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Ke Y, Xu M, Hwarari D, Chen J, Yang L. Genomic Survey of Heat Shock Proteins in Liriodendron chinense Provides Insight into Evolution, Characterization, and Functional Diversities. Int J Mol Sci 2022; 23:ijms232315051. [PMID: 36499378 PMCID: PMC9739435 DOI: 10.3390/ijms232315051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Heat shock proteins (HSPs) are conserved molecular chaperones whose main role is to facilitate the regulation of plant growth and stress responses. The HSP gene family has been characterized in most plants and elucidated as generally stress-induced, essential for their cytoprotective roles in cells. However, the HSP gene family has not yet been analyzed in the Liriodendron chinense genome. In current study, 60 HSP genes were identified in the L. chinense genome, including 7 LchiHSP90s, 23 LchiHSP70s, and 30 LchiHSP20s. We investigated the phylogenetic relationships, gene structure and arrangement, gene duplication events, cis-acting elements, 3D-protein structures, protein-protein interaction networks, and temperature stress responses in the identified L. chinense HSP genes. The results of the comparative phylogenetic analysis of HSP families in 32 plant species showed that LchiHSPs are closely related to the Cinnamomum kanehirae HSP gene family. Duplication events analysis showed seven segmental and six tandem duplication events that occurred in the LchiHSP gene family, which we speculated to have played an important role in the LchiHSP gene expansion and evolution. Furthermore, the Ka/Ks analysis indicated that these genes underwent a purifying selection. Analysis in the promoter region evidenced that the promoter region LchiHSPs carry many stress-responsive and hormone-related cis-elements. Investigations in the gene expression patterns of the LchiHSPs using transcriptome data and the qRT-PCR technique indicated that most LchiHSPs were responsive to cold and heat stress. In total, our results provide new insights into understanding the LchiHSP gene family function and their regulatory mechanisms in response to abiotic stresses.
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Affiliation(s)
- Yongchao Ke
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Mingyue Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (J.C.); (L.Y.)
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (J.C.); (L.Y.)
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Ji XR, Yu YH, Ni PY, Zhang GH, Guo DL. Genome-wide identification of small heat-shock protein (HSP20) gene family in grape and expression profile during berry development. BMC PLANT BIOLOGY 2019; 19:433. [PMID: 31623556 PMCID: PMC6798335 DOI: 10.1186/s12870-019-2031-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/11/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND Studies have shown that HSP20 (heat-shock protein 20) genes play important roles in regulating plant growth, development, and stress response. However, the grape HSP20 gene family has not been well studied. RESULTS A total of 48 VvHSP20 genes were identified from the grape genome, which were divided into 11 subfamilies (CI, CII, CIII, CV, CVI, CVII, MI, MII, ER, CP and PX/Po) based on a phylogenetic analysis and subcellular localization. Further structural analysis showed that most of the VvHSP20 genes (93.8%) had no intron or only one intron, while genes that clustered together based on a phylogenetic tree had similar motifs and evolutionarily conserved structures. The HSP20s share a conservedα-crystalline domain (ACD) and the different components of the ACD domain suggest the functional diversity of VvHSP20s. In addition, the 48 VvHSP20 genes were distributed on 12 grape chromosomes and the majority of VvHSP20 genes were located at the proximal or distal ends of chromosomes. Chromosome mapping indicated that four groups of VvHSP20 genes were identified as tandem duplication genes. Phytohormone responsive, abiotic and biotic stress-responsive, and plant development-related cis-elements were identified from the cis-regulatory elements analysis of VvHSP20s. The expression profiles of VvHSP20s genes (VvHSP20-1, 11, 14, 17, 18, 19, 20, 24, 25, 28, 31, 39, 42, and 43) were largely similar between RNA-Seq and qRT-PCR analysis after hydrogen peroxide (H2O2) treatment. The results showed that most VvHSP20s were down-regulated by H2O2 treatment during fruit development. VvHSP20s genes were indeed found to be involved in the grape berry development and differences in their transcriptional levels may be the result of functional differentiation during evolution. CONCLUSIONS Our results provide valuable information on the evolutionary relationship of genes in the VvHSP20 family, which is useful for future studies on the functional characteristics of VvHSP20 genes in grape.
