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Glad HM, Tralamazza SM, Croll D. The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici. Microb Genom 2023; 9. [PMID: 37991492 DOI: 10.1099/mgen.0.001136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.
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Affiliation(s)
- Hanna M Glad
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Sabina Moser Tralamazza
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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2
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Francisco CS, McDonald BA, Palma-Guerrero J. A transcription factor and a phosphatase regulate temperature-dependent morphogenesis in the fungal plant pathogen Zymoseptoria tritici. Fungal Genet Biol 2023; 167:103811. [PMID: 37196910 DOI: 10.1016/j.fgb.2023.103811] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Naturally fluctuating temperatures provide a constant environmental stress that requires adaptation. Some fungal pathogens respond to heat stress by producing new morphotypes that maximize their overall fitness. The fungal wheat pathogen Zymoseptoria tritici responds to heat stress by switching from its yeast-like blastospore form to hyphae or chlamydospores. The regulatory mechanisms underlying this switch are unknown. Here, we demonstrate that a differential heat stress response is ubiquitous in Z. tritici populations around the world. We used QTL mapping to identify a single locus associated with the temperature-dependent morphogenesis and we found two genes, the transcription factor ZtMsr1 and the protein phosphatase ZtYvh1, regulating this mechanism. We find that ZtMsr1 regulates repression of hyphal growth and induces chlamydospore formation whereas ZtYvh1 is required for hyphal growth. We next showed that chlamydospore formation is a response to the intracellular osmotic stress generated by the heat stress. This intracellular stress stimulates the cell wall integrity (CWI) and high-osmolarity glycerol (HOG) MAPK pathways resulting in hyphal growth. If cell wall integrity is compromised, however, ZtMsr1 represses the hyphal development program and may induce the chlamydospore-inducing genes as a stress-response survival strategy. Taken together, these results suggest a novel mechanism through which morphological transitions are orchestrated in Z. tritici - a mechanism that may also be present in other pleomorphic fungi.
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Affiliation(s)
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, 8092 ETH Zürich, Switzerland
| | - Javier Palma-Guerrero
- Plant Pathology Group, Institute of Integrative Biology, 8092 ETH Zürich, Switzerland.
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3
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Qi H, Chen X, Luo S, Fan H, Guo J, Zhang X, Ke Y, Yang P, Yu F. Genome-Wide Identification and Characterization of Heat Shock Protein 20 Genes in Maize. Life (Basel) 2022; 12:life12091397. [PMID: 36143433 PMCID: PMC9505046 DOI: 10.3390/life12091397] [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: 08/21/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Maize is an important cereal crop worldwide and is sensitive to abiotic stresses in fluctuant environments that seriously affect its growth, yield, and quality. The small heat shock protein (HSP20) plays a crucial role in protecting plants from abiotic stress. However, little is known about HSP20 in maize (ZmHSP20). In this study, 44 ZmHSP20s were identified, which were unequally distributed over 10 chromosomes, and 6 pairs of ZmHSP20s were tandemly presented. The gene structure of ZmHSP20s was highly conserved, with 95% (42) of the genes having no more than one intron. The analysis of the cis-element in ZmHSP20s promoter demonstrated large amounts of elements related to hormonal and abiotic stress responses, including abscisic acid (ABA), high temperature, and hypoxia. The ZmHSP20s protein had more than two conserved motifs that were predictably localized in the cytoplasm, nucleus, endoplasmic reticulum, peroxisome, mitochondria, and plasma. Phylogenetic analysis using HSP20s in Arabidopsis, rice, maize, and Solanum tuberosum indicated that ZmHSP20s were classified into 11 categories, of which each category had unique subcellular localization. Approximately 80% (35) of ZmHSP20 were upregulated under heat stress at the maize seedling stage, whereas the opposite expression profiling of 10 genes under 37 and 48 °C was detected. A total of 20 genes were randomly selected to investigate their expression under treatments of ABA, gibberellin (GA), ethylene, low temperature, drought, and waterlogging, and the results displayed that more than half of these genes were downregulated while ZmHSP20-3, ZmHSP20-7, ZmHSP20-24, and ZmHSP20-44 were upregulated under 1 h treatment of ethylene. A yeast-one-hybrid experiment was conducted to analyze the binding of four heat stress transcription factors (ZmHSFs) with eight of the ZmHSP20s promoter sequences, in which ZmHSF3, ZmHSF13, and ZmHSF17 can bind to most of these selected ZmHSP20s promoters. Our results provided a valuable resource for studying HSP20s function and offering candidates for genetic improvement under abiotic stress.
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Affiliation(s)
- Huanhuan Qi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoke Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Sen Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Hongzeng Fan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jinghua Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Yinggen Ke
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Feng Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
- Correspondence:
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Characterization of curly branch of Gracilariopsis lemaneiformis (Rhodophyta) at morphological, physiological, and molecular levels. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Korotko U, Chwiałkowska K, Sańko-Sawczenko I, Kwasniewski M. DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22041555. [PMID: 33557095 PMCID: PMC7913789 DOI: 10.3390/ijms22041555] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific.
