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Routray D, Ghatak A, Chaturvedi P, Petijová L, Weckwerth W, Ručová D, Bačkor M, Lang I, Goga M. Comparative analysis of geotypic variations in the proteome of Nostoc commune. PLANT SIGNALING & BEHAVIOR 2024; 19:2370719. [PMID: 38913942 PMCID: PMC11197914 DOI: 10.1080/15592324.2024.2370719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 06/26/2024]
Abstract
Cyanobacterium Nostoc commune is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of N. commune with the aim to elucidate the differences of physiological trails between distant geotypes, namely Antarctic (AN) and central European (CE). The result obtained clearly showed that the AN geotype demonstrates elevated levels of total phenols, flavonoids, carotenoids, and phycobiliproteins, indicative of its adaptation to environmental stress as referred by comparison to CE sample. Additionally, we employed LC-MS analysis to investigate the proteomes of N. commune from AN and CE geotypes. In total, 1147 proteins were identified, among which 646 proteins expressed significant (up-regulation) changes in both accessions. In the AN geotype, 83 exclusive proteins were identified compared to 25 in the CE geotype. Functional classification of the significant proteins showed a large fraction involved in photosynthesis, amino acid metabolism, carbohydrate metabolism and protein biosynthesis. Further analysis revealed some defense-related proteins such as, superoxide dismutase (SOD) and glutathione reductase, which are rather explicitly expressed in the AN N. commune. The last two proteins suggest a more stressful condition in AN N. commune. In summary, our findings highlight biochemical processes that safeguard the AN geotype of N. commune from extreme environmental challenges, not recorded in CE accession, probably due to less stressful environment in Europe. This study brings the first ever proteomic analysis of N. commune, emphasizing the need for additional investigations into the climate adaptation of this species with rather plastic genome.
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Affiliation(s)
- Deepti Routray
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Arindam Ghatak
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Linda Petijová
- Department of Genetics, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Dajana Ručová
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Martin Bačkor
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ingeborg Lang
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Goga
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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2
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Kudapa H, Ghatak A, Barmukh R, Chaturvedi P, Khan A, Kale S, Fragner L, Chitikineni A, Weckwerth W, Varshney RK. Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.). THE PLANT GENOME 2024; 17:e20337. [PMID: 37165696 DOI: 10.1002/tpg2.20337] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 05/12/2023]
Abstract
Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.
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Affiliation(s)
- Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aamir Khan
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip Kale
- The Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Lena Fragner
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Centre (VIME), University of Vienna, Vienna, Austria
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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3
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Zhang S, Ghatak A, Mohammadi Bazargani M, Kramml H, Zang F, Gao S, Ramšak Ž, Gruden K, Varshney RK, Jiang D, Chaturvedi P, Weckwerth W. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:555-571. [PMID: 38050335 DOI: 10.1111/pbi.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.
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Affiliation(s)
- Shuang Zhang
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | | | - Hannes Kramml
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Fujuan Zang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Shuang Gao
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Živa Ramšak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop Ecophysiology, Ministry of Agriculture/Nanjing Agricultural University, Nanjing, China
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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5
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Bollier N, Micol-Ponce R, Dakdaki A, Maza E, Zouine M, Djari A, Bouzayen M, Chevalier C, Delmas F, Gonzalez N, Hernould M. Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1278608. [PMID: 37965003 PMCID: PMC10642206 DOI: 10.3389/fpls.2023.1278608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023]
Abstract
Climate change is one of the biggest threats that human society currently needs to face. Heat waves associated with global warming negatively affect plant growth and development and will increase in intensity and frequency in the coming years. Tomato is one of the most produced and consumed fruit in the world but remarkable yield losses occur every year due to the sensitivity of many cultivars to heat stress (HS). New insights into how tomato plants are responding to HS will contribute to the development of cultivars with high yields under harsh temperature conditions. In this study, the analysis of microsporogenesis and pollen germination rate of eleven tomato cultivars after exposure to a chronic HS revealed differences between genotypes. Pollen development was either delayed and/or desynchronized by HS depending on the cultivar considered. In addition, except for two, pollen germination was abolished by HS in all cultivars. The transcriptome of floral buds at two developmental stages (tetrad and pollen floral buds) of five cultivars revealed common and specific molecular responses implemented by tomato cultivars to cope with chronic HS. These data provide valuable insights into the diversity of the genetic response of floral buds from different cultivars to HS and may contribute to the development of future climate resilient tomato varieties.
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Affiliation(s)
- N. Bollier
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | | | - A. Dakdaki
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - E. Maza
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - M. Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - A. Djari
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - M. Bouzayen
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
| | - C. Chevalier
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - F. Delmas
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - N. Gonzalez
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
| | - M. Hernould
- INRAE, Université de Bordeaux, BFP, Bordeaux, France
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6
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Carbó M, Chaturvedi P, Álvarez A, Pineda-Cevallos D, Ghatak A, González PR, Cañal MJ, Weckwerth W, Valledor L. Ferroptosis is the key cellular process mediating Bisphenol A responses in Chlamydomonas and a promising target for enhancing microalgae-based bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130997. [PMID: 36860062 DOI: 10.1016/j.jhazmat.2023.130997] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Microplastics are one of the major pollutants in aquatic environments. Among their components, Bisphenol A (BPA) is one of the most abundant and dangerous, leading to endocrine disorders deriving even in different types of cancer in mammals. However, despite this evidence, the xenobiotic effects of BPA over plantae and microalgae still need to be better understood at the molecular level. To fill this gap, we characterized the physiological and proteomic response of Chlamydomonas reinhardtii during long-term BPA exposure by analyzing physiological and biochemical parameters combined with proteomics. BPA imbalanced iron and redox homeostasis, disrupting cell function and triggering ferroptosis. Intriguingly, this microalgae defense against this pollutant is recovering at both molecular and physiological levels while starch accumulation at 72 h of BPA exposure. In this work, we addressed the molecular mechanisms involved in BPA exposure, demonstrating for the first time the induction of ferroptosis in a eukaryotic alga and how ROS detoxification mechanisms and other specific proteomic rearrangements reverted this situation. These results are of great significance not only for understanding the BPA toxicology or exploring the molecular mechanisms of ferroptosis in microalgae but also for defining novel target genes for microplastic bioremediation efficient strain development.
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Affiliation(s)
- María Carbó
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ana Álvarez
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | | | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | | | - María Jesús Cañal
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Luis Valledor
- Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Asturias, Spain.
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7
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Yang D, Wang Z, Huang X, Xu C. Molecular regulation of tomato male reproductive development. ABIOTECH 2023; 4:72-82. [PMID: 37220538 PMCID: PMC10199995 DOI: 10.1007/s42994-022-00094-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/30/2022] [Indexed: 05/25/2023]
Abstract
The reproductive success of flowering plants, which directly affects crop yield, is sensitive to environmental changes. A thorough understanding of how crop reproductive development adapts to climate changes is vital for ensuring global food security. In addition to being a high-value vegetable crop, tomato is also a model plant used for research on plant reproductive development. Tomato crops are cultivated under highly diverse climatic conditions worldwide. Targeted crosses of hybrid varieties have resulted in increased yields and abiotic stress resistance; however, tomato reproduction, especially male reproductive development, is sensitive to temperature fluctuations, which can lead to aborted male gametophytes, with detrimental effects on fruit set. We herein review the cytological features as well as genetic and molecular pathways influencing tomato male reproductive organ development and responses to abiotic stress. We also compare the shared features among the associated regulatory mechanisms of tomato and other plants. Collectively, this review highlights the opportunities and challenges related to characterizing and exploiting genic male sterility in tomato hybrid breeding programs.
