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Babaei S, Bhalla PL, Singh MB. Identifying long non-coding RNAs involved in heat stress response during wheat pollen development. Front Plant Sci 2024; 15:1344928. [PMID: 38379952 PMCID: PMC10876783 DOI: 10.3389/fpls.2024.1344928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Introduction Wheat is a staple food crop for over one-third of the global population. However, the stability of wheat productivity is threatened by heat waves associated with climate change. Heat stress at the reproductive stage can result in pollen sterility and failure of grain development. Methods This study used transcriptome data analysis to explore the specific expression of long non-coding RNAs (lncRNAs) in response to heat stress during pollen development in four wheat cultivars. Results and discussion We identified 11,054 lncRNA-producing loci, of which 5,482 lncRNAs showed differential expression in response to heat stress. Heat-responsive lncRNAs could target protein-coding genes in cis and trans and in lncRNA-miRNA-mRNA regulatory networks. Gene ontology analysis predicted that target protein-coding genes of lncRNAs regulate various biological processes such as hormonal responses, protein modification and folding, response to stress, and biosynthetic and metabolic processes. We also noted some paired lncRNA/protein-coding gene modules and some lncRNA-miRNA-mRNA regulatory modules shared in two or more wheat cultivars. These modules were related to regulating plant responses to heat stress, such as heat-shock proteins and transcription factors, and protein domains, such as MADS-box, Myc-type, and Alpha crystallin/Hsp20 domain. Conclusion Our results provide the basic knowledge and molecular resources for future functional studies investigating wheat reproductive development under heat stress.
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Affiliation(s)
| | | | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Melbourne, VIC, Australia
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Naqvi RZ, Mahmood MA, Mansoor S, Amin I, Asif M. Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops. Front Plant Sci 2024; 14:1273859. [PMID: 38259913 PMCID: PMC10800452 DOI: 10.3389/fpls.2023.1273859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Arslan Mahmood
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
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Liu H, Chong P, Yan S, Liu Z, Bao X, Tan B. Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress. Plants (Basel) 2023; 12:3542. [PMID: 37896006 PMCID: PMC10609793 DOI: 10.3390/plants12203542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023]
Abstract
This work aims at studying the molecular mechanisms underlying the response of Reaumuria soongorica to salt stress. We used RNA sequencing (RNA-Seq) and Tandem Mass Tag (TMT) techniques to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in R. soongorica leaves treated with 0, 200, and 500 mM NaCl for 72 h. The results indicated that compared with the 0 mM NaCl treatment group, 2391 and 6400 DEGs were identified in the 200 and 500 mM NaCl treatment groups, respectively, while 47 and 177 DEPs were also identified. Transcriptome and proteome association analysis was further performed on R. soongorica leaves in the 0/500 mM NaCl treatment group, and 32 genes with consistent mRNA and protein expression trends were identified. SYP71, CS, PCC13-62, PASN, ZIFL1, CHS2, and other differential genes are involved in photosynthesis, vesicle transport, auxin transport, and other functions of plants, and might play a key role in the salt tolerance of R. soongorica. In this study, transcriptome and proteome association techniques were used to screen candidate genes associated with salt tolerance in R. soongorica, which provides an important theoretical basis for understanding the molecular mechanism of salt tolerance in R. soongorica and breeding high-quality germplasm resources.
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Affiliation(s)
- Hanghang Liu
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Peifang Chong
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Shipeng Yan
- School of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China;
| | - Zehua Liu
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Xinguang Bao
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
| | - Bingbing Tan
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China; (H.L.); (Z.L.); (X.B.); (B.T.)
