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Ma Z, Chen S, Wang Z, Liu J, Zhang B. Proteome analysis of bermudagrass stolons and rhizomes provides new insights into the adaptation of plant stems to aboveground and underground growth. J Proteomics 2021; 241:104245. [PMID: 33901681 DOI: 10.1016/j.jprot.2021.104245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
As an important perennial warm-season turfgrass species, bermudagrass (Cynodon dactylon L.) forms underground-growing rhizomes and aboveground-growing stolons simultaneously, making it a fast propagating clonal plant with strong regeneration ability. In the current study, we compared the internode proteomes of rhizomes and stolons at the same developmental stage in the bermudagrass cultivar Yangjiang using iTRAQ. The results indicated that 228 protein species were differentially accumulated in the two specialized stems. In agreement with the different contents of starch, chlorophyll, anthocyanin and H2O2 in the two types of stems, photosynthesis and flavonoid biosynthesis were enriched with differentially accumulated protein species (DAPs) in stolons, whereas starch and sucrose metabolism, glycolysis, and H2O2 metabolism were enriched with DAPs in rhizomes. Burying stolons in the soil resulted in the gradual degradation of chlorophyll and anthocyanin, accumulation of starch, and increment of H2O2, which is similar to the physiological characteristics of rhizomes. These results collectively revealed that stolons and rhizomes of bermudagrass have significant differences at the proteome level and light might play important regulatory roles in the discrepancy of the proteome profiles and specialization of the two stems, providing new insights into the adaptation of plant stems to aboveground and underground growth. BIOLOGICAL SIGNIFICANCE: As two types of specialized stems that grow underground and aboveground respectively, rhizomes and stolons play important roles in overwintering and ecological invasion of many perennial and clonal plants. However, because rhizomes and stolons rarely coexist in single plant species, the differences between the two stems remain unclear at the molecular level. In this study, through an iTRAQ comparative proteomic analysis, we reported the identification of 228 differentially accumulated protein species (DAPs) in rhizomes and stolons of bermudagrass for the first time. We found that the 228 DAPs were interconnected to form protein networks in regulating diverse cellular activities and biochemical reactions. We also observed that stolons growing underground showed similar physiological activities and DAP expression as those of underground-growing rhizomes, suggesting that light might play important regulatory roles in the specialization of stolons and rhizomes. These results expanded our understanding of the mysterious adaption of plant stems to different growth conditions.
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Affiliation(s)
- Ziyan Ma
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhizhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Bing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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Yin X, Yi K, Zhao Y, Hu Y, Li X, He T, Liu J, Cui G. Revealing the full-length transcriptome of caucasian clover rhizome development. BMC PLANT BIOLOGY 2020; 20:429. [PMID: 32938399 PMCID: PMC7493993 DOI: 10.1186/s12870-020-02637-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/03/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. RESULT We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. CONCLUSIONS This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.
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Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Xu Li
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China.
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Ma X, Yu J, Zhuang L, Shi Y, Meyer W, Huang B. Differential regulatory pathways associated with drought-inhibition and post-drought recuperation of rhizome development in perennial grass. ANNALS OF BOTANY 2020; 126:481-497. [PMID: 32445476 PMCID: PMC7424744 DOI: 10.1093/aob/mcaa099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND AND AIMS Rhizomes are key organs for the establishment of perennial grass stands and adaptation to environmental stress. However, mechanisms regulating rhizome initiation and elongation under drought stress and during post-drought recovery remain unclear. The objective of this study is to investigate molecular factors and metabolic processes involved in drought effects and post-drought recovery in rhizome growth in perennial grass species by comparative transcriptomic and proteomic profiling. METHODS Tall fescue (Festuca arundinacea) (B-type rhizome genotype, 'BR') plants were exposed to drought stress and re-watering in growth chambers. The number and length of rhizomes were measured following drought stress and re-watering. Hormone and sugar contents were analysed, and transcriptomic and proteomic analyses were performed to identify metabolic factors, genes and proteins associated with rhizome development. KEY RESULTS Rhizome initiation and elongation were inhibited by drought stress, and were associated with increases in the contents of abscisic acid (ABA) and soluble sugars, but declines in the contents of indoleacetic acid (IAA), zeatin riboside (ZR) and gibberellin (GA4). Genes involved in multiple metabolic processes and stress defence systems related to rhizome initiation exhibited different responses to drought stress, including ABA signalling, energy metabolism and stress protection. Drought-inhibition of rhizome elongation could be mainly associated with the alteration of GA4 and antioxidants contents, energy metabolism and stress response proteins. Upon re-watering, new rhizomes were regenerated from rhizome nodes previously exposed to drought stress, which was accompanied by the decline in ABA content and increases in IAA, ZR and GA4, as well as genes and proteins for auxin, lipids, lignin and nitrogen metabolism. CONCLUSIONS Drought-inhibition of rhizome initiation and elongation in tall fescue was mainly associated with adjustments in hormone metabolism, carbohydrate metabolism and stress-defence systems. Rhizome regeneration in response to re-watering involved reactivation of hormone and lipid metabolism, secondary cell-wall development, and nitrogen remobilization and cycling.