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Affiliation(s)
- Dandan Yang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhao Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaozhen Huang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Cao Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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8
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Kumar R, Ghatak A, Goyal I, Sarkar NK, Weckwerth W, Grover A, Chaturvedi P. Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes. FRONTIERS IN PLANT SCIENCE 2023; 13:1083971. [PMID: 36756226 PMCID: PMC9901367 DOI: 10.3389/fpls.2022.1083971] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/02/2022] [Indexed: 06/18/2023]
Abstract
Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteome regulation associated with mature anther in response to heat stress. We identified several genotype - specific protein alterations in rice anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moderately heat tolerant), and Nagina22 (Aus, heat tolerant) in the short-term (ST_HS; one cycle of 42°C, 4 hours before anthesis) and long-term (LT_HS; 6 cycles of 38°C, 6 hours before anthesis) heat stress. The proteins upregulated in long-term heat stress in Nagina22 were enriched in biological processes related to unfolded protein binding and carboxylic acid metabolism, including amino acid metabolism. In short-term heat stress, Nagina22 anthers were enriched in proteins associated with vitamin E biosynthesis and GTPase activator activity. In contrast, downregulated proteins were related to ribosomal proteins. The expression of different Hsp20 and DnaJ was genotype specific. Overall, the heat response in Nagina22 was associated with its capacity for adequate metabolic control and cellular homeostasis, which may be critical for its higher reproductive thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis and lays a foundation for breeding thermotolerant varieties via molecular breeding.
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Affiliation(s)
- Ritesh Kumar
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Isha Goyal
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Neelam K. Sarkar
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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9
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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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10
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Klodová B, Potěšil D, Steinbachová L, Michailidis C, Lindner AC, Hackenberg D, Becker JD, Zdráhal Z, Twell D, Honys D. Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. PLANT REPRODUCTION 2022:10.1007/s00497-022-00452-5. [PMID: 36282332 PMCID: PMC10363097 DOI: 10.1007/s00497-022-00452-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronized gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.
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Affiliation(s)
- Božena Klodová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Praha 2, 128 00, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ann-Cathrin Lindner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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11
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Masoomi‐Aladizgeh F, Kamath KS, Haynes PA, Atwell BJ. Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat. PLANT, CELL & ENVIRONMENT 2022; 45:1242-1256. [PMID: 35092006 PMCID: PMC9415111 DOI: 10.1111/pce.14268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
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Affiliation(s)
| | | | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Brian J. Atwell
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
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12
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Zhang S, Ghatak A, Bazargani MM, Bajaj P, Varshney RK, Chaturvedi P, Jiang D, Weckwerth W. Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:669-687. [PMID: 34227164 PMCID: PMC9291999 DOI: 10.1111/tpj.15410] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 05/03/2023]
Abstract
Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.
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Affiliation(s)
- Shuang Zhang
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Arindam Ghatak
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | | | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
| | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Hyderabad502324India
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationMurdoch UniversityMurdochWA6150Australia
| | - Palak Chaturvedi
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjing210095China
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary EcologyMolecular Systems Biology Lab (MOSYS)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Vienna Metabolomics Center (VIME)University of ViennaAlthanstrasse 14ViennaA‐1090Austria
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13
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Poidevin L, Forment J, Unal D, Ferrando A. Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth. PLANT, CELL & ENVIRONMENT 2021. [PMID: 33289138 DOI: 10.1101/2020.05.29.122937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant reproduction is one key biological process that is very sensitive to heat stress and, as a result, enhanced global warming becomes a serious threat to agriculture. In this work, we have studied the effects of heat on germinated pollen of Arabidopsis thaliana both at the transcriptional and translational level. We have used a high-resolution ribosome profiling technology to provide a comprehensive study of the transcriptome and the translatome of germinated pollen at permissive and restrictive temperatures. We have found significant down-regulation of key membrane transporters required for pollen tube growth by heat, thus uncovering heat-sensitive targets. A subset of the heat-repressed transporters showed coordinated up-regulation with canonical heat-shock genes at permissive conditions. We also found specific regulations at the translational level and we have uncovered the presence of ribosomes on sequences annotated as non-coding. Our results demonstrate that heat impacts mostly on membrane transporters thus explaining the deleterious effects of heat stress on pollen growth. The specific regulations at the translational level and the presence of ribosomes on non-coding RNAs highlights novel regulatory aspects on plant fertilization.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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14
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Poidevin L, Forment J, Unal D, Ferrando A. Transcriptome and translatome changes in germinated pollen under heat stress uncover roles of transporter genes involved in pollen tube growth. PLANT, CELL & ENVIRONMENT 2021; 44:2167-2184. [PMID: 33289138 DOI: 10.1111/pce.13972] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 05/12/2023]
Abstract
Plant reproduction is one key biological process that is very sensitive to heat stress and, as a result, enhanced global warming becomes a serious threat to agriculture. In this work, we have studied the effects of heat on germinated pollen of Arabidopsis thaliana both at the transcriptional and translational level. We have used a high-resolution ribosome profiling technology to provide a comprehensive study of the transcriptome and the translatome of germinated pollen at permissive and restrictive temperatures. We have found significant down-regulation of key membrane transporters required for pollen tube growth by heat, thus uncovering heat-sensitive targets. A subset of the heat-repressed transporters showed coordinated up-regulation with canonical heat-shock genes at permissive conditions. We also found specific regulations at the translational level and we have uncovered the presence of ribosomes on sequences annotated as non-coding. Our results demonstrate that heat impacts mostly on membrane transporters thus explaining the deleterious effects of heat stress on pollen growth. The specific regulations at the translational level and the presence of ribosomes on non-coding RNAs highlights novel regulatory aspects on plant fertilization.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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15
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Masoomi-Aladizgeh F, Najeeb U, Hamzelou S, Pascovici D, Amirkhani A, Tan DKY, Mirzaei M, Haynes PA, Atwell BJ. Pollen development in cotton (Gossypium hirsutum) is highly sensitive to heat exposure during the tetrad stage. PLANT, CELL & ENVIRONMENT 2021; 44:2150-2166. [PMID: 33047317 DOI: 10.1111/pce.13908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 05/22/2023]
Abstract
The development of gametes in plants is acutely susceptible to heatwaves as brief as a few days, adversely affecting pollen maturation and reproductive success. Pollen in cotton (Gossypium hirsutum) was differentially affected when tetrad and binucleate stages were exposed to heat, revealing new insights into the interaction between heat and pollen development. Squares were tagged and exposed to 36/25°C (day/night, moderate heat) or 40/30°C (day/night, extreme heat) for 5 days. Mature pollen grains and leaves were collected for physiological and proteomic responses. While photosynthetic competence was not compromised even at 40°C, leaf tissues became leakier. In contrast, pollen grains were markedly smaller after the tetrad stage was exposed to 40°C and boll production was reduced by 65%. Sugar levels in pollen grains were elevated after exposure to heat, eliminating carbohydrate deficits as a likely cause of poor reproductive capacity. Proteomic analysis of pure pollen samples revealed a particularly high abundance of 70-kDa heat shock (Hsp70s) and cytoskeletal proteins. While short-term bursts of heat had a minor impact on leaves, male gametophyte development was profoundly damaged. Cotton acclimates to maxima of 36°C at both the vegetative and reproductive stages but 5-days exposure to 40°C significantly impairs reproductive development.
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Affiliation(s)
| | - Ullah Najeeb
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Toowoomba, Australia
| | - Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Daniel K Y Tan
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Plant Breeding Institute, Sydney Institute of Agriculture, Sydney, New South Wales, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
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16
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Chaturvedi P, Wiese AJ, Ghatak A, Záveská Drábková L, Weckwerth W, Honys D. Heat stress response mechanisms in pollen development. THE NEW PHYTOLOGIST 2021; 231:571-585. [PMID: 33818773 PMCID: PMC9292940 DOI: 10.1111/nph.17380] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 05/03/2023]
Abstract
Being rooted in place, plants are faced with the challenge of responding to unfavourable local conditions. One such condition, heat stress, contributes massively to crop losses globally. Heatwaves are predicted to increase, and it is of vital importance to generate crops that are tolerant to not only heat stress but also to several other abiotic stresses (e.g. drought stress, salinity stress) to ensure that global food security is protected. A better understanding of the molecular mechanisms that underlie the temperature stress response in pollen will be a significant step towards developing effective breeding strategies for high and stable production in crop plants. While most studies have focused on the vegetative phase of plant growth to understand heat stress tolerance, it is the reproductive phase that requires more attention as it is more sensitive to elevated temperatures. Every phase of reproductive development is affected by environmental challenges, including pollen and ovule development, pollen tube growth, male-female cross-talk, fertilization, and embryo development. In this review we summarize how pollen is affected by heat stress and the molecular mechanisms employed during the stress period, as revealed by classical and -omics experiments.
