unshaven (UNS) and Floral Binding Protein 21 (FBP21), but not FBP28, are positively correlated with developmental age. In contrast to A. thaliana, petunia SOC1-like gene expression did not increase with longer photoperiods, and FBP28 transcripts were actually more abundant under short days. Despite evidence of functional redundancy, differential spatio-temporal expression data suggest that SOC1-like genes might fine-tune petunia flowering in response to photoperiod and developmental stage. This likely resulted from modification of SOC1-like gene regulatory elements following recent duplication, and is a possible mechanism to ensure flowering under both inductive and non-inductive photoperiods.
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Affiliation(s)
- Jill C. Preston
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, United States of America
| | - Stacy A. Jorgensen
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, United States of America
| | - Suryatapa G. Jha
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, United States of America
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Liu D, Wang D, Qin Z, Zhang D, Yin L, Wu L, Colasanti J, Li A, Mao L. The SEPALLATA MADS-box protein SLMBP21 forms protein complexes with JOINTLESS and MACROCALYX as a transcription activator for development of the tomato flower abscission zone. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:284-96. [PMID: 24274099 DOI: 10.1111/tpj.12387] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/11/2013] [Accepted: 11/15/2013] [Indexed: 05/20/2023]
Abstract
Organ abscission is a key step in a plant's life cycle and is one of the most important agronomic traits for crops. In tomato, two MADS-box genes, JOINTLESS (J) and MACROCAYLYX (MC), have been shown to be implicated in development of the flower abscission zone (AZ), but the molecular mechanisms underlying this process are not well known. We report here that the SEPALLATA (SEP) MADS-box gene SLMBP21 acts as an additional factor for development of the AZ in tomato. We show that knockdown of SLMBP21 abolishes development of the flower AZ, while overexpression of SLMBP21 produces small cells at the proximal section of the pedicel and the peduncle. Bimolecular fluorescence complementation analysis confirms that SLMBP21 interacts with J and MC, and co-immunoprecipitation assays further demonstrates that these three proteins may form higher-order protein complexes. In situ hybridization shows that SLMBP21, J, and MC transcripts accumulate in distinct regions, but overlap at the AZ vasculature. In addition, transactivation assays in yeast show that, of the three interacting proteins, only SLMBP21 can activate reporter gene transcription. RNA-seq analysis furthermore reveals that loss of function of SLMBP21, J, or MC affects a common subset of meristem activity genes including LeWUS and LATERAL SUPPRESSOR that were specifically expressed in the AZ on the tomato flower pedicel. Since SLMBP21 belongs to the FBP9/23 subclade of the SEP gene family, which is absent in Arabidopsis, the SLMBP21-J-MC complex may represent a distinct mechanism for development of the AZ in plants.
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Affiliation(s)
- Danmei Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
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Su CL, Chen WC, Lee AY, Chen CY, Chang YCA, Chao YT, Shih MC. A modified ABCDE model of flowering in orchids based on gene expression profiling studies of the moth orchid Phalaenopsis aphrodite. PLoS One 2013; 8:e80462. [PMID: 24265826 PMCID: PMC3827201 DOI: 10.1371/journal.pone.0080462] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/02/2013] [Indexed: 12/21/2022] Open
Abstract
Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns.
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Affiliation(s)
- Chun-lin Su
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ann-Ying Lee
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chun-Yi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yao-Chien Alex Chang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Ya-Ting Chao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Fan CM, Wang X, Wang YW, Hu RB, Zhang XM, Chen JX, Fu YF. Genome-wide expression analysis of soybean MADS genes showing potential function in the seed development. PLoS One 2013; 8:e62288. [PMID: 23638026 PMCID: PMC3640087 DOI: 10.1371/journal.pone.0062288] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 03/20/2013] [Indexed: 11/19/2022] Open
Abstract
The MADS family is an ancient and best-studied transcription factor and plays fundamental roles in almost every developmental process in plants. In the plant evolutionary history, the whole genome duplication (WGD) events are important not only to the plant species evolution, but to expansion of members of the gene families. Soybean as a model legume crop has experience three rounds of WGD events. Members of some MIKC(C) subfamilies, such as SOC, AGL6, SQUA, SVP, AGL17 and DEF/GLO, were expanded after soybean three rounds of WGD events. And some MIKC(C) subfamilies, MIKC* and type I MADS families had experienced faster birth-and-death evolution and their traces before the Glycine WGD event were not found. Transposed duplication played important roles in tandem arrangements among the members of different subfamilies. According to the expression profiles of type I and MIKC paralog pair genes, the fates of MIKC paralog gene pairs were subfunctionalization, and the fates of type I MADS paralog gene pairs were nonfunctionalization. 137 out of 163 MADS genes were close to 186 loci within 2 Mb genomic regions associated with seed-relative QTLs, among which 115 genes expressed during the seed development. Although MIKC(C) genes kept the important and conserved functions of the flower development, most MIKC(C) genes showed potentially essential roles in the seed development as well as the type I MADS.