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Affiliation(s)
- Xiqing Ma
- College of Grassland Science and Technology, China Agricultural University, Beijing, PR China
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Jingjin Yu
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, PR China
| | - Lili Zhuang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, PR China
| | - Yi Shi
- College of Grassland Science, Gansu Agricultural University, Lanzhou, PR China
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - William Meyer
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Bingru Huang
- Department of Plant Biology and Pathology Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
- For correspondence. E-mail
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Heringer AS, Santa-Catarina C, Silveira V. Insights from Proteomic Studies into Plant Somatic Embryogenesis. Proteomics 2018; 18:e1700265. [DOI: 10.1002/pmic.201700265] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/08/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Angelo Schuabb Heringer
- Laboratório de Biotecnologia; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
- Unidade de Biologia Integrativa; Setor de Genômica e Proteômica; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia; Centro de Biociências e Biotecnologia; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
- Unidade de Biologia Integrativa; Setor de Genômica e Proteômica; Universidade Estadual do Norte Fluminense Darcy Ribeiro; Rio de Janeiro Brazil
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Ahsan N, Chen M, Salvato F, Wilson RS, Shyama Prasad Rao R, Thelen JJ. Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis. J Proteomics 2017; 165:51-60. [DOI: 10.1016/j.jprot.2017.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/26/2017] [Accepted: 06/05/2017] [Indexed: 01/21/2023]
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Sivakumar G, Alba K, Phillips GC. Biorhizome: A Biosynthetic Platform for Colchicine Biomanufacturing. FRONTIERS IN PLANT SCIENCE 2017; 8:1137. [PMID: 28713407 PMCID: PMC5491623 DOI: 10.3389/fpls.2017.01137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
Colchicine is one of the oldest plant-based medicines used to treat gout and one of the most important alkaloid-based antimitotic drugs with anticancer potential, which is commercially extracted from Gloriosa superba. Clinical trials suggest that colchicine medication could prevent atrial fibrillation recurrence after cardiac surgery. In addition, therapeutic colchicine is undergoing clinical trials to treat non-diabetic metabolic syndrome and diabetic nephropathy. However, the industrial-scale biomanufacturing of colchicine have not yet been established. Clearly, further studies on detailed biorhizome-specific transcriptome analysis, gene expression, and candidate gene validation are required before uncover the mechanism of colchicine biosynthesis and biorhizome-based colchicine biomanufacturing. Annotation of 32312 assembled multiple-tissues transcripts of G. superba represented 15088 unigenes in known plant specific gene ontology. This could help understanding colchicine biosynthesis in G. superba. This review highlights the biorhizomes, rhizome specific genes or gene what expressed with high level in rhizomes, and deep fluid dynamics in a bioreactor specifically for the biomanufacture of colchicine.
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Affiliation(s)
- Ganapathy Sivakumar
- Department of Engineering Technology, College of Technology, University of Houston, HoustonTX, United States
| | - Kamran Alba
- Department of Engineering Technology, College of Technology, University of Houston, HoustonTX, United States
| | - Gregory C. Phillips
- College of Agriculture and Technology, Arkansas State University, JonesboroAR, United States
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Krishnan HB, Natarajan SS, Oehrle NW, Garrett WM, Darwish O. Proteomic Analysis of Pigeonpea (Cajanus cajan) Seeds Reveals the Accumulation of Numerous Stress-Related Proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4572-4581. [PMID: 28532149 DOI: 10.1021/acs.jafc.7b00998] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pigeonpea is one of the major sources of dietary protein for more than a billion people living in South Asia. This hardy legume is often grown in low-input and risk-prone marginal environments. Considerable research effort has been devoted by a global research consortium to develop genomic resources for the improvement of this legume crop. These efforts have resulted in the elucidation of the complete genome sequence of pigeonpea. Despite these developments, little is known about the seed proteome of this important crop. Here, we report the proteome of pigeonpea seed. To enable the isolation of maximum number of seed proteins, including those that are present in very low amounts, three different protein fractions were obtained by employing different extraction media. High-resolution two-dimensional (2-D) electrophoresis followed by MALDI-TOF-TOF-MS/MS analysis of these protein fractions resulted in the identification of 373 pigeonpea seed proteins. Consistent with the reported high degree of synteny between the pigeonpea and soybean genomes, a large number of pigeonpea seed proteins exhibited significant amino acid homology with soybean seed proteins. Our proteomic analysis identified a large number of stress-related proteins, presumably due to its adaptation to drought-prone environments. The availability of a pigeonpea seed proteome reference map should shed light on the roles of these identified proteins in various biological processes and facilitate the improvement of seed composition.
