1
|
Tomato MicroRNAs and Their Functions. Int J Mol Sci 2022; 23:ijms231911979. [PMID: 36233279 PMCID: PMC9569937 DOI: 10.3390/ijms231911979] [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] [Received: 08/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.
Collapse
|
2
|
Cui J, Yi Z, Fu Y, Liu H. Simulated microgravity shapes the endophytic bacterial community by affecting wheat root metabolism. Environ Microbiol 2022; 24:3355-3368. [PMID: 35437853 DOI: 10.1111/1462-2920.16015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
To improve nutrient utilization and pathogenic resistance of plants in space, it is crucial to understand the effects of microgravity on the plant root microbiome. However, the finer details of whether and how microgravity affects the root microbiome remain unclear. Here, we found that simulated microgravity elicits no significant changes in fungal community composition and diversity, whether rhizosphere or endophytic. However, simulated microgravity caused a significant change in the composition and diversity of endophytic bacteria of wheat seedlings, but not in rhizosphere bacteria. The alteration of endophytic bacterial communities demonstrates that wheat seedlings adopt strategies to recruit additional endophytic Enterobacteriaceae and increase the stability of the endophytic bacterial network to respond to the challenge of simulated microgravity. Furthermore, our results also suggest that the corresponding changes in endophytic bacteria under simulated microgravity is closely related to a significant decrease in metabolites of the host's carbon metabolism, flavonoid biosynthesis, benzoxazinoid biosynthesis, and tryptophan metabolism pathways. Our findings reveal details important to our understanding of the impact of gravity on the microbial community of plant seedlings and the theoretical basis for manipulation of microorganisms to ensure efficient plant production in space. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Jingjing Cui
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhihao Yi
- China School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, 100083, China
| | - Yuming Fu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.,State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China.,International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China
| | - Hong Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.,State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083, China.,International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100083, China
| |
Collapse
|
3
|
Sathasivam M, Hosamani R, K Swamy B, Kumaran G S. Plant responses to real and simulated microgravity. LIFE SCIENCES IN SPACE RESEARCH 2021; 28:74-86. [PMID: 33612182 DOI: 10.1016/j.lssr.2020.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 06/12/2023]
Abstract
Plant biology experiments in real and simulated microgravity have significantly contributed to our understanding of physiology and behavior of plants. How do plants perceive microgravity? How that perception translates into stimulus? And in turn plant's response and adaptation to microgravity through physiological, cellular, and molecular changes have been reasonably well documented in the literature. Knowledge gained through these plant biology experiments in microgravity helped to successfully cultivate crops in space. For instance, salad crop such as red romaine lettuce grown on the International Space Station (ISS) is allowed to incorporate into the crew's supplementary diet. However, the use of plants as a sustainable bio-regenerative life support system (BLSS) to produce fresh food and O2, reduce CO2 level, recycle metabolic waste, and efficient water management for long-duration space exploration missions requires critical gap filling research. Hence, it is inevitable to reflect and review plant biology microgravity research findings time and again with a new set of data available in the literature. With that in focus, the current article discusses phenotypic, physiological, biochemical, cell cycle, cell wall changes and molecular responses of plants to microgravity both in real and simulated conditions with the latest literature.
Collapse
Affiliation(s)
- Malarvizhi Sathasivam
- Institute of Agricultural Biotechnology (IABT), University of Agricultural Sciences, Dharwad, Karnataka, 580005, India
| | - Ravikumar Hosamani
- Institute of Agricultural Biotechnology (IABT), University of Agricultural Sciences, Dharwad, Karnataka, 580005, India.
| | - Basavalingayya K Swamy
- Institute of Agricultural Biotechnology (IABT), University of Agricultural Sciences, Dharwad, Karnataka, 580005, India
| | | |
Collapse
|
4
|
Makino Y, Ichinose K, Yoshimura M, Kawahara Y, Yuge L. Efficient preservation of sprouting vegetables under simulated microgravity conditions. PLoS One 2020; 15:e0240809. [PMID: 33057413 PMCID: PMC7561153 DOI: 10.1371/journal.pone.0240809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/02/2020] [Indexed: 01/05/2023] Open
Abstract
The effectiveness of a simulated microgravity environment as a novel method for preserving the freshness of vegetables was investigated. Three types of vegetables were selected: vegetable soybean, mung bean sprouts, and white radish sprouts. These selected vegetables were fixed on a three-dimensional rotary gravity controller, rotated slowly. The selected vegetables were stored at 25°C and 66% of relative humidity for 9, 6, or 5 d while undergoing this process. The simulated microgravity was controlled utilizing a gravity controller around 0 m s-2. The mung bean sprouts stored for 6 d under simulated microgravity conditions maintained higher thickness levels than the vegetable samples stored under normal gravity conditions (9.8 m s-2) for the same duration. The mass of all three items decreased with time without regard to the gravity environment, though the samples stored within the simulated microgravity environment displayed significant mass retention on and after 3 d for mung bean sprout samples and 1 d for white radish sprout samples. In contrast, the mass retention effect was not observed in the vegetable soybean samples. Hence, it was confirmed that the mass retention effect of microgravity was limited to sprout vegetables. As a result of analysis harnessing a mathematical model, assuming that the majority of the mass loss is due to moisture loss, a significant difference in mass reduction coefficient occurs among mung bean sprouts and white radish sprouts due to the microgravity environment, and the mass retention effect of simulated microgravity is quantitatively evaluated utilizing mathematical models. Simulated microgravity, which varies significantly from conventional refrigeration, ethylene control, and modified atmosphere, was demonstrated effective as a novel method for preserving and maintaining the freshness of sprout vegetables. This founding will support long-term space flight missions by prolonging shelf life of sprout vegetables.