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Affiliation(s)
- Cheng-Ming Fan
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Wang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan-Wei Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Rui-Bo Hu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Xiao-Mei Zhang
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian-Xin Chen
- College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yong-Fu Fu
- MOA Key Lab of Soybean Biology (Beijing), National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Pabón-Mora N, Sharma B, Holappa LD, Kramer EM, Litt A. The Aquilegia FRUITFULL-like genes play key roles in leaf morphogenesis and inflorescence development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:197-212. [PMID: 23294330 DOI: 10.1111/tpj.12113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 05/03/2023]
Abstract
The APETALA1/FRUITFULL (AP1/FUL) MADS box transcription factors are best known for the role of AP1 in Arabidopsis sepal and petal identity, the canonical A function of the ABC model of flower development. However, this gene lineage underwent multiple duplication events during angiosperm evolution, providing different taxa with unique gene complements. One such duplication correlates with the origin of the core eudicots, and produced the euAP1 and euFUL clades. Together, euAP1 and euFUL genes function in proper floral meristem identity and repression of axillary meristem growth. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth and fruit development. To investigate the impact of the core eudicot duplication on the functional diversification of this gene lineage, we studied the role of pre-duplication FUL-like genes in columbine (Aquilegia coerulea). Our results show that AqcFL1 genes are broadly expressed in vegetative and reproductive meristems, leaves and flowers. Virus-induced gene silencing of the loci results in plants with increased branching, shorter inflorescences with fewer flowers, and dramatic changes in leaf shape and complexity. However, aqcfl1 plants have normal flowers and fruits. Our results show that, in contrast to characterized AP1/FUL genes, the AqcFL1 loci are either genetically redundant or have been decoupled from the floral genetic program, and play a major role in leaf morphogenesis. We analyze the results in the context of the core eudicot duplication, and discuss the implications of our findings in terms of the genetic regulation of leaf morphogenesis in Aquilegia and other flowering plants.
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Braun P, Aubourg S, Van Leene J, De Jaeger G, Lurin C. Plant protein interactomes. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:161-87. [PMID: 23330791 DOI: 10.1146/annurev-arplant-050312-120140] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps.
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Affiliation(s)
- Pascal Braun
- Department of Plant Systems Biology, Center for Life and Food Sciences Weihenstephan, Technische Universität München (TUM), 85354 Freising-Weihenstephan, Germany.
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Smaczniak C, Immink RGH, Angenent GC, Kaufmann K. Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 2012; 139:3081-98. [PMID: 22872082 DOI: 10.1242/dev.074674] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Members of the MADS-box transcription factor family play essential roles in almost every developmental process in plants. Many MADS-box genes have conserved functions across the flowering plants, but some have acquired novel functions in specific species during evolution. The analyses of MADS-domain protein interactions and target genes have provided new insights into their molecular functions. Here, we review recent findings on MADS-box gene functions in Arabidopsis and discuss the evolutionary history and functional diversification of this gene family in plants. We also discuss possible mechanisms of action of MADS-domain proteins based on their interactions with chromatin-associated factors and other transcriptional regulators.
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Affiliation(s)
- Cezary Smaczniak
- Laboratory of Molecular Biology, Wageningen University, 6708PB Wageningen, The Netherlands
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Zhang J, Khan MR, Tian Y, Li Z, Riss S, He C. Divergences of MPF2-like MADS-domain proteins have an association with the evolution of the inflated calyx syndrome within Solanaceae. PLANTA 2012; 236:1247-1260. [PMID: 22711285 DOI: 10.1007/s00425-012-1684-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/31/2012] [Indexed: 06/01/2023]
Abstract
The inflated calyx syndrome (ICS) is a post-floral novelty within Solanaceae. Previous work has shown that MPF2-like MADS-box genes have been recruited for the development and evolution of ICS through heterotopic expression from vegetative to floral organs. ICS seems to be a plesiomorphic trait in Physaleae, but it has been secondarily lost in some lineages during evolution. We hypothesized that molecular and functional divergences of MPF2-like proteins might play a role in the loss of ICS. In this study we analyzed the phylogeny, selection and various functions of MPF2-like proteins with respect to the evolution of ICS. Directional selection of MPF2-like orthologs toward evolution of ICS was detected. While auto-activation capacity between proteins varies in yeast, MPF2-like interaction with floral MADS-domain proteins is robustly detected, hence substantiating their integration into the floral developmental programs. Dimerization with A- (MPF3) and E-function (PFSEP1/3) proteins seems to be essential for ICS development within Solanaceae. Moreover, the occurrence of the enlarged sepals, reminiscent of ICS, and MPF2-like interactions with these specific partners were observed in transgenic Arabidopsis. The interaction spectrum relevant to ICS seems to be plesiomorphic, reinforcing the plesiomorphy of this trait. The inability of some MPF2-like to interact with either the A-function or any of the E-function partners characterized is correlated with the loss of ICS in the lineages that showed a MPF2-like expression in the calyx. Our findings suggest that, after recruitment of MPF2-like genes for floral development, diversification in their coding region due to directional selection leads to a modification of the MADS-domain protein interacting spectrum, which might serve as a constraint for the evolution of ICS within Solanaceae.
