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Zhang Y, Chen Z, Zhang W, Sarwar R, Wang Z, Tan X. Genome-wide analysis of the NYN domain gene family in Brassica napus and its function role in plant growth and development. Gene 2024; 930:148864. [PMID: 39151674 DOI: 10.1016/j.gene.2024.148864] [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] [Received: 05/08/2024] [Revised: 07/21/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
The NYN domain gene family consists of genes that encode ribonucleases that are characterized by a newly identified NYN domain. Members of the family were widely distributed in all life kingdoms and play a crucial role in various RNA regulation processes, although the wide genome overview of the NYN domain gene family is not yet available in any species. Rapeseed (Brassica napus L.), a polyploid model species, is an important oilseed crop. Here, the phylogenetic analysis of these BnaNYNs revealed five distinct groups strongly supported by gene structure, conserved domains, and conserved motifs. The survey of the expansion of the gene family showed that the birth of BnaNYNs is explained by various duplication events. Furthermore, tissue-specific expression analysis, protein-protein interaction prediction, and cis-element prediction suggested a role for BnaNYNs in plant growth and development. Interestingly, the data showed that three tandem duplicated BnaNYNs (TDBs) exhibited distinct expression patterns from those other BnaNYNs and had a high similarity in protein sequence level. Furthermore, the analysis of one of these TDBs, BnaNYN57, showed that overexpression of BnaNYN57 in Arabidopsis thaliana and B. napus accelerated plant growth and significantly increased silique length, while RNA interference resulted in the opposite growth pattern. It suggesting a key role for the TDBs in processes related to plant growth and development.
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Affiliation(s)
- Yijie Zhang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China.
| | - Zhuo Chen
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China
| | - Wenhua Zhang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China
| | - Rehman Sarwar
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China
| | - Zheng Wang
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China.
| | - Xiaoli Tan
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, PR China.
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2
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Zhou M, Ferl RJ, Paul AL. Light has a principal role in the Arabidopsis transcriptomic response to the spaceflight environment. NPJ Microgravity 2024; 10:82. [PMID: 39107298 PMCID: PMC11303767 DOI: 10.1038/s41526-024-00417-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
The Characterizing Arabidopsis Root Attractions (CARA) spaceflight experiment provides comparative transcriptome analyses of plants grown in both light and dark conditions within the same spaceflight. CARA compared three genotypes of Arabidopsis grown in ambient light and in the dark on board the International Space Station (ISS); Col-0, Ws, and phyD, a phytochrome D mutant in the Col-0 background. In all genotypes, leaves responded to spaceflight with a higher number of differentially expressed genes (DEGs) than root tips, and each genotype displayed distinct light / dark transcriptomic patterns that were unique to the spaceflight environment. The Col-0 leaves exhibited a substantial dichotomy, with ten-times as many spaceflight DEGs exhibited in light-grown plants versus dark-grown plants. Although the total number of DEGs in phyD leaves is not very different from Col-0, phyD altered the manner in which light-grown leaves respond to spaceflight, and many genes associated with the physiological adaptation of Col-0 to spaceflight were not represented. This result is in contrast to root tips, where a previous CARA study showed that phyD substantially reduced the number of DEGs. There were few DEGs, but a series of space-altered gene categories, common to genotypes and lighting conditions. This commonality indicates that key spaceflight genes are associated with signal transduction for light, defense, and oxidative stress responses. However, these key signaling pathways enriched from DEGs showed opposite regulatory direction in response to spaceflight under light and dark conditions, suggesting a complex interaction between light as a signal, and light-signaling genes in acclimation to spaceflight.
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Affiliation(s)
- Mingqi Zhou
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Robert J Ferl
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA.
- UF Research, University of Florida, 1523 Union Rd, Grinter Hall, Gainesville, FL, 32611, USA.
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA.
- Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA.
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3
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Grudzińska M, Galanty A, Prochownik E, Kołodziejczyk A, Paśko P. Can Simulated Microgravity and Darkness Conditions Influence the Phytochemical Content and Bioactivity of the Sprouts?-A Preliminary Study on Selected Fabaceae Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:1515. [PMID: 38891323 PMCID: PMC11174765 DOI: 10.3390/plants13111515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Sprouts' consumption has become popular due to their wide availability, easy cultivation process, and proven biological activity. Moreover, stress factors, such as limited access to light or disturbed gravity during growth, may contribute to the increased activity and the synthesis of bioactive compounds. In this study, for the first time, the examination of the impact of darkness and simulated microgravity conditions on the white clover sprouts from the Fabaceae family was conducted. Among several species, used in the preliminary attempts, only white clover was satisfactory sprouting in the disturbed gravity conditions, and thus was chosen for further examination. A random positioning machine setup was used during the cultivation process to simulate microgravity conditions. Additionally, the sprouts were cultivated in total darkness. Simulated microgravity and/or darkness during the first few days of the sprouts' growth caused biomass reduction, the increased synthesis of bioactive compounds (isoflavones and phenolics), and changes in the level of abscisic acid and phenylalanine ammonia-lyase. Moreover, it increased the antioxidant properties of the sprouts, while the enhancement of their cytotoxic impact was observed only for androgen-dependent prostate cancer LNCaP cells. To conclude, the presented results are promising in searching for novel functional food candidates and further studies are necessary, directed at other plant families.
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Affiliation(s)
- Marta Grudzińska
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, 16 Łazarza St., 31-530 Cracow, Poland;
- Department of Food Chemistry and Nutrition, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland;
| | - Agnieszka Galanty
- Department of Pharmacognosy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland;
| | - Ewelina Prochownik
- Department of Food Chemistry and Nutrition, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland;
| | - Agata Kołodziejczyk
- Space Technology Centre, AGH University of Technology, 36 Czarnowiejska St., 30-054 Cracow, Poland;
| | - Paweł Paśko
- Department of Food Chemistry and Nutrition, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland;
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4
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Bowlby B. Extraterrestrial agriculture: plant cultivation in space. Biotechniques 2024; 76:169-173. [PMID: 38602376 DOI: 10.2144/btn-2024-0033] [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] [Received: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
[Formula: see text] Researchers are using various techniques and technologies to study how plants grow in extraterrestrial conditions with the hopes of sustaining longer missions for exploring deep space as well as being able to one day cultivate crops on other planets.
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Affiliation(s)
- Beatrice Bowlby
- Expert Publishing Science Ltd, Unitec House, 2 Albert Place, London, N3 1QB, UK
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5
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Yemets A, Shadrina R, Blume R, Plokhovska S, Blume Y. Autophagy formation, microtubule disorientation, and alteration of ATG8 and tubulin gene expression under simulated microgravity in Arabidopsis thaliana. NPJ Microgravity 2024; 10:31. [PMID: 38499552 PMCID: PMC10948825 DOI: 10.1038/s41526-024-00381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
Autophagy plays an important role in plant growth and development, pathogen invasion and modulates plant response and adaptation to various abiotic stress stimuli. The biogenesis and trafficking of autophagosomes involve microtubules (MTs) as important actors in the autophagic process. However, initiation of autophagy in plants under microgravity has not been previously studied. Here we demonstrate how simulated microgravity induces autophagy development involving microtubular reorganization during period of autophagosome formation. It was shown that induction of autophagy with maximal autophagosome formation in root cells of Arabidopsis thaliana is observed after 6 days of clinostating, along with MT disorganization, which leads to visible changes in root morphology. Gradual decrease of autophagosome number was indicated on 9th and 12th days of the experiment as well as no significant re-orientation of MTs were identified. Respectively, analysis of α- and β-tubulins and ATG8 gene expression was carried out. In particular, the most pronounced increase of expression on both 6th and 9th days in response to simulated microgravity was detected for non-paralogous AtATG8b, AtATG8f, AtATG8i, and AtTUA2, AtTUA3 genes, as well as for the pair of β-tubulin duplicates, namely AtTUB2 and AtTUB3. Overall, the main autophagic response was observed after 6 and 9 days of exposure to simulated microgravity, followed by adaptive response after 12 days. These findings provide a key basis for further studies of cellular mechanisms of autophagy and involvement of cytoskeletal structures in autophagy biogenesis under microgravity, which would enable development of new approaches, aimed on enhancing plant adaptation to microgravity.
