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Sun J, Zheng Y, Guo J, Zhang Y, Liu Y, Tao Y, Wang M, Liu T, Liu Y, Li X, Zhang X, Zhao L. GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height. PLANT PHYSIOLOGY 2023; 193:775-791. [PMID: 37204820 DOI: 10.1093/plphys/kiad293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/13/2023] [Accepted: 04/26/2023] [Indexed: 05/20/2023]
Abstract
Flowering time, maturity, and plant height are crucial agronomic traits controlled by photoperiod that affect soybean (Glycine max [L.] Merr.) yield and regional adaptability. It is important to cultivate soybean cultivars of earlier maturity that adapt to high latitudes. GAMYB-binding protein 1 (GmGBP1), a member of the SNW/SKIP family of transcriptional coregulators in soybean, is induced by short days and interacts with transcription factor GAMYB (GmGAMYB) during photoperiod control of flowering time and maturity. In the present study, GmGBP1:GmGBP1 soybean showed the phenotypes of earlier maturity and higher plant height. Chromatin immunoprecipitation sequencing (ChIP-seq) assays of GmGBP1-binding sites and RNA sequencing (RNA-seq) of differentially expressed transcripts in GmGBP1:GmGBP1 further identified potential targets of GmGBP1, including small auxin-up RNA (GmSAUR). GmSAUR:GmSAUR soybean also showed earlier maturity and higher plant height. GmGBP1 interacted with GmGAMYB, bound to the promoter of GmSAUR and promoted the expression of FLOWER LOCUS T homologs 2a (GmFT2a) and FLOWERING LOCUS D LIKE 19 (GmFDL19). Flowering repressors such as GmFT4 were negatively regulated, resulting in earlier flowering and maturity. Furthermore, the interaction of GmGBP1 with GmGAMYB increased the gibberellin (GA) signal to promote height and hypocotyl elongation by activating GmSAUR and GmSAUR bound to the promoter of the GA-positive activating regulator gibberellic acid-stimulated Arabidopsis 32 (GmGASA32). These results suggested a photoperiod regulatory pathway in which the interaction of GmGBP1 with GmGAMYB directly activated GmSAUR to promote earlier maturity and plant height in soybean.
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Affiliation(s)
- Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yuhong Zheng
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Jinpeng Guo
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yuntong Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Ying Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yahan Tao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Mengyuan Wang
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Tianmeng Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Yangyang Liu
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | - Xin Li
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
| | | | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China
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Wu T, Lu S, Cai Y, Xu X, Zhang L, Chen F, Jiang B, Zhang H, Sun S, Zhai H, Zhao L, Xia Z, Hou W, Kong F, Han T. Molecular breeding for improvement of photothermal adaptability in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:60. [PMID: 37496825 PMCID: PMC10366068 DOI: 10.1007/s11032-023-01406-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
Soybean (Glycine max (L.) Merr.) is a typical short-day and temperate crop that is sensitive to photoperiod and temperature. Responses of soybean to photothermal conditions determine plant growth and development, which affect its architecture, yield formation, and capacity for geographic adaptation. Flowering time, maturity, and other traits associated with photothermal adaptability are controlled by multiple major-effect and minor-effect genes and genotype-by-environment interactions. Genetic studies have identified at least 11 loci (E1-E4, E6-E11, and J) that participate in photoperiodic regulation of flowering time and maturity in soybean. Molecular cloning and characterization of major-effect flowering genes have clarified the photoperiod-dependent flowering pathway, in which the photoreceptor gene phytochrome A, circadian evening complex (EC) components, central flowering repressor E1, and FLOWERING LOCUS T family genes play key roles in regulation of flowering time, maturity, and adaptability to photothermal conditions. Here, we provide an overview of recent progress in genetic and molecular analysis of traits associated with photothermal adaptability, summarizing advances in molecular breeding practices and tools for improving these traits. Furthermore, we discuss methods for breeding soybean varieties with better adaptability to specific ecological regions, with emphasis on a novel strategy, the Potalaization model, which allows breeding of widely adapted soybean varieties through the use of multiple molecular tools in existing elite widely adapted varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01406-z.