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Yang Y, Pian Y, Li J, Xu L, Lu Z, Dai Y, Li Q. Integrative analysis of genome and transcriptome reveal the genetic basis of high temperature tolerance in pleurotus giganteus (Berk. Karun & Hyde). BMC Genomics 2023; 24:552. [PMID: 37723428 PMCID: PMC10506213 DOI: 10.1186/s12864-023-09669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Pleurotus giganteus is a commonly cultivated mushroom with notable high temperature resistance, making it significant for the growth of the edible fungi industry in the tropics. Despite its practical importance,, the genetic mechanisms underlying its ability to withstand high temperature tolerance remain elusive. RESULTS In this study, we performed high-quality genome sequencing of a monokaryon isolated from a thermotolerant strain of P. giganteus. The genome size was found to be 40.11 Mb, comprising 17 contigs and 13,054 protein-coding genes. Notably, some genes related to abiotic stress were identified in genome, such as genes regulating heat shock protein, protein kinase activity and signal transduction. These findings provide valuable insights into the genetic basis of P. giganteus' high temperature resistance. Furthermore, the phylogenetic tree showed that P. giganteus was more closely related to P. citrinopileatus than other Pleurotus species. The divergence time between Pleurotus and Lentinus was estimated as 153.9 Mya, and they have a divergence time with Panus at 168.3 Mya, which proved the taxonomic status of P. giganteus at the genome level. Additionally, a comparative transcriptome analysis was conducted between mycelia treated with 40 °C heat shock for 18 h (HS) and an untreated control group (CK). Among the 2,614 differentially expressed genes (DEGs), 1,303 genes were up-regulated and 1,311 were down-regulated in the HS group. The enrichment analysis showed that several genes related to abiotic stress, including heat shock protein, DnaJ protein homologue, ubiquitin protease, transcription factors, DNA mismatch repair proteins, and zinc finger proteins, were significantly up-regulated in the HS group. These genes may play important roles in the high temperature adaptation of P. giganteus. Six DEGs were selected according to fourfold expression changes and were validated by qRT-PCR, laying a good foundation for further gene function analysis. CONCLUSION Our study successfully reported a high-quality genome of P. giganteus and identified genes associated with high-temperature tolerance through an integrative analysis of the genome and transcriptome. This study lays a crucial foundation for understanding the high-temperature tolerance mechanism of P. giganteus, providing valuable insights for genetic modification of P. giganteus strains and the development of high-temperature strains for the edible fungus industry, particularly in tropical regions.
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Affiliation(s)
- Yang Yang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
| | - Yongru Pian
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Jingyi Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Lin Xu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China
| | - Zhu Lu
- Jilin Academy of Vegetables and Flowers Sciences, Changchun, China
| | - Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.
| | - Qinfen Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
- Key Laboratory of Low Carbon Green Agriculture in Tropical China, Ministry of Agriculture and Rural Affairs, Haikou, P. R. China.
- National Agricultural Experimental Station for Agricultural Environment, Danzhou, China.
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Luo D, Ding Q, Ma X, Zhu J, Zou K, Hong W, Wang J, Mao C, Xie Z, Wu B, Khan I, Wang X, Feng G, Huang L. Proteomic and physiological responses of contrasting two different heat-resistant orchardgrass genotypes to heat stress. Int J Biol Macromol 2023:125463. [PMID: 37348590 DOI: 10.1016/j.ijbiomac.2023.125463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/20/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
As an important forage crop worldwide, the growth and productivity of orchardgrass are greatly impacted by high temperatures. However, little information is known about how orchardgrass proteomic changes under heat conditions. Therefore, the present study investigated the proteomics and physiological changes in 667 [AKZ-NRGR667 (heat-tolerant)] and 7602 [PI237602 (heat-sensitive)] under heat stress (40/35 °C). In addition, the responses of translational regulating of heat stress in orchardgrass were analyzed through proteomic changes using the tandem mass tags (TMT) technique. Together, 410 differentially expressed proteins (DEPs) were identified from two orchardgrass genotypes under heat at 24 h. Proteomics analyses indicated that proteins related to substance metabolism, photosynthesis, and heat shock proteins (HSPs) were differentially expressed under heat stress and control conditions. Moreover, a large proportion of HSPs were expressed in the heat-tolerant genotype as compared to the heat-sensitive genotype. In conclusion, genotype 667 has higher adaptability and repairing capability due to stronger heat tolerance capacity that can make it more suited to sustaining its survival and growth than genotype 7602. These findings can provide the basis for genetic improvements in orchardgrass and other crops facing high-temperature stress or heat environment that may lead to heat resistance or tolerance.
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Affiliation(s)
- Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiong Ding
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xixi Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kun Zou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenkai Hong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunli Mao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Imran Khan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730020 Lanzhou, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Zhang J, Diao F, Hao B, Xu L, Jia B, Hou Y, Ding S, Guo W. Multiomics reveals Claroideoglomus etunicatum regulates plant hormone signal transduction, photosynthesis and La compartmentalization in maize to promote growth under La stress. Ecotoxicol Environ Saf 2023; 262:115128. [PMID: 37315361 DOI: 10.1016/j.ecoenv.2023.115128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
Rare earth elements (REEs) have been widely used in traditional and high-tech fields, and high doses of REEs are considered a risk to the ecosystem. Although the influence of arbuscular mycorrhizal fungi (AMF) in promoting host resistance to heavy metal (HM) stress has been well documented, the molecular mechanism by which AMF symbiosis enhances plant tolerance to REEs is still unclear. A pot experiment was conducted to investigate the molecular mechanism by which the AMF Claroideoglomus etunicatum promotes maize (Zea mays) seedling tolerance to lanthanum (La) stress (100 mg·kg-1 La). C. etunicatum symbiosis significantly improved maize seedling growth, P and La uptake and photosynthesis. Transcriptome, proteome, and metabolome analyses performed alone and together revealed that differentially expressed genes (DEGs) related to auxin /indole-3-acetic acid (AUX/IAA) and the DEGs and differentially expressed proteins (DEPs) related to ATP-binding cassette (ABC) transporters, natural resistance-associated macrophage proteins (Nramp6), vacuoles and vesicles were upregulated. In contrast, photosynthesis-related DEGs and DEPs were downregulated, and 1-phosphatidyl-1D-myo-inositol 3-phosphate (PI(3)P) was more abundant under C. etunicatum symbiosis. C. etunicatum symbiosis can promote plant growth by increasing P uptake, regulating plant hormone signal transduction, photosynthesis and glycerophospholipid metabolism pathways and enhancing La transport and compartmentalization in vacuoles and vesicles. The results provide new insights into the promotion of plant REE tolerance by AMF symbiosis and the possibility of utilizing AMF-maize interactions in REE phytoremediation and recycling.
