1
|
Lee Y, Kim SJ, Kim YJ, Kim YH, Yoon JY, Shin J, Ok SM, Kim EJ, Choi EJ, Oh JW. Sensor development for multiple simultaneous classifications using genetically engineered M13 bacteriophages. Biosens Bioelectron 2023; 241:115642. [PMID: 37703643 DOI: 10.1016/j.bios.2023.115642] [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: 03/06/2023] [Revised: 07/17/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023]
Abstract
Sensors for detecting infinitesimal amounts of chemicals in air have been widely developed because they can identify the origin of chemicals. These sensing technologies are also used to determine the variety and freshness of fresh food and detect explosives, hazardous chemicals, environmental hormones, and diseases using exhaled gases. However, there is still a need to rapidly develop portable and highly sensitive sensors that respond to complex environments. Here, we show an efficient method for optimising an M13 bacteriophage-based multi-array colourimetric sensor for multiple simultaneous classifications. Apples, which are difficult to classify due to many varieties in distribution, were selected for classifying targets. M13 was adopted to fabricate a multi-array colourimetric sensor using the self-templating process since a chemical property of major coat protein p8 consisting of the M13 body can be manipulated by genetic engineering to respond to various target substances. The twenty sensor units, which consisted of different types of manipulated M13, exhibited colour changes because of the change of photonic crystal-like nanostructure when they were exposed to target substances associated with apples. The classification success rate of the optimal sensor combinations was achieved with high accuracy for the apple variety (100%), four standard fragrances (100%), and aging (84.5%) simultaneously. We expect that this optimisation technique can be used for rapid sensor development capable of multiple simultaneous classifications in various fields, such as medical diagnosis, hazardous environment monitoring, and the food industry, where sensors need to be developed in response to complex environments consisting of various targets.
Collapse
Affiliation(s)
- Yujin Lee
- Department of Nano Fusion Technology, Pusan National University, 46241, Busan, Republic of Korea.
| | - Sung-Jo Kim
- Bio-IT Fusion Technology Research Institute, Pusan National University, 46241, Busan, Republic of Korea
| | - Ye-Ji Kim
- Department of Nano Fusion Technology, Pusan National University, 46241, Busan, Republic of Korea
| | - You Hwan Kim
- Department of Nano Fusion Technology, Pusan National University, 46241, Busan, Republic of Korea
| | - Ji-Young Yoon
- Dental Research Institute, Dental and Life Science Institute, Pusan National University, 50612, Yangsan, Republic of Korea; Department of Dental Anesthesia and Pain Medicine, School of Dentistry, Pusan National University, 50612, Yangsan, Republic of Korea
| | - Jonghyun Shin
- Dental Research Institute, Dental and Life Science Institute, Pusan National University, 50612, Yangsan, Republic of Korea; Department of Pediatric Dentistry, School of Dentistry, Pusan National University, 50612, Yangsan, Republic of Korea
| | - Soo-Min Ok
- Dental Research Institute, Dental and Life Science Institute, Pusan National University, 50612, Yangsan, Republic of Korea; Department of Oral Medicine, School of Dentistry, Pusan National University, 50612, Yangsan, Republic of Korea
| | - Eun-Jung Kim
- Dental Research Institute, Dental and Life Science Institute, Pusan National University, 50612, Yangsan, Republic of Korea; Department of Dental Anesthesia and Pain Medicine, School of Dentistry, Pusan National University, 50612, Yangsan, Republic of Korea
| | - Eun Jung Choi
- Bio-IT Fusion Technology Research Institute, Pusan National University, 46241, Busan, Republic of Korea; Korea Nanobiotechnology Center, Pusan National University, 46241, Busan, Republic of Korea
| | - Jin-Woo Oh
- Department of Nano Fusion Technology, Pusan National University, 46241, Busan, Republic of Korea; Bio-IT Fusion Technology Research Institute, Pusan National University, 46241, Busan, Republic of Korea; Korea Nanobiotechnology Center, Pusan National University, 46241, Busan, Republic of Korea; Department of Nanoenergy Engineering and Research Center for Energy Convergence Technology, Pusan National University, 46241, Busan, Republic of Korea
| |
Collapse
|
2
|
Xu J, Wang F, Zhan J, Li Y, Wang T, Ma R, Tian Y. Construction of TiO2/starch nanocomposite cryogel for ethylene removal and banana preservation. Carbohydr Polym 2023; 312:120825. [PMID: 37059552 DOI: 10.1016/j.carbpol.2023.120825] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023]
Abstract