Collapse
Affiliation(s)
- Yoshio Makino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Kanji Ichinose
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masatoshi Yoshimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Louis Yuge
- Space Bio-Laboratories Co., Ltd., Hiroshima, Japan
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| |
Collapse
|
5
|
Cardoso TCDS, Alves TC, Caneschi CM, Santana DDRG, Fernandes-Brum CN, Reis GLD, Daude MM, Ribeiro THC, Gómez MMD, Lima AA, Gomes LAA, Gomes MDS, Gandolfi PE, Amaral LRD, Chalfun-Júnior A, Maluf WR, de Souza Gomes M. New insights into tomato microRNAs. Sci Rep 2018; 8:16069. [PMID: 30375421 PMCID: PMC6207730 DOI: 10.1038/s41598-018-34202-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
Abstract
Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.
Collapse
Affiliation(s)
- Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Tamires Caixeta Alves
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Carolina Milagres Caneschi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Douglas Dos Reis Gomes Santana
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | | | - Gabriel Lasmar Dos Reis
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus Martins Daude
- Laboratory of Molecular Analysis, Federal University of Tocantins (UFT), Gurupi, 77402-970, Brazil
| | | | - Miguel Maurício Díaz Gómez
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - André Almeida Lima
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | | | - Marcos de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Peterson Elizandro Gandolfi
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil
| | - Antonio Chalfun-Júnior
- Laboratory of Plant Molecular Physiology, Federal University of Lavras (UFLA), Lavras, 3037 - 37200-000, Brazil
| | - Wilson Roberto Maluf
- Department of Agriculture, Federal University of Lavras (UFLA), Lavras, 37 - 37200-000, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, 38700-128, Patos de Minas, Brazil.
| |
Collapse
|
6
|
Yang X, Liu F, Zhang Y, Wang L, Cheng YF. Cold-responsive miRNAs and their target genes in the wild eggplant species Solanum aculeatissimum. BMC Genomics 2017; 18:1000. [PMID: 29287583 PMCID: PMC5747154 DOI: 10.1186/s12864-017-4341-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Low temperature is an important abiotic stress in plant growth and development, especially for thermophilic plants. Eggplants are thermophilic vegetables, although the molecular mechanism of their response to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although the role of many plant miRNAs in facilitating chilling tolerance has been verified, little is known about the mechanisms of eggplant chilling tolerance. Results Here, we used high-throughput sequencing to extract the miRNA and target genes expression profiles of Solanum aculeatissimum (S. aculeatissimum) under low temperature stress at different time periods(0 h, 2 h, 6 h, 12 h, 24 h). Differentially regulated miRNAs and their target genes were analyzed by comparing the small RNA (sRNA) and miRBase 20.0 databases using BLAST or BOWTIE, respectively. Fifty-six down-regulated miRNAs and 28 up-regulated miRNAs corresponding to 220 up-regulated mRNAs and 94 down-regulated mRNAs, respectively, were identified in S. aculeatissimum. Nine significant differentially expressed miRNAs and twelve mRNAs were identified by quantitative Real-time PCR and association analysis, and analyzed for their GO function enrichment and KEGG pathway association. Conclusions In summary, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, which provides a theoretical basis for the further study of low temperature stress-related miRNAs and the regulation of cold-tolerance mechanisms of eggplant at the miRNA level. Electronic supplementary material The online version of this article (10.1186/s12864-017-4341-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xu Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Fei Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Lu Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yu-Fu Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
| |
Collapse
|
7
|
Grimm D, Wehland M, Pietsch J, Aleshcheva G, Wise P, van Loon J, Ulbrich C, Magnusson NE, Infanger M, Bauer J. Growing tissues in real and simulated microgravity: new methods for tissue engineering. TISSUE ENGINEERING PART B-REVIEWS 2014; 20:555-66. [PMID: 24597549 DOI: 10.1089/ten.teb.2013.0704] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tissue engineering in simulated (s-) and real microgravity (r-μg) is currently a topic in Space medicine contributing to biomedical sciences and their applications on Earth. The principal aim of this review is to highlight the advances and accomplishments in the field of tissue engineering that could be achieved by culturing cells in Space or by devices created to simulate microgravity on Earth. Understanding the biology of three-dimensional (3D) multicellular structures is very important for a more complete appreciation of in vivo tissue function and advancing in vitro tissue engineering efforts. Various cells exposed to r-μg in Space or to s-μg created by a random positioning machine, a 2D-clinostat, or a rotating wall vessel bioreactor grew in the form of 3D tissues. Hence, these methods represent a new strategy for tissue engineering of a variety of tissues, such as regenerated cartilage, artificial vessel constructs, and other organ tissues as well as multicellular cancer spheroids. These aggregates are used to study molecular mechanisms involved in angiogenesis, cancer development, and biology and for pharmacological testing of, for example, chemotherapeutic drugs or inhibitors of neoangiogenesis. Moreover, they are useful for studying multicellular responses in toxicology and radiation biology, or for performing coculture experiments. The future will show whether these tissue-engineered constructs can be used for medical transplantations. Unveiling the mechanisms of microgravity-dependent molecular and cellular changes is an up-to-date requirement for improving Space medicine and developing new treatment strategies that can be translated to in vivo models while reducing the use of laboratory animals.
Collapse
Affiliation(s)
- Daniela Grimm
- 1 Institute of Biomedicine, Pharmacology, Aarhus University , Aarhus, Denmark
| | | | | | | | | | | | | | | | | | | |
Collapse
|