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Affiliation(s)
- Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Anna J. Wiese
- Laboratory of Pollen BiologyInstitute of Experimental Botany of the Czech Academy of SciencesRozvojová 263Prague 6165 02Czech Republic
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaAlthanstrasse 14Vienna1090Austria
| | - Lenka Záveská Drábková
- Laboratory of Pollen BiologyInstitute of Experimental Botany of the Czech Academy of SciencesRozvojová 263Prague 6165 02Czech Republic
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaAlthanstrasse 14Vienna1090Austria
- Vienna Metabolomics Center (VIME)University of ViennaAlthanstrasse 14Vienna1090Austria
| | - David Honys
- Laboratory of Pollen BiologyInstitute of Experimental Botany of the Czech Academy of SciencesRozvojová 263Prague 6165 02Czech Republic
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17
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Abstract
The gametophyte represents the sexual phase in the alternation of generations in plants; the other, nonsexual phase is the sporophyte. Here, we review the evolutionary origins of the male gametophyte among land plants and, in particular, its ontogenesis in flowering plants. The highly reduced male gametophyte of angiosperm plants is a two- or three-celled pollen grain. Its task is the production of two male gametes and their transport to the female gametophyte, the embryo sac, where double fertilization takes place. We describe two phases of pollen ontogenesis-a developmental phase leading to the differentiation of the male germline and the formation of a mature pollen grain and a functional phase representing the pollen tube growth, beginning with the landing of the pollen grain on the stigma and ending with double fertilization. We highlight recent advances in the complex regulatory mechanisms involved, including posttranscriptional regulation and transcript storage, intracellular metabolic signaling, pollen cell wall structure and synthesis, protein secretion, and phased cell-cell communication within the reproductive tissues.
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Affiliation(s)
- Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, 165 02 Prague 6, Czech Republic; ,
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18
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Ghatak A, Chaturvedi P, Bachmann G, Valledor L, Ramšak Ž, Bazargani MM, Bajaj P, Jegadeesan S, Li W, Sun X, Gruden K, Varshney RK, Weckwerth W. Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat. FRONTIERS IN PLANT SCIENCE 2021; 11:600278. [PMID: 33519854 DOI: 10.3389/fpls.2020.600278.pmid:33519854;pmcid:pmc7838129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/17/2020] [Indexed: 05/24/2023]
Abstract
Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gert Bachmann
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Luis Valledor
- Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Živa Ramšak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Weimin Li
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Xiaoliang Sun
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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19
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Tang M, Li Z, Luo D, Wei F, Kashif MH, Lu H, Hu Y, Yue J, Huang Z, Tan W, Li R, Chen P. A comprehensive integrated transcriptome and metabolome analyses to reveal key genes and essential metabolic pathways involved in CMS in kenaf. PLANT CELL REPORTS 2021; 40:223-236. [PMID: 33128088 DOI: 10.1007/s00299-020-02628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Numbers of critical genes and pathways were found from the levels of transcriptome and metabolome, which were useful information for understanding of kenaf CMS mechanism. Cytoplasmic male sterility (CMS) is a maternally inherited trait in higher plants that leads to the inability to produce or release functional pollen. However, there is lack of comprehensive studies to reveal the molecular basis of CMS occurrence in kenaf. Herein, we performed transcriptome and UPLC-MS-based metabolome analyses in the anthers of a CMS (UG93A) and its maintainer (UG93B) to sort out essential genes and metabolites responding to CMS in kenaf. Transcriptome characterized 7769 differentially expressed genes (DEGs) between these two materials, and pathway enrichment analysis indicated that these DEGs were involved mainly in pentose and glucuronate interconversions, starch and sucrose metabolism, taurine and hypotaurine metabolism. In the metabolome assay, a total of 116 significantly different metabolites (SDMs) were identified between the CMS and its maintainer line, and these SDMs were involved in eight KEGG pathways, including flavone and flavonol biosynthesis, glycerophospholipid metabolism, flavonoid biosynthesis, glycosylphosphatidylinositol-anchor biosynthesi. Integrated analyses of transcriptome and metabolome showed that 50 genes had strong correlation coefficient values (R2 > 0.9) with ten metabolites enriched in six pathways; notably, most genes and metabolites of flavonoid biosynthesis pathways and flavone and flavonol biosynthesis pathways involved in flavonoids biosynthetic pathways were downregulated in CMS compared to those in maintainer. Taken together, the decreased accumulation of flavonoids resulted from the compromised biosynthesis pathways coupled with energy deficiency in the anthers may contribute largely to CMS in UG93A of kenaf.
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Affiliation(s)
- Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China
| | - Zengqiang Li
- 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
| | - Fan Wei
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- 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
| | - Jiao Yue
- 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
| | - Wenye Tan
- 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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20
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Shabrangy A, Ghatak A, Zhang S, Priller A, Chaturvedi P, Weckwerth W. Magnetic Field Induced Changes in the Shoot and Root Proteome of Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:622795. [PMID: 33708230 PMCID: PMC7940674 DOI: 10.3389/fpls.2021.622795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/13/2021] [Indexed: 05/04/2023]
Abstract
The geomagnetic field (GMF) has been present since the beginning of plant evolution. Recently, some researchers have focused their efforts on employing magnetic fields (MFs) higher than GMF to improve the seed germination, growth, and harvest of agriculturally important crop plants, as the use of MFs is an inexpensive and environment-friendly technique. In this study, we have employed different treatments of MF at 7 mT (milliTesla) at different time points of exposure, including 1, 3, and 6 h. The extended exposure was followed by five consecutive days at 6 h per day in barley seeds. The results showed a positive impact of MF on growth characteristics for 5-day-old seedlings, including seed germination rate, root and shoot length, and biomass weight. Furthermore, ~5 days of delay of flowering in pre-treated plants was also observed. We used a shotgun proteomics approach to identify changes in the protein signatures of root and shoot tissues under MF effects. In total, we have identified 2,896 proteins. Thirty-eight proteins in the shoot and 15 proteins in the root showed significant changes under the MF effect. Proteins involved in primary metabolic pathways were increased in contrast to proteins with a metal ion binding function, proteins that contain iron ions in their structure, and proteins involved in electron transfer chain, which were all decreased significantly in the treated tissues. The upregulated proteins' overall biological processes included carbohydrate metabolic process, oxidation-reduction process, and cell redox homeostasis, while down-regulated processes included translation and protein refolding. In general, shoot response was more affected by MF effect than root tissue, leading to the identification of 41 shoot specific proteins. This study provides an initial insight into the proteome regulation response to MF during barley's seedling stage.
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Affiliation(s)
- Azita Shabrangy
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Azita Shabrangy
| | - Arindam Ghatak
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Shuang Zhang
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Alfred Priller
- VERA Laboratory, Isotope Physics, Faculty of Physics, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
- *Correspondence: Wolfram Weckwerth
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21
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Zhang Z, Hu M, Xu W, Wang Y, Huang K, Zhang C, Wen J. Understanding the molecular mechanism of anther development under abiotic stresses. PLANT MOLECULAR BIOLOGY 2021; 105:1-10. [PMID: 32930929 DOI: 10.1007/s11103-020-01074-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/09/2020] [Indexed: 05/02/2023]
Abstract
The developmental stage of anther development is generally more sensitive to abiotic stress than other stages of growth. Specific ROS levels, plant hormones and carbohydrate metabolism are disturbed in anthers subjected to abiotic stresses. As sessile organisms, plants are often challenged to multiple extreme abiotic stresses, such as drought, heat, cold, salinity and metal stresses in the field, which reduce plant growth, productivity and yield. The development of reproductive stage is more susceptible to abiotic stresses than the vegetative stage. Anther, the male reproductive organ that generate pollen grains, is more sensitive to abiotic stresses than female organs. Abiotic stresses affect all the processes of anther development, including tapetum development and degradation, microsporogenesis and pollen development, anther dehiscence, and filament elongation. In addition, abiotic stresses significantly interrupt phytohormone, lipid and carbohydrate metabolism, alter reactive oxygen species (ROS) homeostasis in anthers, which are strongly responsible for the loss of pollen fertility. At present, the precise molecular mechanisms of anther development under adverse abiotic stresses are still not fully understood. Therefore, more emphasis should be given to understand molecular control of anther development during abiotic stresses to engineer crops with better crop yield.