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Affiliation(s)
- Jisi Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China
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Kakinuma M, Inoue M, Morita T, Tominaga H, Maegawa M, Coury DA, Amano H. Isolation and characterization of a SEPALLATA-like gene, ZjMADS1, from marine angiosperm Zostera japonica. MARINE ENVIRONMENTAL RESEARCH 2012; 76:128-137. [PMID: 22014762 DOI: 10.1016/j.marenvres.2011.09.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/31/2011] [Accepted: 09/27/2011] [Indexed: 05/31/2023]
Abstract
In flowering plants, floral homeotic MADS-box genes, which constitute a large multigene family, play important roles in the specification of floral organs as defined by the ABCDE model. In this study, a MADS-box gene, ZjMADS1, was isolated and characterized from the marine angiosperm Zostera japonica. The predicted length of the ZjMADS1 protein was 246 amino acids (AA), and the AA sequence was most similar to those of the SEPALLATA (SEP) subfamily, corresponding to E-function genes. Southern blot analysis suggested the presence of two SEP3-like genes in the Z. japonica genome. ZjMADS1 mRNA levels were extremely high in the spadices, regardless of the developmental stage, compared to other organs from the reproductive and vegetative shoots. These results suggest that the ZjMADS1 gene may be involved in spadix development in Z. japonica and act as an E-function gene in floral organ development in marine angiosperms.
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Affiliation(s)
- Makoto Kakinuma
- Laboratory of Marine Biochemistry, Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan.
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Ruokolainen S, Ng YP, Albert VA, Elomaa P, Teeri TH. Over-expression of the Gerbera hybrida At-SOC1-like1 gene Gh-SOC1 leads to floral organ identity deterioration. ANNALS OF BOTANY 2011; 107:1491-9. [PMID: 21572092 PMCID: PMC3108810 DOI: 10.1093/aob/mcr112] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/08/2011] [Accepted: 03/30/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS The family of MADS box genes is involved in a number of processes besides controlling floral development. In addition to supplying homeotic functions defined by the ABC model, they influence flowering time and transformation of vegetative meristem into inflorescence meristem, and have functions in roots and leaves. Three Gerbera hybrida At-SOC1-like genes (Gh-SOC1-Gh-SOC3) were identified among gerbera expressed sequence tags. METHODS Evolutionary relationships between SOC1-like genes from gerbera and other plants were studied by phylogenetic analysis. The function of the gerbera gene Gh-SOC1 in gerbera floral development was studied using expression analysis, protein-protein interaction assays and reverse genetics. Transgenic gerbera lines over-expressing or downregulated for Gh-SOC1 were obtained using Agrobacterium transformation and investigated for their floral phenotype. KEY RESULTS Phylogenetic analysis revealed that the closest paralogues of At-SOC1 are Gh-SOC2 and Gh-SOC3. Gh-SOC1 is a more distantly related paralogue, grouping together with a number of other At-SOC1 paralogues from arabidopsis and other plant species. Gh-SOC1 is inflorescence abundant and no expression was seen in vegetative parts of the plant. Ectopic expression of Gh-SOC1 did not promote flowering, but disturbed the development of floral organs. The epidermal cells of ray flower petals appeared shorter and their shape was altered. The colour of ray flower petals differed from that of the wild-type petals by being darker red on the adaxial side and greenish on the abaxial surface. Several protein-protein interactions with other gerbera MADS domain proteins were identified. CONCLUSIONS The At-SOC1 paralogue in gerbera shows a floral abundant expression pattern. A late petal expression might indicate a role in the final stages of flower development. Over-expression of Gh-SOC1 led to partial loss of floral identity, but did not affect flowering time. Lines where Gh-SOC1 was downregulated did not show a phenotype. Several gerbera MADS domain proteins interacted with Gh-SOC1.
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Affiliation(s)
- Satu Ruokolainen
- Gerbera Laboratory, Department of Agricultural Sciences, PO Box 27 (Latokartanonkaari 7), FIN-00014 University of Helsinki, Finland
| | - Yan Peng Ng
- Gerbera Laboratory, Department of Agricultural Sciences, PO Box 27 (Latokartanonkaari 7), FIN-00014 University of Helsinki, Finland
| | - Victor A. Albert
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (SUNY), Buffalo, NY 14260-1300, USA
| | - Paula Elomaa
- Gerbera Laboratory, Department of Agricultural Sciences, PO Box 27 (Latokartanonkaari 7), FIN-00014 University of Helsinki, Finland
| | - Teemu H. Teeri
- Gerbera Laboratory, Department of Agricultural Sciences, PO Box 27 (Latokartanonkaari 7), FIN-00014 University of Helsinki, Finland
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Abstract
Most transcription factors fulfill their role in protein complexes. As a consequence, information about their interaction capacity sheds light on a protein's function and the molecular mechanism underlying this activity. The yeast two-hybrid GAL4 (Y2H) assay is a powerful method to unravel and identify the composition of protein complexes. This in vivo based system makes use of two functional protein domains of the GAL4 transcription factor, each fused to a protein of interest. Upon interaction between the two proteins under study, a transcriptional activator gets reconstituted and reporter genes get activated, allowing the yeast to grow on selective medium. In this chapter protocols are given for Y2H library screening, directed Y2H screening, Y2H matrix screening, and YnH screening involving more than two proteins.
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Affiliation(s)
- Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México.