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Affiliation(s)
- Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
| | - Ruslana Shadrina
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine
| | - Rostyslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
| | - Svitlana Plokhovska
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Baidy-Vyshnevetskoho St., 2a, Kyiv, 04123, Ukraine.
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6
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Land ES, Sheppard J, Doherty CJ, Perera IY. Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments. FRONTIERS IN PLANT SCIENCE 2024; 14:1308713. [PMID: 38259952 PMCID: PMC10800490 DOI: 10.3389/fpls.2023.1308713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Introduction Understanding how plants adapt to the space environment is essential, as plants will be a valuable component of long duration space missions. Several spaceflight experiments have focused on transcriptional profiling as a means of understanding plant adaptation to microgravity. However, there is limited overlap between results from different experiments. Differences in experimental conditions and hardware make it difficult to find a consistent response across experiments and to distinguish the primary effects of microgravity from other spaceflight effects. Methods Plant Signaling (PS) and Plant RNA Regulation (PRR) were two separate spaceflight experiments conducted on the International Space Station utilizing the European Modular Cultivation System (EMCS). The EMCS provided a lighted environment for plant growth with centrifugal capabilities providing an onboard 1 g control. Results and discussion An RNA-Seq analysis of shoot samples from PS and PRR revealed a significant overlap of genes differentially expressed in microgravity between the two experiments. Relative to onboard 1 g controls, genes involved in transcriptional regulation, shoot development, and response to auxin and light were upregulated in microgravity in both experiments. Conversely, genes involved in defense response, abiotic stress, Ca++ signaling, and cell wall modification were commonly downregulated in both datasets. The downregulation of stress responses in microgravity in these two experiments is interesting as these pathways have been previously observed as upregulated in spaceflight compared to ground controls. Similarly, we have observed many stress response genes to be upregulated in the 1 g onboard control compared to ground reference controls; however these genes were specifically downregulated in microgravity. In addition, we analyzed the sRNA landscape of the 1 g and microgravity (μ g) shoot samples from PRR. We identified three miRNAs (miR319c, miR398b, and miR8683) which were upregulated in microgravity, while several of their corresponding target genes were found to be downregulated in microgravity. Interestingly, the downregulated target genes are enriched in those encoding chloroplast-localized enzymes and proteins. These results uncover microgravity unique transcriptional changes and highlight the validity and importance of an onboard 1 g control.
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Affiliation(s)
- Eric S. Land
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - James Sheppard
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Colleen J. Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Imara Y. Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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7
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Ferl RJ, Zhou M, Strickland HF, Haveman NJ, Callaham JB, Bandla S, Ambriz D, Paul AL. Transcriptomic dynamics in the transition from ground to space are revealed by Virgin Galactic human-tended suborbital spaceflight. NPJ Microgravity 2023; 9:95. [PMID: 38123588 PMCID: PMC10733374 DOI: 10.1038/s41526-023-00340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The Virgin Galactic Unity 22 mission conducted the first astronaut-manipulated suborbital spaceflight experiment. The experiment examined the operationalization of Kennedy Space Center Fixation Tubes (KFTs) as a generalizable approach to preserving biology at various phases of suborbital flight. The biology chosen for this experiment was Arabidopsis thaliana, ecotype Col-0, because of the plant history of spaceflight experimentation within KFTs and wealth of comparative data from orbital experiments. KFTs were deployed as a wearable device, a leg pouch attached to the astronaut, which proved to be operationally effective during the course of the flight. Data from the inflight samples indicated that the microgravity period of the flight elicited the strongest transcriptomic responses as measured by the number of genes showing differential expression. Genes related to reactive oxygen species and stress, as well as genes associated with orbital spaceflight, were highly represented among the suborbital gene expression profile. In addition, gene families largely unaffected in orbital spaceflight were diversely regulated in suborbital flight, including stress-responsive transcription factors. The human-tended suborbital experiment demonstrated the operational effectiveness of the KFTs in suborbital flight and suggests that rapid transcriptomic responses are a part of the temporal dynamics at the beginning of physiological adaptation to spaceflight.
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Affiliation(s)
- Robert J Ferl
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA.
- UF Research, University of Florida, 1523 Union Rd, Grinter Hall, Gainesville, FL, 32611, USA.
| | - Mingqi Zhou
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Hunter F Strickland
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Natasha J Haveman
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Jordan B Callaham
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA
| | - Sirisha Bandla
- Virgin Galactic, 1700 Flight Way, 3rd Floor, Tustin, CA, 92782, USA
| | - Daniel Ambriz
- Virgin Galactic, 1700 Flight Way, 3rd Floor, Tustin, CA, 92782, USA
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Fifield Hall, Gainesville, FL, 32611, USA.
- Interdisciplinary Center for Biotechnology Research, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA.
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8
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Barcenilla BB, Meyers AD, Castillo-González C, Young P, Min JH, Song J, Phadke C, Land E, Canaday E, Perera IY, Bailey SM, Aquilano R, Wyatt SE, Shippen DE. Arabidopsis telomerase takes off by uncoupling enzyme activity from telomere length maintenance in space. Nat Commun 2023; 14:7854. [PMID: 38030615 PMCID: PMC10686995 DOI: 10.1038/s41467-023-41510-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/07/2023] [Indexed: 12/01/2023] Open
Abstract
Spaceflight-induced changes in astronaut telomeres have garnered significant attention in recent years. While plants represent an essential component of future long-duration space travel, the impacts of spaceflight on plant telomeres and telomerase have not been examined. Here we report on the telomere dynamics of Arabidopsis thaliana grown aboard the International Space Station. We observe no changes in telomere length in space-flown Arabidopsis seedlings, despite a dramatic increase in telomerase activity (up to 150-fold in roots), as well as elevated genome oxidation. Ground-based follow up studies provide further evidence that telomerase is induced by different environmental stressors, but its activity is uncoupled from telomere length. Supporting this conclusion, genetically engineered super-telomerase lines with enhanced telomerase activity maintain wildtype telomere length. Finally, genome oxidation is inversely correlated with telomerase activity levels. We propose a redox protective capacity for Arabidopsis telomerase that may promote survivability in harsh environments.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Alexander D Meyers
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
- NASA Postdoctoral Program, Oak Ridge Associated Universities, Kennedy Space Center FL, Merritt Island, FL, 32899, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Pierce Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Ji-Hee Min
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Jiarui Song
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Chinmay Phadke
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Eric Land
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emma Canaday
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
| | - Imara Y Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Roberto Aquilano
- National Technological University, Rosario Regional Faculty, Zeballos 1341, S2000, Rosario, Argentina
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA.
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA.
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA.
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9
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Olanrewaju GO, Haveman NJ, Naldrett MJ, Paul AL, Ferl RJ, Wyatt SE. Integrative transcriptomics and proteomics profiling of Arabidopsis thaliana elucidates novel mechanisms underlying spaceflight adaptation. FRONTIERS IN PLANT SCIENCE 2023; 14:1260429. [PMID: 38089794 PMCID: PMC10712242 DOI: 10.3389/fpls.2023.1260429] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/08/2023] [Indexed: 10/16/2024]
Abstract
Spaceflight presents a unique environment with complex stressors, including microgravity and radiation, that can influence plant physiology at molecular levels. Combining transcriptomics and proteomics approaches, this research gives insights into the coordination of transcriptome and proteome in Arabidopsis' molecular and physiological responses to Spaceflight environmental stress. Arabidopsis seedlings were germinated and grown in microgravity (µg) aboard the International Space Station (ISS) in NASA Biological Research in Canisters - Light Emitting Diode (BRIC LED) hardware, with the ground control established on Earth. At 10 days old, seedlings were frozen in RNA-later and returned to Earth. RNA-seq transcriptomics and TMT-labeled LC-MS/MS proteomic analysis of cellular fractionates from the plant tissues suggest the alteration of the photosynthetic machinery (PSII and PSI) in spaceflight, with the plant shifting photosystem core-regulatory proteins in an organ-specific manner to adapt to the microgravity environment. An overview of the ribosome, spliceosome, and proteasome activities in spaceflight revealed a significant abundance of transcripts and proteins involved in protease binding, nuclease activities, and mRNA binding in spaceflight, while those involved in tRNA binding, exoribonuclease activity, and RNA helicase activity were less abundant in spaceflight. CELLULOSE SYNTHASES (CESA1, CESA3, CESA5, CESA7) and CELLULOSE-LIKE PROTEINS (CSLE1, CSLG3), involved in cellulose deposition and TUBULIN COFACTOR B (TFCB) had reduced abundance in spaceflight. This contrasts with the increased expression of UDP-ARABINOPYRANOSE MUTASEs, involved in the biosynthesis of cell wall non-cellulosic polysaccharides, in spaceflight. Both transcripts and proteome suggested an altered polar auxin redistribution, lipid, and ionic intracellular transportation in spaceflight. Analyses also suggest an increased metabolic energy requirement for plants in Space than on Earth, hence, the activation of several shunt metabolic pathways. This study provides novel insights, based on integrated RNA and protein data, on how plants adapt to the spaceflight environment and it is a step further at achieving sustainable crop production in Space.