Perishability caused by natural plant hormone ethylene has attracted great attention in the field of fruit and vegetable (F&V) preservation. Various physical and chemical methods have been applied to remove ethylene, but the eco-unfriendliness and toxicity of these methods limit their application. Herein, a novel starch-based ethylene scavenger was developed by introducing TiO2 nanoparticles into starch cryogel and applying ultrasonic treatment to further improve ethylene removal efficiency. As a porous carrier, the pore wall of cryogel provided dispersion space, which increased the area of TiO2 exposed to UV light, thereby endowing starch cryogel with ethylene removal capacity. The photocatalytic performance of scavenger reached the maximum ethylene degradation efficiency of 89.60 % when the TiO2 loading was 3 %. Ultrasonic treatment interrupted starch molecular chains and then promoted their rearrangement, increasing the material specific surface area from 54.6 m2/g to 225.15 m2/g and improving the ethylene degradation efficiency by 63.23 % compared with the non-sonicated cryogel. Furthermore, the scavenger exhibits good practicability for removing ethylene as a banana package. This work provides a new carbohydrate-based ethylene scavenger, utilizing as a non-food contact inner filler of F&V packaging in practical applications, which exhibits great potential in F&V preservation and broadens the application fields of starch.
Collapse
|
3
|
Kusuma HS, Yugiani P, Himana AI, Aziz A, Putra DAW. Reflections on food security and smart packaging. Polym Bull (Berl) 2023; 81:1-47. [PMID: 36852383 PMCID: PMC9947446 DOI: 10.1007/s00289-023-04734-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/24/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023]
Abstract
Estimating the number of COVID-19 cases in 2020 exacerbated the food contamination and food supply issues. These problems make consumers more concerned about food and the need to access accurate information on food quality. One of the main methods for preserving the quality of food commodities for export, storage, and finished products is food packaging itself. In the food industry, food packaging has a significant role in the food supply which acts as a barrier against unwanted substances and preserves the quality of the food. Meanwhile, packaging waste can also harm the environment; namely, it can become waste in waterways or become garbage that accumulates because it is nonrenewable and nonbiodegradable. The problem of contaminated food caused by product packaging is also severe. Therefore, to overcome these challenges of safety, environmental impact, and sustainability, the role of food packaging becomes very important and urgent. In this review, the authors will discuss in more detail about new technologies applied in the food industry related to packaging issues to advance the utilization of Smart Packaging and Active Packaging.
Collapse
Affiliation(s)
- Heri Septya Kusuma
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional “Veteran” Yogyakarta, Sleman, Indonesia
| | - Puput Yugiani
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional “Veteran” Yogyakarta, Sleman, Indonesia
| | - Ayu Iftah Himana
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional “Veteran” Yogyakarta, Sleman, Indonesia
| | - Amri Aziz
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional “Veteran” Yogyakarta, Sleman, Indonesia
| | - Deva Afriga Wardana Putra
- Department of Chemical Engineering, Faculty of Industrial Technology, Universitas Pembangunan Nasional “Veteran” Yogyakarta, Sleman, Indonesia
| |
Collapse
|
4
|
Kim SJ, Lee Y, Choi EJ, Lee JM, Kim KH, Oh JW. The development progress of multi-array colourimetric sensors based on the M13 bacteriophage. NANO CONVERGENCE 2023; 10:1. [PMID: 36595116 PMCID: PMC9808696 DOI: 10.1186/s40580-022-00351-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Techniques for detecting chemicals dispersed at low concentrations in air continue to evolve. These techniques can be applied not only to manage the quality of agricultural products using a post-ripening process but also to establish a safety prevention system by detecting harmful gases and diagnosing diseases. Recently, techniques for rapid response to various chemicals and detection in complex and noisy environments have been developed using M13 bacteriophage-based sensors. In this review, M13 bacteriophage-based multi-array colourimetric sensors for the development of an electronic nose is discussed. The self-templating process was adapted to fabricate a colour band structure consisting of an M13 bacteriophage. To detect diverse target chemicals, the colour band was utilised with wild and genetically engineered M13 bacteriophages to enhance their sensing abilities. Multi-array colourimetric sensors were optimised for application in complex and noisy environments based on simulation and deep learning analysis. The development of a multi-array colourimetric sensor platform based on the M13 bacteriophage is likely to result in significant advances in the detection of various harmful gases and the diagnosis of various diseases based on exhaled gas in the future.