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Affiliation(s)
- Jingxia Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; Inner Mongolia Key Laboratory of Environmental Chemistry, School of Chemistry and Environment, Inner Mongolia Normal University, Hohhot 010021, China
| | - Fengwei Diao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Baihui Hao
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Lei Xu
- Service Support Center, Ecology and Environmental Department of Inner Mongolia Autonomous Region, Hohhot 010010, China
| | - Bingbing Jia
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yazhou Hou
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Shengli Ding
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Wei Guo
- Inner Mongolia Key Laboratory of Environmental Pollution Control and Waste Resource Recycle, Ministry of Education Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
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Zheng L, Liu Q, Wu R, Zhu M, Dorjee T, Zhou Y, Gao F. The alteration of proteins and metabolites in leaf apoplast and the related gene expression associated with the adaptation of Ammopiptanthus mongolicus to winter freezing stress. Int J Biol Macromol 2023; 240:124479. [PMID: 37072058 DOI: 10.1016/j.ijbiomac.2023.124479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/20/2023]
Abstract
Ammopiptanthus mongolicus, an evergreen broad-leaved plant, can tolerate severe freezing stress (temperatures as low as -20 °C in winter). The apoplast is the space outside the plasma membrane that plays an important role in plant responses to environmental stress. Here, we investigated, using a multi-omics approach, the dynamic alterations in the levels of proteins and metabolites in the apoplast and related gene expression changes involved in the adaptation of A. mongolicus to winter freezing stress. Of the 962 proteins identified in the apoplast, the abundance of several PR proteins, including PR3 and PR5, increased significantly in winter, which may contribute to winter freezing-stress tolerance by functioning as antifreeze proteins. The increased abundance of the cell-wall polysaccharides and cell wall-modifying proteins, including PMEI, XTH32, and EXLA1, may enhance the mechanical properties of the cell wall in A. mongolicus. Accumulation of flavonoids and free amino acids in the apoplast may be beneficial for ROS scavenging and the maintenance of osmotic homeostasis. Integrated analyses revealed gene expression changes associated with alterations in the levels of apoplast proteins and metabolites. Our study improved the current understanding of the roles of apoplast proteins and metabolites in plant adaptation to winter freezing stress.
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Affiliation(s)
- Lamei Zheng
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Rongqi Wu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ming Zhu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tashi Dorjee
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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Yu T, Tian X, Li D, He Y, Yang P, Cheng Y, Zhao X, Sun J, Yang G. Transcriptome, proteome and metabolome analysis provide insights on fat deposition and meat quality in pig. Food Res Int 2023; 166:112550. [PMID: 36914311 DOI: 10.1016/j.foodres.2023.112550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/19/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Intramuscular fat (IMF) content, which is an important determinant of meat quality characteristics such as tenderness, juiciness and flavor, has long been a research hotspot. Chinese local pig breeds are famous for their excellent meat quality which is mainly reflected in the high IMF content, strong hydraulic system and et al. However, there are few analysis of meat quality by omics methods. In our study, we identified 12 different fatty acids, 6 different amino acids, 1,262 differentially expression genes (DEGs), 140 differentially abundant proteins (DAPs) and 169 differentially accumulated metabolites (DAMs) (p < 0.05) with metabolome, transcriptome, and proteome. It has been found that DEGs, DAPs and DAMs were enriched in the Wnt signaling pathway, PI3K-Akt signaling pathway, Rap1 signaling pathway, and Ras signaling pathway which were related to meat quality. Moreover, our Weighted genes co-expression network construction (WGCNA) showed RapGEF1 was the key gene related to IMF content and the RT-qPCR analysis was used to perform validation of the significant genes. In summary, our study provided both fundamental data and new insights to further uncover the secret of pig IMF content.