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Affiliation(s)
- Gbolaga O. Olanrewaju
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental and Plant Biology, Ohio University Athens, OH, United States
| | - Natasha J. Haveman
- NASA Utilization & Life Sciences Office (UB-A), Kennedy Space Center, Merritt Island, FL, United States
| | - Michael J. Naldrett
- Proteomics & Metabolomics Facility, Nebraska Center for Biotechnology, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Robert J. Ferl
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- Office of Research, University of Florida, Gainesville, FL, United States
| | - Sarah E. Wyatt
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
- Department of Environmental and Plant Biology, Ohio University Athens, OH, United States
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10
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Olanrewaju GO, Kruse CPS, Wyatt SE. Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments. Int J Mol Sci 2023; 24:14425. [PMID: 37833871 PMCID: PMC10573023 DOI: 10.3390/ijms241914425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.
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Affiliation(s)
- Gbolaga O. Olanrewaju
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Colin P. S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA;
| | - Sarah E. Wyatt
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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11
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Nakashima J, Pattathil S, Avci U, Chin S, Alan Sparks J, Hahn MG, Gilroy S, Blancaflor EB. Glycome profiling and immunohistochemistry uncover changes in cell walls of Arabidopsis thaliana roots during spaceflight. NPJ Microgravity 2023; 9:68. [PMID: 37608048 PMCID: PMC10444889 DOI: 10.1038/s41526-023-00312-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
A large and diverse library of glycan-directed monoclonal antibodies (mAbs) was used to determine if plant cell walls are modified by low-gravity conditions encountered during spaceflight. This method called glycome profiling (glycomics) revealed global differences in non-cellulosic cell wall epitopes in Arabidopsis thaliana root extracts recovered from RNA purification columns between seedlings grown on the International Space Station-based Vegetable Production System and paired ground (1-g) controls. Immunohistochemistry on 11-day-old seedling primary root sections showed that ten of twenty-two mAbs that exhibited spaceflight-induced increases in binding through glycomics, labeled space-grown roots more intensely than those from the ground. The ten mAbs recognized xyloglucan, xylan, and arabinogalactan epitopes. Notably, three xylem-enriched unsubstituted xylan backbone epitopes were more intensely labeled in space-grown roots than in ground-grown roots, suggesting that the spaceflight environment accelerated root secondary cell wall formation. This study highlights the feasibility of glycomics for high-throughput evaluation of cell wall glycans using only root high alkaline extracts from RNA purification columns, and subsequent validation of these results by immunohistochemistry. This approach will benefit plant space biological studies because it extends the analyses possible from the limited amounts of samples returned from spaceflight and help uncover microgravity-induced tissue-specific changes in plant cell walls.
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Affiliation(s)
- Jin Nakashima
- Analytical Instrumentation Facility, North Carolina State University, 2410 Campus Shore Drive, Raleigh, NC, 27606, USA
| | - Sivakumar Pattathil
- Mascoma LLC (Lallemand Inc.), 67 Etna Road, Lebanon, NH, 03766, USA
- The University of Georgia, Complex Carbohydrate Research Center, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Utku Avci
- The University of Georgia, Complex Carbohydrate Research Center, 315 Riverbend Road, Athens, GA, 30602, USA
- Department of Agricultural Biotechnology, Faculty of Agriculture, Eskisehir Osmangazi University, 26160, Eskisehir, Turkey
| | - Sabrina Chin
- Department of Botany, 430 Lincoln Drive, University of Wisconsin, Madison, WI, 53706, USA
| | - J Alan Sparks
- Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Michael G Hahn
- Department of Agricultural Biotechnology, Faculty of Agriculture, Eskisehir Osmangazi University, 26160, Eskisehir, Turkey
| | - Simon Gilroy
- Department of Botany, 430 Lincoln Drive, University of Wisconsin, Madison, WI, 53706, USA
| | - Elison B Blancaflor
- Utilization & Life Sciences Office, Exploration Research and Technology Programs, NASA John F. Kennedy Space Center, Merritt Island, FL, 32899, USA.
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12
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Kuya N, Nishijima R, Kitomi Y, Kawakatsu T, Uga Y. Transcriptome profiles of rice roots under simulated microgravity conditions and following gravistimulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1193042. [PMID: 37360733 PMCID: PMC10288856 DOI: 10.3389/fpls.2023.1193042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023]
Abstract
Root system architecture affects the efficient uptake of water and nutrients in plants. The root growth angle, which is a critical component in determining root system architecture, is affected by root gravitropism; however, the mechanism of root gravitropism in rice remains largely unknown. In this study, we conducted a time-course transcriptome analysis of rice roots under conditions of simulated microgravity using a three-dimensional clinostat and following gravistimulation to detect candidate genes associated with the gravitropic response. We found that HEAT SHOCK PROTEIN (HSP) genes, which are involved in the regulation of auxin transport, were preferentially up-regulated during simulated microgravity conditions and rapidly down-regulated by gravistimulation. We also found that the transcription factor HEAT STRESS TRANSCRIPTION FACTOR A2s (HSFA2s) and HSFB2s, showed the similar expression patterns with the HSPs. A co-expression network analysis and an in silico motif search within the upstream regions of the co-expressed genes revealed possible transcriptional control of HSPs by HSFs. Because HSFA2s are transcriptional activators, whereas HSFB2s are transcriptional repressors, the results suggest that the gene regulatory networks governed by HSFs modulate the gravitropic response through transcriptional control of HSPs in rice roots.
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Affiliation(s)
- Noriyuki Kuya
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yuka Kitomi
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan
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13
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Li Y, Collins DA, Grintzalis K. A Simple Biochemical Method for the Detection of Proteins as Biomarkers of Life on Martian Soil Simulants and the Impact of UV Radiation. Life (Basel) 2023; 13:life13051150. [PMID: 37240795 DOI: 10.3390/life13051150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The search for life on other planets relies on the detection of biosignatures of life. Many macromolecules have been suggested as potential targets, among which are proteins that are considered vital components of life due to their essential roles in forming cellular structures, facilitating cellular communication and signaling, and catalyzing metabolic reactions. In this context, accurate quantification of protein signatures in soil would be advantageous, and while several proposed methods exist, which are limited by their sensitivity and specificity, their applicability needs further testing and validation. To this aim, we optimized a Bradford-based assay with high sensitivity and reproducibility and a simple protocol to quantify protein extracted from a Martian soil simulant. Methods for protein spiking, extraction, and recovery were optimized, using protein standards and bacterial proteins as representative models. The proposed method achieved high sensitivity and reproducibility. Taking into account that life remains could exist on the surface of Mars, which is subjected to UV radiation, a simulation of UV exposure was performed on a spiked soil simulant. UV radiation degraded the protein spike, thus highlighting the importance of searching for the remaining signal from degraded proteins. Finally, the applicability of the method was explored in relation to the storage of the reagent which was stable even up to 12 months, thus making its application possible for future planetary exploration missions.
