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Arefian M, Bhagya N, Prasad TSK. Phosphorylation-mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biol Rev Camb Philos Soc 2021; 96:2164-2191. [PMID: 34047006 DOI: 10.1111/brv.12748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a major post-translational modification, regulating protein function, stability, and subcellular localization. To date, annotated phosphorylation data are available mainly for model organisms and humans, despite the economic importance of crop species and their large kinomes. Our understanding of the phospho-regulation of flowering in relation to the biology and interaction between the pollen and pistil is still significantly lagging, limiting our knowledge on kinase signalling and its potential applications to crop production. To address this gap, we bring together relevant literature that were previously disconnected to present an overview of the roles of phosphoproteomic signalling pathways in modulating molecular and cellular regulation within specific tissues at different morphological stages of flowering. This review is intended to stimulate research, with the potential to increase crop productivity by providing a platform for novel molecular tools.
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Affiliation(s)
- Mohammad Arefian
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - N Bhagya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, 575018, India
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2
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Chen MX, Lu CC, Sun PC, Nie YX, Tian Y, Hu QJ, Das D, Hou XX, Gao B, Chen X, Liu SX, Zheng CC, Zhao XY, Dai L, Zhang J, Liu YG. Comprehensive transcriptome and proteome analyses reveal a novel sodium chloride responsive gene network in maize seed tissues during germination. PLANT, CELL & ENVIRONMENT 2021; 44:88-101. [PMID: 32677712 DOI: 10.1111/pce.13849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/25/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Germination is a plant developmental process by which radicle of mature seeds start to penetrate surrounding barriers for seedling establishment and multiple environmental factors have been shown to affect it. Little is known how high salinity affects seed germination of C4 plant, Zea mays. Preliminary germination assay suggested that isolated embryo alone was able to germinate under 200 mM NaCl treatment, whereas the intact seeds were highly repressed. We hypothesized that maize endosperm may function in perception and transduction of salt signal to surrounding tissues such as embryo, showing a completely different response to that in Arabidopsis. Since salt response involves ABA, we analysed in vivo ABA distribution and quantity and the result demonstrated that ABA level in isolated embryo under NaCl treatment failed to increase in comparison with the water control, suggesting that the elevation of ABA level is an endosperm dependent process. Subsequently, by using advanced profiling techniques such as RNA sequencing and SWATH-MS-based quantitative proteomics, we found substantial differences in post-transcriptional and translational changes between salt-treated embryo and endosperm. In summary, our results indicate that these regulatory mechanisms, such as alternative splicing, are likely to mediate early responses to salt stress during maize seed germination.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chong-Chong Lu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Peng-Cheng Sun
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yong-Xin Nie
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Qi-Juan Hu
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xuan-Xuan Hou
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Bei Gao
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xi Chen
- Wuhan Institute of Biotechnology, Wuhan, China
| | - Shou-Xu Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Cheng-Chao Zheng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Xiang-Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianhua Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
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3
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Chen MX, Zhu FY, Gao B, Ma KL, Zhang Y, Fernie AR, Chen X, Dai L, Ye NH, Zhang X, Tian Y, Zhang D, Xiao S, Zhang J, Liu YG. Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation. PLANT PHYSIOLOGY 2020; 182:1510-1526. [PMID: 31857423 PMCID: PMC7054881 DOI: 10.1104/pp.19.00430] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/26/2019] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa) molecular breeding has gained considerable attention in recent years, but inaccurate genome annotation hampers its progress and functional studies of the rice genome. In this study, we applied single-molecule long-read RNA sequencing (lrRNA_seq)-based proteogenomics to reveal the complexity of the rice transcriptome and its coding abilities. Surprisingly, approximately 60% of loci identified by lrRNA_seq are associated with natural antisense transcripts (NATs). The high-density genomic arrangement of NAT genes suggests their potential roles in the multifaceted control of gene expression. In addition, a large number of fusion and intergenic transcripts have been observed. Furthermore, 906,456 transcript isoforms were identified, and 72.9% of the genes can generate splicing isoforms. A total of 706,075 posttranscriptional events were subsequently categorized into 10 subtypes, demonstrating the interdependence of posttranscriptional mechanisms that contribute to transcriptome diversity. Parallel short-read RNA sequencing indicated that lrRNA_seq has a superior capacity for the identification of longer transcripts. In addition, over 190,000 unique peptides belonging to 9,706 proteoforms/protein groups were identified, expanding the diversity of the rice proteome. Our findings indicate that the genome organization, transcriptome diversity, and coding potential of the rice transcriptome are far more complex than previously anticipated.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271000, Shandong, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People’s Republic of China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Bei Gao
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kai-Long Ma
- BGI-Shenzhen, Shenzhen 518083, People’s Republic of China
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Xi Chen
- SpecAlly Life Technology Co., Ltd., Wuhan 430075, China
| | - Lei Dai
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Neng-Hui Ye
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xue Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271000, Shandong, China
| | - Di Zhang
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian 271000, Shandong, China
- Author for Contact:
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4
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Bradley D, Beltrao P. Evolution of protein kinase substrate recognition at the active site. PLoS Biol 2019; 17:e3000341. [PMID: 31233486 PMCID: PMC6611643 DOI: 10.1371/journal.pbio.3000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/05/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
Protein kinases catalyse the phosphorylation of target proteins, controlling most cellular processes. The specificity of serine/threonine kinases is partly determined by interactions with a few residues near the phospho-acceptor residue, forming the so-called kinase-substrate motif. Kinases have been extensively duplicated throughout evolution, but little is known about when in time new target motifs have arisen. Here, we show that sequence variation occurring early in the evolution of kinases is dominated by changes in specificity-determining residues. We then analysed kinase specificity models, based on known target sites, observing that specificity has remained mostly unchanged for recent kinase duplications. Finally, analysis of phosphorylation data from a taxonomically broad set of 48 eukaryotic species indicates that most phosphorylation motifs are broadly distributed in eukaryotes but are not present in prokaryotes. Overall, our results suggest that the set of eukaryotes kinase motifs present today was acquired around the time of the eukaryotic last common ancestor and that early expansions of the protein kinase fold rapidly explored the space of possible target motifs.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
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5
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Conserved phosphorylation hotspots in eukaryotic protein domain families. Nat Commun 2019; 10:1977. [PMID: 31036831 PMCID: PMC6488607 DOI: 10.1038/s41467-019-09952-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 04/08/2019] [Indexed: 02/07/2023] Open
Abstract
Protein phosphorylation is the best characterized post-translational modification that regulates almost all cellular processes through diverse mechanisms such as changing protein conformations, interactions, and localization. While the inventory for phosphorylation sites across different species has rapidly expanded, their functional role remains poorly investigated. Here, we combine 537,321 phosphosites from 40 eukaryotic species to identify highly conserved phosphorylation hotspot regions within domain families. Mapping these regions onto structural data reveals that they are often found at interfaces, near catalytic residues and tend to harbor functionally important phosphosites. Notably, functional studies of a phospho-deficient mutant in the C-terminal hotspot region within the ribosomal S11 domain in the yeast ribosomal protein uS11 shows impaired growth and defective cytoplasmic 20S pre-rRNA processing at 16 °C and 20 °C. Altogether, our study identifies phosphorylation hotspots for 162 protein domains suggestive of an ancient role for the control of diverse eukaryotic domain families. Protein phosphorylation has various regulatory functions. Here, the authors map 241 phosphorylation hotspot regions across 40 eukaryotic species, showing that they are enriched at interfaces and near catalytic residues, and enable the discovery of functionally important phospho-sites.