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Affiliation(s)
- Hari B Krishnan
- Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri , Columbia, Missouri 65211, United States
| | - Savithiry S Natarajan
- Soybean Genomics and Improvement Laboratory, PSI, Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Nathan W Oehrle
- Plant Genetics Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Missouri , Columbia, Missouri 65211, United States
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service, U.S. Department of Agriculture , Beltsville, Maryland 20705, United States
| | - Omar Darwish
- Department of Computer and Information Sciences, Towson University , Towson, Maryland 21252, United States
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Ma X, Xu Q, Meyer WA, Huang B. Hormone regulation of rhizome development in tall fescue (Festuca arundinacea) associated with proteomic changes controlling respiratory and amino acid metabolism. ANNALS OF BOTANY 2016; 118:481-94. [PMID: 27443301 PMCID: PMC4998981 DOI: 10.1093/aob/mcw120] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/17/2016] [Accepted: 04/18/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Rhizomes are underground stems with meristematic tissues capable of generating shoots and roots. However, mechanisms controlling rhizome formation and growth are yet to be completely understood. The objectives of this study were to investigate whether rhizome development could be regulated by cytokinins (CKs) and gibberellic acids (GAs), and determine underlying mechanisms of regulation of rhizome formation and growth of tall fescue (Festuca arundinacea) by a CK or GA through proteomic and transcript analysis. METHODS A rhizomatous genotype of tall fescue ('BR') plants were treated with 6-benzylaminopurine (BAP, a synthetic cytokinin) or GA3 in hydroponic culture in growth chambers. Furthermore, comparative proteomic analysis of two-dimensional electrophoresis and mass spectrometry were performed to investigate proteins and associated metabolic pathways imparting increased rhizome number by BAP and rhizome elongation by GA3 KEY RESULTS: BAP stimulated rhizome formation while GA3 promoted rhizome elongation. Proteomic analysis identified 76 differentially expressed proteins (DEPs) due to BAP treatment and 37 DEPs due to GA3 treatment. Cytokinin-related genes and cell division-related genes were upregulated in the rhizome node by BAP and gibberellin-related and cell growth-related genes in the rhizome by GA3 CONCLUSIONS: Most of the BAP- or GA-responsive DEPs were involved in respiratory metabolism and amino acid metabolism. Transcription analysis demonstrated that genes involved in hormone metabolism, signalling pathways, cell division and cell-wall loosening were upregulated by BAP or GA3 The CK and GA promoted rhizome formation and growth, respectively, by activating metabolic pathways that supply energy and amino acids to support cell division and expansion during rhizome initiation and elongation in tall fescue.
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Affiliation(s)
- Xiqing Ma
- College of Agro-grassland Science Nanjing Agricultural University, Nanjing 210095, PR China Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Qian Xu
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, PR China
| | - William A Meyer
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Bingru Huang
- Department of Plant Biology and Pathology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
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Pathania S, Bagler G, Ahuja PS. Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus. FRONTIERS IN PLANT SCIENCE 2016; 7:1229. [PMID: 27588023 PMCID: PMC4988974 DOI: 10.3389/fpls.2016.01229] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 08/02/2016] [Indexed: 05/07/2023]
Abstract
Comparative co-expression analysis of multiple species using high-throughput data is an integrative approach to determine the uniformity as well as diversification in biological processes. Rauvolfia serpentina and Catharanthus roseus, both members of Apocyanacae family, are reported to have remedial properties against multiple diseases. Despite of sharing upstream of terpenoid indole alkaloid pathway, there is significant diversity in tissue-specific synthesis and accumulation of specialized metabolites in these plants. This led us to implement comparative co-expression network analysis to investigate the modules and genes responsible for differential tissue-specific expression as well as species-specific synthesis of metabolites. Toward these goals differential network analysis was implemented to identify candidate genes responsible for diversification of metabolites profile. Three genes were identified with significant difference in connectivity leading to differential regulatory behavior between these plants. These genes may be responsible for diversification of secondary metabolism, and thereby for species-specific metabolite synthesis. The network robustness of R. serpentina, determined based on topological properties, was also complemented by comparison of gene-metabolite networks of both plants, and may have evolved to have complex metabolic mechanisms as compared to C. roseus under the influence of various stimuli. This study reveals evolution of complexity in secondary metabolism of R. serpentina, and key genes that contribute toward diversification of specific metabolites.
