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Shi X, Zhang R, Liu Z, Zhao G, Guo J, Mao X, Fan B. Alternative Splicing Reveals Acute Stress Response of Litopenaeus vannamei at High Alkalinity. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:103-115. [PMID: 38206418 DOI: 10.1007/s10126-023-10281-w] [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: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Alkalinity is regarded as one of the primary stressors for aquatic animals in saline-alkaline water. Alternative splicing (AS) can significantly increase the diversity of transcripts and play key roles in stress response; however, the studies on AS under alkalinity stress of crustaceans are still limited. In the present study, we devoted ourselves to the study of AS under acute alkalinity stress at control (50 mg/L) and treatment groups (350 mg/L) by RNA-seq in pacific white shrimp (Litopenaeus vannamei). We identified a total of 10,556 AS events from 4865 genes and 619 differential AS (DAS) events from 519 DAS genes in pacific white shrimp. Functional annotation showed that the DAS genes primarily involved in spliceosome. Five splicing factors (SFs), U2AF1, PUF60, CHERP, SR140 and SRSF2 were significantly up-regulated and promoted AS. Furthermore, alkalinity activated the Leukocyte transendothelial migration, mTOR signaling pathway and AMPK signaling pathway, which regulated MAPK1, EIF3B and IGFP-RP1 associated with these pathways. We also studied three SFs (HSFP1, SRSF2 and NHE-RF1), which underwent AS to form different transcript isoforms. The above results demonstrated that AS was a regulatory mechanism in pacific white shrimp in response to acute alkalinity stress. SFs played vital roles in AS of pacific white shrimp, such as HSFP1, SRSF2 and NHE-RF1. DAS genes were significantly modified in immunity of pacific white shrimp to cope with alkalinity stress. This is the first study on the response of AS to acute alkalinity stress, which provided scientific basis for AS mechanism of crustaceans response to alkalinity stress.
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Affiliation(s)
- Xiang Shi
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Ruiqi Zhang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China.
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Guiyan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Jintao Guo
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Xue Mao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Baoyi Fan
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
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Dong CL, Feng Z, Lu MX, Du YZ. Chilo suppressalis heat shock proteins are regulated by heat shock factor 1 during heat stress. INSECT MOLECULAR BIOLOGY 2023; 32:69-78. [PMID: 36279182 DOI: 10.1111/imb.12814] [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: 04/26/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Heat shock factor 1 (HSF1) functions to maintain cellular and organismal homeostasis by regulating the expression of target genes, including those encoding heat shock proteins (HSPs). In the present study, the gene encoding HSF1 was cloned from the rice pest Chilo suppressalis, and designated Cshsf1. The deduced protein product, CsHSF1, contained conserved domains typical of the HSF1 family, including a DNA-binding domain, two hydrophobic heptad repeat domains, and a C-terminal transactivation domain. Real-time quantitative PCR showed that Cshsf1 was highly expressed in hemocytes. Expression analysis in different developmental stages of C. suppressalis revealed that Cshsf1 was most highly expressed in male adults. RNAi-mediated silencing of Cshsf1 expression reduced C. suppressalis survival at high temperatures. To investigate the regulatory interactions between Cshsf1 and Cshsps, the promoters and expression patterns of 18 identified Cshsps in C. suppressalis were analysed; four types of heat shock elements (HSEs) were identified in promoter regions including canonical, tail-tail, head-head, and step/gap. The expression of Cshsp19.0, Cshsp21.7B, Cshsp60, Cshsp70 and Cshsp90 was positively regulated by Cshsf1; however, Cshsp22.8, Cshsp702, Cshsp705 and Cshsp706 gene expression was not altered. This study provides a foundation for future studies of HSF1 in insects during thermal stress.
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Affiliation(s)
- Chuan-Lei Dong
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Zhu Feng
- Plant Protection and Quarantine Station of Jiangsu Province, Nanjing, China
| | - Ming-Xing Lu
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Yu-Zhou Du
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education, Yangzhou University, Yangzhou, China
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Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats. BIOLOGY 2022; 11:biology11121740. [PMID: 36552250 PMCID: PMC9774719 DOI: 10.3390/biology11121740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Abstract
The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This study identified the differentially expressed mRNA isoforms which narrowed down the most reliable DEG markers and molecular pathways that underlie the mechanisms of thermoregulation. This experiment was performed on Sprague Dawley rats housed at 22 °C (control group; CT), and three acute heat-stressed groups housed at 42 °C for 30 min (H30), 60 min (H60), and 120 min (H120). Earlier, we demonstrated that acute heat stress increased the rectal temperature of rats, caused abnormal changes in the blood biochemical parameters, as well as induced dramatic changes in the expression levels of genes through epigenetics and post-transcriptional regulation. Transcriptomic analysis using RNA-Sequencing (RNA-Seq) data obtained previously from blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120) was performed. The differentially expressed mRNA isoforms (DEIs) were identified and annotated by the CLC Genomics Workbench. Biological process and metabolic pathway analyses were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 225, 5764, and 4988 DEIs in the blood, liver, and adrenal glands were observed. Furthermore, the number of novel differentially expressed transcript lengths with annotated genes and novel differentially expressed transcript with non-annotated genes were 136 and 8 in blood, 3549 and 120 in the liver, as well as 3078 and 220 in adrenal glands, respectively. About 35 genes were involved in the heat stress response, out of which, Dnaja1, LOC680121, Chordc1, AABR07011951.1, Hsp90aa1, Hspa1b, Cdkn1a, Hmox1, Bag3, and Dnaja4 were commonly identified in the liver and adrenal glands, suggesting that these genes may regulate heat stress response through interactions between the liver and adrenal glands. In conclusion, this study would enhance our understanding of the complex underlying mechanisms of acute heat stress, and the identified mRNA isoforms and genes can be used as potential candidates for thermotolerance selection in mammals.
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Meng JY, Yang CL, Wang HC, Cao Y, Zhang CY. Molecular characterization of six heat shock protein 70 genes from Arma chinensis and their expression patterns in response to temperature stress. Cell Stress Chaperones 2022; 27:659-671. [PMID: 36264419 PMCID: PMC9672165 DOI: 10.1007/s12192-022-01303-y] [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: 06/23/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 01/25/2023] Open
Abstract
Arma chinensis is an important predatory enemy of many agricultural and forest pests. Heat shock protein 70 (Hsp70) plays an essential role in insect adaptation to various stress factors. To explore the functions of Hsp70s in relation to thermal tolerance of A. chinensis, full-length cDNAs of six Hsp70 genes (AcHsp70Ba, AcHsp70-4, AcHsp68a, AcHsp68b, AcHsp70-2, and AcHsc70-4) were cloned. Their open reading frames (ORFs) were 1902, 2454, 1884, 1905, 1872, and 1947 bp, respectively. Developmental expression profiles showed that AcHsp70Ba, AcHsp70-4, and AcHsc70-4 were extremely highly expressed in adult stages. AcHsp68a and AcHsp70-2 showed the highest level of expression in nymph stages, and AcHsp68b was mainly expressed in male adults. Tissue distribution analysis demonstrated that the AcHsp70s were ubiquitously expressed but showing gene-specific and sex-driven patterns of expression. High temperature induced the expression of the six AcHsp70s. Among them, AcHsp70Ba, AcHsp70-4, AcHsp68a, and AcHsc70-4 were significantly induced at 38 °C for 6 h, while all six AcHsp70s were significantly induced at 38 °C for 24 h. There were differences in responses of the six AcHsp70s to low-temperature stress. The expressions of AcHsp70-4, AcHsp68a, and AcHsp68b in male adults were significantly repressed at 4 °C for 6 h, whereas AcHsp70Ba and AcHsp70-2 were significantly induced. The levels of AcHsp70Ba, AcHsp68b, and AcHsp70-2 in female adults were significantly repressed at 4 °C for 24 h, whereas AcHsc70-4 was significantly induced. These results suggested that AcHsp70s play important roles in various developmental stages and tissue function, and contribute to the tolerance of A. chinensis to extreme temperatures.
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Affiliation(s)
- Jian-Yu Meng
- Guizhou Tobacco Science Research Institute, Guiyang, 550081, China
| | - Chang-Li Yang
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, 550025, China
| | - Han-Cheng Wang
- Guizhou Tobacco Science Research Institute, Guiyang, 550081, China
| | - Yi Cao
- Guizhou Tobacco Science Research Institute, Guiyang, 550081, China
| | - Chang-Yu Zhang
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, 550025, China.
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Knockdown of heat shock transcription factor 1 decreases temperature stress tolerance in Bemisia tabaci MED. Sci Rep 2022; 12:16059. [PMID: 36163391 PMCID: PMC9512819 DOI: 10.1038/s41598-022-19788-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
The primary function of heat shock transcription factor (HSF) in the heat shock response is to activate the transcription of genes encoding heat shock proteins (HSPs). The phloem-feeding insect Bemisia tabaci (Gennadius) is an important pest of cotton, vegetables and ornamentals that transmits several plant viruses and causes enormous agricultural losses. In this study, the gene encoding HSF (Bthsf1) was characterized in MED B. tabaci. The full-length cDNA encoded a protein of 652 amino acids with an isoelectric point of 5.55. The BtHSF1 deduced amino acid sequence showed strong similarity to HSF in other insects. Expression analyses using quantitative real-time PCR indicated that Bthsf1 was significantly up-regulated in B. tabaci adults and pupae during thermal stress. Although Bthsf1 was induced by both hot and cold stress, the amplitude of expression was greater in the former. Bthsf1 had distinct, significant differences in expression pattern during different duration of high but not low temperature stress. Oral ingestion of dsBthsf1 repressed the expression of Bthsf1 and four heat shock proteins (Bthsp90, Bthsp70-3, Bthsp20 and Bthsp19.5) in MED B. tabaci during hot and cold stress. In conclusion, our results show that Bthsf1 is differentially expressed during high and low temperature stress and regulates the transcription of multiple hsps in MED B. tabaci.