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Affiliation(s)
- Xiao-Ru Ji
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Yi-He Yu
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Pei-Yi Ni
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
| | - Guo-Hai Zhang
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
| | - Da-Long Guo
- College of Forestry, Henan University of Science and Technology, Luoyang, 471023 Henan Province China
- Henan Engineering Technology Research Center of Quality Regulation and Controlling of Horticultural Plants, Luoyang, 471023 Henan Province China
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Gudys K, Guzy-Wrobelska J, Janiak A, Dziurka MA, Ostrowska A, Hura K, Jurczyk B, Żmuda K, Grzybkowska D, Śróbka J, Urban W, Biesaga-Koscielniak J, Filek M, Koscielniak J, Mikołajczak K, Ogrodowicz P, Krystkowiak K, Kuczyńska A, Krajewski P, Szarejko I. Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2018; 9:769. [PMID: 29946328 PMCID: PMC6005862 DOI: 10.3389/fpls.2018.00769] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 05/18/2018] [Indexed: 05/27/2023]
Abstract
Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs), followed by their prioritization based on Gene Ontology (GO) enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin up-regulated RNAs, nitric oxide synthase, ATP sulfurylases, and proteins involved in regulation of flowering time. This global approach may be proposed for identification of new CGs that underlies QTLs responsible for complex traits.
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Affiliation(s)
- Kornelia Gudys
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
- Department of Botany and Nature Protection, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Justyna Guzy-Wrobelska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Agnieszka Janiak
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Michał A. Dziurka
- Department of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, Poland
| | - Agnieszka Ostrowska
- Department of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, Poland
| | - Katarzyna Hura
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, Poland
| | - Barbara Jurczyk
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, Poland
| | - Katarzyna Żmuda
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, Poland
| | - Daria Grzybkowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Joanna Śróbka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Wojciech Urban
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Jolanta Biesaga-Koscielniak
- Department of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, Poland
| | - Maria Filek
- Department of Developmental Biology, Institute of Plant Physiology, Polish Academy of Sciences, Krakow, Poland
| | - Janusz Koscielniak
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture, Krakow, Poland
| | - Krzysztof Mikołajczak
- Department of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Piotr Ogrodowicz
- Department of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Karolina Krystkowiak
- Department of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Plant Functional Metabolomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anetta Kuczyńska
- Department of Biotechnology, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
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Jaspard E, Hunault G. sHSPdb: a database for the analysis of small Heat Shock Proteins. BMC PLANT BIOLOGY 2016; 16:135. [PMID: 27297221 PMCID: PMC4906601 DOI: 10.1186/s12870-016-0820-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/24/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND small Heat Shock Proteins (sHSP) is a wide proteins family. SHSP are found in all kingdoms and they play critical roles in plant stress tolerance mechanisms (as well as in pathogenic microorganisms and are implicated in human diseases). RESULTS sHSPdb (small Heat Shock Proteins database) is an integrated resource containing non-redundant, full-length and curated sequences of sHSP, classified on the basis of amino acids motifs and physico-chemical properties. sHSPdb gathers data about sHSP defined by various databases (Uniprot, PFAM, CDD, InterPro). It provides a browser interface for retrieving information from the whole database and a search interface using various criteria for retrieving a refined subset of entries. Physicochemical properties, amino acid composition and combinations are calculated for each entry. sHSPdb provides automatic statistical analysis of all sHSP properties. Among various possibilities, sHSPdb allows BLAST searches, alignment of selected sequences and submission of sequences. CONCLUSIONS sHSPdb is a new database containing information about sHSP from all kingdoms. sHSPdb provides a classification of sHSP, as well as tools and data for the analysis of the structure - function relationships of sHSP. Data are mainly related to various physico-chemical properties of the amino acids sequences of sHSP. sHSPdb is accessible at http://forge.info.univ-angers.fr/~gh/Shspdb/index.php .
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Affiliation(s)
- Emmanuel Jaspard
- Université d'Angers, UMR 1345 IRHS, SFR 4207 QUASAV, Angers, France.
- INRA, UMR 1345 IRHS, Beaucouzé, France.
- Agrocampus-Ouest, UMR 1345 IRHS, Angers, France.
| | - Gilles Hunault
- Université d'Angers, Laboratoire d'Hémodynamique, Interaction Fibrose et Invasivité tumorale hépatique, UPRES 3859, IFR 132, F-49045, Angers, France
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