Collapse
Affiliation(s)
- Sung-Jo Kim
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, Republic of Korea
| | - Yujin Lee
- Department of Nano Fusion Technology, Pusan National University, Busan, Republic of Korea
| | - Eun Jung Choi
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, Republic of Korea
- Korea Nanobiotechnology Center, Pusan National University, Busan, Republic of Korea
| | - Jong-Min Lee
- School of Nano Convergence Technology, Hallym University, Chuncheon, Republic of Korea
- Korea and Nano Convergence Technology Center, Hallym University, Chuncheon, Republic of Korea
| | - Kwang Ho Kim
- School of Materials Science and Engineering, Pusan National University, Busan, Republic of Korea
- Global Frontier Research and Development Center for Hybrid Interface Materials, Pusan National University, Busan, Republic of Korea
| | - Jin-Woo Oh
- Bio-IT Fusion Technology Research Institute, Pusan National University, Busan, Republic of Korea
- Department of Nano Fusion Technology, Pusan National University, Busan, Republic of Korea
- Korea Nanobiotechnology Center, Pusan National University, Busan, Republic of Korea
- Department of Nanoenergy Engineering and Research Center for Energy Convergence Technology, Pusan National University, Busan, Republic of Korea
| |
Collapse
|
5
|
Yang Z, Yuan L, Zhu H, Jiang J, Yang H, Li L. Small RNA profiling reveals the involvement of microRNA-mediated gene regulation in response to symbiosis in raspberry. Front Microbiol 2022; 13:1082494. [PMID: 36620006 PMCID: PMC9810812 DOI: 10.3389/fmicb.2022.1082494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Dark septate endophytes (DSEs) can form reciprocal symbioses with most terrestrial plants, providing them with mineral nutrients in exchange for photosynthetic products. Although the mechanism of plant-DSEs is well understood at the transcriptional level, little is known about their post-transcriptional regulation, and microRNAs (miRNAs) for the symbiotic process of DSE infestation of raspberry have not been identified. In this study, we comprehensively identified the miRNAs of DSE-infested raspberry symbiosis using Illumina sequencing. A total of 361 known miRNAs and 95 novel miRNAs were identified in the roots. Similar to other dicotyledons, most of the identified raspberry miRNAs were 21 nt in length. Thirty-seven miRNAs were differentially expressed during colonization after inoculation with Phialocephala fortinii F5, suggesting a possible role for these miRNAs in the symbiotic process. Notably, two miRNAs (miR171h and miR396) previously reported to be responsive to symbiotic processes in alfalfa also had altered expression during raspberry symbiosis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggests that miRNAs are mainly involved in regulatory mechanisms, such as biological processes, cellular metabolic processes, biosynthesis of secondary metabolites, plant-pathogen interactions, and phytohormone signaling pathways. This study revealed the potential conservation of miRNA-mediated post-transcriptional regulation in symbiotic processes among plants and provides some novel miRNAs for understanding the regulatory mechanisms of DSE-raspberry symbiosis.
Collapse
Affiliation(s)
- Zhiyu Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Lianmei Yuan
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Haifeng Zhu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Jing Jiang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China
| | - Hongyi Yang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, China,College of Life Science, Northeast Forestry University, Harbin, China,*Correspondence: Hongyi Yang,
| | - Lili Li
- Institute of Forestry Science of Heilongjiang Province, Harbin, China,Lili Li,
| |
Collapse
|
6
|
Bhakta S, Tak H, Ganapathi TR. Exploring diverse roles of micro RNAs in banana: Current status and future prospective. PHYSIOLOGIA PLANTARUM 2021; 173:1323-1334. [PMID: 33305854 DOI: 10.1111/ppl.13311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/17/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Micro RNAs (miRNAs) are 20-24 nucleotides long non-coding RNA sequences identified and characterized in multiple plant and animal systems. miRNAs play multifarious roles ranging from plant development to stress tolerance by synchronizing physiological processes at the level of transcription and translation. Banana is a major horticultural crop with colossal production worldwide. Despite the recent encouraging developments, the information on functions of miRNAs in banana plants is still in its infancy. The available literature pertaining to miRNAs in banana plants hints towards their contribution as master regulators in crucial physiological processes for instance abiotic stress responses, pathogenic defence response, fruit ripening and so on. This review is focused on biogenesis of miRNAs, their identification and deciphering their respective roles in banana plants with special emphasis on abiotic stress responses, plant immune responses, fruit ripening and storage. Based on the prior reports, we identified a few miRNAs with prospective roles in stress tolerance and illustrated the potential applications of miRNAs in banana crop improvement utilizing recent biotechnological tools such as CRISPR cas9, RNAi and the nano particle based foliar spray of miRNAs. The review briefly explained the future directions in banana research with a special emphasis on miRNA regulatory networks and agronomic traits improvement. Finally, future domains in miRNA research in plants and their possible applications towards crop improvement in agriculture are described briefly.