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Transcriptome Analyses Reveal Essential Roles of Alternative Splicing Regulation in Heat-Stressed Holstein Cows. Int J Mol Sci 2022; 23:ijms231810664. [PMID: 36142577 PMCID: PMC9505234 DOI: 10.3390/ijms231810664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/03/2022] Open
Abstract
Heat stress (HS) severely impacts the productivity and welfare of dairy cows. Investigating the biological mechanisms underlying HS response is crucial for developing effective mitigation and breeding strategies. Therefore, we evaluated the changes in milk yield, physiological indicators, blood biochemical parameters, and alternative splicing (AS) patterns of lactating Holstein cows during thermoneutral (TN, N = 19) and heat-stress (HS, N = 17) conditions. There was a significant (p < 0.05) decline in milk yield as physiological indicators increased after exposure to natural HS conditions. The levels of eight out of 13 biochemical parameters of HS were also significantly altered in the presence of HS (p < 0.05). These results demonstrate that HS negatively influences various biological processes of Holstein cows. Furthermore, we investigated AS events based on the RNA-seq data from blood samples. With HS, five common types of AS events were generally increased by 6.7−38.9%. A total of 3470 AS events corresponding to 3143 unique genes were differentially alternatively spliced (DSGs) (p-adjusted < 0.05) between TN and HS groups. The functional annotation results show that the majority of DSGs are involved in mRNA splicing and spliceosomal complex, followed by enrichment in immune and metabolic processes. Eighty-seven out of 645 differentially expressed genes (DEGs) (fold change ≥ 1.5 and false discovery rate < 0.05) overlapped with DSGs. Further analyses showed that 20 of these genes were significantly enriched for the RNA splicing, RNA binding, and RNA transport. Among them, two genes (RBM25 and LUC7L3) had strong interrelation and co-expression pattern with other genes and were identified as candidate genes potentially associated with HS responses in dairy cows. In summary, AS plays a crucial role in changing the transcriptome diversity of heat-stress-related genes in multiple biological pathways and provides a different regulation mechanism from DEGs.
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Xiao W, Sun Y, Xu J, Zhang N, Dong L. uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response. J Mol Evol 2022; 90:375-388. [PMID: 35962830 PMCID: PMC9375200 DOI: 10.1007/s00239-022-10068-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Diseases and environmental stresses are two distinct challenges for virtually all living organisms. In light of evolution, cellular responses to diseases and stresses might share similar molecular mechanisms, but the detailed regulation pathway is not reported yet. We obtained the transcriptomes and translatomes from several NSCLC (non-small-cell lung cancer) patients as well as from different species under normal or stress conditions. We found that the translation level of gene ATF4 is remarkably enhanced in NSCLC due to the reduced number of ribosomes binding to its upstream open reading frames (uORFs). We also showed the evolutionary conservation of this uORF-ATF4 regulation in the stress response of other species. Molecular experiments showed that knockdown of ATF4 reduced the cell growth rate while overexpression of ATF4 enhanced cell growth, especially for the ATF4 allele with mutated uORFs. Population genetics analyses in multiple species verified that the mutations that abolish uATGs (start codon of uORFs) are highly deleterious, suggesting the functional importance of uORFs. Our study proposes an evolutionarily conserved pattern that enhances the ATF4 translation by uORFs upon stress or disease. We generalized the concept of cellular response to diseases and stresses. These two biological processes may share similar molecular mechanisms.
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Affiliation(s)
- Wenjing Xiao
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| | - Yang Sun
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jinpeng Xu
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Na Zhang
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lina Dong
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Sun J, Liu Z, Quan J, Li L, Zhao G, Lu J. RNA-seq Analysis Reveals Alternative Splicing Under Heat Stress in Rainbow Trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:5-17. [PMID: 34787764 DOI: 10.1007/s10126-021-10082-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) is one of the most economically important cold-water farmed species in the world, and transcriptomic studies in response to heat stress have been conducted and will be studied in depth. Alternative splicing (AS), a post-transcriptional regulatory process that regulates gene expression and increases proteomic diversity, is still poorly understood in rainbow trout under heat stress. In the present study, 18,623 alternative splicing events were identified from 9936 genes using RNA transcriptome sequencing technology (RNA-Seq) and genomic information. A total of 2731 differential alternative splicing (DAS) events were found among 2179 differentially expressed genes (DEGs). Gene ontology analysis revealed that the DEGs were mainly enriched in cellular metabolic process, cell part, and organic cyclic compound binding under heat stress. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis displayed that the DEGs were enriched for 39 pathways, and some key pathways, such as lysine degradation, are involved in the regulation of heat stress in liver tissues of rainbow trout. The results were validated by qRT-PCR, confirming reliability of our bioinformatics analysis.
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Affiliation(s)
- Jun Sun
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China.
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
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Qi X, Wang Y, Zhang G, Cao S, Xu P, Ren X, Mansour A, Niu C. Transcriptome analysis uncovers different avenues for manipulating cold performance in Chrysomya megacephala (Diptera, Calliphoridae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2022; 112:1-12. [PMID: 35225171 DOI: 10.1017/s0007485321001073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Temperature strongly impacts the rates of physiological and biochemical processes, which in turn can determine the survival and population size of insects. At low temperatures performance is limited, however, cold tolerance and performance at low temperature can be improved after short- or long-term acclimation in many insect species. To understand mechanisms underlying acclimation, we sequenced and compared the transcriptome of the blowfly Chrysomya megacephala under rapid cold hardening (RCH) and long-term cold acclimation (LCA) conditions. The RCH response was dominated by genes related to immune response, spliceosome, and protein processing in endoplasmic reticulum with up-regulation during recovery from RCH. In contrast, LCA was associated with genes related to carbohydrate metabolism and cytoskeleton branching and stabilizing. Meanwhile, mRNA levels of genes related to glycerophospholipid metabolism, and some heat shock proteins (Hsps) were collectively up-regulated by both RCH and LCA. There were more genes and pathway adjustments associated with LCA than RCH. Overall, the transcriptome data provide basic information of molecular mechanisms underpinning the RCH and LCA response. The partly independent molecular responses to RCH and LCA suggest that several avenues for manipulating cold performance exist and RCH might be more effective as it only triggers fewer genes and affects the general metabolisms less. These observations provide some appropriate methods to improve cold tolerance of C. megacephala, and hold promise for developing an extended use of mass-reared C. megacephala with better cold performance as a pollinator of crops at low temperatures.
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Affiliation(s)
- Xuewei Qi
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Yaohui Wang
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Guijian Zhang
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Shuai Cao
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Penghui Xu
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Xueming Ren
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
| | - Abdelaziz Mansour
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613Giza, Egypt
| | - Changying Niu
- Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan430070, China
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Huang S, Dou J, Li Z, Hu L, Yu Y, Wang Y. Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data. Genes (Basel) 2022; 13:genes13020358. [PMID: 35205403 PMCID: PMC8871965 DOI: 10.3390/genes13020358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Heat stress is one of the most severe challenges faced in livestock production in summer. Alternative splicing as an important post-transcriptional regulation is rarely studied in heat-stressed animals. Here, we performed and analyzed RNA-sequencing assays on the liver of Sprague-Dawley rats in control (22 °C, n = 5) and heat stress (4 °C for 120 min, H120; n = 5) groups, resulting in the identification of 636 differentially expressed genes. Identification analysis of the alternative splicing events revealed that heat stress-induced alternative splicing events increased by 20.18%. Compared with other types of alternative splicing events, the alternative start increased the most (43.40%) after heat stress. Twenty-eight genes were differentially alternatively spliced (DAS) between the control and H120 groups, among which Acly, Hnrnpd and mir3064 were also differentially expressed. For DAS genes, Srebf1, Shc1, Srsf5 and Ensa were associated with insulin, while Cast, Srebf1, Tmem33, Tor1aip2, Slc39a7 and Sqstm1 were enriched in the composition of the endoplasmic reticulum. In summary, our study conducts a comprehensive profile of alternative splicing in heat-stressed rats, indicating that alternative splicing is one of the molecular mechanisms of heat stress response in mammals and providing reference data for research on heat tolerance in mammalian livestock.
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Affiliation(s)
- Shangzhen Huang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Jinhuan Dou
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 100193, China
- Correspondence: (J.D.); (Y.W.)
| | - Zhongshu Li
- Agricultural College, Yanbian University, Yanji 133002, China;
| | - Lirong Hu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Ying Yu
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
| | - Yachun Wang
- National Engineering Laboratory of Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (S.H.); (L.H.); (Y.Y.)
- Correspondence: (J.D.); (Y.W.)
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John S, Olas JJ, Mueller-Roeber B. Regulation of alternative splicing in response to temperature variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6150-6163. [PMID: 34028544 PMCID: PMC8483784 DOI: 10.1093/jxb/erab232] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 05/08/2023]
Abstract
Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.
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Affiliation(s)
- Sheeba John
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Correspondence: or
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
- Correspondence: or
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Chang YW, Wang YC, Zhang XX, Iqbal J, Lu MX, Du YZ. Transcriptional regulation of small heat shock protein genes by heat shock factor 1 (HSF1) in Liriomyza trifolii under heat stress. Cell Stress Chaperones 2021; 26:835-843. [PMID: 34337672 PMCID: PMC8492843 DOI: 10.1007/s12192-021-01224-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/26/2021] [Accepted: 07/27/2021] [Indexed: 01/02/2023] Open
Abstract
Small heat shock proteins (sHSPs) function as molecular chaperones in multiple physiological processes and are active during thermal stress. sHSP expression is controlled by heat shock transcription factor (HSF); however, few studies have been conducted on HSF in agricultural pests. Liriomyza trifolii is an introduced insect pest of horticultural and vegetable crops in China. In this study, the master regulator, HSF1, was cloned and characterized from L. trifolii, and the expression levels of HSF1 and five sHSPs were studied during heat stress. HSF1 expression in L. trifolii generally decreased with rising temperatures, whereas expression of the five sHSPs showed an increasing trend that correlated with elevated temperatures. All five sHSPs and HSF1 showed an upward trend in expression with exposure to 40 ℃ without a recovery period. When a recovery period was incorporated after thermal stress, the expression patterns of HSF1 and sHSPs in L. trifolii exposed to 40 °C was significantly lower than expression with no recovery period. To elucidate potential interactions between HSF1 and sHSPs, double-stranded RNA was synthesized to knock down HSF1 in L. trifolii by RNA interference. The knockdown of HSF1 by RNAi decreased the survival rate and expression of HSP19.5, HSP20.8, and HSP21.3 during high-temperature stress. This study expands our understanding of HSF1-regulated gene expression in L. trifolii exposed to heat stress.
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Affiliation(s)
- Ya-Wen Chang
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Yu-Cheng Wang
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Xiao-Xiang Zhang
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Junaid Iqbal
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Ming-Xing Lu
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Yu-Zhou Du
- College of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China.