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Affiliation(s)
- Zaibao Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Menghui Hu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Weiwei Xu
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Yuan Wang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Ke Huang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Chi Zhang
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Jie Wen
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
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Keller M, Schleiff E, Simm S. miRNAs involved in transcriptome remodeling during pollen development and heat stress response in Solanum lycopersicum. Sci Rep 2020; 10:10694. [PMID: 32612181 PMCID: PMC7329895 DOI: 10.1038/s41598-020-67833-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 06/10/2020] [Indexed: 01/11/2023] Open
Abstract
Cellular transitions during development and stress response depend on coordinated transcriptomic and proteomic alterations. Pollen is particular because its development is a complex process that includes meiotic and mitotic divisions which causes a high heat sensitivity of these cells. Development and stress response are accompanied by a reprogramming of the transcriptome, e.g. by post-transcriptional regulation via miRNAs. We identified known and potentially novel miRNAs in the transcriptome of developing and heat-stressed pollen of Solanum lycopersicum (tomato). The prediction of target mRNAs yielded an equal number of predicted target-sites in CDS and 3'UTR regions of target mRNAs. The result enabled the postulation of a possible link between miRNAs and a fine-tuning of transcription factor abundance during pollen development. miRNAs seem to play a role in the pollen heat stress response as well. We identified several heat stress transcription factors and heat shock proteins as putative targets of miRNAs in response to heat stress, thereby placing these miRNAs as important elements of thermotolerance. Moreover, for members of the AP2, SBP and ARF family members we could predict a miRNA-mediated regulation during development via the miR172, mir156 and mir160-family strengthening the current concept of a cross-connection between development and stress response in plants.
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Affiliation(s)
- Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438, Frankfurt am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt am Main, Germany.
- Frankfurt Institute of Advanced Studies, 60438, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, 60438, Frankfurt am Main, Germany.
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt am Main, Germany
- Frankfurt Institute of Advanced Studies, 60438, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, 17475, Greifswald, Germany
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Pazhamala LT, Chaturvedi P, Bajaj P, Srikanth S, Ghatak A, Chitikineni A, Bellaire A, Hingane A, Kumar CVS, Saxena KB, Weckwerth W, Saxena RK, Varshney RK. Multiomics approach unravels fertility transition in a pigeonpea line for a two-line hybrid system. THE PLANT GENOME 2020; 13:e20028. [PMID: 33016616 DOI: 10.1002/tpg2.20028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/05/2020] [Accepted: 04/18/2020] [Indexed: 05/17/2023]
Abstract
Pigeonpea [Cajanus cajan (L.) Millsp.] is a pulse crop cultivated in the semi-arid regions of Asia and Africa. It is a rich source of protein and capable of alleviating malnutrition, improving soil health and the livelihoods of small-holder farmers. Hybrid breeding has provided remarkable improvements for pigeonpea productivity, but owing to a tedious and costly seed production system, an alternative two-line hybrid technology is being explored. In this regard, an environment-sensitive male sterile line has been characterized as a thermosensitive male sterile line in pigeonpea precisely responding to day temperature. The male sterile and fertile anthers from five developmental stages were studied by integrating transcriptomics, proteomics and metabolomics supported by precise phenotyping and scanning electron microscopic study. Spatio-temporal analysis of anther transcriptome and proteome revealed 17 repressed DEGs/DEPs in sterile anthers that play a critical role in normal cell wall morphogenesis and tapetal cell development. The male fertility to sterility transition was mainly due to a perturbation in auxin homeostasis, leading to impaired cell wall modification and sugar transport. Limited nutrient utilization thus leads to microspore starvation in response to moderately elevated day temperature which could be restored with auxin-treatment in the male sterile line. Our findings outline a molecular mechanism that underpins fertility transition responses thereby providing a process-oriented two-line hybrid breeding framework for pigeonpea.
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Affiliation(s)
- Lekha T Pazhamala
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Sandhya Srikanth
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, 1030, Austria
| | - Anupama Hingane
- Crop Improvement Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - C V Sameer Kumar
- Crop Improvement Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - K B Saxena
- Crop Improvement Theme, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Rachit K Saxena
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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Weckwerth W, Ghatak A, Bellaire A, Chaturvedi P, Varshney RK. PANOMICS meets germplasm. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1507-1525. [PMID: 32163658 PMCID: PMC7292548 DOI: 10.1111/pbi.13372] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, translational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment-dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker-dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.
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Affiliation(s)
- Wolfram Weckwerth
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Anke Bellaire
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS)Department of Functional and Evolutionary EcologyFaculty of Life SciencesUniversity of ViennaViennaAustria
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadTelanganaIndia
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25
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Structural and Functional Heat Stress Responses of Chloroplasts of Arabidopsis thaliana. Genes (Basel) 2020; 11:genes11060650. [PMID: 32545654 PMCID: PMC7349189 DOI: 10.3390/genes11060650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 11/17/2022] Open
Abstract
Temperature elevations constitute a major threat to plant performance. In recent years, much was learned about the general molecular mode of heat stress reaction of plants. The current research focuses on the integration of the knowledge into more global networks, including the reactions of cellular compartments. For instance, chloroplast function is central for plant growth and survival, and the performance of chloroplasts is tightly linked to the general status of the cell and vice versa. We examined the changes in photosynthesis, chloroplast morphology and proteomic composition posed in Arabidopsis thaliana chloroplasts after a single or repetitive heat stress treatment over a period of two weeks. We observed that the acclimation is potent in the case of repetitive application of heat stress, while a single stress results in lasting alterations. Moreover, the physiological capacity and its adjustment are dependent on the efficiency of the protein translocation process as judged from the analysis of mutants of the two receptor units of the chloroplast translocon, TOC64, and TOC33. In response to repetitive heat stress, plants without TOC33 accumulate Hsp70 proteins and plants without TOC64 have a higher content of proteins involved in thylakoid structure determination when compared to wild-type plants.
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26
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Ghatak A, Chaturvedi P, Bachmann G, Valledor L, Ramšak Ž, Bazargani MM, Bajaj P, Jegadeesan S, Li W, Sun X, Gruden K, Varshney RK, Weckwerth W. Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:600278. [PMID: 33519854 PMCID: PMC7838129 DOI: 10.3389/fpls.2020.600278] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/17/2020] [Indexed: 05/20/2023]
Abstract
Presently, pearl millet and wheat are belonging to highly important cereal crops. Pearl millet, however, is an under-utilized crop, despite its superior resilience to drought and heat stress in contrast to wheat. To investigate this in more detail, we performed comparative physiological screening and large scale proteomics of drought stress responses in drought-tolerant and susceptible genotypes of pearl millet and wheat. These chosen genotypes are widely used in breeding and farming practices. The physiological responses demonstrated large differences in the regulation of root morphology and photosynthetic machinery, revealing a stay-green phenotype in pearl millet. Subsequent tissue-specific proteome analysis of leaves, roots and seeds led to the identification of 12,558 proteins in pearl millet and wheat under well-watered and stress conditions. To allow for this comparative proteome analysis and to provide a platform for future functional proteomics studies we performed a systematic phylogenetic analysis of all orthologues in pearl millet, wheat, foxtail millet, sorghum, barley, brachypodium, rice, maize, Arabidopsis, and soybean. In summary, we define (i) a stay-green proteome signature in the drought-tolerant pearl millet phenotype and (ii) differential senescence proteome signatures in contrasting wheat phenotypes not capable of coping with similar drought stress. These different responses have a significant effect on yield and grain filling processes reflected by the harvest index. Proteome signatures related to root morphology and seed yield demonstrated the unexpected intra- and interspecies-specific biochemical plasticity for stress adaptation for both pearl millet and wheat genotypes. These quantitative reference data provide tissue- and phenotype-specific marker proteins of stress defense mechanisms which are not predictable from the genome sequence itself and have potential value for marker-assisted breeding beyond genome assisted breeding.