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6
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Chen MX, Zhu FY, Wang FZ, Ye NH, Gao B, Chen X, Zhao SS, Fan T, Cao YY, Liu TY, Su ZZ, Xie LJ, Hu QJ, Wu HJ, Xiao S, Zhang J, Liu YG. Alternative splicing and translation play important roles in hypoxic germination in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:817-833. [PMID: 30535157 PMCID: PMC6363088 DOI: 10.1093/jxb/ery393] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/27/2018] [Indexed: 05/04/2023]
Abstract
Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Feng-Zhu Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Neng-Hui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
| | - Bei Gao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xi Chen
- SpecAlly Life Technology Co., Ltd, Wuhan, China
| | - Shan-Shan Zhao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Yun-Ying Cao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Tie-Yuan Liu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ze-Zhuo Su
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Li-Juan Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qi-Juan Hu
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Hui-Jie Wu
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Correspondence: or
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Correspondence: or
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7
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Lu ZS, Chen QS, Zheng QX, Shen JJ, Luo ZP, Fan K, Xu SH, Shen Q, Liu PP. Proteomic and Phosphoproteomic Analysis in Tobacco Mosaic Virus-Infected Tobacco (Nicotiana tabacum). Biomolecules 2019; 9:E39. [PMID: 30678100 PMCID: PMC6406717 DOI: 10.3390/biom9020039] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 12/11/2022] Open
Abstract
Tobacco mosaic virus (TMV) is a common source of biological stress that significantly affects plant growth and development. It is also useful as a model in studies designed to clarify the mechanisms involved in plant viral disease. Plant responses to abiotic stress were recently reported to be regulated by complex mechanisms at the post-translational modification (PTM) level. Protein phosphorylation is one of the most widespread and major PTMs in organisms. Using immobilized metal ion affinity chromatography (IMAC) enrichment, high-pH C18 chromatography fraction, and high-accuracy mass spectrometry (MS), a set of proteins and phosphopeptides in both TMV-infected tobacco and control tobacco were identified. A total of 4905 proteins and 3998 phosphopeptides with 3063 phosphorylation sites were identified. These 3998 phosphopeptides were assigned to 1311 phosphoproteins, as some proteins carried multiple phosphorylation sites. Among them, 530 proteins and 337 phosphopeptides corresponding to 277 phosphoproteins differed between the two groups. There were 43 upregulated phosphoproteins, including phosphoglycerate kinase, pyruvate phosphate dikinase, protein phosphatase 2C, and serine/threonine protein kinase. To the best of our knowledge, this is the first phosphoproteomic analysis of leaves from a tobacco cultivar, K326. The results of this study advance our understanding of tobacco development and TMV action at the protein phosphorylation level.
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Affiliation(s)
- Zi-Shu Lu
- Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450000, China.
| | - Qian-Si Chen
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Qing-Xia Zheng
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Juan-Juan Shen
- Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450000, China.
| | - Zhao-Peng Luo
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Kai Fan
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
| | - Sheng-Hao Xu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Qi Shen
- Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450000, China.
| | - Ping-Ping Liu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, China.
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8
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Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, Yang JF, Cao YY, Zhang Y, Yoshida T, Fernie AR, Fan GY, Wen B, Zhou R, Liu TY, Fan T, Gao B, Zhang D, Hao GF, Xiao S, Liu YG, Zhang J. Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:518-533. [PMID: 28407323 DOI: 10.1111/tpj.13571] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 05/19/2023]
Abstract
In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.
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Affiliation(s)
- Fu-Yuan Zhu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mo-Xian Chen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Neng-Hui Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Lu Shi
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Jing-Fang Yang
- College of Chemistry, Central China Normal University, Wuhan, China
| | - Yun-Ying Cao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Bo Wen
- BGI-Shenzhen, Shenzhen, China
| | | | - Tie-Yuan Liu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Bei Gao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Di Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ge-Fei Hao
- College of Chemistry, Central China Normal University, Wuhan, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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9
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del Val C, Bondar AN. Charged groups at binding interfaces of the PsbO subunit of photosystem II: A combined bioinformatics and simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:432-441. [DOI: 10.1016/j.bbabio.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 01/20/2023]
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10
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Tan X, Gao F, Su H, Gong Y, Zhang J, Sullivan MA, Chen J. Genetic and Proteomic characterization of Bile Salt Export Pump (BSEP) in Snake Liver. Sci Rep 2017; 7:43556. [PMID: 28368001 PMCID: PMC5377248 DOI: 10.1038/srep43556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/25/2017] [Indexed: 12/14/2022] Open
Abstract
Snake gallbladder, a traditional Chinese medicine, has been believed in various Asian countries to improve visual acuity and alleviate rheumatism. Bile acids, a major component of the gallbladder, are toxic to the liver and kidney in humans and animals due to its detergent effects, while also exhibiting therapeutic effects due to an increase in the gallbladder contractions of muscle strips in patients with cholesterol gallstones. Secretion of bile acids in human and mammals depends on the bile salt export pump (BSEP), a liver-specific adenosine triphosphate (ATP)-binding cassette transporter encoded by ABCB11. However, the presence of BSEP in snakes has not been thoroughly explored. Here we confirm the existence of BSEP and its coding DNA sequence in snakes on both the proteomic and genetic level. This work provides information on the snake ABCB11 sequence and helps further potential genetic manipulation to affect bile salt metabolism. Our study provides the foundation for research on bile acid production from snakes by using modern genetic and proteomic methodologies.