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Fang H, Kang L, Abbas Z, Hu L, Chen Y, Tan X, Wang Y, Xu Q. Identification of key Genes and Pathways Associated With Thermal Stress in Peripheral Blood Mononuclear Cells of Holstein Dairy Cattle. Front Genet 2021; 12:662080. [PMID: 34178029 PMCID: PMC8222911 DOI: 10.3389/fgene.2021.662080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
The objectives of the present study were to identify key genes and biological pathways associated with thermal stress in Chinese Holstein dairy cattle. Hence, we constructed a cell-model, applied various molecular biology experimental techniques and bioinformatics analysis. A total of 55 candidate genes were screened from published literature and the IPA database to examine its regulation under cold (25°C) or heat (42°C) stress in PBMCs. We identified 29 (3 up-regulated and 26 down-regulated) and 41 (15 up-regulated and 26 down-regulated) significantly differentially expressed genes (DEGs) (fold change ≥ 1.2-fold and P < 0.05) after cold and heat stress treatments, respectively. Furthermore, bioinformatics analyses confirmed that major biological processes and pathways associated with thermal stress include protein folding and refolding, protein phosphorylation, transcription factor binding, immune effector process, negative regulation of cell proliferation, autophagy, apoptosis, protein processing in endoplasmic reticulum, estrogen signaling pathway, pathways related to cancer, PI3K- Akt signaling pathway, and MAPK signaling pathway. Based on validation at the cellular and individual levels, the mRNA expression of the HIF1A gene showed upregulation during cold stress and the EIF2A, HSPA1A, HSP90AA1, and HSF1 genes showed downregulation after heat exposure. The RT-qPCR and western blot results revealed that the HIF1A after cold stress and the EIF2A, HSPA1A, HSP90AA1, and HSF1 after heat stress had consistent trend changes at the cellular transcription and translation levels, suggesting as key genes associated with thermal stress response in Holstein dairy cattle. The cellular model established in this study with PBMCs provides a suitable platform to improve our understanding of thermal stress in dairy cattle. Moreover, this study provides an opportunity to develop simultaneously both high-yielding and thermotolerant Chinese Holstein cattle through marker-assisted selection.
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Affiliation(s)
- Hao Fang
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Ling Kang
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Zaheer Abbas
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Lirong Hu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yumei Chen
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Xiao Tan
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- Institute of Life Sciences and Bio-Engineering, Beijing Jiaotong University, Beijing, China
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Samanta S, Barman M, Chakraborty S, Banerjee A, Tarafdar J. Involvement of small heat shock proteins (sHsps) in developmental stages of fall armyworm, Spodoptera frugiperda and its expression pattern under abiotic stress condition. Heliyon 2021; 7:e06906. [PMID: 33997419 PMCID: PMC8105634 DOI: 10.1016/j.heliyon.2021.e06906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/09/2021] [Accepted: 04/20/2021] [Indexed: 11/03/2022] Open
Abstract
Fall armyworm (FAW), Spodoptera frugiperda a recent invasive pest in India is reported to cause significant damage by feeding voraciously on maize and other economic crops from tropical to temperate provinces. It is becoming an arduous challenge to control the pest as it can survive in a wide range of temperature conditions and is already said to develop resistance towards certain insecticides. The small Heat shock proteins (hereafter, sHsps) are known to play an important role in adaptation of insects under such stress conditions. Our present study involved characterization of the three sHsps genes (sHsp19.74, sHsp20.7 and sHsp19.07) which encoded proteins of about 175, 176 and 165 amino acids with a conserved α-crystalline domain. Phylogenetic analysis of deduced amino acid sequences of the three genes showed strong similarity with the other lepidopteran sHsps. The effect of different growth stages on the expression profile of these stress proteins has also been studied and the Quantitative real time PCR (qRT-PCR) analysis revealed that the transcript level of sHsp19.07 and sHsp20.7 were significantly upregulated under extreme heat (44 °C) and cold (5 °C) stress. However, sHsp19.74 responded only to heat treatment but not to the cold treatment. In addition, the expression profile of all three sHsps was significantly lower in the larval stage (5th instar). Chlorantraniliprole treatment resulted in maximum expression of sHsp19.07 and sHsp20.7 after 12hr of exposure to the insecticide. Meanwhile, the same expression was observed after 8hr of exposure in case of sHsp19.74. These results proved that the sHsp genes of S. frugiperda were induced and modulated in response to abiotic stress, thus influencing the physiological function leading to survival of FAW in diversified climate in India.
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Affiliation(s)
- Snigdha Samanta
- Department of Agricultural Entomology, B.C.K.V, West Bengal, India
| | - Mritunjoy Barman
- Department of Agricultural Entomology, B.C.K.V, West Bengal, India
| | | | - Amitava Banerjee
- Department of Agricultural Entomology, B.C.K.V, West Bengal, India
| | - Jayanta Tarafdar
- Department of Plant Pathology, B.C.K.V, Nadia, West Bengal, India.,Directorate of Research, B.C.K.V, Kalyani, 741235, India
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Molecular Characterization of Heat-Induced HSP11.0 and Master-Regulator HSF from Cotesia chilonis and Their Consistent Response to Heat Stress. INSECTS 2021; 12:insects12040322. [PMID: 33916570 PMCID: PMC8066536 DOI: 10.3390/insects12040322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/27/2022]
Abstract
Simple Summary Small heat shock proteins (sHSPs) are members of the heat shock protein (HSP) family that play an important role in heat stress, and heat shock factors (HSFs) are transcriptional activators that mainly regulate the expression of HSPs. Cotesia chilonis, the major endoparasitoid of Chilo suppressalis, widely distributes in China and other Asian regions. Previous studies have shown that C. chilonis has a certain thermal tolerance. Here, heat-induced HSP11.0 and master-regulator HSF were cloned and characterized from C. chilonis. The transcription patterns of them in response to different temperatures and time course after temperature treatment were analyzed. This study is the first report on the analysis on hsf gene of C. chilonis. The results of expression patterns will provide new insights into thermoregulation of C. chilonis in response to climate change. Abstract Small heat shock proteins (sHSPs) are members of the heat shock protein (HSP) family that play an important role in temperature stress, and heat shock factors (HSFs) are transcriptional activators that regulate HSP expression. Cotesia chilonis, the major endoparasitoid of Chilo suppressalis, modulates the C. suppressalis population in the field. In this study, we cloned and characterized two genes from C.chilonis: the heat-induced HSP11.0 gene (Cchsp11.0) that consisted of a 306-bp ORF, and the master regulator HSF (Cchsf) containing an 1875-bp ORF. CcHSP11.0 contained a chaperonin cpn10 signature motif that is conserved in other hymenopteran insects. CcHSF is a typical HSF and contains a DNA-binding domain, two hydrophobic heptad repeat domains, and a C-terminal trans-activation domain. Neither Cchsp11.0 or Cchsf contain introns. Real-time quantitative PCR revealed that Cchsp11.0 and Cchsf were highly induced at 36 °C and 6 °C after a 2-h exposure. Overall, the induction of Cchsf was lower than Cchsp11.0 at low temperatures, whereas the opposite was true at high temperatures. In conclusion, both Cchsp11.0 and Cchsf are sensitive to high and low temperature stress, and the expression pattern of the two genes were positively correlated during temperature stress.
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Alternative Splicing of Heat Shock Transcription Factor 2 Regulates the Expression of Laccase Gene Family in Response to Copper in Trametes trogii. Appl Environ Microbiol 2021; 87:AEM.00055-21. [PMID: 33579682 PMCID: PMC8091107 DOI: 10.1128/aem.00055-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
White-rot fungi, especially Trametes strains, are the primary source of industrial laccases in bioenergy and bioremediation. Trametes strains express members of the laccase gene family with different physicochemical properties and expression patterns. However, the literature on the expression pattern of the laccase gene family in T. trogii S0301 and the response mechanism to Cu2+, a key laccase inducer, in white-rot fungal strains is scarce. In the present study, we found that Cu2+ could induce the mRNAs and proteins of the two alternative splicing variants of heat shock transcription factor 2 (TtHSF2). Furthermore, the overexpression of alternative splicing variants TtHSF2α and TtHSF2β-I in the homokaryotic T. trogii S0301 strain showed opposite effects on the extracellular total laccase activity, with the maximum laccase activity of approximately 0.6 U mL-1 and 3.0 U mL-1, respectively, on the eighth day, which is 0.4 and 2.3 times that of the wild type strain. Similarly, TtHSF2α and TtHSF2β-I play opposite roles in the oxidation tolerance to H2O2 In addition, the direct binding of TtHSF2α to the promoter regions of the representative laccase isoenzymes (TtLac1 and TtLac13) and protein-protein interactions between TtHSF2α and TtHSF2β-I were detected. Our results demonstrate the crucial roles of TtHSF2 and its alternative splicing variants in response to Cu2+ We believe that these findings will deepen our understanding of alternative splicing of HSFs and their regulatory mechanism of the laccase gene family in white-rot fungi.Importance The members of laccase gene family in Trametes strains are the primary source of industrial laccase and have gained widespread attention. Increasing the yield and enzymatic properties of laccase through various methods has always been a topic worthy of attention, and there is no report on the regulation of laccase expression through HSF transcription factor engineering. Here, we found that two alternative splicing variants of TtHSF2 functioned oppositely in regulating the expression of laccase genes, and copper can induce the expression of almost all members of the laccase gene family. Most importantly, our study suggested that TtHSF2 and its alternative splicing variants are vital for copper-induced production of laccases in T. trogii S0301.
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Qian Y, Cao L, Zhang Q, Amee M, Chen K, Chen L. SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue. BMC PLANT BIOLOGY 2020; 20:366. [PMID: 32746857 PMCID: PMC7397585 DOI: 10.1186/s12870-020-02572-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/23/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND As a cool-season grass species, tall fescue (Festuca arundinacea) is challenged by increasing temperatures. Heat acclimation or activation of leaf senescence, are two main strategies when tall fescue is exposed to heat stress (HS). However, lacking a genome sequence, the complexity of hexaploidy nature, and the short read of second-generation sequencing hinder a comprehensive understanding of the mechanism. This study aims to characterize the molecular mechanism of heat adaptation and heat-induced senescence at transcriptional and post-transcriptional levels. RESULTS Transcriptome of heat-treated (1 h and 72 h) and senescent leaves of tall fescue were generated by combining single-molecular real-time and Illumina sequencing. In total, 4076; 6917, and 11,918 differentially expressed genes (DEGs) were induced by short- and long-term heat stress (HS), and senescence, respectively. Venn and bioinformatics analyses of DEGs showed that short-term HS strongly activated heat shock proteins (Hsps) and heat shock factors (Hsfs), as well as specifically activated FK506-binding proteins (FKBPs), calcium signaling genes, glutathione S-transferase genes, photosynthesis-related genes, and phytohormone signaling genes. By contrast, long-term HS shared most of DEGs with senescence, including the up-regulated chlorophyll catabolic genes, phytohormone synthesis/degradation genes, stress-related genes, and NACs, and the down-regulated photosynthesis-related genes, FKBPs, and catalases. Subsequently, transient overexpression in tobacco showed that FaHsfA2a (up-regulated specifically by short-term HS) reduced cell membrane damages caused by HS, but FaNAC029 and FaNAM-B1 (up-regulated by long-term HS and senescence) increased the damages. Besides, alternative splicing was widely observed in HS and senescence responsive genes, including Hsps, Hsfs, and phytohormone signaling/synthesis genes. CONCLUSIONS The short-term HS can stimulate gene responses and improve thermotolerance, but long-term HS is a damage and may accelerate leaf senescence. These results contribute to our understanding of the molecular mechanism underlying heat adaptation and heat-induced senescence.