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Lü S, Fan Y, Liu L, Liu S, Zhang W, Meng Z. Ectopic expression of TrPI, a Taihangia rupestris (Rosaceae) PI ortholog, causes modifications of vegetative architecture in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2010; 167:1613-21. [PMID: 20828868 DOI: 10.1016/j.jplph.2010.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 05/30/2010] [Accepted: 06/06/2010] [Indexed: 05/13/2023]
Abstract
In eudicotyledonous model plants, the B-function genes encode a pair of partner MADS-domain proteins, APETALA3 (AP3) and PISTILLATA (PI) in Arabidopsis and DEFICIENS (DEF) and GLOBOSA (GLO) in Antirrhinum. These proteins, which must form heterodimers to function, are required to specify petal and stamen identity during flower development. Here, we report cloning and characterization of TrPI (Taihangia rupestris PISTILLATA), a PI/GLO-like gene from the core eudicot species Taihangia rupestris (Rosaceae). DNA gel blot analysis showed that TrPI is a single copy gene in the T. rupestris genome. Quantitative RT-PCR and in situ hybridization analyses revealed that TrPI is transcribed in both the vegetative and reproductive organs at different levels. Ectopic expression of TrPI in Arabidopsis caused severe modifications in vegetative plant architecture, including rosette leaves and cauline leaves arranged in a non-spiral phyllotaxy, and a flattened primary inflorescence stem that produced two or three offshoots at the base, middle or top. Moreover, we show that the TrPI gene is capable of rescuing pi-1 mutant phenotypes. Yeast two-hybrid assays showed that TrPI forms homodimers. Taken together, these results show that TrPI might function in regulating plant architecture in addition to its function as a floral organ identity gene in T. rupestris, suggesting that the TrPI protein has biochemical features that distinguish it from the well-studied orthologs, PI and GLO.
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Affiliation(s)
- Shanhua Lü
- School of Agriculture, Liaocheng University, Liaocheng 252059, China
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Abstract
MADS-box genes encode transcription factors that are key regulators of plant inflorescence and flower development. We examined DNA sequence variation in 32 maize MADS-box genes and 32 randomly chosen maize loci and investigated their involvement in maize domestication and improvement. Using neutrality tests and a test based on coalescent simulation of a bottleneck model, we identified eight MADS-box genes as putative targets of the artificial selection associated with domestication. According to neutrality tests, one additional MADS-box gene appears to have been under selection during modern agricultural improvement of maize. For random loci, two genes were indicated as targets of selection during domestication and four additional genes were indicated to be candidate-selected loci for maize improvement. These results suggest that MADS-box genes were more frequent targets of selection during domestication than genes chosen at random from the genome.
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Wang YQ, Melzer R, Theissen G. Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of 'floral quartets'. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:177-90. [PMID: 21070403 DOI: 10.1111/j.1365-313x.2010.04325.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Several lines of evidence suggest that the identity of floral organs in angiosperms is specified by multimeric transcription factor complexes composed of MADS-domain proteins. These bind to specific cis-regulatory elements ('CArG-boxes') of their target genes involving DNA-loop formation, thus constituting 'floral quartets'. Gymnosperms, angiosperms' closest relatives, contain orthologues of floral homeotic genes, but when and how the interactions constituting floral quartets were established during evolution has remained unknown. We have comprehensively studied the dimerization and DNA-binding of several classes of MADS-domain proteins from the gymnosperm Gnetum gnemon. Determination of protein-protein and protein-DNA interactions by yeast two-hybrid, in vitro pull-down and electrophoretic mobility shift assays revealed complex patterns of homo- and heterodimerization among orthologues of floral homeotic class B, class C and class E proteins and B(sister) proteins. Using DNase I footprint assays we demonstrate that both orthologues of class B with C proteins, and orthologues of class C proteins alone, but not orthologues of class B proteins alone can loop DNA in floral quartet-like complexes. This is in contrast to class B and class C proteins from angiosperms, which require other factors such as class E floral homeotic proteins to 'glue' them together in multimeric complexes. Our findings suggest that the evolutionary origin of floral quartet formation is based on the interaction of different DNA-bound homodimers, does not depend on class E proteins, and predates the origin of angiosperms.
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Affiliation(s)
- Yong-Qiang Wang
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, Germany
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Ruokolainen S, Ng YP, Broholm SK, Albert VA, Elomaa P, Teeri TH. Characterization of SQUAMOSA-like genes in Gerbera hybrida, including one involved in reproductive transition. BMC PLANT BIOLOGY 2010; 10:128. [PMID: 20579337 PMCID: PMC3017819 DOI: 10.1186/1471-2229-10-128] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 06/25/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND The flowering process in plants proceeds through the induction of an inflorescence meristem triggered by several pathways. Many of the genes associated with both the flowering process and floral architecture encode transcription factors of the MADS domain family. Gerbera, a member of the sunflower family, Asteraceae, bears compressed inflorescence heads (capitula) with three different flower types characterized by differences in both sexuality and floral symmetry. To understand how such a complex inflorescence structure is achieved at the molecular level, we have characterized the array of Gerbera MADS box genes. The high number of SQUAMOSA-like genes in Gerbera compared to other model species raised the question as to whether they may relate to Gerbera's complex inflorescence structure and whether or not a homeotic A function is present. RESULTS In this paper we describe six Gerbera genes related to the SQUAMOSA/APETALA1/FRUITFULL genes of snapdragon and Arabidopsis. Based on phylogenetic analysis of the entire gene lineage, our data indicates that GSQUA1 and GSQUA3 are members of the SQUA/AP1 clade, while GSQUA2, GSQUA4, GSQUA5 and GSQUA6 are co-orthologs of the Arabidopsis FUL gene. GSQUA1/GSQUA3 and GSQUA4/GSQUA5/GSQUA6, respectively, represent several gene duplication events unknown in the model systems that may be specific to either Gerbera or Asteraceae. GSQUA genes showed specific expression profiles. GSQUA1, GSQUA2, and GSQUA5 were inflorescence abundant, while GSQUA3, GSQUA4, and GSQUA6 expression was also detected in vegetative organs. Overexpression of GSQUA2 in Gerbera led to accelerated flowering, dwarfism and vegetative abnormalities, all new and specific phenomena observed in transgenic Gerbera plants with modified MADS box gene expression. CONCLUSIONS Based on expression patterns, none of the Gerbera SQUA-like genes are likely to control flower organ identity in the sense of the floral A function. However, our data shows that the FUL-like gene GSQUA2 plays a vital role in meristem transition. The roles of other GSQUA-genes in Gerbera floral development are intriguing, but require still further study.