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Affiliation(s)
- Taiyong Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xuekai Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yulin He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Peiyu Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ye Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xin Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jingchun Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Jiang H, Liu X, Xiao P, Wang Y, Xie Q, Wu X, Ding H. Functional insights of plant bcl-2-associated ahanogene (BAG) proteins: Multi-taskers in diverse cellular signal transduction pathways. Front Plant Sci 2023; 14:1136873. [PMID: 37056491 PMCID: PMC10086319 DOI: 10.3389/fpls.2023.1136873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Bcl-2-associated athanogene (BAG) gene family is a highly conserved molecular chaperone cofactor in evolution from yeast to humans and plants playing important roles in a variety of signal pathways. Plant BAG proteins have special structures, especially those containing CaM-binding IQ motifs which are unique to plants. While early studies focused more on the structure and physiological function of plant BAGs, recent studies have revealed many novel functional mechanisms involved in multiple cellular processes. How to achieve signal specificity has become an interesting topic of plant BAG research. In this review, we have provided a historic view of plant BAG research and summarized recent advances in the establishment of BAG as essential components in normal plant growth, environmental stress response, and plant immunity. Based on the relationship between BAG proteins and their newly interacting proteins, this review highlights the functional mechanisms of various cellular signals mediated by plant BAGs. Future work needs to focus on the post-translational modification of BAG proteins, and on understanding how specificity is achieved among BAG signaling pathways.
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Affiliation(s)
- Hailong Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Xiaoya Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Peixiang Xiao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Yan Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Qihui Xie
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Xiaoxia Wu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China
| | - Haidong Ding
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China
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Guo N, Tang S, Wang J, Hu S, Tang S, Wei X, Shao G, Jiao G, Sheng Z, Hu P. Transcriptome and Proteome Analysis Revealed That Hormone and Reactive Oxygen Species Synergetically Regulate Dormancy of Introgression Line in Rice ( Oryza sativa L.). Int J Mol Sci 2023; 24:ijms24076088. [PMID: 37047061 PMCID: PMC10094489 DOI: 10.3390/ijms24076088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Dormancy is a complex agronomy phenotype controlled by multiple signaling and a key trait repressing pre-harvest sprouting (PHS). However, the signaling network of dormancy remains unclear. In this study, we used Zhonghua11 (ZH11) with a weak dormancy, and Introgression line (IL) with a strong dormancy to study the mechanism of hormones and reactive oxygen species (ROS) crosstalk regulating rice dormancy. The germination experiment showed that the germination rate of ZH11 was 76.86%, while that of IL was only 1.25%. Transcriptome analysis showed that there were 1658 differentially expressed genes (DEGs) between IL and ZH11, of which 577 were up-regulated and 1081 were down-regulated. Additionally, DEGs were mainly enriched in oxidoreductase activity, cell periphery, and plant hormone signal transduction pathways. Tandem mass tags (TMT) quantitative proteomics analysis showed 275 differentially expressed proteins (DEPs) between IL and ZH11, of which 176 proteins were up-regulated, 99 were down-regulated, and the DEPs were mainly enriched in the metabolic process and oxidation-reduction process. The comprehensive transcriptome and proteome analysis showed that their correlation was very low, and only 56 genes were co-expressed. Hormone content detection showed that IL had significantly lower abscisic acid (ABA) contents than the ZH11 while having significantly higher jasmonic acid (JA) contents than the ZH11. ROS content measurement showed that the hydrogen peroxide (H2O2) content of IL was significantly lower than the ZH11, while the production rate of superoxide anion (O2.-) was significantly higher than the ZH11. These results indicate that hormones and ROS crosstalk to regulate rice dormancy. In particular, this study has deepened our mechanism of ROS and JA crosstalk regulating rice dormancy and is conducive to our precise inhibition of PHS.
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Affiliation(s)
- Naihui Guo
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Shengjia Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Jiayu Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
| | - Peisong Hu
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture, China National Rice improvement Centre, China National Rice Research Institute, Hangzhou 310006, China
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Wang Z, Rehman A, Jia Y, Dai P, He S, Wang X, Li H, Wang L, Qayyum A, Peng Z, Du X. Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton. Gene 2023; 868:147374. [PMID: 36934785 DOI: 10.1016/j.gene.2023.147374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.
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Affiliation(s)
- Zhenzhen Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Rehman
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Yinhua Jia
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Panhong Dai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Shoupu He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Xiaoyang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Hongge Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China
| | - Abdul Qayyum
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Zhen Peng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China.
| | - Xiongming Du
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS), Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
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Xiao Y, Zhang P, Zhang H, Wang H, Min G, Wang H, Wang Y, Xu J. Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa. Microorganisms 2023; 11:765. [PMID: 36985338 PMCID: PMC10058807 DOI: 10.3390/microorganisms11030765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.