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Affiliation(s)
- Yiguang Qian
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, People’s Republic of China
| | - Liwen Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Qiang Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Maurice Amee
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Ke Chen
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, People’s Republic of China
| | - Liang Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, People’s Republic of China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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Suresh S, Crease TJ, Cristescu ME, Chain FJJ. Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure. BMC Genomics 2020; 21:433. [PMID: 32586292 PMCID: PMC7318467 DOI: 10.1186/s12864-020-06831-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/15/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. RESULTS By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. CONCLUSIONS Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
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Affiliation(s)
- Sneha Suresh
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- Present address: The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong SAR
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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Li BJ, Zhu ZX, Qin H, Meng ZN, Lin HR, Xia JH. Genome-Wide Characterization of Alternative Splicing Events and Their Responses to Cold Stress in Tilapia. Front Genet 2020; 11:244. [PMID: 32256528 PMCID: PMC7093569 DOI: 10.3389/fgene.2020.00244] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.
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Affiliation(s)
| | | | | | | | | | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Hu F, Fan J, Wu C, Zhu M, Zhou Y, Wang S, Zhang C, Tao M, Zhao R, Tang C, Luo K, Qin Q, Ma M, Chen B, Wang J, Zhou A, Bai L, Liu S. Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:515-525. [PMID: 31203477 PMCID: PMC6679832 DOI: 10.1007/s10126-019-09899-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 50 chromosomes [corrected]. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1-91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma.
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Affiliation(s)
- Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Jingjing Fan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Ming Zhu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yunfan Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Ming Ma
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Bo Chen
- Key Laboratory of Phytochemical R&D of Hunan Province, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Hunan Normal University, Changsha, 410081, China
| | - Jinpu Wang
- Hunan Province Livestock and Fisheries Bureau, Changsha, 410081, China
| | - Aiguo Zhou
- Chenzhou Animal Husbandry-Veterinary & Fisheries Bureau, Changsha, 410081, China
| | - Liangxiong Bai
- Mangshan Forestry Resources Administration Bureau, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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Chen W, Geng SL, Song Z, Li YJ, Wang H, Cao JY. Alternative splicing and expression analysis of HSF1 in diapause pupal brains in the cotton bollworm, Helicoverpa armigera. PEST MANAGEMENT SCIENCE 2019; 75:1258-1269. [PMID: 30324758 DOI: 10.1002/ps.5238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Diapause is the arrest of the development of insects and can be used for the development of effective agricultural pest management strategies. Heat shock protein 70 (Hsp70) is reported to be up-regulated during diapause to maintain survival in some insect species. However, its regulatory mechanism is unknown. RESULTS Expression of hsp70 in Helicoverpa armigera was found to be up-regulated in diapause pupal brains. To elucidate the molecular regulatory mechanisms of hsp70, we focused our attention on its transcription factor, heat shock factor 1 (HSF1). Four alternative splicing variants of HSF1 from pupal brains of H. armigera were identified, and subcellular localization analysis indicated that these variants were exclusively expressed in the nucleus. Real-time PCR analysis showed that all of these variants were up-regulated in diapause pupal brains, and their expression patterns were consistent with that of hsp70. Finally, promoter activity assay and Western blotting detection demonstrated that hsp70 was activated and up-regulated by these variants. CONCLUSION Expression of hsp70 in H. armigera during diapause is regulated by multiple alternatively spliced isoforms of HSF1. The results of this study may provide important information for understanding the regulatory mechanisms of hsps during insect diapause. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Wei Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Shao-Lei Geng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhe Song
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yu-Juan Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Hui Wang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
- School of Biological Medicine, Beijing City University, Beijing, China
| | - Jian-Yun Cao
- School of Economics and Trade, South China University of Technology, Guangzhou, China
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Kühnhold H, Steinmann N, Huang YH, Indriana L, Meyer A, Kunzmann A. Temperature-induced aerobic scope and Hsp70 expression in the sea cucumber Holothuria scabra. PLoS One 2019; 14:e0214373. [PMID: 30901348 PMCID: PMC6430385 DOI: 10.1371/journal.pone.0214373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/12/2019] [Indexed: 11/29/2022] Open
Abstract
The Aerobic Scope (AS), which reflects the functional capacity for biological fitness, is a highly relevant proxy to determine thermal tolerance in various taxa. Despite the importance of this method, its implementation is often hindered, due to lacking techniques to accurately measure standard- (SMR) and maximal- (MMR) metabolic rates, especially in sluggish marine invertebrates with low oxygen consumption rates, such as sea cucumbers. In this study the AS concept was modified to define a Temperature-induced Aerobic Scope (TAS), based on metabolic rate changes due to temperature adjustments rather than traditionally used physical activity patterns. Consequentially, temperature dependent peak and bottom O2 consumption rates, defined as Temperature-induced Maximal- (TMMR) and Standard Metabolic Rates (TSMR), respectively, served as MMR and SMR alternatives for the sea cucumber Holothuria scabra. TMMR and TSMR were induced through acute temperature change (2°C per hour; 17–41°C) until critical warm (WTcrit) and cold (CTcrit) temperatures were reached, respectively. In addition, Hsp70 gene expression linked to respiration rates served as synergistic markers to confirm critical threshold temperatures. O2 consumption of H. scabra peaked distinctly at WTcrit of 38°C (TMMR = 33.2 ± 4.7 μgO2 g-1 h-1). A clear metabolic bottom line was reached at CTcrit of 22°C (TSMR = 2.2 ± 1.4 μgO2 g-1 h-1). Within the thermal window of 22–38°C H. scabra sustained positive aerobic capacity, with assumed optimal performance range between 29–31.5°C (13.85–18.7 μgO2 g-1 h-1). Between 39–41°C H. scabra decreased respiration progressively, while gene expression levels of Hsp70 increased significantly at 41°C, indicating prioritization of heat shock response (HSR) and homeostatic disruption. At the cold end (17–22°C) homeostatic disruption was visible through incrementally increasing energetic expenses to fuel basal maintenance costs, but no Hsp70 overexpression occurred. TMMR, TSMR and TAS proved to be reliable metrics, similar to the traditional energetic key parameters MMR, SMR and AS, to determine a specific aerobic performance window for the sluggish bottom dwelling species H. scabra. In addition, the linkage between respiration physiology and molecular defense mechanisms showed valuable analytical synergies in terms of mechanistic prioritization as response to thermal stress. Overall, this study will help to define lethal temperatures for aquaculture and to predict the effects of environmental stress, such as ocean warming, in H. scabra.
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Affiliation(s)
- Holger Kühnhold
- Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
- * E-mail:
| | - Nuri Steinmann
- Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Yi-Hsuan Huang
- Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Lisa Indriana
- Research Centre for Oceanography, Indonesian Institute of Science (LIPI), Lombok, Indonesia
| | - Achim Meyer
- Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
| | - Andreas Kunzmann
- Department of Ecology, Leibniz Centre for Tropical Marine Research (ZMT), Bremen, Germany
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Peng JX, He PP, Wei PY, Zhang B, Zhao YZ, Li QY, Chen XL, Peng M, Zeng DG, Yang CL, Chen X. Proteomic Responses Under Cold Stress Reveal Unique Cold Tolerance Mechanisms in the Pacific White Shrimp ( Litopenaeus vannamei). Front Physiol 2018; 9:1399. [PMID: 30483139 PMCID: PMC6243039 DOI: 10.3389/fphys.2018.01399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/13/2018] [Indexed: 11/13/2022] Open
Abstract
The Pacific white shrimp (Litopenaeus vannamei), one of the most widely cultured shrimp species in the world, often suffers from cold stress. To understand the molecular mechanism of cold tolerance in Pacific white shrimp, we conducted a proteomic analysis on two contrasting shrimp cultivars, namely, cold-tolerant Guihai2 (GH2) and cold-sensitive Guihai1 (GH1), under normal temperature (28°C), under cold stress (16°C), and during recovery to 28°C. In total, 3,349 proteins were identified, among which 2,736 proteins were quantified. Based on gene ontology annotations, differentially expressed proteins largely belonged to biological processes, cellular components, and molecular functions. KEGG pathway annotations indicated that the main changes were observed in the lysosome, ribosomes, and oxidative phosphorylation. Subcellular localization analysis showed a significant increase in proteins present in cytosol, extracellular regions, and mitochondria. Combining enrichment-based clustering analysis and qRT-PCR analysis, we found that glutathione S-transferase, zinc proteinase, m7GpppX diphosphatase, AP2 transcription complex, and zinc-finger transcription factors played a major role in the cold stress response in Pacific white shrimp. Moreover, structure proteins, including different types of lectin and DAPPUDRAFT, were indispensable for cold stress tolerance of the Pacific white shrimp. Results indicate the molecular mechanisms of the Pacific white shrimp in response to cold stress and provide new insight into breeding new cultivars with increased cold tolerance.
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Affiliation(s)
- Jin-Xia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Ping-Ping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Pin-Yuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yong-Zhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qiang-Yong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiu-Li Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Di-Gang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chun-Ling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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Tan S, Wang W, Tian C, Niu D, Zhou T, Jin Y, Yang Y, Gao D, Dunham R, Liu Z. Heat stress induced alternative splicing in catfish as determined by transcriptome analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 29:166-172. [PMID: 30481682 DOI: 10.1016/j.cbd.2018.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/07/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
Abstract
Heat tolerance is increasingly becoming an important trait for aquaculture species with a changing climate. Transcriptional studies on responses to heat stress have been conducted in catfish, one of the most important economic aquaculture species around the world. The molecular mechanisms underlying heat tolerance is still poorly understood, especially at the post-transcriptional level including regulation of alternative splicing. In this study, existing RNA-Seq datasets were utilized to characterize the change of alternative splicing in catfish following heat treatment. Heat-tolerant and -intolerant catfish were differentiated by the time to lost equilibrium after heat stress. With heat stress, alternative splicing was generally increased. In heat-intolerant fish, the thermal stress induced 29.2% increases in alternative splicing events and 25.8% increases in alternatively spliced genes. A total of 282, 189, and 44 differential alternative splicing (DAS) events were identified in control-intolerant, control-tolerant, and intolerant-tolerant comparisons, corresponding to 252, 171, and 42 genes, respectively. Gene ontology analyses showed that genes involved in the molecular function of RNA binding were significantly enriched in DAS gene sets after heat stress in both heat-intolerant and -tolerant catfish compared with the control group. Similar results were also observed in the DAS genes between heat-intolerant and -tolerant catfish, and the biological process of RNA splicing was also enriched in this comparison, indicating the involvement of RNA splicing-related genes underlying heat tolerance. This is the first comprehensive study of alternative splicing in response to heat stress in fish species, providing insights into the molecular mechanisms of responses to the abiotic stress.
