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Zhang Y, Zhang J, Fan H, Lu R, Nie G. Database construction and comparative genomics analysis of genes involved in nutritional metabolic diseases in fish. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 50:101241. [PMID: 38733902 DOI: 10.1016/j.cbd.2024.101241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/24/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
Nutritional metabolic diseases in fish frequently arise in the setting of intensive aquaculture. The etiology and pathogenesis of these conditions involve energy metabolic disorders influenced by both internal genetic factors and external environmental conditions. The exploration of genes associated with nutritional and metabolic disorder has sparked considerable interest within both the aquaculture scientific community and the industry. High-throughput sequencing technology offers researchers extensive genetic information. Effectively mining, analyzing, and securely storing this data is crucial, especially for advancing disease prevention and treatment strategies. Presently, the exploration and application of gene databases concerning nutritional and metabolic disorders in fish are at a nascent stag. Therefore, this study focused on the model organism zebrafish and five primary economic fish species as the subjects of investigation. Using information from KEGG, OMIM, and existing literature, a novel gene database associated with nutritional metabolic diseases in fish was meticulously constructed. This database encompassed 4583 genes for Danio rerio, 6287 for Cyprinus carpio, 3289 for Takifugu rubripes, 3548 for Larimichthys crocea, 3816 for Oreochromis niloticus, and 5708 for Oncorhynchus mykiss. Through a comparative systems biology approach, we discerned a relatively high conservation of genes linked to nutritional metabolic diseases across these fish species, with over 54.9 % of genes being conserved throughout all six species. Additionally, the analysis pinpointed the existence of 13 species-specific genes within the genomes of large yellow croaker, tilapia, and rainbow trout. These genes exhibit the potential to serve as novel candidate targets for addressing nutritional metabolic diseases.
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Affiliation(s)
- Yuru Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Junmei Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Haiying Fan
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Ronghua Lu
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China
| | - Guoxing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China; College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang 453007, PR China.
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Zhang J, Zhang Y, Feng C. Genome-Wide Analysis of MYB Genes in Primulina eburnea (Hance) and Identification of Members in Response to Drought Stress. Int J Mol Sci 2023; 25:465. [PMID: 38203634 PMCID: PMC10778706 DOI: 10.3390/ijms25010465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Due to periodic water deficiency in karst environments, Primulina eburnea experiences sporadic drought stress in its habitat. Despite being one of the largest gene families and functionally diverse in terms of plant growth and development, MYB transcription factors in P. eburnea have not been studied. Here, a total of 230 MYB genes were identified in P. eburnea, including 67 1R-MYB, 155 R2R3-MYB, six 3R-MYB, and two 4R-MYB genes. The R2R3-type PebMYB genes could be classified into 16 subgroups, while the remaining PebMYB genes (1R-MYB, 3R-MYB, and 4R-MYB genes) were divided into 10 subgroups. Notably, the results of the phylogenetic analysis were further supported by the motif and gene structure analysis, which showed that individuals in the same subgroup had comparable motif and structure organization. Additionally, gene duplication and synteny analyses were performed to better understand the evolution of PebMYB genes, and 291 pairs of segmental duplicated genes were found. Moreover, RNA-seq analysis revealed that the PebMYB genes could be divided into five groups based on their expression characteristics. Furthermore, 11 PebMYB genes that may be involved in drought stress response were identified through comparative analysis with Arabidopsis thaliana. Notably, seven of these genes (PebMYB3, PebMYB13, PebMYB17, PebMYB51, PebMYB142, PebMYB69, and PebMYB95) exhibited significant differences in expression between the control and drought stress treatments, suggesting that they may play important roles in drought stress response. These findings clarified the characteristics of the MYB gene family in P. eburnea, augmenting our comprehension of their potential roles in drought stress adaptation.
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Affiliation(s)
- Jie Zhang
- Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (J.Z.); (Y.Z.)
| | - Yi Zhang
- Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (J.Z.); (Y.Z.)
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Chen Feng
- Jiangxi Provincial Key Laboratory of Ex Situ Plant Conservation and Utilization, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China; (J.Z.); (Y.Z.)
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Félix JW, Granados-Alegría MI, Gómez-Tah R, Tzec-Simá M, Ruíz-May E, Canto-Canché B, Zamora-Briseño JA, Bojórquez-Velázquez E, Oropeza-Salín C, Islas-Flores I. Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation. Int J Mol Sci 2023; 24:10431. [PMID: 37445609 DOI: 10.3390/ijms241310431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.
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Affiliation(s)
- Jean Wildort Félix
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - María Inés Granados-Alegría
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Miguel Tzec-Simá
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Eliel Ruíz-May
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, Colonia El Haya, Xalapa C.P. 91073, Veracruz, Mexico
| | - Carlos Oropeza-Salín
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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Fan D, Smith DL. Mucilaginibacter sp. K Improves Growth and Induces Salt Tolerance in Nonhost Plants via Multilevel Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:938697. [PMID: 35832221 PMCID: PMC9271937 DOI: 10.3389/fpls.2022.938697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Soil salinity negatively modulates plant growth and development, contributing to severe decreases in the growth and production of crops. Mucilaginibacter sp. K is a root endophytic bacterium that was previously reported by our laboratory to stimulate growth and confer salt tolerance in Arabidopsis (Arabidopsis thaliana). The main purpose of the present study is to elucidate the physiological and molecular machinery responsible for the prospective salt tolerance as imparted by Mucilaginibacter sp. K. We first report that auxin, gibberellin, and MPK6 signalings were required for strain K-induced growth promotion and salt tolerance in Arabidopsis. Then, this strain was assessed as a remediation strategy to improve maize performance under salinity stress. Under normal growth conditions, the seed vigor index, nitrogen content, and plant growth were significantly improved in maize. After NaCl exposure, strain K significantly promoted the growth of maize seedlings, ameliorated decline in chlorophyll content and reduced accretion of MDA and ROS compared with the control. The possible mechanisms involved in salt resistance in maize could be the improved activities of SOD and POD (antioxidative system) and SPS (sucrose biosynthesis), upregulated content of total soluble sugar and ABA, and reduced Na+ accumulation. These physiological changes were then confirmed by induced gene expression for ion transportation, photosynthesis, ABA biosynthesis, and carbon metabolism. In summary, these results suggest that strain K promotes plant growth through increases in photosynthesis and auxin- and MPK6-dependent pathways; it also bestows salt resistance on plants through protection against oxidative toxicity, Na+ imbalance, and osmotic stress, along with the activation of auxin-, gibberellin-, and MPK6-dependent signaling pathways. This is the first detailed report of maize growth promotion by a Mucilaginibacter sp. strain from wild plant. This strain could be used as a favorable biofertilizer and a salinity stress alleviator for maize, with further ascertainment as to its reliability of performance under field conditions and in the presence of salt stress.
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Affiliation(s)
- Di Fan
- School of Biology, Food and Environment, Hefei University, Hefei, China
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
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Xu Z, He J, Tehseen Azhar M, Zhang Z, Fan S, Jiang X, Jia T, Shang H, Yuan Y. UDP-glucose pyrophosphorylase: genome-wide identification, expression and functional analyses in Gossypium hirsutum. PeerJ 2022; 10:e13460. [PMID: 35663522 PMCID: PMC9161816 DOI: 10.7717/peerj.13460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/27/2022] [Indexed: 01/14/2023] Open
Abstract
In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased. These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton.
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Affiliation(s)
- Zhongyang Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiasen He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Haihong Shang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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