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Affiliation(s)
- Yongda Li
- School of Biotechnology, Dublin City University, D09 Y5NO Dublin, Ireland
| | - David A Collins
- School of Biotechnology, Dublin City University, D09 Y5NO Dublin, Ireland
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14
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Corydon TJ, Schulz H, Richter P, Strauch SM, Böhmer M, Ricciardi DA, Wehland M, Krüger M, Erzinger GS, Lebert M, Infanger M, Wise PM, Grimm D. Current Knowledge about the Impact of Microgravity on Gene Regulation. Cells 2023; 12:cells12071043. [PMID: 37048115 PMCID: PMC10093652 DOI: 10.3390/cells12071043] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023] Open
Abstract
Microgravity (µg) has a massive impact on the health of space explorers. Microgravity changes the proliferation, differentiation, and growth of cells. As crewed spaceflights into deep space are being planned along with the commercialization of space travelling, researchers have focused on gene regulation in cells and organisms exposed to real (r-) and simulated (s-) µg. In particular, cancer and metastasis research benefits from the findings obtained under µg conditions. Gene regulation is a key factor in a cell or an organism’s ability to sustain life and respond to environmental changes. It is a universal process to control the amount, location, and timing in which genes are expressed. In this review, we provide an overview of µg-induced changes in the numerous mechanisms involved in gene regulation, including regulatory proteins, microRNAs, and the chemical modification of DNA. In particular, we discuss the current knowledge about the impact of microgravity on gene regulation in different types of bacteria, protists, fungi, animals, humans, and cells with a focus on the brain, eye, endothelium, immune system, cartilage, muscle, bone, and various cancers as well as recent findings in plants. Importantly, the obtained data clearly imply that µg experiments can support translational medicine on Earth.
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Affiliation(s)
- Thomas J. Corydon
- Department of Biomedicine, Aarhus University, Hoegh Guldbergs Gade 10, 8000 Aarhus, Denmark
- Department of Ophthalmology, Aarhus University Hospital, Palle Juul-Jensens Blvd. 99, 8200 Aarhus, Denmark
- Correspondence: ; Tel.: +45-28-992-179
| | - Herbert Schulz
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Peter Richter
- Gravitational Biology Group, Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Sebastian M. Strauch
- Postgraduate Program in Health and Environment, University of Joinville Region, Joinville 89219-710, SC, Brazil
| | - Maik Böhmer
- Institute for Molecular Biosciences, Johann Wolfgang Goethe Universität, 60438 Frankfurt am Main, Germany
| | - Dario A. Ricciardi
- Institute for Molecular Biosciences, Johann Wolfgang Goethe Universität, 60438 Frankfurt am Main, Germany
| | - Markus Wehland
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Marcus Krüger
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Gilmar S. Erzinger
- Postgraduate Program in Health and Environment, University of Joinville Region, Joinville 89219-710, SC, Brazil
| | - Michael Lebert
- Gravitational Biology Group, Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Manfred Infanger
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
| | - Petra M. Wise
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- The Saban Research Institute, Children’s Hospital Los Angeles, University of Southern California, 4650 Sunset Blvd, Los Angeles, CA 90027, USA
| | - Daniela Grimm
- Department of Biomedicine, Aarhus University, Hoegh Guldbergs Gade 10, 8000 Aarhus, Denmark
- Department of Microgravity and Translational Regenerative Medicine, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Clinic for Plastic, Aesthetic and Hand Surgery, Medical Faculty, University Hospital Magdeburg, Otto von Guericke University, Leipziger Straße 44, 39120 Magdeburg, Germany
- Research Group ‘Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt-und Schwerelosigkeitsbedingungen’ (MARS), Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
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15
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Barker R, Kruse CPS, Johnson C, Saravia-Butler A, Fogle H, Chang HS, Trane RM, Kinscherf N, Villacampa A, Manzano A, Herranz R, Davin LB, Lewis NG, Perera I, Wolverton C, Gupta P, Jaiswal P, Reinsch SS, Wyatt S, Gilroy S. Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome. NPJ Microgravity 2023; 9:21. [PMID: 36941263 PMCID: PMC10027818 DOI: 10.1038/s41526-023-00247-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/10/2023] [Indexed: 03/23/2023] Open
Abstract
Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration's GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.
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Affiliation(s)
- Richard Barker
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Colin P S Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, 87545, USA
| | | | - Amanda Saravia-Butler
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Logyx, LLC, Mountain View, CA, 94043, USA
| | - Homer Fogle
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
- Bionetics, Yorktown, VA, 23693, USA
| | - Hyun-Seok Chang
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Ralph Møller Trane
- Department of Statistics, University of Wisconsin, Madison, WI, 53706, USA
| | - Noah Kinscherf
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040, Madrid, Spain
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-741, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-741, USA
| | - Imara Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Chris Wolverton
- Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, 43015, USA
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Sigrid S Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Sarah Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA.
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16
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Lu X, Yang Z, Song W, Miao J, Zhao H, Ji P, Li T, Si J, Yin Z, Jing M, Shen D, Dou D. The Phytophthora sojae effector PsFYVE1 modulates immunity-related gene expression by targeting host RZ-1A protein. PLANT PHYSIOLOGY 2023; 191:925-945. [PMID: 36461945 PMCID: PMC9922423 DOI: 10.1093/plphys/kiac552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Oomycete pathogens secrete numerous effectors to manipulate plant immunity and promote infection. However, relatively few effector types have been well characterized. In this study, members of an FYVE domain-containing protein family that are highly expanded in oomycetes were systematically identified, and one secreted protein, PsFYVE1, was selected for further study. PsFYVE1 enhanced Phytophthora capsici infection in Nicotiana benthamiana and was necessary for Phytophthora sojae virulence. The FYVE domain of PsFYVE1 had PI3P-binding activity that depended on four conserved amino acid residues. Furthermore, PsFYVE1 targeted RNA-binding proteins RZ-1A/1B/1C in N. benthamiana and soybean (Glycine max), and silencing of NbRZ-1A/1B/1C genes attenuated plant immunity. NbRZ-1A was associated with the spliceosome complex that included three important components, glycine-rich RNA-binding protein 7 (NbGRP7), glycine-rich RNA-binding protein 8 (NbGRP8), and a specific component of the U1 small nuclear ribonucleoprotein complex (NbU1-70K). Notably, PsFYVE1 disrupted NbRZ-1A-NbGRP7 interaction. RNA-seq and subsequent experimental analysis demonstrated that PsFYVE1 and NbRZ-1A not only modulated pre-mRNA alternative splicing (AS) of the necrotic spotted lesions 1 (NbNSL1) gene, but also co-regulated transcription of hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (NbHCT), ethylene insensitive 2 (NbEIN2), and sucrose synthase 4 (NbSUS4) genes, which participate in plant immunity. Collectively, these findings indicate that the FYVE domain-containing protein family includes potential uncharacterized effector types and also highlight that plant pathogen effectors can regulate plant immunity-related genes at both AS and transcription levels to promote disease.
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Affiliation(s)
- Xinyu Lu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zitong Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Song
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hanqing Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyun Ji
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jierui Si
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Yin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Maofeng Jing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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17
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Yang L, Yang L, Zhao C, Liu J, Tong C, Zhang Y, Cheng X, Jiang H, Shen J, Xie M, Liu S. Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1009998. [PMID: 36311064 PMCID: PMC9608124 DOI: 10.3389/fpls.2022.1009998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.