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Affiliation(s)
- Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Donghong Niu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA; College of Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY 13244, USA.
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Wang J, Wang J, Lu Y, Fang Y, Gao X, Wang Z, Zheng W, Xu S. The heat responsive wheat TaRAD23 rescues developmental and thermotolerant defects of the rad23b mutant in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:23-31. [PMID: 30080608 DOI: 10.1016/j.plantsci.2018.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/30/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
High temperature severely damage the growth and development of crops with climate change. To effectively screen heat responsive proteins in wheat (Triticum aestivum L.), the isobaric tandem mass tag (TMT)-labeled quantitative proteomic analysis and quantitative real-time PCR (qRT-PCR) were performed. Here, we found that a wheat RADIATION SENSITIVE 23 protein, TaRAD23, was up-regulated at both protein and RNA levels by exposing to heat stress. Sequence homology analysis indicated that the TaRAD23 is a conserved protein, which is closely related to the Arabidopsis thaliana proteins AtRAD23B and AtRAD23A. Genetic knockout of AtRAD23B, but not AtRAD23A, shows multiple developmental defects, as well as sensitivity to heat stress. Meanwhile, we observed that constitutive overexpression of TaRAD23 in rad23b fully rescued developmental and thermotolerant defects of the mutant. Furthermore, qRT-PCR analysis of heat responsive genes in rad23b and its complementary lines suggested that suppression of the heat shock transcription factor AtHSFA2 and heat responsive genes (HSP70, HSP90, HSP17.6 and HSA32) may be the cause of the weaker thermotolerance in rad23b. Taken together, the data suggest that the heat responsive TaRAD23 is a functionally highly conserved protein that plays an important role in development, as well as the regulation in heat stress response network.
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Affiliation(s)
- Jun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Junzhe Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Yunze Lu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Yan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China.
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Weijun Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China.
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26
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Azzouz-Olden F, Hunt A, DeGrandi-Hoffman G. Transcriptional response of honey bee (Apis mellifera) to differential nutritional status and Nosema infection. BMC Genomics 2018; 19:628. [PMID: 30134827 PMCID: PMC6106827 DOI: 10.1186/s12864-018-5007-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022] Open
Abstract
Background Bees are confronting several environmental challenges, including the intermingled effects of malnutrition and disease. Intuitively, pollen is the healthiest nutritional choice, however, commercial substitutes, such as Bee-Pro and MegaBee, are widely used. Herein we examined how feeding natural and artificial diets shapes transcription in the abdomen of the honey bee, and how transcription shifts in combination with Nosema parasitism. Results Gene ontology enrichment revealed that, compared with poor diet (carbohydrates [C]), bees fed pollen (P > C), Bee-Pro (B > C), and MegaBee (M > C) showed a broad upregulation of metabolic processes, especially lipids; however, pollen feeding promoted more functions, and superior proteolysis. The superiority of the pollen diet was also evident through the remarkable overexpression of vitellogenin in bees fed pollen instead of MegaBee or Bee-Pro. Upregulation of bioprocesses under carbohydrates feeding compared to pollen (C > P) provided a clear poor nutritional status, uncovering stark expression changes that were slight or absent relatively to Bee-Pro (C > B) or MegaBee (C > M). Poor diet feeding (C > P) induced starvation response genes and hippo signaling pathway, while it repressed growth through different mechanisms. Carbohydrate feeding (C > P) also elicited ‘adult behavior’, and developmental processes suggesting transition to foraging. Finally, it altered the ‘circadian rhythm’, reflecting the role of this mechanism in the adaptation to nutritional stress in mammals. Nosema-infected bees fed pollen compared to carbohydrates (PN > CN) upheld certain bioprocesses of uninfected bees (P > C). Poor nutritional status was more apparent against pollen (CN > PN) than Bee-Pro (CN > BN) or MegaBee (CN > MN). Nosema accentuated the effects of malnutrition since more starvation-response genes and stress response mechanisms were upregulated in CN > PN compared to C > P. The bioprocess ‘Macromolecular complex assembly’ was also enriched in CN > PN, and involved genes associated with human HIV and/or influenza, thus providing potential candidates for bee-Nosema interactions. Finally, the enzyme Duox emerged as essential for guts defense in bees, similarly to Drosophila. Conclusions These results provide evidence of the superior nutritional status of bees fed pollen instead of artificial substitutes in terms of overall health, even in the presence of a pathogen. Electronic supplementary material The online version of this article (10.1186/s12864-018-5007-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Arthur Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
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Zhang X, Zhang M, Su Y, Wang Z, Zhao Q, Zhu H, Qian Z, Xu J, Tang S, Wu D, Lin Y, Kemper N, Hartung J, Bao E. Inhibition of heat stress-related apoptosis of chicken myocardial cells through inducing Hsp90 expression by aspirin administration in vivo. Br Poult Sci 2018; 59:308-317. [PMID: 29557194 DOI: 10.1080/00071668.2018.1454585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
1. This experiment investigated the anti-apoptosis effects and the mechanism of aspirin action in the heat shock response of chicken myocardial cells in vivo, via changes in the heat stress (HS) protein Hsp90 and the rate of apoptosis. Broiler chickens were administered aspirin (1 mg/kg body weight) 2 h before exposure to HS, and then exposed to 40 ± 1°C for 0, 1, 2, 3, 5, 7, 10, 15 and 24 h. 2. The induction and consumption of the HS factor heat shock factor (HSF)-1, and reductions of HSF-2 and HSF-3 induced by HS led to a delay in Hsp90 expression. HSF-1, 2 and 3 regulation of hsp90 expression in turn inhibited the synthesis and activation of protein kinase β (Akt), which resulted in a significant increase in caspase-3 at 2 and 10 h, caspase-9 from 1 to 7 h (except at 5 h), and the heat-stressed apoptosis of the myocardial cells. 3. Administration of aspirin changed the expression patterns of HSF-1, 2 and 3 such that the expression of Hsp90 protein was significantly upregulated (by 2.3-4.1 times compared with that of the non-treated cells). The resultant increase in Akt expression and activation, compared with the HS group, inhibited caspase-3 and caspase-9 activities and reduced the myocardial cells apoptosis rate (by 2.14-2.56 times). 4. Aspirin administration could inhibit heat-stressed apoptosis of myocardial cells in vivo and may be closely associated with its promotion of HS response of chicken hearts, especially Hsp90 expression.
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Affiliation(s)
- X Zhang
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - M Zhang
- b College of Animal Science and Technology , Jinling Institute of Technology , Nanjing , China
| | - Y Su
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - Z Wang
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - Q Zhao
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - H Zhu
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - Z Qian
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - J Xu
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - S Tang
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - D Wu
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - Y Lin
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
| | - N Kemper
- c Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour , University of Veterinary Medicine Hannover , Hannover , Germany
| | - J Hartung
- c Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour , University of Veterinary Medicine Hannover , Hannover , Germany
| | - E Bao
- a College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China
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Sharma V, Kohli S, Brahmachari V. Correlation between desiccation stress response and epigenetic modifications of genes in Drosophila melanogaster: An example of environment-epigenome interaction. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1058-1068. [PMID: 28801151 DOI: 10.1016/j.bbagrm.2017.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/05/2017] [Accepted: 08/05/2017] [Indexed: 01/12/2023]
Abstract
Animals from different phyla including arthropods tolerate water stress to different extent. This tolerance is accompanied by biochemical changes which in turn are due to transcriptional alteration. The changes in transcription can be an indirect effect on some of the genes, ensuing from the effect of stress on the regulators of transcription including epigenetic regulators. Within this paradigm, we investigated the correlation between stress response and epigenetic modification underlying gene expression modulation during desiccation stress in Canton-S. We report altered resistance of flies in desiccation stress for heterozygote mutants of PcG and TrxG members. Pc/+ mutant shows lower survival, while ash1/+ mutants show higher survival under desiccation stress as compared to Canton-S. We detect expression alteration in stress related genes as well the genes of the Polycomb and trithorax complex in Canton-S subjected to desiccation stress. Concomitant with this, there is an altered enrichment of H3K27me3 and H3K4me3 at the upstream regions of the stress responsive genes. The enrichment of activating mark, H3K4me3, is higher in non-stress condition. H3K27me3, the repressive mark, is more pronounced under stress condition, which in turn, can be correlated with the binding of Pc. Our results show that desiccation stress induces dynamic switching in expression and enrichment of PcG and TrxG in the upstream region of genes, which correlates with histone modifications. We provide evidence that epigenetic modulation could be one of the mechanisms to adapt to the desiccation stress in Drosophila. Thus, our study proposes the interaction of epigenome and environmental factors.
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Affiliation(s)
- Vineeta Sharma
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi 110 007, India.
| | - Surbhi Kohli
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi 110 007, India
| | - Vani Brahmachari
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi 110 007, India
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Abstract
The biological activity and geographical distribution of honey bees is strongly temperature-dependent, due to their ectothermic physiology. In China, the endemic Apis cerana cerana exhibits stronger cold hardiness than Western honey bees, making the former species important pollinators of winter-flowering plants. Although studies have examined behavioral and physiological mechanisms underlying cold resistance in bees, data are scarce regarding the exact molecular mechanisms. Here, we investigated gene expression in A. c. cerana under two temperature treatments, using transcriptomic analysis to identify differentially expressed genes (DEGs) and relevant biological processes, respectively. Across the temperature treatments, 501 DEGs were identified. A gene ontology analysis showed that DEGs were enriched in pathways related to sugar and amino acid biosynthesis and metabolism, as well as calcium ion channel activity. Additionally, heat shock proteins, zinc finger proteins, and serine/threonine-protein kinases were differentially expressed between the two treatments. The results of this study provide a general digital expression profile of thermoregulation genes responding to cold hardiness in A. c. cerana. Our data should prove valuable for future research on cold tolerance mechanisms in insects, and may be beneficial in breeding efforts to improve bee hardiness.