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Affiliation(s)
- Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Yupeng Cai
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xin Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Honglei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education of China, Northeast Agricultural University, Harbin, 150030 China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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3
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Rosenkranz RRE, Ullrich S, Löchli K, Simm S, Fragkostefanakis S. Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2022; 13:911277. [PMID: 35812973 PMCID: PMC9260394 DOI: 10.3389/fpls.2022.911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/26/2022] [Indexed: 05/26/2023]
Abstract
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
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Affiliation(s)
| | - Sarah Ullrich
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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4
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Li Z, Tang M, Luo D, Kashif MH, Cao S, Zhang W, Hu Y, Huang Z, Yue J, Li R, Chen P. Integrated Methylome and Transcriptome Analyses Reveal the Molecular Mechanism by Which DNA Methylation Regulates Kenaf Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:709030. [PMID: 34512693 PMCID: PMC8428968 DOI: 10.3389/fpls.2021.709030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/26/2021] [Indexed: 05/03/2023]
Abstract
DNA methylation regulates key biological processes in plants. In this study, kenaf seedlings were pretreated with the DNA methylation inhibitor 5-azacytidine (5-azaC) (at concentrations of 0, 100, 200, 400, and 600 μM), and the results showed that pretreatment with 200 μM 5-azaC promoted flowering most effectively. To elucidate the underlying mechanism, phytohormone, adenosine triphosphate (ATP), and starch contents were determined, and genome-wide DNA methylation and transcriptome analyses were performed on anthers pretreated with 200 μM 5-azaC (5-azaC200) or with no 5-azaC (control conditions; 5-azaC0). Biochemical analysis revealed that 5-azaC pretreatment significantly reduced indoleacetic acid (IAA) and gibberellic acid (GA) contents and significantly increased abscisic acid (ABA) and ATP contents. The starch contents significantly increased in response to 200 and 600 μM 5-azaC. Further genome-wide DNA methylation analysis revealed 451 differentially methylated genes (DMGs) with 209 up- and 242 downregulated genes. Transcriptome analysis showed 3,986 differentially expressed genes (DEGs), with 2,171 up- and 1,815 downregulated genes. Integrated genome-wide DNA methylation and transcriptome analyses revealed 72 genes that were both differentially methylated and differentially expressed. These genes, which included ARFs, PP2C, starch synthase, FLC, PIF1, AGL80, and WRKY32, are involved mainly in plant hormone signal transduction, starch and sucrose metabolism, and flowering regulation and may be involved in early flowering. This study serves as a reference and theoretical basis for kenaf production and provides insights into the effects of DNA methylation on plant growth and development.
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Affiliation(s)
- Zengqiang Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Dengjie Luo
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Shan Cao
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Wenxian Zhang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yali Hu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhen Huang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Jiao Yue
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
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5
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Yang X, Li X, Shan J, Li Y, Zhang Y, Wang Y, Li W, Zhao L. Overexpression of GmGAMYB Accelerates the Transition to Flowering and Increases Plant Height in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:667242. [PMID: 34040624 PMCID: PMC8141843 DOI: 10.3389/fpls.2021.667242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/07/2021] [Indexed: 05/27/2023]
Abstract
The flowering time and plant height of soybean are important agronomic characters, which control the adaptability and yield of soybean. R2R3 MYB transcription factor plays an important regulatory role in plant growth and development. In this study, soybean GmGAMYB gene of R2R3-MYB type was induced by long-days (LDs). GmGAMYB showed higher transcriptional levels in the flowers, leaves and pods of soybean. Overexpression of GmGAMYB in transgenic soybean showed earlier flowering time and maturity in LDs and short-days (SDs). GmGAMYB interacted with GmGBP1 and might promote flowering time by up-regulating the expression of GmFULc gene in soybean. Moreover, the expression level of GmGAMYB was also induced by gibberellins (GAs) and the plant height of GmGAMYB-ox plants was significantly increased, which was caused by the enlargement of internode cell in stem. Furthermore, GmGAMYB overexpression led to increased GA sensitivity in the hypocotyl of soybean seedlings compared with WT. GmGAMYB may be a positive regulator of GA response of promoting plant height by up-regulating the expression of GmGA20ox gene in soybean. Together, our studies preliminarily showed that the partial functions of GmGAMYB in regulating flowering time and GA pathway.