Collapse
Affiliation(s)
- Subham Bhakta
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Himanshu Tak
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Thumballi R Ganapathi
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| |
Collapse
|
7
|
Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
Collapse
Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
| |
Collapse
|
8
|
Cai J, Wu Z, Hao Y, Liu Y, Song Z, Chen W, Li X, Zhu X. Small RNAs, Degradome, and Transcriptome Sequencing Provide Insights into Papaya Fruit Ripening Regulated by 1-MCP. Foods 2021; 10:1643. [PMID: 34359513 PMCID: PMC8303378 DOI: 10.3390/foods10071643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/04/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
As an inhibitor of ethylene receptors, 1-methylcyclopropene (1-MCP) can delay the ripening of papaya. However, improper 1-MCP treatment will cause a rubbery texture in papaya. Understanding of the underlying mechanism is still lacking. In the present work, a comparative sRNA analysis was conducted after different 1-MCP treatments and identified a total of 213 miRNAs, of which 44 were known miRNAs and 169 were novel miRNAs in papaya. Comprehensive functional enrichment analysis indicated that plant hormone signal pathways play an important role in fruit ripening. Through the comparative analysis of sRNAs and transcriptome sequencing, a total of 11 miRNAs and 12 target genes were associated with the ethylene and auxin signaling pathways. A total of 1741 target genes of miRNAs were identified by degradome sequencing, and nine miRNAs and eight miRNAs were differentially expressed under the ethylene and auxin signaling pathways, respectively. The network regulation diagram of miRNAs and target genes during fruit ripening was drawn. The expression of 11 miRNAs and 12 target genes was verified by RT-qPCR. The target gene verification showed that cpa-miR390a and cpa-miR396 target CpARF19-like and CpERF RAP2-12-like, respectively, affecting the ethylene and auxin signaling pathways and, therefore, papaya ripening.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Xiaoyang Zhu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (J.C.); (Z.W.); (Y.H.); (Y.L.); (Z.S.); (W.C.); (X.L.)
| |
Collapse
|
9
|
Luo Y, Wang T, Yang D, Luo B, Wang WP, Yu D, He FL, Wang QM, Rao LQ. Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties, 9311 and Nagina 22. Genome 2021; 64:969-984. [PMID: 33901411 DOI: 10.1139/gen-2020-0175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants, but their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties, 9311 and Nagina 22, remain largely unknown. In this study, 464 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differentially expressed miRNAs were obtained with 9311 libraries as the control group, of which 54 were upregulated and 36 were downregulated. To gain insight into functional significance, 2773 potential target genes of these 90 differentially expressed miRNAs were predicted. GO enrichment analysis showed that the predicted target genes of differentially expressed miRNAs included NACs, LACs, CSD, and Hsp40. KEGG pathway analysis showed that the target genes of these differentially expressed miRNAs were significantly enriched in the plant hormone signal transduction pathway. The expression levels of 10 differentially expressed miRNAs and their target genes obtained by qRT-PCR were largely consistent with the sequencing results. This study lays a foundation for the elucidation of the miRNA-mediated regulatory mechanisms in rice at elevated temperatures.
Collapse
Affiliation(s)
- Ying Luo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China.,College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China
| | - Tao Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China
| | - Dan Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China
| | - Biao Luo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China
| | - Wei-Ping Wang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Dong Yu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Fu-Lin He
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, China
| | - Qi-Ming Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China
| | - Li-Qun Rao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410125, China
| |
Collapse
|
10
|
Zhang YP, Zhang YY, Thakur K, Zhang F, Hu F, Zhang JG, Wei PC, Wei ZJ. Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development. FRONTIERS IN PLANT SCIENCE 2021; 12:709197. [PMID: 34394165 PMCID: PMC8358462 DOI: 10.3389/fpls.2021.709197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/30/2021] [Indexed: 05/05/2023]
Abstract
Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.