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Zhao Y, Zhao J, Hu M, Sun L, Liu Q, Zhang Y, Li Q, Wang P, Ma W, Li H, Gao H, Zhang Y. Transcriptome and Proteome Analysis Revealed the Influence of High-Molecular-Weight Glutenin Subunits (HMW-GSs) Deficiency on Expression of Storage Substances and the Potential Regulatory Mechanism of HMW-GSs. Foods 2023; 12:foods12020361. [PMID: 36673453 PMCID: PMC9857648 DOI: 10.3390/foods12020361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
The processing quality of wheat is affected by seed storage substances, such as protein and starch. High-molecular-weight glutenin subunits (HMW-GSs) are the major components of wheat seed storage proteins (SSPs); they are also key determinators of wheat end-use quality. However, the effects of HMW-GSs absence on the expression of other storage substances and the regulation mechanism of HMW-GSs are still limited. Previously, a wheat transgenic line LH-11 with complete deletions of HMW-GSs was obtained through introducing an exogenous gene Glu-1Ebx to the wild-type cultivar Bobwhite by transgenic approach. In this study, comparative seed transcriptomics and proteomics of transgenic and non-transgenic lines at different seed developmental stages were carried out to explore the changes in genes and proteins and the underlying regulatory mechanism. Results revealed that a number of genes, including genes related to SSPs, carbohydrates metabolism, amino acids metabolism, transcription, translation, and protein process were differentially enriched. Seed storage proteins displayed differential expression patterns between the transgenic and non-transgenic line, a major rise in the expression levels of gliadins were observed at 21 and 28 days post anthesis (DPA) in the transgenic line. Changes in expressions of low-molecular-weight glutenins (LMW-GSs), avenin-like proteins (ALPs), lipid transfer proteins (LTPs), and protease inhibitors (PIs) were also observed. In addition, genes related to carbohydrate metabolism were differentially expressed, which probably leads to a difference in starch component and deposition. A list of gene categories participating in the accumulation of SSPs was proposed according to the transcriptome and proteome data. Six genes from the MYB and eight genes from the NAC transcription families are likely important regulators of HMW-GSs accumulation. This study will provide data support for understanding the regulatory network of wheat storage substances. The screened candidate genes can lay a foundation for further research on the regulation mechanism of HMW-GSs.
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Affiliation(s)
- Yun Zhao
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Jie Zhao
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Mengyun Hu
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Lijing Sun
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Qian Liu
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Yelun Zhang
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Qianying Li
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Peinan Wang
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Perth 6150, Australia
| | - Hui Li
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Huimin Gao
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Correspondence: (H.G.); (Y.Z.)
| | - Yingjun Zhang
- Laboratory of Crop Genetics and Breeding of Hebei, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
- Correspondence: (H.G.); (Y.Z.)
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Cheng SS, Ku YS, Cheung MY, Lam HM. Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification. Front Plant Sci 2022; 13:1001920. [PMID: 36247637 PMCID: PMC9557097 DOI: 10.3389/fpls.2022.1001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.
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Momo J, Kumar A, Islam K, Ahmad I, Rawoof A, Ramchiary N. A comprehensive update on Capsicum proteomics: Advances and future prospects. J Proteomics 2022; 261:104578. [DOI: 10.1016/j.jprot.2022.104578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 10/18/2022]
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Jiang H, Ji Y, Sheng J, Wang Y, Liu X, Xiao P, Ding H. Genome-Wide Identification of the Bcl-2 Associated Athanogene (BAG) Gene Family in Solanum lycopersicum and the Functional Role of SlBAG9 in Response to Osmotic Stress. Antioxidants (Basel) 2022; 11:598. [PMID: 35326248 DOI: 10.3390/antiox11030598] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
The Bcl-2-associated athanogene (BAG) proteins are a family of multi-functional group of co-chaperones regulators, modulating diverse processes from plant growth and development to stress response. Here, 10 members of SlBAG gene family were identified based on the available tomato (Solanum lycopersicum) genomic information and named as SlBAG1-10 according to their chromosomal location. All SlBAG proteins harbor a characteristic BAG domain, categorized into two groups, and SlBAG4, SlBAG7, and SlBAG9 of group I contain a plant-specific isoleucine glutamine (IQ) calmodulin-binding motif located in the N terminus. The quantitative real-time PCR expression analysis revealed that these SlBAG genes had organ-specific expression patterns and most SlBAG genes were differentially expressed in multiple abiotic stresses including drought, salt, high temperature, cold, and cadmium stress as well as abscisic acid and H2O2. In addition, heterologous overexpression of SlBAG9 increased the sensitivity of Arabidopsis to drought, salt, and ABA during seed germination and seedling growth. The decreased tolerance may be due to the downregulation of stress-related genes expression and severe oxidative stress. The expression levels of some stress and ABA-related genes, such as ABI3, RD29A, DREB2A, and P5CS1, were significantly inhibited by SlBAG9 overexpression under osmotic stress. Meanwhile, the overexpression of SlBAG9 inhibited the expression of FSD1 and CAT1 under stress conditions and the decreased levels of superoxide dismutase and catalase enzyme activities were detected accompanying the trends in the expression of both genes, which resulted in H2O2 accumulation and lipid peroxidation. Taken together, these findings lay a foundation for the future study of the biological function of SlBAG genes in tomato.