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6
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Quantitative Control of Early Flowering in White Lupin ( Lupinus albus L.). Int J Mol Sci 2021; 22:ijms22083856. [PMID: 33917799 PMCID: PMC8068107 DOI: 10.3390/ijms22083856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 12/03/2022] Open
Abstract
White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection.
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7
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Zhang H, Yin L, Song F, Jiang M. SKIP Silencing Decreased Disease Resistance Against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000 in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:593267. [PMID: 33381133 PMCID: PMC7767821 DOI: 10.3389/fpls.2020.593267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/19/2020] [Indexed: 05/29/2023]
Abstract
SKIP, a component of the spliceosome, is involved in numerous signaling pathways. However, there is no direct genetic evidence supporting the function of SKIP in defense responses. In this paper, two SKIPs, namely, SlSKIP1a and SlSKIP1b, were analyzed in tomato. qRT-PCR analysis showed that the SlSKIP1b expression was triggered via Pseudomonas syringae pv. tomato (Pst) DC3000 and Botrytis cinerea (B. cinerea), together with the defense-associated signals. In addition, the functions of SlSKIP1a and SlSKIP1b in disease resistance were analyzed in tomato through the virus-induced gene silencing (VIGS) technique. VIGS-mediated SlSKIP1b silencing led to increased accumulation of reactive oxygen species (ROS), along with the decreased expression of defense-related genes (DRGs) after pathogen infection, suggesting that it reduced B. cinerea and Pst DC3000 resistance. There was no significant difference in B. cinerea and Pst DC3000 resistance in TRV-SlSKIP1a-infiltrated plants compared with the TRV-GUS-silencing counterparts. As suggested by the above findings, SlSKIP1b plays a vital role in disease resistance against pathogens possibly by regulating the accumulation of ROS as well as the expression of DRGs.
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Affiliation(s)
- Huijuan Zhang
- Life Science Collegue, Taizhou University, Taizhou, China
| | - Longfei Yin
- Life Science Collegue, Taizhou University, Taizhou, China
| | - Fengming Song
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Ming Jiang
- Life Science Collegue, Taizhou University, Taizhou, China
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8
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Tognacca RS, Kubaczka MG, Servi L, Rodríguez FS, Godoy Herz MA, Petrillo E. Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana's life cycle. Transcription 2020; 11:117-133. [PMID: 32748694 DOI: 10.1080/21541264.2020.1796473] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.
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Affiliation(s)
- Rocío S Tognacca
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - M Guillermina Kubaczka
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Lucas Servi
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Florencia S Rodríguez
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina.,Departamento De Biodiversidad Y Biología Experimental, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Micaela A Godoy Herz
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Ezequiel Petrillo
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
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9
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Cao Y, Ma L. To Splice or to Transcribe: SKIP-Mediated Environmental Fitness and Development in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1222. [PMID: 31632433 PMCID: PMC6785753 DOI: 10.3389/fpls.2019.01222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/04/2019] [Indexed: 05/04/2023]
Abstract
Gene expression in eukaryotes is controlled at multiple levels, including transcriptional and post-transcriptional levels. The transcriptional regulation of gene expression is complex and includes the regulation of the initiation and elongation phases of transcription. Meanwhile, the post-transcriptional regulation of gene expression includes precursor messenger RNA (pre-mRNA) splicing, 5' capping, and 3' polyadenylation. Among these events, pre-mRNA splicing, conducted by the spliceosome, plays a key role in the regulation of gene expression, and the efficiency and precision of pre-mRNA splicing are critical for gene function. Ski-interacting protein (SKIP) is an evolutionarily conserved protein from yeast to humans. In plants, SKIP is a bifunctional regulator that works as a splicing factor as part of the spliceosome and as a transcriptional regulator via interactions with the transcriptional regulatory complex. Here, we review how the functions of SKIP as a splicing factor and a transcriptional regulator affect environmental fitness and development in plants.