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Affiliation(s)
- Satu Ruokolainen
- Gerbera Laboratory, Department of Agricultural Sciences, P.O. Box 27 (Latokartanonkaari 7), FIN - 00014 University of Helsinki, Finland
| | - Yan Peng Ng
- Biomedicum Helsinki, P.O. Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, Finland
| | - Suvi K Broholm
- Gerbera Laboratory, Department of Agricultural Sciences, P.O. Box 27 (Latokartanonkaari 7), FIN - 00014 University of Helsinki, Finland
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY, 14260, USA
| | - Paula Elomaa
- Gerbera Laboratory, Department of Agricultural Sciences, P.O. Box 27 (Latokartanonkaari 7), FIN - 00014 University of Helsinki, Finland
| | - Teemu H Teeri
- Gerbera Laboratory, Department of Agricultural Sciences, P.O. Box 27 (Latokartanonkaari 7), FIN - 00014 University of Helsinki, Finland
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Matias-Hernandez L, Battaglia R, Galbiati F, Rubes M, Eichenberger C, Grossniklaus U, Kater MM, Colombo L. VERDANDI is a direct target of the MADS domain ovule identity complex and affects embryo sac differentiation in Arabidopsis. THE PLANT CELL 2010; 22:1702-15. [PMID: 20581305 PMCID: PMC2910977 DOI: 10.1105/tpc.109.068627] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 05/23/2010] [Accepted: 06/10/2010] [Indexed: 05/19/2023]
Abstract
In Arabidopsis thaliana, the three MADS box genes SEEDSTICK (STK), SHATTERPROOF1 (SHP1), and SHP2 redundantly regulate ovule development. Protein interaction studies have shown that a multimeric complex composed of the ovule identity proteins together with the SEPALLATA MADS domain proteins is necessary to determine ovule identity. Despite the extensive knowledge that has become available about these MADS domain transcription factors, little is known regarding the genes that they regulate. Here, we show that STK, SHP1, and SHP2 redundantly regulate VERDANDI (VDD), a putative transcription factor that belongs to the plant-specific B3 superfamily. The vdd mutant shows defects during the fertilization process resulting in semisterility. Analysis of the vdd mutant female gametophytes indicates that antipodal and synergid cell identity and/or differentiation are affected. Our results provide insights into the pathways regulated by the ovule identity factors and the role of the downstream target gene VDD in female gametophyte development.
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Affiliation(s)
| | - Raffaella Battaglia
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, 20133 Milano, Italy
| | - Francesca Galbiati
- Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milano, Italy
| | - Marco Rubes
- Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milano, Italy
| | - Christof Eichenberger
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland
| | - Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland
| | - Martin M. Kater
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, 20133 Milano, Italy
| | - Lucia Colombo
- Dipartimento di Biologia, Università degli Studi di Milano, 20133 Milano, Italy
- Address correspondence to
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Elitzur T, Vrebalov J, Giovannoni JJ, Goldschmidt EE, Friedman H. The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:1523-35. [PMID: 20200120 PMCID: PMC2837265 DOI: 10.1093/jxb/erq017] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 01/19/2010] [Accepted: 01/20/2010] [Indexed: 05/18/2023]
Abstract
Six MaMADS-box genes have been cloned from the banana fruit cultivar Grand Nain. The similarity of these genes to tomato LeRIN is low and neither MaMADS2 nor MaMADS1 complement the tomato rin mutation. Nevertheless, the expression patterns, specifically in fruit and the induction during ripening and in response to ethylene and 1-MCP, suggest that some of these genes may participate in ripening. MaMADS1, 2, and 3, are highly expressed in fruit only, while the others are expressed in fruit as well as in other organs. Moreover, the suites of MaMADS-box genes and their temporal expression differ in peel and pulp during ripening. In the pulp, the increase in MaMADS2, 3, 4, and 5 expression preceded an increase in ethylene production, but coincides with the CO(2) peak. However, MaMADS1 expression in pulp coincided with ethylene production, but a massive increase in its expression occurred late during ripening, together with a second wave in the expression of MaMADS2, 3, and 4. In the peel, on the other hand, an increase in expression of MaMADS1, 3, and to a lesser degree also of MaMADS4 and 2 coincided with an increase in ethylene production. Except MaMADS3, which was induced by ethylene in pulp and peel, only MaMADS4, and 5 in pulp and MaMADS1 in peel were induced by ethylene. 1-MCP applied at the onset of the increase in ethylene production, increased the levels of MaMADS4 and MaMADS1 in pulp, while it decreased MaMADS1, 3, 4, and 5 in peel, suggesting that MaMADS4 and MaMADS1 are negatively controlled by ethylene at the onset of ethylene production only in pulp. Only MaMADS2 is neither induced by ethylene nor by 1-MCP, and it is expressed mainly in pulp. Our results suggest that two independent ripening programs are employed in pulp and peel which involve the activation of mainly MaMADS2, 4, and 5 and later on also MaMADS1 in pulp, and mainly MaMADS1, and 3 in peel. Hence, our results are consistent with MaMADS2, a SEP3 homologue, acting in the pulp upstream of the increase in ethylene production similarly to LeMADS-RIN.