Collapse
Affiliation(s)
- Yin-Ping Zhang
- Anhui Academy of Agricultural Sciences, Crop Research Institute, Hefei, China
| | - Yuan-Yuan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Fan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Fei Hu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Jian-Guo Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Peng-Cheng Wei
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
- *Correspondence: Peng-Cheng Wei,
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
- Zhao-Jun Wei,
| |
Collapse
|
11
|
Li T, Gonzalez N, Inzé D, Dubois M. Emerging Connections between Small RNAs and Phytohormones. TRENDS IN PLANT SCIENCE 2020; 25:912-929. [PMID: 32381482 DOI: 10.1016/j.tplants.2020.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 05/20/2023]
Abstract
Small RNAs (sRNAs), mainly including miRNAs and siRNAs, are ubiquitous in eukaryotes. sRNAs mostly negatively regulate gene expression via (post-)transcriptional gene silencing through DNA methylation, mRNA cleavage, or translation inhibition. The mechanisms of sRNA biogenesis and function in diverse biological processes, as well as the interactions between sRNAs and environmental factors, like (a)biotic stress, have been deeply explored. Phytohormones are central in the plant's response to stress, and multiple recent studies highlight an emerging role for sRNAs in the direct response to, or the regulation of, plant hormonal pathways. In this review, we discuss recent progress on the unraveling of crossregulation between sRNAs and nine plant hormones.
Collapse
Affiliation(s)
- Ting Li
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- INRAE, Université de Bordeaux, UMR1332 Biologie du fruit et Pathologie, F-33882 Villenave d'Ornon cedex, France
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
| | - Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| |
Collapse
|
12
|
Wei H, Seidi F, Zhang T, Jin Y, Xiao H. Ethylene scavengers for the preservation of fruits and vegetables: A review. Food Chem 2020; 337:127750. [PMID: 32861166 DOI: 10.1016/j.foodchem.2020.127750] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/15/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
The phytohormone ethylene is the main cause of postharvest spoilage of fruit and vegetables (F&V). To address the global challenge of reducing postharvest losses of F&V, effective management of ethylene is of great importance. This review summarizes the various ethylene scavengers/inhibitors and emerging technologies recently developed for the effective removal of ethylene released, paying particular attention to the ethylene scavenger/inhibitors containing catalysts to promote the in-situ oxidation of ethylene without inducing further pollution. Packing ethylene scavengers, such as zeolite, titanium dioxide and transition metals, in a small sachet has been practically used and widely reported. However, incorporating ethylene scavenger into food packaging materials or films along with the in-situ oxidation of ethylene has been rarely reviewed. The current review fills up this gap, covering the latest research progress on ethylene scavengers/inhibitors and discussion on the mechanisms of ethylene elimination and oxidation associated with F&V packaging.
Collapse
Affiliation(s)
- Haiying Wei
- Joint International Research Lab of Lignocellulosic Functional Materials and Provincial Key Lab of Pulp and Paper Sci & Tech, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Farzad Seidi
- Joint International Research Lab of Lignocellulosic Functional Materials and Provincial Key Lab of Pulp and Paper Sci & Tech, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Tingwei Zhang
- Joint International Research Lab of Lignocellulosic Functional Materials and Provincial Key Lab of Pulp and Paper Sci & Tech, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yongcan Jin
- Joint International Research Lab of Lignocellulosic Functional Materials and Provincial Key Lab of Pulp and Paper Sci & Tech, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB E3B 5A3, Canada.
| |
Collapse
|
13
|
Bai S, Tian Y, Tan C, Bai S, Hao J, Hasi A. Genome-wide identification of microRNAs involved in the regulation of fruit ripening and climacteric stages in melon ( Cucumis melo). HORTICULTURE RESEARCH 2020; 7:106. [PMID: 32637134 PMCID: PMC7327070 DOI: 10.1038/s41438-020-0331-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 05/31/2023]
Abstract
Fruit ripening is influenced by multiple plant hormones and the regulation of genes. However, studies on posttranscriptional regulators (e.g., miRNAs) of fruit growth and ripening are limited. We used miRNA sequencing and degradome methods to identify miRNAs and their target genes in melon (Cucumis melo cv. Hetao melon). A total of 61 conserved miRNAs and 36 novel miRNAs were identified from fruit growth, ripening, climacteric, and postclimacteric developmental stage samples, of which 32 conserved miRNAs were differentially expressed between developmental stage samples. Sixty-two target genes of 43 conserved miRNAs and 1 novel miRNA were identified from degradome sequencing. To further investigate miRNA influencing fruit ripening, transgenic melon plants overexpressing pre-cme-miR393 (cme-miR393-OE) were generated and characterized. The results showed that fruit ripening was delayed in cme-miR393-OE transgenic lines compared to nontransgenic fruits. The target of cme-miR393 was also identified, and the expression of CmAFB2 was repressed in transgenic plants. These results provide evidence that miRNA regulates melon fruit ripening and provide potential targets to improve the horticultural traits of melon fruit.