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10
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Zhao L, Li M, Xu C, Yang X, Li D, Zhao X, Wang K, Li Y, Zhang X, Liu L, Ding F, Du H, Wang C, Sun J, Li W. Natural variation in GmGBP1 promoter affects photoperiod control of flowering time and maturity in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:147-162. [PMID: 30004144 DOI: 10.1111/tpj.14025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 05/13/2023]
Abstract
The present study screened for polymorphisms in coding and non-coding regions of the GmGBP1 gene in 278 soybean accessions with variable maturity and growth habit characteristics under natural field conditions in three different latitudes in China. The results showed that the promoter region was highly diversified compared with the coding sequence of GmGBP1. Five polymorphisms and four haplotypes were closely related to soybean flowering time and maturity through association and linkage disequilibrium analyses. Varieties with the polymorphisms SNP_-796G, SNP_-770G, SNP_-307T, InDel_-242normal, SNP_353A, or haplotypes Hap-3 and Hap-4 showed earlier flowering time and maturity in different environments. The shorter growth period might be largely due to higher GmGBP1 expression levels in soybean that were caused by the TCT-motif with SNP_-796G in the promoter. In contrast, the lower expression level of GmGBP1 in soybean caused by RNAi interference of GmGBP1 resulted in a longer growth period under different day lengths. Furthermore, the gene interference of GmGBP1 also caused a reduction in photoperiod response sensitivity (PRS) before flowering in soybean. RNA-seq analysis on GmGBP1 underexpression in soybean showed that 94 and 30 predicted genes were significantly upregulated and downregulated, respectively. Of these, the diurnal photoperiod-specific expression pattern of three significant flowering time genes GmFT2a, GmFT5a, and GmFULc also showed constantly lower mRNA levels in GmGBP1-i soybean than in wild type, especially under short day conditions. Together, the results showed that GmGBP1 functioned as a positive regulator upstream of GmFT2a and GmFT5a to activate the expression of GmFULc to promote flowering on short days.
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Affiliation(s)
- Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Minmin Li
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Chongjing Xu
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Xue Yang
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Kuo Wang
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Yinghua Li
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Lixue Liu
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Fuquan Ding
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Hailong Du
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Chunsheng Wang
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology of Ministry of Education China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, 150030, China
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Li Y, Xia C, Feng J, Yang D, Wu F, Cao Y, Li L, Ma L. The SNW Domain of SKIP Is Required for Its Integration into the Spliceosome and Its Interaction with the Paf1 Complex in Arabidopsis. MOLECULAR PLANT 2016; 9:1040-50. [PMID: 27130079 DOI: 10.1016/j.molp.2016.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/03/2016] [Accepted: 04/18/2016] [Indexed: 05/07/2023]
Abstract
SKIP is a conserved protein from yeasts to plants and humans. In plant cells, SKIP is a bifunctional regulator that works in the nucleus as a splicing factor by integrating into the spliceosome and as a transcriptional activator by interacting with the Paf1 complex. In this study, we identified two nuclear localization signals in SKIP and confirmed that each is sufficient to target SKIP to the nucleus. The SNW domain of SKIP is required for both its function as a splicing factor by promoting integration into the spliceosome in response to stress, and its function as a transcriptional activator by controlling its interaction with the Paf1 complex to participate in flowering. Truncated proteins that included the SNW domain and the N- or C-terminus of SKIP were still able to carry out the functions of the full-length protein in gene splicing and transcriptional activation in Arabidopsis. In addition, we found that SKIP undergoes 26S proteasome-mediated degradation, and that the C-terminus of SKIP is required to maintain the stability of the protein in plant cells. Together, our findings demonstrate the structural domain organization of SKIP and reveal the core domains and motifs underlying SKIP function in plants.