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Affiliation(s)
- Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- *Correspondence: Palak Chaturvedi,
| | - Gert Bachmann
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Luis Valledor
- Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Spain
| | - Živa Ramšak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | | | - Weimin Li
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Xiaoliang Sun
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Ljubljana, Slovenia
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- Wolfram Weckwerth,
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Santiago JP, Sharkey TD. Pollen development at high temperature and role of carbon and nitrogen metabolites. PLANT, CELL & ENVIRONMENT 2019; 42:2759-2775. [PMID: 31077385 DOI: 10.1111/pce.13576] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 05/11/2023]
Abstract
Fruit and seed crop production heavily relies on successful stigma pollination, pollen tube growth, and fertilization of female gametes. These processes depend on production of viable pollen grains, a process sensitive to high-temperature stress. Therefore, rising global temperatures threaten worldwide crop production. Close observation of plant development shows that high-temperature stress causes morpho-anatomical changes in male reproductive tissues that contribute to reproductive failure. These changes include early tapetum degradation, anther indehiscence, and deformity of pollen grains, all of which are contributing factors to pollen fertility. At the molecular level, reactive oxygen species (ROS) accumulate when plants are subjected to high temperatures. ROS is a signalling molecule that can be beneficial or detrimental for plant cells depending on its balance with the endogenous cellular antioxidant system. Many metabolites have been linked with ROS over the years acting as direct scavengers or molecular stabilizers that promote antioxidant enzyme activity. This review highlights recent advances in research on anther and pollen development and how these might explain the aberrations seen during high-temperature stress; recent work on the role of nitrogen and carbon metabolites in anther and pollen development is discussed including their potential role at high temperature.
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Affiliation(s)
- James P Santiago
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, 48824
| | - Thomas D Sharkey
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan, 48824
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, 48824
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Comparative Analysis of Proteomics and Transcriptomics during Fertility Transition in a Two-Line Hybrid Rice Line Wuxiang S. Int J Mol Sci 2019; 20:ijms20184542. [PMID: 31540278 PMCID: PMC6770272 DOI: 10.3390/ijms20184542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022] Open
Abstract
The two-line hybrid rice is an important factor of a global crop, but its fertility transition mechanism is unclear. Here, a comparative proteomics and transcriptomics analysis was completed on the two-line hybrid rice line Wuxiang S (WXS) to explore its molecular mechanism and protein regulation during fertility transition. A total of 340 differentially abundant proteins (DAPs) were identified using iTRAQ between the pollen mother cell formation stage (P2) and the meiosis stage (P3). There were 3541 and 4247 differentially expressed genes (DEGs) in P2 and P3 between WXS (Sterile, S)-WXS(S) and WXS (Fertile, F)-WXS(F), respectively, of which 92 and 71 DEGs had corresponding DAPs. Among the DAPs and DEGs, 65 (SP2 vs. FP2) and 55 (SP3 vs. FP3) corresponding DEGs and DAPs (cor-DEGs-DAPs) showed the same expression trend, indicating the cor-DEGs-DAPs genes might play vital roles in WXS fertility transition. Further analysis indicated that cor-DEGs-DAPs proteins were related to energy metabolism-related proteins in anther development and were accompanied by the activation of the stress response pathway and modifications to the cell wall, which ultimately affected the fertility transition of the PTGMS rice line WXS.
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29
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Ghatak A, Chaturvedi P, Weckwerth W. Metabolomics in Plant Stress Physiology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 164:187-236. [PMID: 29470599 DOI: 10.1007/10_2017_55] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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Paupière MJ, Tikunov YM, Firon N, de Vos RCH, Maliepaard C, Visser RGF, Bovy AG. The effect of isolation methods of tomato pollen on the results of metabolic profiling. Metabolomics 2019; 15:11. [PMID: 30830456 PMCID: PMC6326007 DOI: 10.1007/s11306-018-1471-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/31/2018] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Untargeted metabolomics is a powerful tool to detect hundreds of metabolites within a given tissue and to compare the metabolite composition of samples in a comprehensive manner. However, with regard to pollen research such comprehensive metabolomics approaches are yet not well developed. To enable isolation of pollen that is tightly enclosed within the anthers of the flower, such as immature pollen, the current pollen isolation protocols require the use of a watery solution. These protocols raise a number of concerns for their suitability in metabolomics analyses, in view of possible metabolic activities in the pollen and contamination with anther metabolites. OBJECTIVES We assessed the effect of different sample preparation procedures currently used for pollen isolation for their suitability to perform metabolomics of tomato pollen. METHODS Pollen were isolated using different methods and the metabolic profiles were analysed by liquid chromatography-mass spectrometry (LC-MS). RESULTS Our results demonstrated that pollen isolation in a watery solution led to (i) rehydration of the pollen grains, inducing marked metabolic changes in flavonoids, phenylpropanoids and amino acids and thus resulting in a metabolite profile that did not reflect the one of mature dry pollen, (ii) hydrolysis of sucrose into glucose and fructose during subsequent metabolite extraction, unless the isolated and rehydrated pollen were lyophilized prior to extraction, and (iii) contamination with anther-specific metabolites, such as alkaloids, thus compromising the metabolic purity of the pollen fraction. CONCLUSION We conclude that the current practices used to isolate pollen are suboptimal for metabolomics analyses and provide recommendations on how to improve the pollen isolation protocol, in order to obtain the most reliable metabolic profile from pollen tissue.
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Affiliation(s)
- Marine J Paupière
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Yury M Tikunov
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Nurit Firon
- Institute of Plant Sciences, The Volcani Center, ARO, Bet Dagan, Israel
| | - Ric C H de Vos
- Bioscience, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Arnaud G Bovy
- Plant Breeding, Wageningen University & Research, PO Box 386, 6700 AJ, Wageningen, The Netherlands.
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Jegadeesan S, Beery A, Altahan L, Meir S, Pressman E, Firon N. Ethylene production and signaling in tomato (Solanum lycopersicum) pollen grains is responsive to heat stress conditions. PLANT REPRODUCTION 2018; 31:367-383. [PMID: 29948007 DOI: 10.1007/s00497-018-0339-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Tomato pollen grains have the capacity for ethylene production, possessing specific components of the ethylene-biosynthesis and -signaling pathways, being affected/responsive to high-temperature conditions. Exposure of plants to heat stress (HS) conditions reduces crop yield and quality, mainly due to sensitivity of pollen grains. Recently, it was demonstrated that ethylene, a gaseous plant hormone, plays a significant role in tomato pollen heat-tolerance. It is not clear, however, whether, or to what extent, pollen grains are dependent on the capacity of the surrounding anther tissues for ethylene synthesis and signaling, or can synthesize this hormone and possess an active signaling pathway. The aim of this work was (1) to investigate if isolated, maturing and mature, tomato pollen grains have the capacity for ethylene production, (2) to find out whether pollen grains possess an active ethylene-biosynthesis and -signaling pathway and characterize the respective tomato pollen components at the transcript level, (3) to look into the effect of short-term HS conditions. Results from accumulation studies showed that pollen, anthers, and flowers produced ethylene and HS affected differentially ethylene production by (rehydrated) mature pollen, compared to anthers and flowers, causing elevated ethylene levels. Furthermore, several ethylene synthesis genes were expressed, with SlACS3 and SlACS11 standing out as highly HS-induced genes of the pollen ethylene biosynthesis pathway. Specific components of the ethylene-signaling pathway as well as several ethylene-responsive factors were expressed in pollen, with SlETR3 (ethylene receptor; named also NR, for never ripe) and SlCTR2 (constitutive triple response2) being HS responsive. This work shows that tomato pollen grains have the capacity for ethylene production, possessing active ethylene-biosynthesis and -signaling pathways, highlighting specific pollen components that serve as a valuable resource for future research on the role of ethylene in pollen thermotolerance.
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Affiliation(s)
- Sridharan Jegadeesan
- Department of Vegetable Research, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avital Beery
- Department of Vegetable Research, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Leviah Altahan
- Department of Vegetable Research, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Shimon Meir
- Postharvest Science of Fresh Produce, Postharvest and Food Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Etan Pressman
- Department of Vegetable Research, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel
| | - Nurit Firon
- Department of Vegetable Research, Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 50250, Bet Dagan, Israel.