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Taheri S, Gantait S, Azizi P, Mazumdar P. Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing. 3 Biotech 2022; 12:63. [PMID: 35186660 DOI: 10.1007/s13205-022-03132-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.
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Ding H, Qian L, Jiang H, Ji Y, Fang Y, Sheng J, Xu X, Ge C. Overexpression of a Bcl-2-associated athanogene SlBAG9 negatively regulates high-temperature response in tomato. Int J Biol Macromol 2022; 194:695-705. [PMID: 34822834 DOI: 10.1016/j.ijbiomac.2021.11.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 12/18/2022]
Abstract
The Bcl-2-associated athanogene (BAG) gene is a multi-functional family of co-chaperones regulator, modulating plant stress response. Our previous study revealed that the SlBAG9 of tomato (Solanum lycopersicum) had the higher expression level induced by high-temperature (HT) at the transcriptional and protein levels, but its biological function was still unclear. Here, we conducted an in-depth analysis of SlBAG9. SlBAG9 protein was not located in the mitochondria but in the cytoplasm and nucleus. Many cis-acting elements involved in plant stress and hormone responses were located in the promoter regions of SlBAG9 including heat-shock element (HSE1). The β-glucuronidase (GUS) histochemical analysis showed that SlBAG9 promoter could drive GUS gene expression in transiently transformed Nicotiana tabacum leaves under non-inducing condition and HSE1 is critical for HT-induced GUS activity under HT. The transcription of SlBAG9 was expressed in different organs and was regulated by HT, cold, drought, and salt stresses as well as exogenous abscisic acid (ABA) and H2O2. To further elucidate SlBAG9 function in response to HT, the transgenic tomato plants overexpressing SlBAG9 were developed. Compared to the wild-type plants, SlBAG9-overexpressing plants exhibited more sensitivity to HT stress, reflected by the burning symptoms, the degradation of chlorophyll, and the reduction of photosynthetic rates. Additionally, SlBAG9-overexpressing lines showed higher accumulation of lipid peroxidation production (MDA) and H2O2, but lower activities of superoxide dismutase, catalase, and peroxidase. Therefore, it is speculated that SlBAG9 plays a negative role in thermotolerance probably by inhibition of antioxidant enzyme system leading to the oxidative damage, consequently aggravating the HT-caused injury phenotype.
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Affiliation(s)
- Haidong Ding
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China.
| | - Lu Qian
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Hailong Jiang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Yurong Ji
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Yifang Fang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Jiarong Sheng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoying Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Cailin Ge
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
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Ahammed GJ, Guang Y, Yang Y, Chen J. Mechanisms of elevated CO 2-induced thermotolerance in plants: the role of phytohormones. Plant Cell Rep 2021; 40:2273-2286. [PMID: 34269828 DOI: 10.1007/s00299-021-02751-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/29/2021] [Indexed: 05/20/2023]
Abstract
Rising atmospheric CO2 is a key driver of climate change, intensifying drastic changes in meteorological parameters. Plants can sense and respond to changes in environmental parameters including atmospheric CO2 and temperatures. High temperatures beyond the physiological threshold can significantly affect plant growth and development and thus attenuate crop productivity. However, elevated atmospheric CO2 can mitigate the deleterious effects of heat stress on plants. Despite a large body of literature supporting the positive impact of elevated CO2 on thermotolerance, the underlying biological mechanisms and precise molecular pathways that lead to enhanced tolerance to heat stress remain largely unclear. Under heat stress, elevated CO2-induced expression of respiratory burst oxidase homologs (RBOHs) and reactive oxygen species (ROS) signaling play a critical role in stomatal movement, which optimizes gas exchange to enhance photosynthesis and water use efficiency. Notably, elevated CO2 also fortifies antioxidant defense and redox homeostasis to alleviate heat-induced oxidative damage. Both hormone-dependent and independent pathways have been shown to mediate high CO2-induced thermotolerance. The activation of heat-shock factors and subsequent expression of heat-shock proteins are thought to be the essential mechanism downstream of hormone and ROS signaling. Here we review the role of phytohormones in plant response to high atmospheric CO2 and temperatures. We also discuss the potential mechanisms of elevated CO2-induced thermotolerance by focusing on several key phytohormones such as ethylene. Finally, we address some limitations of our current understanding and the need for further research to unveil the yet-unknown crosstalk between plant hormones in mediating high CO2-induced thermotolerance in plants.