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Affiliation(s)
- Yan Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China; Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Congcong Xia
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jinlin Feng
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Dong Yang
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Fangming Wu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ying Cao
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Legong Li
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ligeng Ma
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, Beijing 100048, China; College of Life Sciences, Capital Normal University, Beijing 100048, China.
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12
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Song L, Prince S, Valliyodan B, Joshi T, Maldonado dos Santos JV, Wang J, Lin L, Wan J, Wang Y, Xu D, Nguyen HT. Genome-wide transcriptome analysis of soybean primary root under varying water-deficit conditions. BMC Genomics 2016; 17:57. [PMID: 26769043 PMCID: PMC4714440 DOI: 10.1186/s12864-016-2378-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean is a major crop that provides an important source of protein and oil to humans and animals, but its production can be dramatically decreased by the occurrence of drought stress. Soybeans can survive drought stress if there is a robust and deep root system at the early vegetative growth stage. However, little is known about the genome-wide molecular mechanisms contributing to soybean root system architecture. This study was performed to gain knowledge on transcriptome changes and related molecular mechanisms contributing to soybean root development under water limited conditions. RESULTS The soybean Williams 82 genotype was subjected to very mild stress (VMS), mild stress (MS) and severe stress (SS) conditions, as well as recovery from the severe stress after re-watering (SR). In total, 6,609 genes in the roots showed differential expression patterns in response to different water-deficit stress levels. Genes involved in hormone (Auxin/Ethylene), carbohydrate, and cell wall-related metabolism (XTH/lipid/flavonoids/lignin) pathways were differentially regulated in the soybean root system. Several transcription factors (TFs) regulating root growth and responses under varying water-deficit conditions were identified and the expression patterns of six TFs were found to be common across the stress levels. Further analysis on the whole plant level led to the finding of tissue-specific or water-deficit levels specific regulation of transcription factors. Analysis of the over-represented motif of different gene groups revealed several new cis-elements associated with different levels of water deficit. The expression patterns of 18 genes were confirmed byquantitative reverse transcription polymerase chain reaction method and demonstrated the accuracy and effectiveness of RNA-Seq. CONCLUSIONS The primary root specific transcriptome in soybean can enable a better understanding of the root response to water deficit conditions. The genes detected in root tissues that were associated with key hormones, carbohydrates, and cell wall-related metabolism could play a vital role in achieving drought tolerance and could be promising candidates for future functional characterization. TFs involved in the soybean root and at the whole plant level could be used for future network analysis between TFs and cis-elements. All of these findings will be helpful in elucidating the molecular mechanisms associated with water stress responses in soybean roots.
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Affiliation(s)
- Li Song
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Silvas Prince
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Babu Valliyodan
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Trupti Joshi
- Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
| | - Joao V Maldonado dos Santos
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Jiaojiao Wang
- Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Li Lin
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Jinrong Wan
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Yongqin Wang
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
| | - Dong Xu
- Department of Computer Science, and Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- MU Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
| | - Henry T Nguyen
- Division of Plant Science and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Lee SS, Park HJ, Yoon DH, Kim BG, Ahn JC, Luan S, Cho HS. Rice cyclophilin OsCYP18-2 is translocated to the nucleus by an interaction with SKIP and enhances drought tolerance in rice and Arabidopsis. PLANT, CELL & ENVIRONMENT 2015; 38:2071-87. [PMID: 25847193 DOI: 10.1111/pce.12531] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 05/19/2023]
Abstract