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Affiliation(s)
- Shivalika Pathania
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial ResearchPalampur, India
- *Correspondence: Shivalika Pathania
| | - Ganesh Bagler
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial ResearchPalampur, India
- Center for Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi)New Delhi, India
- Centre for Biologically Inspired System Science, Indian Institute of Technology JodhpurJodhpur, India
- Dhirubhai Ambani Institute of Information and Communication TechnologyGandhinagar, India
- Ganesh Bagler
| | - Paramvir S. Ahuja
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial ResearchPalampur, India
- Indian Institute of Science Education and Research (IISER) MohaliMohali, India
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Zhao Q, Gao J, Suo J, Chen S, Wang T, Dai S. Cytological and proteomic analyses of horsetail (Equisetum arvense L.) spore germination. FRONTIERS IN PLANT SCIENCE 2015; 6:441. [PMID: 26136760 PMCID: PMC4469821 DOI: 10.3389/fpls.2015.00441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/29/2015] [Indexed: 05/25/2023]
Abstract
Spermatophyte pollen tubes and root hairs have been used as single-cell-type model systems to understand the molecular processes underlying polar growth of plant cells. Horsetail (Equisetum arvense L.) is a perennial herb species in Equisetopsida, which creates separately growing spring and summer stems in its life cycle. The mature chlorophyllous spores produced from spring stems can germinate without dormancy. Here we report the cellular features and protein expression patterns in five stages of horsetail spore germination (mature spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells). Using 2-DE combined with mass spectrometry, 80 proteins were found to be abundance changed upon spore germination. Among them, proteins involved in photosynthesis, protein turnover, and energy supply were over-represented. Thirteen proteins appeared as proteoforms on the gels, indicating the potential importance of post-translational modification. In addition, the dynamic changes of ascorbate peroxidase, peroxiredoxin, and dehydroascorbate reductase implied that reactive oxygen species homeostasis is critical in regulating cell division and tip-growth. The time course of germination and diverse expression patterns of proteins in photosynthesis, energy supply, lipid and amino acid metabolism indicated that heterotrophic and autotrophic metabolism were necessary in light-dependent germination of the spores. Twenty-six proteins were involved in protein synthesis, folding, and degradation, indicating that protein turnover is vital to spore germination and rhizoid tip-growth. Furthermore, the altered abundance of 14-3-3 protein, small G protein Ran, actin, and caffeoyl-CoA O-methyltransferase revealed that signaling transduction, vesicle trafficking, cytoskeleton dynamics, and cell wall modulation were critical to cell division and polar growth. These findings lay a foundation toward understanding the molecular mechanisms underlying fern spore asymmetric division and rhizoid polar growth.
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Affiliation(s)
- Qi Zhao
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
| | - Jing Gao
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry UniversityHarbin, China
| | - Jinwei Suo
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Alkali Soil Natural Environmental Science Center, Northeast Forestry UniversityHarbin, China
| | - Sixue Chen
- Department of Biology, Interdisciplinary Center for Biotechnology Research, Genetics Institute, Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | - Tai Wang
- Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal UniversityShanghai, China
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11
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Salvato F, Balbuena TS, Nelson W, Rao RSP, He R, Soderlund CA, Gang DR, Thelen JJ. Comparative proteomic analysis of developing rhizomes of the ancient vascular plant Equisetum hyemale and different monocot species. J Proteome Res 2015; 14:1779-91. [PMID: 25716083 DOI: 10.1021/pr501157w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rhizome is responsible for the invasiveness and competitiveness of many plants with great economic and agricultural impact worldwide. Besides its value as an invasive organ, the rhizome plays a role in the establishment and massive growth of forage, providing biomass for biofuel production. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development, and function in plants. In this work, we characterized the proteome of rhizome apical tips and elongation zones from different species using a GeLC-MS/MS (one-dimensional electrophoresis in combination with liquid chromatography coupled online with tandem mass spectrometry) spectral-counting proteomics strategy. Five rhizomatous grasses and an ancient species were compared to study the protein regulation in rhizomes. An average of 2200 rhizome proteins per species were confidently identified and quantified. Rhizome-characteristic proteins showed similar functional distributions across all species analyzed. The over-representation of proteins associated with central roles in cellular, metabolic, and developmental processes indicated accelerated metabolism in growing rhizomes. Moreover, 61 rhizome-characteristic proteins appeared to be regulated similarly among analyzed plants. In addition, 36 showed conserved regulation between rhizome apical tips and elongation zones across species. These proteins were preferentially expressed in rhizome tissues regardless of the species analyzed, making them interesting candidates for more detailed investigative studies about their roles in rhizome development.