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Affiliation(s)
- Golam Jalal Ahammed
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yelan Guang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Youxin Yang
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jinyin Chen
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruits and Vegetables, Collaborative Innovation Center of Post-Harvest Key Technology and Quality Safety of Fruits and Vegetables, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China.
- Pingxiang University, Pingxiang, Jiangxi, China.
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Wai AH, Cho LH, Peng X, Waseem M, Lee DJ, Lee JM, Kim CK, Chung MY. Genome-wide identification and expression profiling of Alba gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.). BMC Plant Biol 2021; 21:530. [PMID: 34772358 PMCID: PMC8588595 DOI: 10.1186/s12870-021-03310-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/02/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Alba (Acetylation lowers binding affinity) proteins are an ancient family of nucleic acid-binding proteins that function in gene regulation, RNA metabolism, mRNA translatability, developmental processes, and stress adaptation. However, comprehensive bioinformatics analysis on the Alba gene family of Solanum lycopersicum has not been reported previously. RESULTS In the present study, we undertook the first comprehensive genome-wide characterization of the Alba gene family in tomato (Solanum lycopersicum L.). We identified eight tomato Alba genes, which were classified into two groups: genes containing a single Alba domain and genes with a generic Alba domain and RGG/RG repeat motifs. Cis-regulatory elements and target sites for miRNAs, which function in plant development and stress responses, were prevalent in SlAlba genes. To explore the structure-function relationships of tomato Alba proteins, we predicted their 3D structures, highlighting their likely interactions with several putative ligands. Confocal microscopy revealed that SlAlba-GFP fusion proteins were localized to the nucleus and cytoplasm, consistent with putative roles in various signalling cascades. Expression profiling revealed the differential expression patterns of most SlAlba genes across diverse organs. SlAlba1 and SlAlba2 were predominantly expressed in flowers, whereas SlAlba5 expression peaked in 1 cm-diameter fruits. The SlAlba genes were differentially expressed (up- or downregulated) in response to different abiotic stresses. All but one of these genes were induced by abscisic acid treatment, pointing to their possible regulatory roles in stress tolerance via an abscisic acid-dependent pathway. Furthermore, co-expression of SlAlba genes with multiple genes related to several metabolic pathways spotlighted their crucial roles in various biological processes and signalling. CONCLUSIONS Our characterization of SlAlba genes should facilitate the discovery of additional genes associated with organ and fruit development as well as abiotic stress adaptation in tomato.
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Affiliation(s)
- Antt Htet Wai
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950 Republic of Korea
- Department of Biology, Yangon University of Education, Kamayut Township, Yangon Region 11041 Myanmar
| | - Lae-Hyeon Cho
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang-si, Gyeongsangnam-do 50463 Republic of Korea
| | - Xin Peng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Muhammad Waseem
- College of horticulture, South China Agricultural University, Guangzhou, China
| | - Do-jin Lee
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950 Republic of Korea
| | - Je-Min Lee
- Department of Horticulture, Kyungpook National University, Daegu, Republic of Korea
| | - Chang-Kil Kim
- Department of Horticulture, Kyungpook National University, Daegu, Republic of Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950 Republic of Korea
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21
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Ding H, Qian Y, Fang Y, Ji Y, Sheng J, Ge C. Characteristics of SlCML39, a Tomato Calmodulin-like Gene, and Its Negative Role in High Temperature Tolerance of Arabidopsis thaliana during Germination and Seedling Growth. Int J Mol Sci 2021; 22:ijms222111479. [PMID: 34768907 PMCID: PMC8584099 DOI: 10.3390/ijms222111479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/19/2022] Open
Abstract
Calmodulin-like (CML) proteins are primary calcium sensors and function in plant growth and response to stress stimuli. However, so far, the function of plant CML proteins, including tomato, is still unclear. Previously, it was found that a tomato (Solanum lycopersicum) CML, here named SlCML39, was significantly induced by high temperature (HT) at transcription level, but its biological function is scarce. In this study, the characteristics of SlCML39 and its role in HT tolerance were studied. SlCML39 encodes a protein of 201 amino acids containing four EF hand motifs. Many cis-acting elements related to plant stress and hormone response appear in the promoter regions of SlCML39. SlCML39 is mainly expressed in the root, stem, and leaf and can be regulated by HT, cold, drought, and salt stresses as well as ABA and H2O2. Furthermore, heterologous overexpression of SlCML39 reduces HT tolerance in Arabidopsis thaliana at the germination and seedling growth stages. To better understand the molecular mechanism of SlCML39, the downstream gene network regulated by SlCML39 under HT was analyzed by RNA-Seq. Interestingly, we found that many genes involved in stress responses as well as ABA signal pathway are down-regulated in the transgenic seedlings under HT stress, such as KIN1, RD29B, RD26, and MAP3K18. Collectively, these data indicate that SlCML39 acts as an important negative regulator in response to HT stress, which might be mediated by the ABA signal pathway.