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Affiliation(s)
- Lingli Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Yang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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18
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Red Light Enhances Plant Adaptation to Spaceflight and Mars g-Levels. Life (Basel) 2022; 12:life12101484. [PMID: 36294919 PMCID: PMC9605285 DOI: 10.3390/life12101484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022] Open
Abstract
Understanding how plants respond and adapt to extraterrestrial conditions is essential for space exploration initiatives. Deleterious effects of the space environment on plant development have been reported, such as the unbalance of cell growth and proliferation in the root meristem, or gene expression reprogramming. However, plants are capable of surviving and completing the seed-to-seed life cycle under microgravity. A key research challenge is to identify environmental cues, such as light, which could compensate the negative effects of microgravity. Understanding the crosstalk between light and gravity sensing in space was the major objective of the NASA-ESA Seedling Growth series of spaceflight experiments (2013–2018). Different g-levels were used, with special attention to micro-g, Mars-g, and Earth-g. In spaceflight seedlings illuminated for 4 days with a white light photoperiod and then photostimulated with red light for 2 days, transcriptomic studies showed, first, that red light partially reverted the gene reprogramming induced by microgravity, and that the combination of microgravity and photoactivation was not recognized by seedlings as stressful. Two mutant lines of the nucleolar protein nucleolin exhibited differential requirements in response to red light photoactivation. This observation opens the way to directed-mutagenesis strategies in crop design to be used in space colonization. Further transcriptomic studies at different g-levels showed elevated plastid and mitochondrial genome expression in microgravity, associated with disturbed nucleus–organelle communication, and the upregulation of genes encoding auxin and cytokinin hormonal pathways. At the Mars g-level, genes of hormone pathways related to stress response were activated, together with some transcription factors specifically related to acclimation, suggesting that seedlings grown in partial-g are able to acclimate by modulating genome expression in routes related to space-environment-associated stress.
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19
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Baba AI, Mir MY, Riyazuddin R, Cséplő Á, Rigó G, Fehér A. Plants in Microgravity: Molecular and Technological Perspectives. Int J Mol Sci 2022; 23:10548. [PMID: 36142459 PMCID: PMC9505700 DOI: 10.3390/ijms231810548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 01/19/2023] Open
Abstract
Plants are vital components of our ecosystem for a balanced life here on Earth, as a source of both food and oxygen for survival. Recent space exploration has extended the field of plant biology, allowing for future studies on life support farming on distant planets. This exploration will utilize life support technologies for long-term human space flights and settlements. Such longer space missions will depend on the supply of clean air, food, and proper waste management. The ubiquitous force of gravity is known to impact plant growth and development. Despite this, we still have limited knowledge about how plants can sense and adapt to microgravity in space. Thus, the ability of plants to survive in microgravity in space settings becomes an intriguing topic to be investigated in detail. The new knowledge could be applied to provide food for astronaut missions to space and could also teach us more about how plants can adapt to unique environments. Here, we briefly review and discuss the current knowledge about plant gravity-sensing mechanisms and the experimental possibilities to research microgravity-effects on plants either on the Earth or in orbit.
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Affiliation(s)
- Abu Imran Baba
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Mohd Yaqub Mir
- Doctoral School of Neuroscience, Semmelweis University, H-1083 Budapest, Hungary
- Theoretical Neuroscience and Complex Systems Group, Department of Computational Sciences, Wigner Research Centre for Physics, H-1121 Budapest, Hungary
| | - Riyazuddin Riyazuddin
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Biological Research Centre (BRC), Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), H-6726 Szeged, Hungary
| | - Ágnes Cséplő
- Biological Research Centre (BRC), Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), H-6726 Szeged, Hungary
| | - Gábor Rigó
- Biological Research Centre (BRC), Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), H-6726 Szeged, Hungary
| | - Attila Fehér
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Biological Research Centre (BRC), Institute of Plant Biology, Eötvös Loránd Research Network (ELKH), H-6726 Szeged, Hungary
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20
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Peng L, Ru M, Liang Z. Variation of photosynthesis, secondary metabolites and antioxidant activities in third generation of spaceflight-induced Salvia miltiorrhiza. CHINESE HERBAL MEDICINES 2022; 14:592-601. [PMID: 36405058 PMCID: PMC9669357 DOI: 10.1016/j.chmed.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/18/2021] [Accepted: 02/18/2022] [Indexed: 10/14/2022] Open
Abstract
Objective Spaceflight has long been perceived as an effective way to improve the quantity and quality of plants with wide applications. In order to obtain stable and inheritable descendants of spaceflight-induced Salvia miltiorrhiza lines, we investigated and analyzed four lines m16, m50, m51, m57 (three individuals of each line) and the ground control (three individuals) of the third generation of spaceflight-induced S. miltiorrhiza from primary/secondary metabolism and antioxidative abilities. Methods A portable photosynthesis system (Li-6400) with red/blue LED light source was used to perform the photosynthetic characteristics to evaluate their primary productivity. The secondary metabolites (phenolic acids, tanshinones, total phenolics and flavonoids) and antioxidant activity of roots were analyzed to assess their quality. Results Compared with control, line m16 presented weak photosynthetic ability, but high apparent quantum yield (AQY), higher contents of secondary metabolites, and stronger antioxidative abilities. Line m57 had a strong gas exchange ability, relatively higher secondary metabolites contents, and ascending antioxidative abilities. Lines m50 and m51 were in the middle level of lines m16 and m57. The principal component analysis for all the original data revealed three components including a root-related index, a leaf-related index, and a CO2 response parameter could be used to distinguish spaceflight-induced S. miltiorrhiza lines. Conclusion Line m57 could be an appropriate material for the investigation of targeted breeding towards high production, and line m16 could be used to identify essential genes and unravel sophisticated pathways underlying the secondary metabolisms.
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21
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Manzano A, Carnero-Diaz E, Herranz R, Medina FJ. Recent transcriptomic studies to elucidate the plant adaptive response to spaceflight and to simulated space environments. iScience 2022; 25:104687. [PMID: 35856037 PMCID: PMC9287483 DOI: 10.1016/j.isci.2022.104687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Discovering the adaptation mechanisms of plants to the space environment is essential for supporting human space exploration. Transcriptomic analyses allow the identification of adaptation response pathways by detecting changes in gene expression at the global genome level caused by the main factors of the space environment, namely altered gravity and cosmic radiation. This article reviews transcriptomic studies carried out from plants grown in spaceflights and in different ground-based microgravity simulators. Despite differences in plant growth conditions, these studies have shown that cell wall remodeling, oxidative stress, defense response, and photosynthesis are common altered processes in plants grown under spaceflight conditions. European scientists have significantly contributed to the acquisition of this knowledge, e.g., by showing the role of red light in the adaptation response of plants (EMCS experiments) and the mechanisms of cellular response and adaptation mostly affecting cell cycle regulation, using cell cultures in microgravity simulators. Cell wall, photosynthesis, and stress response are key in plant adaptation to space DNA methylation and alternative splicing are among the involved molecular mechanisms Light is an essential factor for plant development, even more in the space environment EMCS and simulation cell culture experiments are the main European contributions
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Affiliation(s)
- Aránzazu Manzano
- PCNPμG Lab (Plant Cell Nucleolus, Proliferation and Microgravity), Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Eugénie Carnero-Diaz
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, CNRS, EPHE, UA, Paris, 75005, France
| | - Raúl Herranz
- PCNPμG Lab (Plant Cell Nucleolus, Proliferation and Microgravity), Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - F Javier Medina
- PCNPμG Lab (Plant Cell Nucleolus, Proliferation and Microgravity), Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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22
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Paul AL, Elardo SM, Ferl R. Plants grown in Apollo lunar regolith present stress-associated transcriptomes that inform prospects for lunar exploration. Commun Biol 2022; 5:382. [PMID: 35552509 PMCID: PMC9098553 DOI: 10.1038/s42003-022-03334-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
The extent to which plants can enhance human life support on other worlds depends on the ability of plants to thrive in extraterrestrial environments using in-situ resources. Using samples from Apollo 11, 12, and 17, we show that the terrestrial plant Arabidopsis thaliana germinates and grows in diverse lunar regoliths. However, our results show that growth is challenging; the lunar regolith plants were slow to develop and many showed severe stress morphologies. Moreover, all plants grown in lunar soils differentially expressed genes indicating ionic stresses, similar to plant reactions to salt, metal and reactive oxygen species. Therefore, although in situ lunar regoliths can be useful for plant production in lunar habitats, they are not benign substrates. The interaction between plants and lunar regolith will need to be further elucidated, and likely mitigated, to best enable efficient use of lunar regolith for life support within lunar stations. Arabidopsis plants were seeded onto lunar soil samples taken directly from the Apollo 11, 12, and 17 missions. Transcriptomic analyses reveal that plants grown in lunar soil differentially express genes associated with salt, metal, and ROS stress.