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Understanding the mechanisms of dormancy in an invasive alien Sycamore lace bug, Corythucha ciliata through transcript and metabolite profiling. Sci Rep 2017; 7:2631. [PMID: 28572631 PMCID: PMC5453966 DOI: 10.1038/s41598-017-02876-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/19/2017] [Indexed: 11/08/2022] Open
Abstract
The sycamore lace bug, Corythucha ciliata, is a pest of sycamore trees. In China, it is found in the most northern border where it has been known to become dormant during harsh winters. But the molecular and metabolic basis for dormancy in this insect is still unknown. In this study, we analyzed the transcript and metabolite profiles of this bug to identify key genes and metabolites that are significantly regulated during dormancy in adult females and males. In total, 149 differentially expressed genes (DEGs) were significantly up-regulated and 337 DEGs were significantly down-regulated in dormant adults (both females and males). We found major differences in heat shock protein (HSPs), immunity-responsive genes, NAD-dependent deacetylase sirtuin-1 (SIRT1) and genes involved in the spliceosome pathway that is known to regulate stress. Among the 62 metabolites identified by GC-MS, 12 metabolites including glycerol, trehalose, and alanine were significantly increased during C. ciliata dormancy. By integrating the transcriptome and metabolite datasets, we found that the metabolites in glycolysis/gluconeogenesis and citrate cycle (TCA) were significantly reduced. This study is the first to report both transcript and metabolite profiles of the overwintering responses of C. ciliata to cold stress at the molecular level.
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Wang TY, Chen YM, Chen TY. Molecular cloning of orange-spotted grouper (Epinephelus coioides) heat shock transcription factor 1 isoforms and characterization of their expressions in response to nodavirus. FISH & SHELLFISH IMMUNOLOGY 2016; 59:123-136. [PMID: 27773730 DOI: 10.1016/j.fsi.2016.10.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
Heat shock transcription factor 1 (HSF1) regulates heat shock proteins (HSPs), which assist in protein folding and inhibit protein denaturation following stress. HSF1 was firstly cloned from orange-spotted grouper and exists as two isoforms, one with (osgHSF1a) and one without (osgHSF1b) exon 11. Heat exposure increased the expression of osgHSF1b while cold exposure increased that of osgHSF1a. Both isoforms were mainly expressed in the brains, eyes, and fins. Expression of osgHSF1b was higher than osgHSF1a during development. Poly I:C and LPS could also induce osgHSF1 isoforms expression differentially. Exposure to nervous necrosis virus (NNV) increased the level of both osgHSF1 isoforms at 12 h. GF-1 cells with overexpression of osgHSF1 isoforms enhanced viral loads within 24 h, whereas both pharmacological inhibition and RNA interference of HSF1 reduced virus infection. This study shows that osgHSF1 can support the early stage of virus infection and provides a new insight into the molecular regulation of osgHSF1 between the influence of temperatures and immunity.
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Affiliation(s)
- Ting-Yu Wang
- Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Translational Center for Marine Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Young-Mao Chen
- Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Translational Center for Marine Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Agriculture Biotechnology Research Center, National Cheng Kung University, Tainan 70101, Taiwan
| | - Tzong-Yueh Chen
- Laboratory of Molecular Genetics, Institute of Biotechnology, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Translational Center for Marine Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Agriculture Biotechnology Research Center, National Cheng Kung University, Tainan 70101, Taiwan; University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
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Clemson AS, Sgrò CM, Telonis-Scott M. Thermal plasticity in Drosophila melanogaster populations from eastern Australia: quantitative traits to transcripts. J Evol Biol 2016; 29:2447-2463. [PMID: 27542565 DOI: 10.1111/jeb.12969] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/19/2016] [Accepted: 08/17/2016] [Indexed: 12/19/2022]
Abstract
The flexibility afforded to genotypes in different environments by phenotypic plasticity is of interest to biologists studying thermal adaptation because of the thermal lability of many traits. Differences in thermal performance and reaction norms can provide insight into the evolution of thermal adaptation to explore broader questions such as species distributions and persistence under climate change. One approach is to study the effects of temperature on fitness, morphological and more recently gene expression traits in populations from different climatic origins. The diverse climatic conditions experienced by Drosophila melanogaster along the eastern Australian temperate-tropical gradient are ideal given the high degree of continuous trait differentiation, but reaction norm variation has not been well studied in this system. Here, we reared a tropical and temperate population from the ends of the gradient over six developmental temperatures and examined reaction norm variation for five quantitative traits including thermal performance for fecundity, and reaction norms for thermotolerance, body size, viability and 23 transcript-level traits. Despite genetic variation for some quantitative traits, we found no differentiation between the populations for fecundity thermal optima and breadth, and the reaction norms for the other traits were largely parallel, supporting previous work suggesting that thermal evolution occurs by changes in trait means rather than by reaction norm shifts. We examined reaction norm variation in our expanded thermal regime for a gene set shown to previously exhibit GxE for expression plasticity in east Australian flies, as well as key heat-shock genes. Although there were differences in curvature between the populations suggesting a higher degree of thermal plasticity in expression patterns than for the quantitative traits, we found little evidence to support a role for genetic variation in maintaining expression plasticity.
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Affiliation(s)
- A S Clemson
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - C M Sgrò
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - M Telonis-Scott
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
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Global Gene Expression Profiling and Alternative Splicing Events during the Chondrogenic Differentiation of Human Cartilage Endplate-Derived Stem Cells. BIOMED RESEARCH INTERNATIONAL 2015; 2015:604972. [PMID: 26649308 PMCID: PMC4662983 DOI: 10.1155/2015/604972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/07/2023]
Abstract
Low back pain (LBP) is a very prevalent disease and degenerative disc diseases (DDDs) usually account for the LBP. However, the pathogenesis of DDDs is complicated and difficult to elucidate. Alternative splicing is a sophisticated regulatory process which greatly increases cellular complexity and phenotypic diversity of eukaryotic organisms. In addition, the cartilage endplate-derived stem cells have been discovered and identified by our research group. In this paper, we continue to investigate gene expression profiling and alternative splicing events during chondrogenic differentiation of cartilage endplate-derived stem cells. We adopted Affymetrix Human Transcriptome Array 2.0 (HTA 2.0) to compare the transcriptional and splicing changes between the control and differentiated samples. RT-PCR and quantitative PCR are used to validate the microarray results. The GO and KEGG pathway analysis was also performed. After bioinformatics analysis of the data, we detected 1953 differentially expressed genes. In terms of alternative splicing, the Splicing Index algorithm was used to select alternatively spliced genes. We detected 4411 alternatively spliced genes. GO and KEGG pathway analysis also revealed several functionally involved biological processes and signaling pathways. To our knowledge, this is the first study to investigate the alternative splicing mechanisms in chondrogenic differentiation of stem cells on a genome-wide scale.
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Štětina T, Koštál V, Korbelová J. The Role of Inducible Hsp70, and Other Heat Shock Proteins, in Adaptive Complex of Cold Tolerance of the Fruit Fly (Drosophila melanogaster). PLoS One 2015; 10:e0128976. [PMID: 26034990 PMCID: PMC4452724 DOI: 10.1371/journal.pone.0128976] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/01/2015] [Indexed: 12/14/2022] Open
Abstract
Background The ubiquitous occurrence of inducible Heat Shock Proteins (Hsps) up-regulation in response to cold-acclimation and/or to cold shock, including massive increase of Hsp70 mRNA levels, often led to hasty interpretations of its role in the repair of cold injury expressed as protein denaturation or misfolding. So far, direct functional analyses in Drosophila melanogaster and other insects brought either limited or no support for such interpretations. In this paper, we analyze the cold tolerance and the expression levels of 24 different mRNA transcripts of the Hsps complex and related genes in response to cold in two strains of D. melanogaster: the wild-type and the Hsp70- null mutant lacking all six copies of Hsp70 gene. Principal Findings We found that larvae of both strains show similar patterns of Hsps complex gene expression in response to long-term cold-acclimation and during recovery from chronic cold exposures or acute cold shocks. No transcriptional compensation for missing Hsp70 gene was seen in Hsp70- strain. The cold-induced Hsps gene expression is most probably regulated by alternative splice variants C and D of the Heat Shock Factor. The cold tolerance in Hsp70- null mutants was clearly impaired only when the larvae were exposed to severe acute cold shock. No differences in mortality were found between two strains when the larvae were exposed to relatively mild doses of cold, either chronic exposures to 0°C or acute cold shocks at temperatures down to -4°C. Conclusions The up-regulated expression of a complex of inducible Hsps genes, and Hsp70 mRNA in particular, is tightly associated with cold-acclimation and cold exposure in D. melanogaster. Genetic elimination of Hsp70 up-regulation response has no effect on survival of chronic exposures to 0°C or mild acute cold shocks, while it negatively affects survival after severe acute cold shocks at temperaures below -8°C.
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Affiliation(s)
- Tomáš Štětina
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vladimír Koštál
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- * E-mail:
| | - Jaroslava Korbelová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Li Z, Long Y, Zhong L, Song G, Zhang X, Yuan L, Cui Z, Dai H. RNA sequencing provides insights into the toxicogenomic response of ZF4 cells to methyl methanesulfonate. J Appl Toxicol 2015; 36:94-104. [DOI: 10.1002/jat.3147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/10/2015] [Accepted: 02/10/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Zhouquan Li
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Yong Long
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Liqiao Zhong
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Guili Song
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Xiaohua Zhang
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Li Yuan
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Zongbin Cui
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Heping Dai
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
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Telonis-Scott M, Clemson AS, Johnson TK, Sgrò CM. Spatial analysis of gene regulation reveals new insights into the molecular basis of upper thermal limits. Mol Ecol 2014; 23:6135-51. [PMID: 25401770 DOI: 10.1111/mec.13000] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/06/2014] [Accepted: 11/13/2014] [Indexed: 12/11/2022]
Abstract
The cellular stress response has long been the primary model for studying the molecular basis of thermal adaptation, yet the link between gene expression, RNA metabolism and physiological responses to thermal stress remains largely unexplored. We address this by comparing the transcriptional and physiological responses of three geographically distinct populations of Drosophila melanogaster from eastern Australia in response to, and recovery from, a severe heat stress with and without a prestress hardening treatment. We focus on starvin (stv), recently identified as an important thermally responsive gene. Intriguingly, stv encodes seven transcripts from alternative transcription sites and alternative splicing, yet appears to be rapidly heat inducible. First, we show genetic differences in upper thermal limits of the populations tested. We then demonstrate that the stv locus does not ubiquitously respond to thermal stress but is expressed as three distinct thermal and temporal RNA phenotypes (isoforms). The shorter transcript isoforms are rapidly upregulated under stress in all populations and show similar molecular signatures to heat-shock proteins. Multiple stress exposures seem to generate a reserve of pre-mRNAs, effectively 'priming' the cells for subsequent stress. Remarkably, we demonstrate a bypass in the splicing blockade in these isoforms, suggesting an essential role for these transcripts under heat stress. Temporal profiles for the weakly heat responsive stv isoform subset show opposing patterns in the two most divergent populations. Innate and induced transcriptome responses to hyperthermia are complex, and warrant moving beyond gene-level analyses.