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Teixeira FM, Shah M, Domont GB, Nogueira FCS, Campos FAP. In-Depth Proteome Analysis of Ricinus communis Pollens. Proteomics 2018; 19:e1800347. [PMID: 30474183 DOI: 10.1002/pmic.201800347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/10/2018] [Indexed: 11/07/2022]
Abstract
Pollen grains are tiny structures vital for sexual reproduction and consequently seed and fruit production in angiosperms, and a source of many allergenic components responsible for deleterious implications for health worldwide. Current pollen research is mainly focused on unraveling the molecular mechanisms underlying the pollen germination and tube formation passing from the quiescent stage. In this context, an in-depth proteome analysis of the pollens from Ricinus communis at three different stages-that is, mature, hydrated, and in vitro germinated-is performed. This analysis results in the identification of 1950 proteins, including 1773, 1313, and 858, from mature, hydrated, and germinated pollens, respectively. Based on label-free quantification, 164 proteins are found to be significantly differentially abundant from mature to hydrated pollens, 40 proteins from hydrated to germinated, and 57 proteins from mature to germinated pollens, respectively. Most of the differentially abundant proteins are related to protein, carbohydrate, and energy metabolism and signaling. Besides other functional classes, a reasonable number of the proteins are predicted to be allergenic proteins, previously undiscovered. This is the first in-deep proteome analysis of the R. communis pollens and, to the best of our knowledge, one of the most complete proteome dataset identified from the pollens of any plant species, thus providing a reference proteome for researchers interested in pollen biology.
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Affiliation(s)
- Fabiano M Teixeira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, 60455-900, Brazil
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, 60800, Pakistan
| | - Gilberto B Domont
- Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Fábio C S Nogueira
- Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Francisco A P Campos
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, 60455-900, Brazil
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Jegadeesan S, Chaturvedi P, Ghatak A, Pressman E, Meir S, Faigenboim A, Rutley N, Beery A, Harel A, Weckwerth W, Firon N. Proteomics of Heat-Stress and Ethylene-Mediated Thermotolerance Mechanisms in Tomato Pollen Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:1558. [PMID: 30483278 PMCID: PMC6240657 DOI: 10.3389/fpls.2018.01558] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/04/2018] [Indexed: 05/19/2023]
Abstract
Heat stress is a major cause for yield loss in many crops, including vegetable crops. Even short waves of high temperature, becoming more frequent during recent years, can be detrimental. Pollen development is most heat-sensitive, being the main cause for reduced productivity under heat-stress across a wide range of crops. The molecular mechanisms involved in pollen heat-stress response and thermotolerance are however, not fully understood. Recently, we have demonstrated that ethylene, a gaseous plant hormone, plays a role in tomato (Solanum lycopersicum) pollen thermotolerance. These results were substantiated in the current work showing that increasing ethylene levels by using an ethylene-releasing substance, ethephon, prior to heat-stress exposure, increased pollen quality. A proteomic approach was undertaken, to unravel the mechanisms underlying pollen heat-stress response and ethylene-mediated pollen thermotolerance in developing pollen grains. Proteins were extracted and analyzed by means of a gel LC-MS fractionation protocol, and a total of 1,355 proteins were identified. A dataset of 721 proteins, detected in three biological replicates of at least one of the applied treatments, was used for all analyses. Quantitative analysis was performed based on peptide count. The analysis revealed that heat-stress affected the developmental program of pollen, including protein homeostasis (components of the translational and degradation machinery), carbohydrate, and energy metabolism. Ethephon-pre-treatment shifted the heat-stressed pollen proteome closer to the proteome under non-stressful conditions, namely, by showing higher abundance of proteins involved in protein synthesis, degradation, tricarboxylic acid cycle, and RNA regulation. Furthermore, up-regulation of protective mechanisms against oxidative stress was observed following ethephon-treatment (including higher abundance of glutathione-disulfide reductase, glutaredoxin, and protein disulfide isomerase). Taken together, the findings identified systemic and fundamental components of pollen thermotolerance, and serve as a valuable quantitative protein database for further research.
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Affiliation(s)
- Sridharan Jegadeesan
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture of The Hebrew University of Jerusalem, Rehovot, Israel
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Etan Pressman
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Shimon Meir
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Adi Faigenboim
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Nicholas Rutley
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Avital Beery
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Arye Harel
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Nurit Firon
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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Keller M, Simm S. The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen. BMC Genomics 2018; 19:447. [PMID: 29884134 PMCID: PMC5994098 DOI: 10.1186/s12864-018-4824-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/24/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and proteome. At the same time, pollen development and viability is largely sensitive to stress, particularly to elevated temperatures. The transcriptomic and proteomic changes during pollen development and of different stages in response to elevated temperature was targeted to define the underlying molecular principles. RESULTS The analysis of the transcriptome and proteome of Solanum lycopersicum pollen at tetrad, post-meiotic and mature stage before and after heat stress yielded a decline of the transcriptome but an increase of the proteome size throughout pollen development. Comparison of the transcriptome and proteome led to the discovery of two modes defined as direct and delayed translation. Here, genes of distinct functional processes are under the control of direct and delayed translation. The response of pollen to elevated temperature occurs rather at proteome, but not as drastic at the transcriptome level. Heat shock proteins, proteasome subunits, ribosomal proteins and eukaryotic initiation factors are most affected. On the example of heat shock proteins we demonstrate a decoupling of transcript and protein levels as well as a distinct regulation between the developmental stages. CONCLUSIONS The transcriptome and proteome of developing pollen undergo drastic changes in composition and quantity. Changes at the proteome level are a result of two modes assigned as direct and delayed translation. The response of pollen to elevated temperature is mainly regulated at the proteome level, whereby proteins related to synthesis and degradation of proteins are most responsive and might play a central role in the heat stress response of pollen.
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Affiliation(s)
- Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany
- Frankfurt Institute of Advanced Studies, D-60438 Frankfurt am Main, Germany
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Identification of Wheat Inflorescence Development-Related Genes Using a Comparative Transcriptomics Approach. Int J Genomics 2018; 2018:6897032. [PMID: 29581960 PMCID: PMC5822904 DOI: 10.1155/2018/6897032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/26/2017] [Accepted: 12/03/2017] [Indexed: 12/14/2022] Open
Abstract
Inflorescence represents the highly specialized plant tissue producing the grains. Although key genes regulating flower initiation and development are conserved, the mechanism regulating fertility is still not well explained. To identify genes and gene network underlying inflorescence morphology and fertility of bread wheat, expressed sequence tags (ESTs) from different tissues were analyzed using a comparative transcriptomics approach. Based on statistical comparison of EST frequencies of individual genes in EST pools representing different tissues and verification with RT-PCR and RNA-seq data, 170 genes of 59 gene sets predominantly expressed in the inflorescence were obtained. Nearly one-third of the gene sets displayed differentiated expression profiles in terms of their subgenome orthologs. The identified genes, most of which were predominantly expressed in anthers, encode proteins involved in wheat floral identity determination, anther and pollen development, pollen-pistil interaction, and others. Particularly, 25 annotated gene sets are associated with pollen wall formation, of which 18 encode enzymes or proteins participating in lipid metabolic pathway, including fatty acid ω-hydroxylation, alkane and fatty alcohol biosynthesis, and glycerophospholipid metabolism. We showed that the comparative transcriptomics approach was effective in identifying genes for reproductive development and found that lipid metabolism was particularly active in wheat anthers.
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36
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Cai W, Zhang D. The role of receptor-like kinases in regulating plant male reproduction. PLANT REPRODUCTION 2018; 31:77-87. [PMID: 29508076 DOI: 10.1007/s00497-018-0332-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/19/2018] [Indexed: 05/21/2023]
Abstract
RLKs in anther development. The cell-to-cell communication is essential for specifying different cell types during plant growth, development and adaption to the ever-changing environment. Plant male reproduction, in particular, requires the exquisitely synchronized development of different cell layers within the male tissue, the anther. Receptor-like kinases (RLKs) belong to a large group of kinases localized on the cell surfaces, perceiving extracellular signals and thereafter regulating intracellular processes. Here we update the role of RLKs in early anther development by defining the cell fate and anther patterning, responding to the changing environment and controlling anther carbohydrate metabolism. We provide speculation of the poorly characterized ligands and substrates of these RLKs. The conserved and diversified aspects underlying the function of RLKs in anther development are discussed.
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Affiliation(s)
- Wenguo Cai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia.