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Affiliation(s)
- Tomer Elitzur
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), the Volcani Center, PO Box 6, Bet Dagan 50250, Israel
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Kennedy-Leigh Centre for Horticultural Research, Faculty of Agriculture, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel
| | - Julia Vrebalov
- Boyce Thompson Institute for Plant Research and USDA-ARS, Tower Road, Cornell Campus, Ithaca NY, USA
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research and USDA-ARS, Tower Road, Cornell Campus, Ithaca NY, USA
| | - Eliezer E. Goldschmidt
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Kennedy-Leigh Centre for Horticultural Research, Faculty of Agriculture, Food and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot, Israel
| | - Haya Friedman
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization (ARO), the Volcani Center, PO Box 6, Bet Dagan 50250, Israel
- To whom correspondence should be addressed: E-mail:
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Immink RG, Kaufmann K, Angenent GC. The ‘ABC’ of MADS domain protein behaviour and interactions. Semin Cell Dev Biol 2010; 21:87-93. [DOI: 10.1016/j.semcdb.2009.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 10/23/2009] [Indexed: 02/05/2023]
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Litt A, Kramer EM. The ABC model and the diversification of floral organ identity. Semin Cell Dev Biol 2009; 21:129-37. [PMID: 19948236 DOI: 10.1016/j.semcdb.2009.11.019] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 11/16/2009] [Accepted: 11/23/2009] [Indexed: 01/22/2023]
Abstract
Broad studies of the ABC program across angiosperms have found that interactions between gene duplication, biochemical evolution, shifts in gene expression and modification of existing identity programs have been critical to the evolution of floral morphology. Several themes can be recognized in this context. First, the original concept of "A" function applies only very narrowly to Arabidopsis and its close relatives. Second, while many types of petaloid organs are associated with the expression of AP3/PI homologs, there is growing evidence that there are other genetic mechanisms for producing petaloidy, especially in first whorl organs. Third, pre-existing organ identity programs can be modified to yield novel organ types, often in association with gene duplications. Lastly, there are many aspects of ABC gene function outside the major model systems that remain a mystery, perhaps none more so than the C-terminal amino acid motifs that distinguish specific ABC gene lineages.
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Affiliation(s)
- Amy Litt
- The New York Botanical Garden, Bronx, NY 10458, USA.
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Wang Z, Zhang Q. Genome-wide identification and evolutionary analysis of the animal specific ETS transcription factor family. Evol Bioinform Online 2009; 5:119-31. [PMID: 20011068 PMCID: PMC2789578 DOI: 10.4137/ebo.s2948] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified 207 ETS genes which encode 321 ETS TFs from ten animal species. Of the 321 ETS TFs, 155 contain only an ETS domain, about 50% contain a ETS_PEA3_N or a SAM_PNT domain in addition to an ETS domain, the rest (only four) contain a second ETS domain or a second ETS_PEA3_N domain or an another domain (AT_hook or DNA_pol_B). A Neighbor-Joining phylogenetic tree was constructed using the amino acid sequences of the ETS domain of the ETS TFs. The results revealed that the ETS genes of the ten species can be divided into two distinct groups. Group I contains one nematode ETS gene and 18 vertebrate animal ETS genes. Group II contains the majority of the ETS TFs and can be further divided into eleven subgroups. The sequence motifs outside the DNA-binding domain and the conservation of the exon-intron structural patterns of the ETS TFs in human, cattle, and chicken further support the phylogenetic classification among these ETS TFs. Extensive duplication of the ETS genes was found in the genome of each species. The duplicated ETS genes account for ~69% of the total of ETS genes. Furthermore, we also found there are ETS gene clusters in all of the ten animal species. Statistical analysis of the Gene Ontology annotations of the ETS genes showed that the ETS proteins tend to be related to RNA biosynthetic process, biopolymer metabolic process and macromolecule metabolic process expected from the common GO categories of transcriptional factors. We also discussed the functional conservation and diversification of ETS TFs.