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Affiliation(s)
- Marina Telonis-Scott
- School of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia
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Song HM, Mu XD, Gu DE, Luo D, Yang YX, Xu M, Luo JR, Zhang JE, Hu YC. Molecular characteristics of the HSP70 gene and its differential expression in female and male golden apple snails (Pomacea canaliculata) under temperature stimulation. Cell Stress Chaperones 2014; 19:579-89. [PMID: 24368711 PMCID: PMC4041941 DOI: 10.1007/s12192-013-0485-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/05/2013] [Accepted: 12/06/2013] [Indexed: 01/09/2023] Open
Abstract
Heat-shock protein 70 (HSP70) is one of the most important heat-shock proteins that helps organisms to modulate stress response via over-expression. The HSP70 gene from Pomacea canaliculata was cloned using the RACE approach; the gene is 2,767 bp in length and contains an open reading frame of 1,932 bp, which is encoded by a polypeptide of 643 amino acids. BLAST analysis showed that the predicted amino acid sequence of the P. canaliculata HSP70 gene shared a relatively high similarity with that of other known eukaryotic species that display conserved HSP characteristics. The phylogeny demonstrated a separate clustering of the apple snail HSP70 with other constitutive members from other mollusk species. Quantitative real-time RT-PCR was used to detect the differential expression of HSP70 in both sexes of P. canaliculata at different temperature conditions. These results showed that HSP70 transcript levels decreased slightly under cold shock and increased significantly under heat-shock conditions in both sexes compared to normal temperatures (26 °C). Under cold-shock treatment, the sex effect was not significant. With heat treatment, HSP70 expression could be induced at 36 °C in both females and males, and it peaked at 42 and 39 °C in females and males, respectively. In addition, a clear time-dependent HSP70 expression pattern of the apple snail exposed to the same high temperature (36 °C) was observed at different time points. The maximal induction of HSP70 expression appeared at 12 and 48 h in males and females after heat shock, respectively. The maximal induction in females was significantly higher compared to males under heat stimulus. Taken together, these results strongly suggested that males were more susceptible to heat than females and provided useful molecular information for the ecological adaptability of P. canaliculata against extreme environmental stress.
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Affiliation(s)
- Hong-Mei Song
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Xi-Dong Mu
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Dang-En Gu
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Du Luo
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Ye-Xin Yang
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Meng Xu
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Jian-Ren Luo
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
| | - Jia-En Zhang
- />Department of Ecology, College of Agriculture, South China Agricultural University, Key Laboratory of Ecological Agriculture, Guangzhou, 510642 China
| | - Yin-Chang Hu
- />Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Guangzhou, Guangdong 510380 China
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Chang CY, Lin WD, Tu SL. Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens. PLANT PHYSIOLOGY 2014; 165:826-840. [PMID: 24777346 PMCID: PMC4044832 DOI: 10.1104/pp.113.230540] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Plant growth and development are constantly influenced by temperature fluctuations. To respond to temperature changes, different levels of gene regulation are modulated in the cell. Alternative splicing (AS) is a widespread mechanism increasing transcriptome complexity and proteome diversity. Although genome-wide studies have revealed complex AS patterns in plants, whether AS impacts the stress defense of plants is not known. We used heat shock (HS) treatments at nondamaging temperature and messenger RNA sequencing to obtain HS transcriptomes in the moss Physcomitrella patens. Data analysis identified a significant number of novel AS events in the moss protonema. Nearly 50% of genes are alternatively spliced. Intron retention (IR) is markedly repressed under elevated temperature but alternative donor/acceptor site and exon skipping are mainly induced, indicating differential regulation of AS in response to heat stress. Transcripts undergoing heat-sensitive IR are mostly involved in specific functions, which suggests that plants regulate AS with transcript specificity under elevated temperature. An exonic GAG-repeat motif in these IR regions may function as a regulatory cis-element in heat-mediated AS regulation. A conserved AS pattern for HS transcription factors in P. patens and Arabidopsis (Arabidopsis thaliana) reveals that heat regulation for AS evolved early during land colonization of green plants. Our results support that AS of specific genes, including key HS regulators, is fine-tuned under elevated temperature to modulate gene regulation and reorganize metabolic processes.
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Affiliation(s)
- Chiung-Yun Chang
- Institute of Plant and Microbial Biology (C.-Y.C., W.-D.L., S.-L.T.) and Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program (C.-Y.C., S.-L.T.), Academia Sinica, Taipei 11529, Taiwan; andGraduate Institute of Biotechnology (C.-Y.C.) and Biotechnology Center (S.-L.T.), National Chung-Hsing University, Taichung 402, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology (C.-Y.C., W.-D.L., S.-L.T.) and Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program (C.-Y.C., S.-L.T.), Academia Sinica, Taipei 11529, Taiwan; andGraduate Institute of Biotechnology (C.-Y.C.) and Biotechnology Center (S.-L.T.), National Chung-Hsing University, Taichung 402, Taiwan
| | - Shih-Long Tu
- Institute of Plant and Microbial Biology (C.-Y.C., W.-D.L., S.-L.T.) and Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program (C.-Y.C., S.-L.T.), Academia Sinica, Taipei 11529, Taiwan; andGraduate Institute of Biotechnology (C.-Y.C.) and Biotechnology Center (S.-L.T.), National Chung-Hsing University, Taichung 402, Taiwan
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Neueder A, Achilli F, Moussaoui S, Bates GP. Novel isoforms of heat shock transcription factor 1, HSF1γα and HSF1γβ, regulate chaperone protein gene transcription. J Biol Chem 2014; 289:19894-906. [PMID: 24855652 PMCID: PMC4106310 DOI: 10.1074/jbc.m114.570739] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The heat shock response, resulting in the production of heat shock proteins or molecular chaperones, is triggered by elevated temperature and a variety of other stressors. Its master regulator is heat shock transcription factor 1 (HSF1). Heat shock factors generally exist in multiple isoforms. The two known isoforms of HSF1 differ in the inclusion (HSF1α) or exclusion (HSF1β) of exon 11. Although there are some data concerning the differential expression patterns and transcriptional activities of HSF2 isoforms during development, little is known about the distinct properties of the HSF1 isoforms. Here we present evidence for two novel HSF1 isoforms termed HSF1γα and HSF1γβ, and we show that the HSF1 isoform ratio differentially regulates heat shock protein gene transcription. Hsf1γ isoforms are expressed in various mouse tissues and are translated into protein. Furthermore, after heat shock, HSF1γ isoforms are exported from the nucleus more rapidly or degraded more quickly than HSF1α or HSF1β. We also show that each individual HSF1 isoform is sufficient to induce the heat shock response and that expression of combinations of HSF1 isoforms, in particular HSF1α and HSF1β, results in a synergistic enhancement of the transcriptional response. In addition, HSF1γ isoforms potentially suppress the synergistic effect of HSF1α and HSF1β co-expression. Collectively, our observations suggest that the expression of HSF1 isoforms in a specific ratio provides an additional layer in the regulation of heat shock protein gene transcription.
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Affiliation(s)
- Andreas Neueder
- From the Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, United Kingdom and
| | - Francesca Achilli
- From the Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, United Kingdom and
| | - Saliha Moussaoui
- Neuroscience Discovery, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Gillian P Bates
- From the Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, United Kingdom and
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Transcriptomic characterization of cold acclimation in larval zebrafish. BMC Genomics 2013; 14:612. [PMID: 24024969 PMCID: PMC3847098 DOI: 10.1186/1471-2164-14-612] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 09/04/2013] [Indexed: 11/10/2022] Open
Abstract
Background Temperature is one of key environmental parameters that affect the whole life of fishes and an increasing number of studies have been directed towards understanding the mechanisms of cold acclimation in fish. However, the adaptation of larvae to cold stress and the cold-specific transcriptional alterations in fish larvae remain largely unknown. In this study, we characterized the development of cold-tolerance in zebrafish larvae and investigated the transcriptional profiles under cold stress using RNA-seq. Results Pre-exposure of 96 hpf zebrafish larvae to cold stress (16°C) for 24 h significantly increased their survival rates under severe cold stress (12°C). RNA-seq generated 272 million raw reads from six sequencing libraries and about 92% of the processed reads were mapped to the reference genome of zebrafish. Differential expression analysis identified 1,431 up- and 399 down-regulated genes. Gene ontology enrichment analysis of cold-induced genes revealed that RNA splicing, ribosome biogenesis and protein catabolic process were the most highly overrepresented biological processes. Spliceosome, proteasome, eukaryotic ribosome biogenesis and RNA transport were the most highly enriched pathways for genes up-regulated by cold stress. Moreover, alternative splicing of 197 genes and promoter switching of 64 genes were found to be regulated by cold stress. A shorter isoform of stk16 that lacks 67 amino acids at the N-terminus was specifically generated by skipping the second exon in cold-treated larvae. Alternative promoter usage was detected for per3 gene under cold stress, which leading to a highly up-regulated transcript encoding a truncated protein lacking the C-terminal domains. Conclusions These findings indicate that zebrafish larvae possess the ability to build cold-tolerance under mild low temperature and transcriptional and post-transcriptional regulations are extensively involved in this acclimation process.
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Exon array analysis of alternative splicing of genes in SOD1G93A transgenic mice. Appl Biochem Biotechnol 2013; 170:301-19. [PMID: 23508861 DOI: 10.1007/s12010-013-0155-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 02/18/2013] [Indexed: 01/15/2023]
Abstract
Alternative splicing is a common strategy for creating functional diversities of proteins. While conventional identification of splice variants generally targets individual genes in amyotrophic lateral sclerosis, we present a novel exon-centric array that allows genome-wide identification of splice variants and concurrently provides analysis of gene expression. Compare 1 was asymptomatic SOD1G93A transgenic mice with nontransgenic littermates; compare 2 was symptomatic with asymptomatic transgenic mice. RT-PCR was performed to validate. Pathway and GO analysis were performed on abnormal genes. These findings could guide us to demonstrated the potential influence of mutant human CuZn-SOD1 and of splicing regulation in pathological processes.