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Affiliation(s)
- Anna-Lisa Paul
- Interdisciplinary Center for Biotechnology Research and Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| | - Stephen M Elardo
- Department of Geological Sciences, University of Florida, Gainesville, FL, USA
| | - Robert Ferl
- UF Research and Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
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23
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Villacampa A, Fañanás‐Pueyo I, Medina FJ, Ciska M. Root growth direction in simulated microgravity is modulated by a light avoidance mechanism mediated by flavonols. PHYSIOLOGIA PLANTARUM 2022; 174:e13722. [PMID: 35606933 PMCID: PMC9327515 DOI: 10.1111/ppl.13722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/11/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
In a microgravity environment, without any gravitropic signal, plants are not able to define and establish a longitudinal growth axis. Consequently, absorption of water and nutrients by the root and exposure of leaves to sunlight for efficient photosynthesis is hindered. In these conditions, other external cues can be explored to guide the direction of organ growth. Providing a unilateral light source can guide the shoot growth, but prolonged root exposure to light causes a stress response, affecting growth and development, and also affecting the response to other environmental factors. Here, we have investigated how the protection of the root from light exposure, while the shoot is illuminated, influences the direction of root growth in microgravity. We report that the light avoidance mechanism existing in roots guides their growth towards diminishing light and helps establish the proper longitudinal seedling axis in simulated microgravity conditions. This process is regulated by flavonols, as shown in the flavonoid-accumulating mutant transparent testa 3, which shows an increased correction of the root growth direction in microgravity, when the seedling is grown with the root protected from light. This finding may improve the efficiency of water and nutrient sourcing and photosynthesis under microgravity conditions, as they exist in space, contributing to better plant fitness and biomass production in space farming enterprises, necessary for space exploration by humans.
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Affiliation(s)
- Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas – CSICMadridSpain
| | | | - F. Javier Medina
- Centro de Investigaciones Biológicas Margarita Salas – CSICMadridSpain
| | - Malgorzata Ciska
- Centro de Investigaciones Biológicas Margarita Salas – CSICMadridSpain
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24
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Kato S, Murakami M, Saika R, Soga K, Wakabayashi K, Hashimoto H, Yano S, Matsumoto S, Kasahara H, Kamada M, Shimazu T, Hashimoto T, Hoson T. Suppression of Cortical Microtubule Reorientation and Stimulation of Cell Elongation in Arabidopsis Hypocotyls under Microgravity Conditions in Space. PLANTS 2022; 11:plants11030465. [PMID: 35161447 PMCID: PMC8837939 DOI: 10.3390/plants11030465] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 11/16/2022]
Abstract
How microgravity in space influences plant cell growth is an important issue for plant cell biology as well as space biology. We investigated the role of cortical microtubules in the stimulation of elongation growth in Arabidopsis (Arabidopsis thaliana) hypocotyls under microgravity conditions with the Resist Tubule space experiment. The epidermal cells in the lower half of the hypocotyls of wild-type Columbia were longer in microgravity than at on-orbit 1 g, which precipitated an increase in the entire hypocotyl length. In the apical region, cortical microtubules adjacent to the outer tangential wall were predominantly transverse to the long axis of the cell, whereas longitudinal microtubules were predominant in the basal region. In the 9th to 12th epidermal cells (1 to 3 mm) from the tip, where the modification of microtubule orientation from transverse to longitudinal directions (reorientation) occurred, cells with transverse microtubules increased, whereas those with longitudinal microtubules decreased in microgravity, and the average angle with respect to the transverse cell axis decreased, indicating that the reorientation was suppressed in microgravity. The expression of tubulin genes was suppressed in microgravity. These results suggest that under microgravity conditions, the expression of genes related to microtubule formation was downregulated, which may cause the suppression of microtubule reorientation from transverse to longitudinal directions, thereby stimulating cell elongation in Arabidopsis hypocotyls.
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Affiliation(s)
- Shiho Kato
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (S.K.); (M.M.); (R.S.); (K.S.); (K.W.)
| | - Mana Murakami
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (S.K.); (M.M.); (R.S.); (K.S.); (K.W.)
| | - Ryo Saika
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (S.K.); (M.M.); (R.S.); (K.S.); (K.W.)
| | - Kouichi Soga
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (S.K.); (M.M.); (R.S.); (K.S.); (K.W.)
| | - Kazuyuki Wakabayashi
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (S.K.); (M.M.); (R.S.); (K.S.); (K.W.)
| | - Hirofumi Hashimoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara 252-5210, Japan;
| | - Sachiko Yano
- Japan Aerospace Exploration Agency, Tsukuba 305-8505, Japan;
| | - Shohei Matsumoto
- Japan Manned Space Systems, Tokyo 100-0004, Japan; (S.M.); (H.K.)
| | - Haruo Kasahara
- Japan Manned Space Systems, Tokyo 100-0004, Japan; (S.M.); (H.K.)
| | | | | | - Takashi Hashimoto
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan;
| | - Takayuki Hoson
- Department of Biology, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan; (S.K.); (M.M.); (R.S.); (K.S.); (K.W.)
- Correspondence:
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25
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Schulz H, Strauch SM, Richter P, Wehland M, Krüger M, Sahana J, Corydon TJ, Wise P, Baran R, Lebert M, Grimm D. Latest knowledge about changes in the proteome in microgravity. Expert Rev Proteomics 2022; 19:43-59. [PMID: 35037812 DOI: 10.1080/14789450.2022.2030711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION : A long-term stay of humans in space causes a large number of well-known health problems and changes in protists and plants. Deep space exploration will increase the time humans or rodents will spend in microgravity (µg). Moreover, they are exposed to cosmic radiation, hypodynamia, and isolation. OMICS investigations will increase our knowledge of the underlying mechanisms of µg-induced alterations in vivo and in vitro. AREAS COVERED : We summarize the findings over the recent 3 years on µg-induced changes in the proteome of protists, plants, rodent and human cells. Considering the thematic orientation of microgravity-related publications in that time frame, we focus on medicine-associated findings such as the µg-induced antibiotic resistance of bacteria, the myocardial consequences of µg-induced calpain activation and the role of MMP13 in osteoarthritis. All these point to the fact that µg is an extreme stressor that could not be evolutionarily addressed on Earth. EXPERT COMMENTARY : In conclusion, when interpreting µg-experiments, the direct, mostly unspecific stress response, must be distinguished from specific µg-effects. For this reason, recent studies often do not consider single protein findings but place them in the context of protein-protein interactions. This enables an estimation of functional relationships, especially if these are supported by epigenetic and transcriptional data (multi-omics).