Collapse
Affiliation(s)
- Selinge Bai
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, 010070 Hohhot, China
| | - Yunyun Tian
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, 010070 Hohhot, China
| | - Chao Tan
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, 010070 Hohhot, China
| | - Shunbuer Bai
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, 010070 Hohhot, China
| | - Jinfeng Hao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, 010070 Hohhot, China
| | - Agula Hasi
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, 010070 Hohhot, China
| |
Collapse
|
14
|
Roles of transcription factor SQUAMOSA promoter binding protein-like gene family in papaya (Carica papaya) development and ripening. Genomics 2020; 112:2734-2747. [PMID: 32194147 DOI: 10.1016/j.ygeno.2020.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 02/05/2023]
Abstract
SQUAMOSA promoter binding protein-like (SPL) family plays vital regulatory roles in plant growth and development. The SPL family in climacteric fruit Carica papaya has not been reported. This study identified 14 papaya SPLs (CpSPL) from papaya genome and analyzed their sequence features, phylogeny, intron/exon structure, conserved motif, miR156-mediated posttranscriptional regulation, and expression patterns. 14 CpSPLs were clustered into 8 groups, and two distinct expression patterns were revealed for miR156-targeted and nontargeted CpSPLs in different tissues and fruit development stages. The expression changes of CpSPLs in ethephon and 1-MCP treated fruit during ripening suggested that the CpSPLs guided by CpmiR156 play crucial roles in ethylene signaling pathway. This study sheds light on the new function of SPL family in fruit development and ripening, providing insights on understanding evolutionary divergence of the members of SPL family among plant species.
Collapse
|
15
|
Ye J, Han W, Fan R, Liu M, Li L, Jia X. Integration of Transcriptomes, Small RNAs, and Degradome Sequencing to Identify Putative miRNAs and Their Targets Related to Eu-Rubber Biosynthesis in Eucommia ulmoides. Genes (Basel) 2019; 10:genes10080623. [PMID: 31430866 PMCID: PMC6722833 DOI: 10.3390/genes10080623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 01/24/2023] Open
Abstract
Eucommia ulmoides has attracted much attention as a valuable natural rubber (Eu-rubber) production tree. As a strategic material, Eu-rubber plays a vital role in general and defence industries. However, the study of Eu-rubber biosynthesis at a molecular level is scarce, and the regulatory network between microRNAs (miRNAs) and messenger RNAs (mRNAs) in Eu-rubber biosynthesis has not been assessed. In this study, we comprehensively analyzed the transcriptomes, small RNAs (sRNAs) and degradome to reveal the regulatory network of Eu-rubber biosynthesis in E. ulmoides. A total of 82,065 unigenes and 221 miRNAs were identified using high-throughput sequencing; 20,815 targets were predicted using psRNATarget software. Of these targets, 779 miRNA-target pairs were identified via degradome sequencing. Thirty-one miRNAs were differentially expressed; 22 targets of 34 miRNAs were annotated in the terpenoid backbone biosynthesis pathway (ko00900) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG). These miRNAs were putatively related to Eu-rubber biosynthesis. A regulatory network was constructed according to the expression profiles of miRNAs and their targets. These results provide a comprehensive analysis of transcriptomics, sRNAs and degradome to reveal the Eu-rubber accumulation, and provide new insights into genetic engineering techniques which may improve the content of Eu-rubber in E. ulmoides.
Collapse
Affiliation(s)
- Jing Ye
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Wenjing Han
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Ruisheng Fan
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Minhao Liu
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Long Li
- College of Forestry, Northwest A&F University, Shaanxi 712100, China
| | - Xiaoming Jia
- College of Forestry, Northwest A&F University, Shaanxi 712100, China.
| |
Collapse
|