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Zhang M, Yue Z, Liu Z, Islam A, Rehana B, Tang S, Bao E, Hartung J. Hsp70 and HSF-1 expression is altered in the tissues of pigs transported for various periods of times. J Vet Sci 2013; 13:253-9. [PMID: 23000582 PMCID: PMC3467400 DOI: 10.4142/jvs.2012.13.3.253] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to assess changes of Hsp70 and HSF-1 protein and mRNA expression in stress-sensitive organs of pigs during transportation for various periods of time. Twenty pigs were randomly divided into four groups (0 h, 1 h, 2 h, and 4 h of transportation). A significant increased activity of AST and CK was observed after 1 h and 2 h of transportation. Histopathological changes in the heart, liver, and stomach indicated that these organs sustained different degrees of injury. Hsp70 protein expression in the heart and liver of transported pigs did not change significantly while it increased significantly (p < 0.05) in the stomach. Hsp70 mRNA levels decreased significantly (p < 0.05) in the heart after 4 h of transportation. However, mRNA expression increased significantly in the liver after 1 (p < 0.05) and 4 h (p < 0.01) of transportation, and increased significantly in the stomach of the transported pigs after 1, 4 (p < 0.01), and 2 h (p < 0.05). HSF-1 levels were reduced at 1 and 4 h (p < 0.05) only in the hearts of transported pigs. These results indicate that Hsp70 mediates distinct stress-related functions in different tissues during transportation.
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Affiliation(s)
- Miao Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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Kihara F, Niimi T, Yamashita O, Yaginuma T. Heat shock factor binds to heat shock elements upstream of heat shock protein 70a and Samui genes to confer transcriptional activity in Bombyx mori diapause eggs exposed to 5°C. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 41:843-851. [PMID: 21782023 DOI: 10.1016/j.ibmb.2011.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Revised: 06/23/2011] [Accepted: 06/30/2011] [Indexed: 05/31/2023]
Abstract
To understand the molecular mechanisms of how 5°C-incubation activates mRNA expression of Hsp70a and Samui genes in Bombyx mori diapause eggs, we first searched the 5'-upstream regions of the Hsp70a and Samui genes for heat shock elements (HSEs) and found two regions [Hsp70aHSE-1 (-95 to -58) and -2 (-145 to -121), and SamuiHSE-1 (-84 to -55) and -2 (-304 to -290)] corresponding to HSEs (repeats of nGAAn and/or nTTCn). We cloned four cDNAs encoding heat shock factor (HSF)-a2 (627 amino acids), -b (685 aa), -c (682 aa) and -d (705 aa), which were produced by alternative splicing. When we exposed diapause eggs to 5°C beginning at 2 day post-oviposition to break diapause, HSFd mRNA only increased after chilling for 6-8 days, a pattern very similar to those of Hsp70a and Samui mRNAs. To examine further whether HSFd binds to the respective HSEs, we carried out a gel shift assay using HSFd protein expressed in a cell-free system and the isolated HSEs; migration of the respective digoxigenin(DIG)-labeled HSE-1 and -2 of Hsp70a and Samui was retarded by addition of HSFd; the retarded bands disappeared after addition of the corresponding unlabeled HSE-1 and -2 as competitors, but were not affected by addition of the respective mutated unlabeled HSE-1 and -2. These results indicated that HSFd protein binds to the respective HSEs and may activate mRNA expression of Hsp70a and Samui genes upon exposure of diapause eggs to 5°C.
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Affiliation(s)
- Fukashi Kihara
- Laboratory of Sericulture & Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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Diversity in DNA recognition by heat shock transcription factors (HSFs) from model organisms. FEBS Lett 2011; 585:1293-8. [PMID: 21510947 DOI: 10.1016/j.febslet.2011.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/30/2011] [Accepted: 04/05/2011] [Indexed: 11/22/2022]
Abstract
Heat shock transcription factor (HSF), an evolutionarily conserved heat-responsive regulator, binds to heat shock elements (HSEs) comprising continuous inverted repeats of the pentamer nGAAn. Here, we analyzed DNA-binding ability, particularly for the discontinuously arranged nGAAn units, of HSFs from various organisms, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio. Among these, only C. elegans HSF failed to bind the discontinuous nGAAn units, which suggests that the target genes of HSFs in many, but not all, organisms contain discontinuous HSEs, as well as continuous HSEs. Further analysis of alternatively spliced HSF isoforms showed the importance of the C-terminal region in HSF-HSE interaction.
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Kawabe S, Yokoyama Y. Novel isoforms of heat shock transcription factor 1 are induced by hypoxia in the Pacific oyster Crassostrea gigas. ACTA ACUST UNITED AC 2011; 315:394-407. [PMID: 21455948 DOI: 10.1002/jez.685] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 12/22/2022]
Abstract
The Pacific oyster Crassostrea gigas inhabits the intertidal zone and shows tolerance to various stress conditions such as hypoxia and heat shock. However, little is known about the cellular mechanism of responses to these stresses. Heat shock transcription factor 1 (HSF1) regulates the transcription of several genes, including heat shock proteins (HSPs). In this study, we cloned HSF1 from the oyster and investigated its response to air-exposure. The cDNA of oyster Hsf1 contains 2,931 bp, of which 1,389 bp encode a protein of 463 amino acid residues. Moreover, we found that the oyster has seven novel alternatively spliced isoforms, Hsf1b-h, consisting of insertion A with 48 bp, insertion B with 42 bp and/or insertion C with 42 bp. We determined the sequences of oyster genomic DNA containing Hsf1 insertions A, B and C. The results indicated that eight isoforms of Hsf1 are generated from a single Hsf1 gene by alternative splicing without frameshifting. Real-time PCR analysis showed that Hsf1a is expressed constitutively, and the expression of Hsf1b-h and Hsp70 mRNA is induced by air exposure and/or hypoxia. In addition, we found that 11 putative hypoxia response elements, which are hypoxia-inducible factor 1 (HIF-1) binding sequences, are located in the Hsf1 promoter region. These data suggest that the oyster has an HIF-HSF pathway in which HSPs are induced in an HIF-dependent manner, and that it also has a novel mechanism of alternative splicing of Hsf1 in response to hypoxia.
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Affiliation(s)
- Shinya Kawabe
- Department of Marine Bioscience, Faculty of Marine Bioscience, Fukui Prefectural University, Fukui, Japan
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Yue Z, Hao Q, Tang S, Bao E, Hartung J. Variation in Hsp90, HSF-1, and hsp90 mRNA expression in tissues of pigs exposed to different durations of transport. Livest Sci 2010. [DOI: 10.1016/j.livsci.2010.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Said Ali K, Ferencz A, Nemcsók J, Hermesz E. Expressions of heat shock and metallothionein genes in the heart of common carp (Cyprinus carpio): effects of temperature shock and heavy metal exposure. ACTA BIOLOGICA HUNGARICA 2010; 61:10-23. [PMID: 20194095 DOI: 10.1556/abiol.61.2010.1.2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Heat shock proteins (HSPs) and metallothioneins (MTs) play important roles in protection against environmental stressors. The present study analyzes and compares the regulation of heat shock ( hsp70, hsc70-1 and hsp90alpha ) and metallothionein (MT-1 and MT-2) genes in the heart of common carp, in response to elevated temperature, cold shock and exposure to several heavy metal ions (As 3+ , Cd 2+ and Cu 2+ ), in whole-animal experiments. Among these metals, arsenate proved to be the most potent inducer of the examined stress genes; the hsp90alpha and MT-1 mRNA levels were elevated 11- and 10-fold, respectively, after a 24-h exposure. In contrast, Cd 2+ at 10 mg/L had no impact on the expression of hsp90alpha , and the MT genes also proved to be rather insensitive to Cd 2+ treatment in the heart: only a 2-2.5-fold induction was observed in response to 10 mg/L Cd 2+ . Heat shock resulted in a transient induction of hsp70 (19-fold) and hsp90alpha (15-fold), while elevated temperature had no effect on the expression of the MTs. Direct cold shock induced hsp70 expression (14-fold), while the hsp90alpha (26-fold) and MT-2 (2-fold) expressions peaked after the recovery period following a direct cold shock. The five stress genes examined in this study exhibited a unique, tissue-specific basal expression pattern and a characteristic sensitivity to metal treatments and temperature shocks.
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Affiliation(s)
- K Said Ali
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Szeged, Szeged, Hungary
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Sonoda S, Tsumuki H. Characterization of alternatively spliced transcripts encoding heat shock transcription factor in cultured cells of the cabbage armyworm, Mamestra brassicae. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2010; 73:49-60. [PMID: 19750550 DOI: 10.1002/arch.20339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A gene encoding heat shock transcription factor (HSF) was cloned and sequenced from cultured cells of the cabbage armyworm, Mamestra brassicae. The cDNA potentially encoded a 699-aa protein, with a calculated molecular weight of 77.8 kDa. Deduced amino acid identities to HSFs from Aedes aegypti and Drosophila melanogaster were 36 and 34%, respectively. Analysis of the genomic DNA revealed eight exons and three optional exons: a, b, and c. Exon a contained a premature in-frame stop codon that would generate a truncated protein. When the cells were exposed to high temperature or cadmium, no particular alternative transcripts showed significant up- or down-regulated expression relative to the total amount of the transcripts. These results suggest that alternative splicing may not be a principal mechanism for regulation of M. brassicae HSF gene expression in response to heat shock and cadmium.
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Affiliation(s)
- Shoji Sonoda
- Research Institute for Bioresources, Okayama University, Kurashiki, Okayama, Japan.
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Colinet H, Lee SF, Hoffmann A. Temporal expression of heat shock genes during cold stress and recovery from chill coma in adult Drosophila melanogaster. FEBS J 2009; 277:174-85. [PMID: 19968716 DOI: 10.1111/j.1742-4658.2009.07470.x] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A common physiological response of organisms to environmental stresses is the increase in expression of heat shock proteins (Hsps). In insects, this process has been widely examined for heat stress, but the response to cold stress has been far less studied. In the present study, we focused on 11 Drosophila melanogaster Hsp genes during the stress exposure and recovery phases. The temporal gene expression of adults was analyzed during 9 h of cold stress at 0 degrees C and during 8 h of recovery at 25 degrees C. Increased expression of some, but not all, Hsp genes was elicited in response to cold stress. The transcriptional activity of Hsp genes was not modulated during the cold stress, and peaks of expression occurred during the recovery phase. On the basis of their response, we consider that Hsp60, Hsp67Ba and Hsc70-1 are not cold-inducible, whereas Hsp22, Hsp23, Hsp26, Hsp27, Hsp40, Hsp68, Hsp70Aa and Hsp83 are induced by cold. This study suggests the importance of the recovery phase for repairing chilling injuries, and highlights the need to further investigate the contributions of specific Hsp genes to thermal stress responses. Parallels are drawn between the stress response networks resulting from heat and cold stress.
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Affiliation(s)
- Hervé Colinet
- Unité d'Ecologie et de Biogéographie, Biodiversity Research Centre, Université Catholique de Louvain, Louvain-la-Neuve, Belgium.
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