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Affiliation(s)
- Xinle Tan
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,The University of Queensland, School of Chemistry &Molecular Bioscience, Brisbane, QLD 4072, Australia
| | - Fei Gao
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hexiu Su
- Department of Hematology, Affiliated Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yajun Gong
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Jie Zhang
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Mitchell A Sullivan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Jiachun Chen
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
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Shchennikova AV, Beletsky AV, Shulga OA, Mazur AM, Prokhortchouk EB, Kochieva EZ, Ravin NV, Skryabin KG. Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys. PLANT MOLECULAR BIOLOGY 2016; 91:441-458. [PMID: 27097902 DOI: 10.1007/s11103-016-0478-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Myco-heterotroph Monotropa hypopitys is a widely spread perennial herb used to study symbiotic interactions and physiological mechanisms underlying the development of non-photosynthetic plant. Here, we performed, for the first time, transcriptome-wide characterization of M. hypopitys miRNA profile using high throughput Illumina sequencing. As a result of small RNA library sequencing and bioinformatic analysis, we identified 55 members belonging to 40 families of known miRNAs and 17 putative novel miRNAs unique for M. hypopitys. Computational screening revealed 206 potential mRNA targets for known miRNAs and 31 potential mRNA targets for novel miRNAs. The predicted target genes were described in Gene Ontology terms and were found to be involved in a broad range of metabolic and regulatory pathways. The identification of novel M. hypopitys-specific miRNAs, some with few target genes and low abundances, suggests their recent evolutionary origin and participation in highly specialized regulatory mechanisms fundamental for non-photosynthetic biology of M. hypopitys. This global analysis of miRNAs and their potential targets in M. hypopitys provides a framework for further investigation of miRNA role in the evolution and establishment of non-photosynthetic myco-heterotrophs.
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Affiliation(s)
- Anna V Shchennikova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Olga A Shulga
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Alexander M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Egor B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Elena Z Kochieva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Nikolay V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071
| | - Konstantin G Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, bld. 2, Moscow, Russia, 119071.
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12
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Tan X, Sullivan MA, Gao F, Li S, Schulz BL, Gilbert RG. A new non-degradative method to purify glycogen. Carbohydr Polym 2016; 147:165-170. [PMID: 27178921 DOI: 10.1016/j.carbpol.2016.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/22/2022]
Abstract
Liver glycogen, a complex branched glucose polymer containing a small amount of protein, is important for maintaining glucose homeostasis (blood-sugar control) in humans. It has recently been found that glycogen molecular structure is impaired in diabetes. Isolating the carbohydrate polymer and any intrinsically-attached protein(s) is an essential prerequisite for studying this structural impairment. This requires an effective, non-degradative and efficient purification method to exclude the many other proteins present in liver. Proteins and glycogen have different ranges of molecular sizes. Despite the plethora of proteins that might still be present in significant abundance after other isolation techniques, SEC (size exclusion chromatography, also known as GPC), which separates by molecular size, should separate those extraneous to glycogen from glycogen with any intrinsically associated protein(s). A novel purification method is developed for this, based on preparative SEC following sucrose gradient centrifugation. Proteomics is used to show that the new method compares favourably with current methods in the literature.
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Affiliation(s)
- Xinle Tan
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia
| | - Mitchell A Sullivan
- The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Fei Gao
- Tongji School of Pharmacy, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Shihan Li
- The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3052, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert G Gilbert
- The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia; Joint International Research Laboratory of Agriculture and Agri-Product Safety, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, PR China.
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13
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Silva-Sanchez C, Li H, Chen S. Recent advances and challenges in plant phosphoproteomics. Proteomics 2015; 15:1127-41. [PMID: 25429768 DOI: 10.1002/pmic.201400410] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 09/29/2014] [Accepted: 11/24/2014] [Indexed: 12/13/2022]
Abstract
Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and MS are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review, we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
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