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Affiliation(s)
- Fernanda Salvato
- †Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Tiago S Balbuena
- †Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - William Nelson
- ‡BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - R Shyama Prasad Rao
- †Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Ruifeng He
- §Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Carol A Soderlund
- ‡BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - David R Gang
- §Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Jay J Thelen
- †Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
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He R, Salvato F, Park JJ, Kim MJ, Nelson W, Balbuena TS, Willer M, Crow JA, May GD, Soderlund CA, Thelen JJ, Gang DR. A systems-wide comparison of red rice (Oryza longistaminata) tissues identifies rhizome specific genes and proteins that are targets for cultivated rice improvement. BMC PLANT BIOLOGY 2014; 14:46. [PMID: 24521476 PMCID: PMC3933257 DOI: 10.1186/1471-2229-14-46] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 02/07/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant. RESULTS We used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease. CONCLUSIONS A significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.
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Affiliation(s)
- Ruifeng He
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA
| | - Fernanda Salvato
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
- Current Address: Departamento de Tecnologia, Universidade Estadual Paulista, Jaboticabal, SP 14884-900, Brazil
| | - Jeong-Jin Park
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA
| | - Min-Jeong Kim
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA
| | - William Nelson
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
| | - Tiago S Balbuena
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
- Current Address: Departamento de Tecnologia, Universidade Estadual Paulista, Jaboticabal, SP 14884-900, Brazil
| | - Mark Willer
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
| | - John A Crow
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Greg D May
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | | | - Jay J Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO 65211, USA
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, PO Box 646340, Pullman, WA 99164, USA
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Havelund JF, Thelen JJ, Møller IM. Biochemistry, proteomics, and phosphoproteomics of plant mitochondria from non-photosynthetic cells. FRONTIERS IN PLANT SCIENCE 2013; 4:51. [PMID: 23494127 PMCID: PMC3595712 DOI: 10.3389/fpls.2013.00051] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/26/2013] [Indexed: 05/24/2023]
Abstract
Mitochondria fulfill some basic roles in all plant cells. They supply the cell with energy in the form of ATP and reducing equivalents [NAD(P)H] and they provide the cell with intermediates for a range of biosynthetic pathways. In addition to this, mitochondria contribute to a number of specialized functions depending on the tissue and cell type, as well as environmental conditions. We will here review the biochemistry and proteomics of mitochondria from non-green cells and organs, which differ from those of photosynthetic organs in a number of respects. We will briefly cover purification of mitochondria and general biochemical properties such as oxidative phosphorylation. We will then mention a few adaptive properties in response to water stress, seed maturation and germination, and the ability to function under hypoxic conditions. The discussion will mainly focus on Arabidopsis cell cultures, etiolated germinating rice seedlings and potato tubers as model plants. It will cover the general proteome as well as the posttranslational modification protein phosphorylation. To date 64 phosphorylated mitochondrial proteins with a total of 103 phosphorylation sites have been identified.
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Affiliation(s)
- Jesper F. Havelund
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
| | - Jay J. Thelen
- Department of Biochemistry and Interdisciplinary Plant Group, University of Missouri-ColumbiaColumbia, MO, USA
| | - Ian M. Møller
- Department of Molecular Biology and Genetics, Science and Technology, Aarhus UniversitySlagelse, Denmark
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Flores-Nascimento MC, Paes-Leme AF, Mazetto BM, Zanella JL, De Paula EV, Annichino-Bizzacchi JM. Inflammatory, immune and lipid transportation proteins are differentially expressed in spontaneous and proximal deep vein thrombosis patients. Thromb Res 2012; 130:e246-50. [DOI: 10.1016/j.thromres.2012.08.306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/11/2012] [Accepted: 08/21/2012] [Indexed: 12/25/2022]
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