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Affiliation(s)
- Haidong Ding
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.Q.); (Y.F.); (Y.J.); (J.S.)
- Correspondence: (H.D.); (C.G.); Tel./Fax: +86-514-8797-9204
| | - Ying Qian
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.Q.); (Y.F.); (Y.J.); (J.S.)
| | - Yifang Fang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.Q.); (Y.F.); (Y.J.); (J.S.)
| | - Yurong Ji
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.Q.); (Y.F.); (Y.J.); (J.S.)
| | - Jiarong Sheng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.Q.); (Y.F.); (Y.J.); (J.S.)
| | - Cailin Ge
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (Y.Q.); (Y.F.); (Y.J.); (J.S.)
- Correspondence: (H.D.); (C.G.); Tel./Fax: +86-514-8797-9204
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22
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Leite GGF, Ferreira BL, Tashima AK, Nishiduka ES, Cunha-Neto E, Brunialti MKC, Assuncao M, Azevedo LCP, Freitas F, van der Poll T, Scicluna BP, Salomão R. Combined Transcriptome and Proteome Leukocyte's Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis. Front Immunol 2021; 12:744799. [PMID: 34594344 PMCID: PMC8477441 DOI: 10.3389/fimmu.2021.744799] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/24/2021] [Indexed: 01/20/2023] Open
Abstract
Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in “omics” technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co‐differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down‐regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up‐regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host‐defense system.
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Affiliation(s)
- Giuseppe Gianini Figueirêdo Leite
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Bianca Lima Ferreira
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Erika Sayuri Nishiduka
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Edecio Cunha-Neto
- Laboratorio de Imunologia, Instituto do Coracao, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Milena Karina Colo Brunialti
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Murillo Assuncao
- Intensive Care Unit, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | - Flávio Freitas
- Intensive Care Unit, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Applied Biomedical Sciences, Faculty of Health Sciences, Mater Dei hospital, University of Malta, Msida, Malta
| | - Reinaldo Salomão
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
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23
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Garai S, Citu, Singla-Pareek SL, Sopory SK, Kaur C, Yadav G. Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants. Front Plant Sci 2021; 12:707286. [PMID: 34381483 PMCID: PMC8350573 DOI: 10.3389/fpls.2021.707286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/29/2021] [Indexed: 08/01/2023]
Abstract
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its "prionome." In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Citu
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sudhir K. Sopory
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Charanpreet Kaur
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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24
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Callwood J, Melmaiee K, Kulkarni KP, Vennapusa AR, Aicha D, Moore M, Vorsa N, Natarajan P, Reddy UK, Elavarthi S. Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species. Int J Mol Sci 2021; 22:ijms22052481. [PMID: 33804571 PMCID: PMC7957502 DOI: 10.3390/ijms22052481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 01/07/2023] Open
Abstract
Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.
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Affiliation(s)
- Jodi Callwood
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA; (J.C.); (K.P.K.); (A.R.V.); (D.A.); (S.E.)
| | - Kalpalatha Melmaiee
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA; (J.C.); (K.P.K.); (A.R.V.); (D.A.); (S.E.)
- Correspondence:
| | - Krishnanand P. Kulkarni
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA; (J.C.); (K.P.K.); (A.R.V.); (D.A.); (S.E.)
| | - Amaranatha R. Vennapusa
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA; (J.C.); (K.P.K.); (A.R.V.); (D.A.); (S.E.)
| | - Diarra Aicha
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA; (J.C.); (K.P.K.); (A.R.V.); (D.A.); (S.E.)
| | - Michael Moore
- Optical Science Center for Applied Research (OSCAR), Delaware State University, Dover, DE 19901, USA;
| | - Nicholi Vorsa
- Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, Chatsworth, NJ 08019, USA;
| | - Purushothaman Natarajan
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112, USA; (P.N.); (U.K.R.)
| | - Umesh K. Reddy
- Department of Biology and Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112, USA; (P.N.); (U.K.R.)
| | - Sathya Elavarthi
- Department of Agriculture and Natural Resources, Delaware State University, Dover, DE 19901, USA; (J.C.); (K.P.K.); (A.R.V.); (D.A.); (S.E.)
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