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Affiliation(s)
- Zhipeng Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Rijpkema AS, Zethof J, Gerats T, Vandenbussche M. The petunia AGL6 gene has a SEPALLATA-like function in floral patterning. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 60:1-9. [PMID: 19453449 DOI: 10.1111/j.1365-313x.2009.03917.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
SEPALLATA (SEP) MADS-box genes are required for the regulation of floral meristem determinacy and the specification of sepals, petals, stamens, carpels and ovules, specifically in angiosperms. The SEP subfamily is closely related to the AGAMOUS LIKE6 (AGL6) and SQUAMOSA (SQUA) subfamilies. So far, of these three groups only AGL6-like genes have been found in extant gymnosperms. AGL6 genes are more similar to SEP than to SQUA genes, both in sequence and in expression pattern. Despite the ancestry and wide distribution of AGL6-like MADS-box genes, not a single loss-of-function mutant exhibiting a clear phenotype has yet been reported; consequently the function of AGL6-like genes has remained elusive. Here, we characterize the Petunia hybrida AGL6 (PhAGL6, formerly called PETUNIA MADS BOX GENE4/pMADS4) gene, and show that it functions redundantly with the SEP genes FLORAL BINDING PROTEIN2 (FBP2) and FBP5 in petal and anther development. Moreover, expression analysis suggests a function for PhAGL6 in ovary and ovule development. The PhAGL6 and FBP2 proteins interact in in vitro experiments overall with the same partners, indicating that the two proteins are biochemically quite similar. It will be interesting to determine the functions of AGL6-like genes of other species, especially those of gymnosperms.
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Affiliation(s)
- Anneke S Rijpkema
- Plant Genetics, IWWR, Radboud University Nijmegen, 6525 ED, Nijmegen, The Netherlands
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Tani E, Polidoros AN, Flemetakis E, Stedel C, Kalloniati C, Demetriou K, Katinakis P, Tsaftaris AS. Characterization and expression analysis of AGAMOUS-like, SEEDSTICK-like, and SEPALLATA-like MADS-box genes in peach (Prunus persica) fruit. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:690-700. [PMID: 19409800 DOI: 10.1016/j.plaphy.2009.03.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 03/23/2009] [Accepted: 03/31/2009] [Indexed: 05/06/2023]
Abstract
MADS-box genes encode transcriptional regulators that are critical for flowering, flower organogenesis and plant development. Although there are extensive reports on genes involved in flower organogenesis in model and economically important plant species, there are few reports on MADS-box genes in woody plants. In this study, we have cloned and characterized AGAMOUS (AG), SEEDSTICK (STK) and SEPALLATA (SEP) homologs from peach tree (Prunus persica L. Batsch) and studied their expression patterns in different tissues as well as in fruit pericarp during pit hardening. AG- STK- and SEP-like homologs, representative of the C-, D-, E-like MADS-box gene lineages, respectively, play key roles in stamen, carpel, ovule and fruit development in Arabidopsis thaliana. Sequence similarities, phylogenetic analysis and structural characteristics were used to provide classification of the isolated genes in type C (PPERAG), type D (PPERSTK) and type E (PPERSEP1, PPERSEP3, PPERFB9) organ identity genes. Expression patterns were determined and in combination with phylogenetic data provided useful indications on the function of these genes. These data suggest the involvement of MADS-box genes in peach flower and fruit development and provide further evidence for the role of these genes in woody perennial trees that is compatible with their function in model plant species.
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Affiliation(s)
- Eleni Tani
- Institute of Agrobiotechnology (IN.A.), CERTH, 6th km Charilaou-Thermis Road, Thermi GR-570 01, Greece
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Shan H, Zahn L, Guindon S, Wall PK, Kong H, Ma H, DePamphilis CW, Leebens-Mack J. Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Mol Biol Evol 2009; 26:2229-44. [PMID: 19578156 DOI: 10.1093/molbev/msp129] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Phylogenomic analyses show that gene and genome duplication events have led to the diversification of transcription factor gene families throughout the evolutionary history of land plants and that gene duplications have played an important role in shaping regulatory networks influencing key phenotypic characters including floral development and flowering time. A molecular evolutionary investigation of the mode and tempo of selection acting on the angiosperm MADS box AP1/SQUA, AP3/PI, AG/AGL11, and SEP gene subfamilies revealed site-specific patterns of shifting evolutionary constraint throughout angiosperm history. Specific positions in the four canonical MADS box gene regions, especially K domains and C-terminal regions of all four of these MADS box gene subfamilies exhibited clade-specific shifts in selective constraint following concerted duplication events. Moreover, the frequency of site-specific shifts in constraint was correlated with gene duplications and early angiosperm diversification. We hypothesize that coevolution among interacting MADS box proteins may be responsible for simultaneous increases in the ratio of nonsynonymous to synonymous substitutions (d(N)/d(S) = omega) early in angiosperm history and following concerted duplication events.
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Affiliation(s)
- Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Xiangshan, Beijing, People's Republic of China
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Mondragón-Palomino M, Hiese L, Härter A, Koch MA, Theissen G. Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses. BMC Evol Biol 2009; 9:81. [PMID: 19383167 PMCID: PMC2680841 DOI: 10.1186/1471-2148-9-81] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Accepted: 04/21/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Positive selection is recognized as the prevalence of nonsynonymous over synonymous substitutions in a gene. Models of the functional evolution of duplicated genes consider neofunctionalization as key to the retention of paralogues. For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification. However, the relative impact of these two factors has not been systematically evaluated. Class B MADS-box genes, comprising DEF-like and GLO-like genes, encode developmental transcription factors essential for establishment of perianth and male organ identity in the flowers of angiosperms. Here, we contrast the role of positive selection and the known divergence in expression patterns of genes encoding class B-like MADS-box transcription factors from monocots, with emphasis on the family Orchidaceae and the order Poales. Although in the monocots these two groups are highly diverse and have a strongly canalized floral morphology, there is no information on the role of positive selection in the evolution of their distinctive flower morphologies. Published research shows that in Poales, class B-like genes are expressed in stamens and in lodicules, the perianth organs whose identity might also be specified by class B-like genes, like the identity of the inner tepals of their lily-like relatives. In orchids, however, the number and pattern of expression of class B-like genes have greatly diverged. RESULTS The DEF-like genes from Orchidaceae form four well-supported, ancient clades of orthologues. In contrast, orchid GLO-like genes form a single clade of ancient orthologues and recent paralogues. DEF-like genes from orchid clade 2 (OMADS3-like genes) are under less stringent purifying selection than the other orchid DEF-like and GLO-like genes. In comparison with orchids, purifying selection was less stringent in DEF-like and GLO-like genes from Poales. Most importantly, positive selection took place before the major organ reduction and losses in the floral axis that eventually yielded the zygomorphic grass floret. CONCLUSION In DEF-like genes of Poales, positive selection on the region mediating interactions with other proteins or DNA could have triggered the evolution of the regulatory mechanisms behind the development of grass-specific reproductive structures. Orchidaceae show a different trend, where gene duplication and transcriptional divergence appear to have played a major role in the canalization and modularization of perianth development.