Cyclophilin 18-2 (CYP18-2) genes, homologues of human peptidyl-prolyl isomerase-like 1 (PPiL1), are conserved across multicellular organisms and Schizosaccharomyces pombe. Although PPiL1 is known to interact with ski-interacting protein (SKIP), a transcriptional co-regulator and spliceosomal component, there have been no functional analyses of PPiL1 homologues in plants. Rice cyclophilin 18-2 (OsCYP18-2) bound directly to amino acids 56-95 of OsSKIP and its binding was independent of cyclosporin A, a cyclophilin-binding drug. Moreover, OsCYP18-2 exhibited PPIase activity regardless of its interaction with OsSKIP. Therefore, the binding site for OsCYP18-2's interaction with SKIP was distinct from the PPIase active site. OsCYP18-2's interaction with SKIP full-length protein enabled OsCYP18-2's translocation from the cytoplasm into the nucleus and AtSKIP interacted in planta with both AtCYP18-2 and OsCYP18-2. Drought and salt stress induced similar expression of OsCYP18-2 and OsSKIP. Overexpression of OsCYP18-2 in transgenic rice and Arabidopsis thaliana plants enhanced drought tolerance and altered expression and pre-mRNA splicing patterns of stress-related genes in Arabidopsis under drought conditions. Furthermore, OsCYP18-2 caused transcriptional activation with/without OsSKIP in the GAL4 system of yeast; thus the OsSKIP-OsCYP18-2 interaction has an important role in the transcriptional and post-transcriptional regulation of stress-related genes and increases tolerance to drought stress.
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Affiliation(s)
- Sang Sook Lee
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | - Hyun Ji Park
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | - Dae Hwa Yoon
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
- Department of Pharmacology, College of Medicine, Seonam University, Namwon, 590-170, Korea
| | - Beom-Gi Kim
- Divisions of Bio-Crops Development, National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, Korea
| | - Jun Cheul Ahn
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
- Department of Pharmacology, College of Medicine, Seonam University, Namwon, 590-170, Korea
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, 73072, USA
| | - Hye Sun Cho
- Sustainable Bioresource Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
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15
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Feng J, Li J, Gao Z, Lu Y, Yu J, Zheng Q, Yan S, Zhang W, He H, Ma L, Zhu Z. SKIP Confers Osmotic Tolerance during Salt Stress by Controlling Alternative Gene Splicing in Arabidopsis. MOLECULAR PLANT 2015; 8:1038-52. [PMID: 25617718 DOI: 10.1016/j.molp.2015.01.011] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 05/18/2023]
Abstract
Deciphering the mechanisms underlying plant responses to abiotic stress is key for improving plant stress resistance. Much is known about the regulation of gene expression in response to salt stress at the transcriptional level; however, little is known about this process at the posttranscriptional level. Recently, we demonstrated that SKIP is a component of spliceosome that interacts with clock gene pre-mRNAs and is essential for regulating their alternative splicing and mRNA maturation. In this study, we found that skip-1 plants are hypersensitive to both salt and osmotic stresses, and that SKIP is required for the alternative splicing and mRNA maturation of several salt-tolerance genes, including NHX1, CBL1, P5CS1, RCI2A, and PAT10. A genome-wide analysis revealed that SKIP mediates the alternative splicing of many genes under salt-stress conditions, and that most of the alternative splicing events in skip-1 involve intron retention and can generate a premature termination codon in the transcribed mRNA. SKIP also controls alternative splicing by modulating the recognition or cleavage of 5' and 3' splice donor and acceptor sites under salt-stress conditions. Therefore, this study addresses the fundamental question of how the mRNA splicing machinery in plants contributes to salt-stress responses at the posttranscriptional level, and provides a link between alternative splicing and salt tolerance.
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Affiliation(s)
- Jinlin Feng
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China; College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jingjing Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China
| | - Zhaoxu Gao
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China; College of Life Sciences, Peking University, Beijing 100871, China
| | - Yaru Lu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China
| | - Junya Yu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qian Zheng
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China
| | - Shuning Yan
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China
| | - Wenjiao Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China
| | - Hang He
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Ligeng Ma
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
| | - Zhengge Zhu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei 050021, China.