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Affiliation(s)
- Herbert Schulz
- Department of Microgravity and Translational Regenerative Medicine, Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Research Group 'Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen' (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | - Sebastian M Strauch
- Postgraduate Program in Health and Environment, University of Joinville Region, Rua Paulo Malschitzki, 10 - Zona Industrial Norte, Joinville, SC, CEP 89219-710, Brazil
| | - Peter Richter
- Gravitational Biology Group, Department of Biology, Friedrich-Alexander University, Staudtstraße 5, 91058 Erlangen, Germany
| | - Markus Wehland
- Department of Microgravity and Translational Regenerative Medicine, Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Research Group 'Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen' (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | - Marcus Krüger
- Department of Microgravity and Translational Regenerative Medicine, Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Research Group 'Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen' (MARS), Otto-von-Guericke University, Magdeburg, Germany
| | | | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.,Department of Ophthalmology, Aarhus University Hospital, Aarhus C, Denmark
| | - Petra Wise
- Department of Microgravity and Translational Regenerative Medicine, Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,The Saban Research Institute, Children's Hospital Los Angeles, University of Southern California, Los Angeles, USA
| | - Ronni Baran
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Michael Lebert
- Gravitational Biology Group, Department of Biology, Friedrich-Alexander University, Staudtstraße 5, 91058 Erlangen, Germany.,Space Biology Unlimited SAS, 24 Cours de l'Intendance, 33000 Bordeaux, France
| | - Daniela Grimm
- Department of Microgravity and Translational Regenerative Medicine, Clinic for Plastic, Aesthetic and Hand Surgery, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany.,Research Group 'Magdeburger Arbeitsgemeinschaft für Forschung unter Raumfahrt- und Schwerelosigkeitsbedingungen' (MARS), Otto-von-Guericke University, Magdeburg, Germany.,Department of Biomedicine, Aarhus University, Aarhus C, Denmark
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26
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Kruse CPS, Wyatt SE. Nitric oxide, gravity response, and a unified schematic of plant signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111105. [PMID: 34895542 DOI: 10.1016/j.plantsci.2021.111105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Plant signaling components are often involved in numerous processes. Calcium, reactive oxygen species, and other signaling molecules are essential to normal biotic and abiotic responses. Yet, the summation of these components is integrated to produce a specific response despite their involvement in a myriad of response cascades. In the response to gravity, the role of many of these individual components has been studied, but a specific sequence of signals has not yet been assembled into a cohesive schematic of gravity response signaling. Herein, we provide a review of existing knowledge of gravity response and differential protein and gene regulation induced by the absence of gravity stimulus aboard the International Space Station and propose an integrated theoretical schematic of gravity response incorporating that information. Recent developments in the role of nitric oxide in gravity signaling provided some of the final contextual pillars for the assembly of the model, where nitric oxide and the role of cysteine S-nitrosation may be central to the gravity response. The proposed schematic accounts for the known responses to reorientation with respect to gravity in roots-the most well studied gravitropic plant tissue-and is supported by the extensive evolutionary conservation of regulatory amino acids within protein components of the signaling schematic. The identification of a role of nitric oxide in regulating the TIR1 auxin receptor is indicative of the broader relevance of the schematic in studying a multitude of environmental and stress responses. Finally, there are several experimental approaches that are highlighted as essential to the further study and validation of this schematic.
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Affiliation(s)
- Colin P S Kruse
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, United States; Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, United States; Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, United States(1)
| | - Sarah E Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, United States; Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, United States.
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27
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Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots. Life (Basel) 2021; 11:life11101010. [PMID: 34685382 PMCID: PMC8539686 DOI: 10.3390/life11101010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Abstract
Although many reports characterize the transcriptional response of Arabidopsis seedlings to microgravity, few investigate the effect of partial or fractional gravity on gene expression. Understanding plant responses to fractional gravity is relevant for plant growth on lunar and Martian surfaces. The plant signaling flight experiment utilized the European Modular Cultivation System (EMCS) onboard the International Space Station (ISS). The EMCS consisted of two rotors within a controlled chamber allowing for two experimental conditions, microgravity (stationary rotor) and simulated gravity in space. Seedlings were grown for 5 days under continuous light in seed cassettes. The arrangement of the seed cassettes within each experimental container results in a gradient of fractional g (in the spinning rotor). To investigate whether gene expression patterns are sensitive to fractional g, we carried out transcriptional profiling of root samples exposed to microgravity or partial g (ranging from 0.53 to 0.88 g). Data were analyzed using DESeq2 with fractional g as a continuous variable in the design model in order to query gene expression across the gravity continuum. We identified a subset of genes whose expression correlates with changes in fractional g. Interestingly, the most responsive genes include those encoding transcription factors, defense, and cell wall-related proteins and heat shock proteins.
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28
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Abstract
Circadian clocks are important to much of life on Earth and are of inherent interest to humanity, implicated in fields ranging from agriculture and ecology to developmental biology and medicine. New techniques show that it is not simply the presence of clocks, but coordination between them that is critical for complex physiological processes across the kingdoms of life. Recent years have also seen impressive advances in synthetic biology to the point where parallels can be drawn between synthetic biological and circadian oscillators. This review will emphasize theoretical and experimental studies that have revealed a fascinating dichotomy of coupling and heterogeneity among circadian clocks. We will also consolidate the fields of chronobiology and synthetic biology, discussing key design principles of their respective oscillators.
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Affiliation(s)
- Chris N Micklem
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK.,The Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CH3 0HE, UK
| | - James C W Locke
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
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29
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Paul AL, Haveman N, Califar B, Ferl RJ. Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:691790. [PMID: 34589093 PMCID: PMC8475764 DOI: 10.3389/fpls.2021.691790] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Background: Plants subjected to the novel environment of spaceflight show transcriptomic changes that resemble aspects of several terrestrial abiotic stress responses. Under investigation here is whether epigenetic modulations, similar to those that occur in terrestrial stress responses, have a functional role in spaceflight physiological adaptation. The Advanced Plant Experiment-04 - Epigenetic Expression experiment examined the role of cytosine methylation in spaceflight adaptation. The experiment was conducted onboard the International Space Station, and evaluated the spaceflight-altered, genome-wide methylation profiles of two methylation-regulating gene mutants [methyltransferase 1 (met1-7) and elongator complex subunit 2 (elp2-5)] along with a wild-type Col-0 control. Results: The elp2-5 plants suffered in their physiological adaptation to spaceflight in that their roots failed to extend away from the seed and the overall development of the plants was greatly impaired in space. The met1-7 plants suffered less, with their morphology affected by spaceflight in a manner similar to that of the Col-0 controls. The differentially expressed genes (DEGs) in spaceflight were dramatically different in the elp2-5 and met1-7 plants compared to Col-0, indicating that the disruptions in these mutants resulted in a reprogramming of their spaceflight responses, especially in elp2-5. Many of the genes comprising the spaceflight transcriptome of each genotype were differentially methylated in spaceflight. In Col-0 the majority of the DEGs were representative of the now familiar spaceflight response, which includes genes associated with cell wall remodeling, pathogen responses and ROS signaling. However, the spaceflight transcriptomes of met1-7 and elp2-5 each presented patterns of DEGs that are almost completely different than Col-0, and to each other. Further, the DEGs of the mutant genotypes suggest a more severe spaceflight stress response in the mutants, particularly in elp2-5. Conclusion: Arabidopsis physiological adaptation to spaceflight results in differential DNA methylation in an organ-specific manner. Disruption of Met1 methyltransferase function does not dramatically affect spaceflight growth or morphology, yet met1-7 reprograms the spaceflight transcriptomic response in a unique manner. Disruption of elp2-5 results in poor development in spaceflight grown plants, together with a diminished, dramatically reprogrammed transcriptomic response.
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Affiliation(s)
- Anna-Lisa Paul
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Natasha Haveman
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Brandon Califar
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Robert J. Ferl
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
- Office of Research, University of Florida, Gainesville, FL, United States
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30
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Manzano A, Pereda-Loth V, de Bures A, Sáez-Vásquez J, Herranz R, Medina FJ. Light signals counteract alterations caused by simulated microgravity in proliferating plant cells. AMERICAN JOURNAL OF BOTANY 2021; 108:1775-1792. [PMID: 34524692 DOI: 10.1002/ajb2.1728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Light and gravity are fundamental cues for plant development. Our understanding of the effects of light stimuli on plants in space, without gravity, is key to providing conditions for plants to acclimate to the environment. Here we tested the hypothesis that the alterations caused by the absence of gravity in root meristematic cells can be counteracted by light. METHODS Seedlings of wild-type Arabidopsis thaliana and two mutants of the essential nucleolar protein nucleolin (nuc1, nuc2) were grown in simulated microgravity, either under a white light photoperiod or under continuous darkness. Key variables of cell proliferation (cell cycle regulation), cell growth (ribosome biogenesis), and auxin transport were measured in the root meristem using in situ cellular markers and transcriptomic methods and compared with those of a 1 g control. RESULTS The incorporation of a photoperiod regime was sufficient to attenuate or suppress the effects caused by gravitational stress at the cellular level in the root meristem. In all cases, values for variables recorded from samples receiving light stimuli in simulated microgravity were closer to values from the controls than values from samples grown in darkness. Differential sensitivities were obtained for the two nucleolin mutants. CONCLUSIONS Light signals may totally or partially replace gravity signals, significantly improving plant growth and development in microgravity. Despite that, molecular alterations are still compatible with the expected acclimation mechanisms, which need to be better understood. The differential sensitivity of nuc1 and nuc2 mutants to gravitational stress points to new strategies to produce more resilient plants to travel with humans in new extraterrestrial endeavors.