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Immink RGH, Tonaco IAN, de Folter S, Shchennikova A, van Dijk ADJ, Busscher-Lange J, Borst JW, Angenent GC. SEPALLATA3: the 'glue' for MADS box transcription factor complex formation. Genome Biol 2009; 10:R24. [PMID: 19243611 PMCID: PMC2688274 DOI: 10.1186/gb-2009-10-2-r24] [Citation(s) in RCA: 200] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 12/16/2008] [Accepted: 02/25/2009] [Indexed: 11/10/2022] Open
Abstract
A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing. Background Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and are thought to assemble into multimeric complexes. In this study a large-scale yeast three-hybrid screen is utilized to provide insight into the higher-order complex formation capacity of the Arabidopsis MADS box family. SEPALLATA3 (SEP3) has been shown to mediate complex formation and, therefore, special attention is paid to this factor in this study. Results In total, 106 multimeric complexes were identified; in more than half of these at least one SEP protein was present. Besides the known complexes involved in determining floral organ identity, various complexes consisting of combinations of proteins known to play a role in floral organ identity specification, and flowering time determination were discovered. The capacity to form this latter type of complex suggests that homeotic factors play essential roles in down-regulation of the MADS box genes involved in floral timing in the flower via negative auto-regulatory loops. Furthermore, various novel complexes were identified that may be important for the direct regulation of the floral transition process. A subsequent detailed analysis of the APETALA3, PISTILLATA, and SEP3 proteins in living plant cells suggests the formation of a multimeric complex in vivo. Conclusions Overall, these results provide strong indications that higher-order complex formation is a general and essential molecular mechanism for plant MADS box protein functioning and attribute a pivotal role to the SEP3 'glue' protein in mediating multimerization.
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Affiliation(s)
- Richard G H Immink
- Plant Research International, Bioscience, Droevendaalsesteeg 1, Wageningen, the Netherlands.
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Yu L, Patibanda V, Smith HMS. A novel role of BELL1-like homeobox genes, PENNYWISE and POUND-FOOLISH, in floral patterning. PLANTA 2009; 229:693-707. [PMID: 19082619 DOI: 10.1007/s00425-008-0867-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 11/18/2008] [Indexed: 05/21/2023]
Abstract
Flowers are determinate shoots comprised of perianth and reproductive organs displayed in a whorled phyllotactic pattern. Floral organ identity genes display region-specific expression patterns in the developing flower. In Arabidopsis, floral organ identity genes are activated by LEAFY (LFY), which functions with region-specific co-regulators, UNUSUAL FLORAL ORGANS (UFO) and WUSCHEL (WUS), to up-regulate homeotic genes in specific whorls of the flower. PENNYWISE (PNY) and POUND-FOOLISH (PNF) are redundant functioning BELL1-like homeodomain proteins that are expressed in shoot and floral meristems. During flower development, PNY functions with a co-repressor complex to down-regulate the homeotic gene, AGAMOUS (AG), in the outer whorls of the flower. However, the function of PNY as well as PNF in regulating floral organ identity in the central whorls of the flower is not known. In this report, we show that combining mutations in PNY and PNF enhance the floral patterning phenotypes of weak and strong alleles of lfy, indicating that these BELL1-like homeodomain proteins play a role in the specification of petals, stamens and carpels during flower development. Expression studies show that PNY and PNF positively regulate the homeotic genes, APETALA3 and AG, in the inner whorls of the flower. Moreover, PNY and PNF function in parallel with LFY, UFO and WUS to regulate homeotic gene expression. Since PNY and PNF interact with the KNOTTED1-like homeodomain proteins, SHOOTMERISTEMLESS (STM) and KNOTTED-LIKE from ARABIDOPSIS THALIANA2 (KNAT2) that regulate floral development, we propose that PNY/PNF-STM and PNY/PNF-KNAT2 complexes function in the inner whorls to regulate flower patterning events.
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Affiliation(s)
- Lifeng Yu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters. Int J Mol Sci 2009; 10:116-132. [PMID: 19333437 PMCID: PMC2662457 DOI: 10.3390/ijms10010116] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Revised: 12/15/2008] [Accepted: 12/18/2008] [Indexed: 11/18/2022] Open
Abstract
The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.
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Chapter 10 FRET and FLIM applications in plants. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s0075-7535(08)00010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
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