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37
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Qi ZY, Wang KX, Yan MY, Kanwar MK, Li DY, Wijaya L, Alyemeni MN, Ahmad P, Zhou J. Melatonin Alleviates High Temperature-Induced Pollen Abortion in Solanum lycopersicum. Molecules 2018; 23:E386. [PMID: 29439470 PMCID: PMC6017144 DOI: 10.3390/molecules23020386] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/21/2022] Open
Abstract
Melatonin is a pleiotropic signal molecule that plays critical roles in regulating plant growth and development, as well as providing physiological protections against various environmental stresses. Nonetheless, the mechanisms for melatonin-mediated pollen thermotolerance remain largely unknown. In this study, we report that irrigation treatment with melatonin (20 µM) effectively ameliorated high temperature-induced inactivation of pollen and inhibition of pollen germination in tomato (Solanum lycopersicum) plants. Melatonin alleviated reactive oxygen species production in tomato anthers under high temperature by the up-regulation of the transcription and activities of several antioxidant enzymes. Transmission electron micrograph results showed that high temperature-induced pollen abortion is associated with a premature degeneration of the tapetum cells and the formation of defective pollen grains with degenerated nuclei at the early uninuclear microspore stage, whilst melatonin protected degradation of organelles by enhancing the expression of heat shock protein genes to refold unfolded proteins and the expression of autophagy-related genes and formation of autophagosomes to degrade denatured proteins. These findings suggest a novel function of melatonin to protect pollen activity under high temperature and support the potential effects of melatonin on reproductive development of plants.
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Affiliation(s)
- Zhen-Yu Qi
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China.
- Agricultural Experiment Station, Zhejiang University, Hangzhou 310058, China.
| | - Kai-Xin Wang
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China.
| | - Meng-Yu Yan
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China.
| | - Mukesh Kumar Kanwar
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China.
| | - Dao-Yi Li
- Chinese Academy of Agricultural Mechanization Sciences, Beijing 10083, China.
| | - Leonard Wijaya
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Mohammed Nasser Alyemeni
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Parvaiz Ahmad
- Department of Botany and Microbiology, Faculty of Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Jie Zhou
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China.
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38
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Zhang Z, Hu M, Feng X, Gong A, Cheng L, Yuan H. Proteomes and Phosphoproteomes of Anther and Pollen: Availability and Progress. Proteomics 2018; 17. [PMID: 28665021 DOI: 10.1002/pmic.201600458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/02/2017] [Indexed: 12/24/2022]
Abstract
In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development. In this review, we summarize the achievements of proteomics and phosphoproteomics with anther and pollen organs from model plant and crop species (i.e. Arabidopsis, rice, tobacco). The increased proteomic information facilitated translation of information from the models to crops and thus aid in agricultural improvement.
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Affiliation(s)
- Zaibao Zhang
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Menghui Hu
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Xiaobing Feng
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Andong Gong
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Lin Cheng
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Hongyu Yuan
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
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40
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Ott E, Kawaguchi Y, Kölbl D, Chaturvedi P, Nakagawa K, Yamagishi A, Weckwerth W, Milojevic T. Proteometabolomic response of Deinococcus radiodurans exposed to UVC and vacuum conditions: Initial studies prior to the Tanpopo space mission. PLoS One 2017; 12:e0189381. [PMID: 29244852 PMCID: PMC5731708 DOI: 10.1371/journal.pone.0189381] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
The multiple extremes resistant bacterium Deinococcus radiodurans is able to withstand harsh conditions of simulated outer space environment. The Tanpopo orbital mission performs a long-term space exposure of D. radiodurans aiming to investigate the possibility of interplanetary transfer of life. The revealing of molecular machinery responsible for survivability of D. radiodurans in the outer space environment can improve our understanding of underlying stress response mechanisms. In this paper, we have evaluated the molecular response of D. radiodurans after the exposure to space-related conditions of UVC irradiation and vacuum. Notably, scanning electron microscopy investigations showed that neither morphology nor cellular integrity of irradiated cells was affected, while integrated proteomic and metabolomic analysis revealed numerous molecular alterations in metabolic and stress response pathways. Several molecular key mechanisms of D. radiodurans, including the tricarboxylic acid cycle, the DNA damage response systems, ROS scavenging systems and transcriptional regulators responded in order to cope with the stressful situation caused by UVC irradiation under vacuum conditions. These results reveal the effectiveness of the integrative proteometabolomic approach as a tool in molecular analysis of microbial stress response caused by space-related factors.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Denise Kölbl
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Kazumichi Nakagawa
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | - Akihiko Yamagishi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
- * E-mail: (TM); (WW)
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41
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Pan C, Ye L, Zheng Y, Wang Y, Yang D, Liu X, Chen L, Zhang Y, Fei Z, Lu G. Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato. BMC Genomics 2017; 18:843. [PMID: 29096602 PMCID: PMC5668977 DOI: 10.1186/s12864-017-4238-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 10/25/2017] [Indexed: 12/18/2022] Open
Abstract
Background Autogamy in cultivated tomato varieties is a derived trait from wild type tomato plants, which are mostly allogamous. However, environmental stresses can cause morphological defects in tomato flowers and hinder autogamy. Under elevated temperatures, tomato plants usually exhibit the phenotype of stigma exsertion, with severely hindered self-pollination and fruit setting, whereas the inherent mechanism of stigma exsertion have been hitherto unknown. Numerous small RNAs (sRNAs) have been shown to play significant roles in plant development and stress responses, however, none of them have been studied with respect to stamen and pistil development under high-temperature conditions. We investigated the associations between stigma exsertion and small RNAs using high-throughput sequencing technology and molecular biology approaches. Results Sixteen sRNA libraries of Micro-Tom were constructed from plants stamen and pistil samples and sequenced after 2 d and 12 d of exposure to heat stress, respectively, from which a total of 110 known and 84 novel miRNAs were identified. Under heat stress conditions, 34 known and 35 novel miRNAs were differentially expressed in stamens, and 20 known and 10 novel miRNAs were differentially expressed in pistils. GO and KEGG pathway analysis showed that the predicted target genes of differentially expressed miRNAs were significantly enriched in metabolic pathways in both stamen and pistil libraries. Potential miRNA-target cleavage cascades that correlated with the regulation of stigma exsertion under heat stress conditions were found and validated through qRT-PCR and RLM-5′ RACE. Conclusion Overall, a global spectrum of known and novel miRNAs involved in tomato stigma exsertion and induced by high temperatures were identified using high-throughput sequencing and molecular biology approaches, laying a foundation for revealing the miRNA-mediated regulatory network involved in the development of tomato stamens and pistils under high-temperature conditions. Electronic supplementary material The online version of this article (10.1186/s12864-017-4238-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Changtian Pan
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Lei Ye
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Yan Wang
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Dandan Yang
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Xue Liu
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Lifei Chen
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Youwei Zhang
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.,USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Gang Lu
- Key Laboratory of Horticultural Plant Growth, Development and Biotechnology, Agricultural Ministry of China, Department of Horticulture, Zhejiang University, Hangzhou, 310085, China. .,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou, 310085, China.
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Rotsch AH, Kopka J, Feussner I, Ischebeck T. Central metabolite and sterol profiling divides tobacco male gametophyte development and pollen tube growth into eight metabolic phases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:129-146. [PMID: 28685881 DOI: 10.1111/tpj.13633] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 05/23/2023]
Abstract
While changes in the transcriptome and proteome of developing pollen have been investigated in tobacco and other species, the metabolic consequences remain rather unclear. Here, a broad range of metabolites was investigated in close succession of developmental stages. Thirteen stages of tobacco male gametophyte development were collected, ranging from tetrads to pollen tubes. Subsequently, the central metabolome and sterol composition were analyzed by GC-mass spectrometry (MS), monitoring 77 metabolites and 29 non-identified analytes. The overall results showed that development and tube growth could be divided into eight metabolic phases with the phase including mitosis I being most distinct. During maturation, compounds such as sucrose and proline accumulated. These were degraded after rehydration, while γ-aminobutyrate transiently increased, possibly deriving from proline breakdown. Sterol analysis revealed that tetrads harbor similar sterols as leaves, but throughout maturation unusual sterols increased. Lastly, two further sterols exclusively accumulated in pollen tubes. This study allows a deeper look into metabolic changes during the development of a quasi-single cell type. Metabolites accumulating during maturation might accelerate pollen germination and tube growth, protect from desiccation, and feed pollinators. Future studies of the underlying processes orchestrating the changes in metabolite levels might give valuable insights into cellular regulation of plant metabolism.