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Affiliation(s)
- Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | | | - Anne de Bures
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, 66860, France
- Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, 66860, France
| | - Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, Perpignan, 66860, France
- Université de Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, 66860, France
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
| | - F Javier Medina
- Centro de Investigaciones Biológicas Margarita Salas - CSIC, Ramiro de Maeztu 9, Madrid, 28040, Spain
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31
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Zeng D, Cui J, Yin Y, Xiong Y, Liu M, Guan S, Cheng D, Sun Y, Lu W. Metabolomics Analysis in Different Development Stages on SP0 Generation of Rice Seeds After Spaceflight. FRONTIERS IN PLANT SCIENCE 2021; 12:700267. [PMID: 34276752 PMCID: PMC8278407 DOI: 10.3389/fpls.2021.700267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Spaceflight is a special abiotic stress condition. In recent years, it has been confirmed that the spaceflight caused the stress response of rice seeds, and the protein level, transcription level, and methylation level will change during the planting process after returning to the ground. However, the changes at the metabolome level are not very clear. In this study, two kinds of rice seeds, Dongnong423 (DN3) and Dongnong416 (DN6), were carried on the ShiJian-10 retractable satellite (SJ-10) for 12.5 days in orbit, returned to the ground and planted in the field until the three-leaf (TLP) and tillering stage (TS). The results of antioxidant enzyme activity, soluble sugar, and electron leakage rate revealed that the spaceflight caused the stress response of rice. The TLP and TS of DN3 identified 110 and 57 different metabolites, respectively, while the TLP and TS of DN6 identified 104 and 74 different metabolites, respectively. These metabolites included amino acids, sugars, fatty acids, organic acids and secondary metabolites. We used qRT-PCR technology to explore the changes of enzyme genes in the tricarboxylic acid cycle (TCA) and amino acid metabolism pathway. Combined with the results of metabolomics, we determined that during the TLP, the TCA cycle rate of DN3 was inhibited and amino acid metabolism was activated, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. In TS, the TCA cycle rate of DN3 was inhibited, and amino acid metabolism was not significantly changed, while the TCA cycle rate of DN6 was activated and amino acid metabolism was inhibited. These results suggested that the response mechanisms of the two different rice strains to spaceflight stress are different, and these differences may be reflected in energy consumption and compound biosynthesis of rice in different growth and development stages. This study provided new insights for further exploring the effects of spaceflight.
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Affiliation(s)
- Deyong Zeng
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Jie Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - YiShu Yin
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Yi Xiong
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Mengyao Liu
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Shuanghong Guan
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Dayou Cheng
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
| | - Yeqing Sun
- Dalian Maritime University, Environmental Systems Biology Institute, Dalian, China
| | - Weihong Lu
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
- National and Local Joint Engineering Laboratory for Synthesis, Transformation and Separation of Extreme Environmental Nutrients, Harbin Institute of Technology, Harbin, China
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Kordyum E, Hasenstein KH. Plant biology for space exploration - Building on the past, preparing for the future. LIFE SCIENCES IN SPACE RESEARCH 2021; 29:1-7. [PMID: 33888282 DOI: 10.1016/j.lssr.2021.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/05/2021] [Accepted: 01/16/2021] [Indexed: 06/12/2023]
Abstract
A review of past insights of space experiments with plants outlines basic space and gravity effects as well as gene expression. Efforts to grow plants in space gradually incorporated basic question on plant productivity, stress response and cultivation. The prospect of extended space missions as well as colonization of the Moon and Mars require better understanding and therefore research efforts on biomass productivity, substrate and water relations, atmospheric composition, pressure and temperature and substrate and volume (growth space) requirements. The essential combination of using plants not only for food production but also for regeneration of waste, and recycling of carbon and oxygen production requires integration of complex biological and engineering aspects. We combine a historical account of plant space research with considerations for future research on plant cultivation, selection, and productivity based on space-related environmental conditions.
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Affiliation(s)
- Elizabeth Kordyum
- Department of Cell Biology and Anatomy, Institute of Botany NASU, Tereschenkivska Str. 2, 01601 Kiev, Ukraine, United States
| | - Karl H Hasenstein
- Biology Department, University of Louisiana at Lafayette, Lafayette, LA, 70504-3602, United States.
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Heyneke E, Hoefgen R. Meeting the complexity of plant nutrient metabolism with multi-omics approaches. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2261-2265. [PMID: 33779750 PMCID: PMC8006596 DOI: 10.1093/jxb/eraa600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article comments on:Henriet C, Balliau T, Aime D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. 2021. Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. Journal of Experimental Botany 72, 2611–2626.
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Affiliation(s)
- Elmien Heyneke
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
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Villacampa A, Ciska M, Manzano A, Vandenbrink JP, Kiss JZ, Herranz R, Medina FJ. From Spaceflight to Mars g-Levels: Adaptive Response of A. Thaliana Seedlings in a Reduced Gravity Environment Is Enhanced by Red-Light Photostimulation. Int J Mol Sci 2021; 22:E899. [PMID: 33477454 PMCID: PMC7830483 DOI: 10.3390/ijms22020899] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/10/2021] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
The response of plants to the spaceflight environment and microgravity is still not well understood, although research has increased in this area. Even less is known about plants' response to partial or reduced gravity levels. In the absence of the directional cues provided by the gravity vector, the plant is especially perceptive to other cues such as light. Here, we investigate the response of Arabidopsis thaliana 6-day-old seedlings to microgravity and the Mars partial gravity level during spaceflight, as well as the effects of red-light photostimulation by determining meristematic cell growth and proliferation. These experiments involve microscopic techniques together with transcriptomic studies. We demonstrate that microgravity and partial gravity trigger differential responses. The microgravity environment activates hormonal routes responsible for proliferation/growth and upregulates plastid/mitochondrial-encoded transcripts, even in the dark. In contrast, the Mars gravity level inhibits these routes and activates responses to stress factors to restore cell growth parameters only when red photostimulation is provided. This response is accompanied by upregulation of numerous transcription factors such as the environmental acclimation-related WRKY-domain family. In the long term, these discoveries can be applied in the design of bioregenerative life support systems and space farming.
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Affiliation(s)
- Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.V.); (M.C.); (A.M.)
| | - Malgorzata Ciska
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.V.); (M.C.); (A.M.)
| | - Aránzazu Manzano
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.V.); (M.C.); (A.M.)
| | | | - John Z. Kiss
- Department of Biology, University of North Carolina-Greensboro, Greensboro, NC 27402, USA;
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.V.); (M.C.); (A.M.)
| | - F. Javier Medina
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.V.); (M.C.); (A.M.)
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Niu L, Liu L, Wang W. Digging for Stress-Responsive Cell Wall Proteins for Developing Stress-Resistant Maize. FRONTIERS IN PLANT SCIENCE 2020; 11:576385. [PMID: 33101346 PMCID: PMC7546335 DOI: 10.3389/fpls.2020.576385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/07/2020] [Indexed: 06/09/2023]
Abstract
As a vital component of plant cell walls, proteins play important roles in stress response by modifying the structure of cell walls and involving in the wall integrity signaling pathway. Recently, we have critically reviewed the predictors, databases, and cross-referencing of the subcellular locations of possible cell wall proteins (CWPs) in plants (Briefings in Bioinformatics 2018;19:1130-1140). Here, we briefly introduce strategies for isolating CWPs during proteomic analysis. Taking maize (Zea mays) as an example, we retrieved 1873 probable maize CWPs recorded in the UniProt KnowledgeBase (UniProtKB). After curation, 863 maize CWPs were identified and classified into 59 kinds of protein families. By referring to gene ontology (GO) annotations and gene differential expression in the Expression Atlas, we have highlighted the potential of CWPs acting in the front line of defense against biotic and abiotic stresses. Moreover, the analysis results of cis-acting elements revealed the responsiveness of the genes encoding CWPs toward phytohormones and various stresses. We suggest that the stress-responsive CWPs could be promising candidates for applications in developing varieties of stress-resistant maize.
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