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16
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Synergistic regulatory networks mediated by microRNAs and transcription factors under drought, heat and salt stresses in Oryza Sativa spp. Gene 2015; 555:127-39. [DOI: 10.1016/j.gene.2014.10.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 09/12/2014] [Accepted: 10/26/2014] [Indexed: 01/16/2023]
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17
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Kostrouch D, Kostrouchová M, Yilma P, Chughtai AA, Novotný JP, Novák P, Kostrouchová V, Kostrouchová M, Kostrouch Z. SKIP and BIR-1/Survivin have potential to integrate proteome status with gene expression. J Proteomics 2014; 110:93-106. [PMID: 25088050 DOI: 10.1016/j.jprot.2014.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/05/2014] [Accepted: 07/22/2014] [Indexed: 11/25/2022]
Abstract
UNLABELLED SKIP and BIR are evolutionarily conserved proteins; SKIP (SKP-1) is a known transcription and splicing cofactor while BIR-1/Survivin regulates cell division, gene expression and development. Their loss of function induces overlapping developmental phenotypes. We searched for SKP-1 and BIR-1 interaction on protein level using yeast two-hybrid screens and identified partially overlapping categories of proteins as SKIP-1 and BIR-1 interactors. The interacting proteins included ribosomal proteins, transcription factors, translation factors and cytoskeletal and motor proteins suggesting involvement in multiple protein complexes. To visualize the effect of BIR-1 on the proteome in Caenorhabditis elegans we induced a short time pulse BIR-1 overexpression in synchronized L1 larvae. This led to a dramatic alteration of the whole proteome pattern indicating that BIR-1 alone has the capacity to alter the chromatographic profile of many target proteins including proteins found to be interactors in yeast two hybrid screens. The results were validated for ribosomal proteins RPS3 and RPL5, non-muscle myosin and TAC-1, a transcription cofactor and a centrosome associated protein. Together, these results suggest that SKP-1 and BIR-1 are multifunctional proteins that form multiple protein complexes in both shared and distinct pathways and have the potential to connect proteome signals with the regulation of gene expression. BIOLOGICAL SIGNIFICANCE The genomic organization of the genes encoding BIR-1 and SKIP (SKP-1) in C. elegans have suggested that these two factors, each evolutionarily conserved, have related functions. However, these functional connections have remained elusive and underappreciated in light of limited information from C. elegans and other biological systems. Our results provide further evidence for a functional link between these two factors and suggest they may transmit proteome signals towards the regulation of gene expression.
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Affiliation(s)
- David Kostrouch
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Markéta Kostrouchová
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Petr Yilma
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Ahmed Ali Chughtai
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Jan Philipp Novotný
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Petr Novák
- Laboratory of Structure Biology and Cell Signaling, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, Prague, Czech Republic
| | - Veronika Kostrouchová
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Marta Kostrouchová
- Laboratory of Molecular Biology and Genetics, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Zdeněk Kostrouch
- Laboratory of Molecular Pathology, Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Czech Republic.
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18
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Liew LC, Singh MB, Bhalla PL. Unique and conserved features of floral evocation in legumes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:714-728. [PMID: 24930396 DOI: 10.1111/jipb.12187] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
Legumes, with their unique ability to fix atmospheric nitrogen, play a vital role in ensuring future food security and mitigating the effects of climate change because they use less fossil energy and produce less greenhouse gases compared with N-fertilized systems. Grain legumes are second only to cereal crops as a source of human and animal food, and they contribute approximately one third of the protein consumed by the human population. The productivity of seed crops, such as grain legumes, is dependent on flowering. Despite the genetic variation and importance of flowering in legume production, studies of the molecular pathways that control flowering in legumes are limited. Recent advances in genomics have revealed that legume flowering pathways are divergent from those of such model species as Arabidopsis thaliana. Here, we discuss the current understanding of flowering time regulation in legumes and highlight the unique and conserved features of floral evocation in legumes.
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Affiliation(s)
- Lim Chee Liew
- Plant Molecular Biology and Biotechnology Laboratory, Melbourne School of Land and Environment, University of Melbourne, Parkville, Victoria, 3010, Australia
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