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Affiliation(s)
- Alexander H Rotsch
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Plant Biochemistry, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
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44
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Paul P, Chaturvedi P, Mesihovic A, Ghatak A, Weckwerth W, Schleiff E. Protocol for Enrichment of the Membrane Proteome of Mature Tomato Pollen. Bio Protoc 2017; 7:e2315. [PMID: 34541080 DOI: 10.21769/bioprotoc.2315] [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: 01/20/2017] [Revised: 03/01/2017] [Accepted: 05/02/2017] [Indexed: 11/02/2022] Open
Abstract
We established and elaborated on a method to enrich the membrane proteome of mature pollen from economically relevant crop using the example of Solanum lycopersicum (tomato). To isolate the pollen protein fraction enriched in membrane proteins, a high salt concentration (750 mM of sodium chloride) was used. The membrane protein-enriched fraction was then subjected to shotgun proteomics for identification of proteins, followed by in silico analysis to annotate and classify the detected proteins.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany.,Current address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Anida Mesihovic
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany.,Cluster of Excellence, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany, Germany
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Paupière MJ, Müller F, Li H, Rieu I, Tikunov YM, Visser RGF, Bovy AG. Untargeted metabolomic analysis of tomato pollen development and heat stress response. PLANT REPRODUCTION 2017; 30:81-94. [PMID: 28508929 PMCID: PMC5486769 DOI: 10.1007/s00497-017-0301-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/02/2017] [Indexed: 05/17/2023]
Abstract
Pollen development metabolomics. Developing pollen is among the plant structures most sensitive to high temperatures, and a decrease in pollen viability is often associated with an alteration of metabolite content. Most of the metabolic studies of pollen have focused on a specific group of compounds, which limits the identification of physiologically important metabolites. To get a better insight into pollen development and the pollen heat stress response, we used a liquid chromatography-mass spectrometry platform to detect secondary metabolites in pollen of tomato (Solanum lycopersicum L.) at three developmental stages under control conditions and after a short heat stress at 38 °C. Under control conditions, the young microspores accumulated a large amount of alkaloids and polyamines, whereas the mature pollen strongly accumulated flavonoids. The heat stress treatment led to accumulation of flavonoids in the microspore. The biological role of the detected metabolites is discussed. This study provides the first untargeted metabolomic analysis of developing pollen under a changing environment that can serve as reference for further studies.
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Affiliation(s)
- Marine J Paupière
- Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Florian Müller
- Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Hanjing Li
- Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Ivo Rieu
- Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yury M Tikunov
- Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Arnaud G Bovy
- Plant Breeding, Wageningen University and Research Centre, PO Box 386, 6700 AJ, Wageningen, The Netherlands.
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Ghatak A, Chaturvedi P, Weckwerth W. Cereal Crop Proteomics: Systemic Analysis of Crop Drought Stress Responses Towards Marker-Assisted Selection Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:757. [PMID: 28626463 PMCID: PMC5454074 DOI: 10.3389/fpls.2017.00757] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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Wang L, Sun X, Weiszmann J, Weckwerth W. System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism. FRONTIERS IN PLANT SCIENCE 2017; 8:1066. [PMID: 28713396 PMCID: PMC5491621 DOI: 10.3389/fpls.2017.01066] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/02/2017] [Indexed: 05/19/2023]
Abstract
Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed similarities to Concord grape and indicates the strong effect of genetic background on metabolic partitioning in primary and secondary metabolism.
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Affiliation(s)
- Lei Wang
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Xiaoliang Sun
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Wolfram Weckwerth
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48
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Wang L, Nägele T, Doerfler H, Fragner L, Chaturvedi P, Nukarinen E, Bellaire A, Huber W, Weiszmann J, Engelmeier D, Ramsak Z, Gruden K, Weckwerth W. System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and preparation of stress resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:318-32. [PMID: 27136060 DOI: 10.1111/tpj.13201] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 03/04/2016] [Accepted: 04/22/2016] [Indexed: 05/19/2023]
Abstract
Theobroma cacao and its popular product, chocolate, are attracting attention due to potential health benefits including antioxidative effects by polyphenols, anti-depressant effects by high serotonin levels, inhibition of platelet aggregation and prevention of obesity-dependent insulin resistance. The development of cacao seeds during fruit ripening is the most crucial process for the accumulation of these compounds. In this study, we analyzed the primary and the secondary metabolome as well as the proteome during Theobroma cacao cv. Forastero seed development by applying an integrative extraction protocol. The combination of multivariate statistics and mathematical modelling revealed a complex consecutive coordination of primary and secondary metabolism and corresponding pathways. Tricarboxylic acid (TCA) cycle and aromatic amino acid metabolism dominated during the early developmental stages (stages 1 and 2; cell division and expansion phase). This was accompanied with a significant shift of proteins from phenylpropanoid metabolism to flavonoid biosynthesis. At stage 3 (reserve accumulation phase), metabolism of sucrose switched from hydrolysis into raffinose synthesis. Lipids as well as proteins involved in lipid metabolism increased whereas amino acids and N-phenylpropenoyl amino acids decreased. Purine alkaloids, polyphenols, and raffinose as well as proteins involved in abiotic and biotic stress accumulated at stage 4 (maturation phase) endowing cacao seeds the characteristic astringent taste and resistance to stress. In summary, metabolic key points of cacao seed development comprise the sequential coordination of primary metabolites, phenylpropanoid, N-phenylpropenoyl amino acid, serotonin, lipid and polyphenol metabolism thereby covering the major compound classes involved in cacao aroma and health benefits.
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Affiliation(s)
- Lei Wang
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME); University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Hannes Doerfler
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Anke Bellaire
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Werner Huber
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Doris Engelmeier
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Ziva Ramsak
- Department of Systems Biology and Biotechnology, National Institute of Biology, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of Biology, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME); University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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49
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Ghatak A, Chaturvedi P, Nagler M, Roustan V, Lyon D, Bachmann G, Postl W, Schröfl A, Desai N, Varshney RK, Weckwerth W. Comprehensive tissue-specific proteome analysis of drought stress responses in Pennisetum glaucum (L.) R. Br. (Pearl millet). J Proteomics 2016; 143:122-135. [DOI: 10.1016/j.jprot.2016.02.032] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/21/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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50
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Ambrosino L, Bostan H, Ruggieri V, Chiusano ML. Bioinformatics resources for pollen. PLANT REPRODUCTION 2016; 29:133-147. [PMID: 27271281 DOI: 10.1007/s00497-016-0284-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/19/2016] [Indexed: 06/06/2023]
Abstract
Bioinformatics for Pollen. Pollen plays a key role in crop production, and its development is the most delicate phase in reproduction. Different metabolic pathways are involved in pollen development, and changes in the level of some metabolites, as well as responses to stress, are correlated with the reduction in pollen viability, leading consequently to a decrease in the fruit production. However, studies on pollen may be hard because gamete development and fertilization are complex processes that occur during a short window of time. The rise of the so-called -omics sciences provided key strategies to promote molecular research in pollen tissues, starting from model organisms and moving to increasing number of species. An integrated multi-level approach based on investigations from genomics, transcriptomics, proteomics and metabolomics appears now feasible to clarify key molecular processes in pollen development and viability. To this aim, bioinformatics has a fundamental role for data production and analysis, contributing varied and ad hoc methodologies, endowed with different sensitivity and specificity, necessary for extracting added-value information from the large amount of molecular data achievable. Bioinformatics is also essential for data management, organization, distribution and integration in suitable resources. This is necessary to catch the biological features of the pollen tissues and to design effective approaches to identifying structural or functional properties, enabling the modeling of the major involved processes in normal or in stress conditions. In this review, we provide an overview of the available bioinformatics resources for pollen, ranging from raw data collections to complete databases or platforms, when available, which include data and/or results from -omics efforts on the male gametophyte. Perspectives in the fields will also be described.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy
| | - Hamed Bostan
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy
| | - Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples "Federico II", via Università 100, Portici (NA), 80055, Italy.
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