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Affiliation(s)
- Urszula Korotko
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Department of Genetics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
| | - Izabela Sańko-Sawczenko
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warszawa, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Correspondence:
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Ding Z, Fu L, Tie W, Yan Y, Wu C, Hu W, Zhang J. Extensive Post-Transcriptional Regulation Revealed by Transcriptomic and Proteomic Integrative Analysis in Cassava under Drought. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3521-3534. [PMID: 30830777 DOI: 10.1021/acs.jafc.9b00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cassava is a major tropical/subtropical food crop and its yield is greatly restrained by drought; however, the mechanism underlying the drought stress remains largely unknown. In this study, totally 1242 and 715 differentially expressed genes (DEGs), together with 237 and 307 differentially expressed proteins (DEPs), were respectively identified in cassava leaves and roots through RNA-seq and iTRAQ techniques. The majority of DEGs and DEPs were exclusively regulated at the mRNA and protein level, respectively, whereas only a few were commonly regulated, indicating the major involvement of post-transcriptional regulation under drought. Subsequently, the functions of these specifically or commonly regulated DEGs and DEPs were analyzed, and the post-transcriptional regulation of genes involved in heat shock protein, secondary metabolism biosynthesis, and hormone biosynthesis was extensively discussed. This is the first report on an integration of transcriptomic and proteomic analysis in cassava, and it provides new insights into the post-transcriptional regulation of cassava drought stress.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Lili Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
- Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology , Huazhong University of Science and Technology (HUST) , Wuhan 430074 , China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Jiaming Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
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7
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He L, Yu H, Dai Y, Wang Y. Analysis of genetic variations of heat shock proteins Hsp70 and Hsp90 in Isaria farinosa strains from the Yunnan province of China. Folia Microbiol (Praha) 2019; 64:521-534. [PMID: 30666590 DOI: 10.1007/s12223-018-00676-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/26/2018] [Indexed: 11/29/2022]
Abstract
In the present study, the cDNA sequences of Hsp70 and Hsp90 genes of Isaria farinosa (designated IFHSP70 and IFHSP90) were cloned and characterized using multiple techniques of molecular biology and bioinformatics. The genetic differentiation of the two genes was investigated among 10 geographically separated populations distributed in the Yunnan province. The complete sequence of the IFHSP70 cDNA had a length of 2158 bp, and contained an open reading frame (ORF) of 1962 bp, encoding a 71-kDa polypeptide comprising of 653 amino acids. IFHSP90 cDNA had a length of 2144 bp, and contained an ORF of 2103 bp, encoding a polypeptide of 79.23 kDa, comprising of 700 amino acids. The deduced amino acid sequences of IFHSP70 and IFHSP90 shared high sequence identities with other fungi. Fundamental information pertaining to the protein families, signatures, and conserved motifs of Hsp70 and Hsp90 were also identified. Analysis of molecular variances (AMOVA) from the Hsp70 and Hsp90 genes showed that the genetic variation within-population (83.26%, 83.08%) was greater than among the populations (16.74%, 16.92%). The values of nucleotide diversity (Pi), haplotype diversity (Hd), coefficient of genetic differentiation (Fst), and gene flow (Nm) were calculated. For Hsp70, Pi = 0.0425, Hd = 0.888, Fst = 0.167, Nm = 1.24; For Hsp90, Pi = 0.0420, Hd = 0.894, Fst = 0.169, and Nm = 1.22. These data indicated that the genetic differentiation among 10 different geographical populations of I. farinosa was limited. This study describes, for the first time, cloning, characterization and identification of Isaria farinosa Hsp70 and Hsp90 genes, and provides a preliminary basis for exploring the genetic structure of the genus Isaria using the sequences of Hsp70 and Hsp90 as molecular markers.
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Affiliation(s)
- Lu He
- Yunnan Herbal Laboratory, Institute of Herb Biotic Resources, School of Life Sciences, Yunnan University, Kunming, 650091, China.,Institute of Tropical Eco-agriculture, Yunnan Academy of Agriculture Science, Yuanmou, 651399, China.,International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China
| | - Hong Yu
- Yunnan Herbal Laboratory, Institute of Herb Biotic Resources, School of Life Sciences, Yunnan University, Kunming, 650091, China. .,International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China.
| | - Yongdong Dai
- Yunnan Herbal Laboratory, Institute of Herb Biotic Resources, School of Life Sciences, Yunnan University, Kunming, 650091, China.,International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China
| | - Yuanbing Wang
- Yunnan Herbal Laboratory, Institute of Herb Biotic Resources, School of Life Sciences, Yunnan University, Kunming, 650091, China.,International Joint Research Center for Sustainable Utilization of Cordyceps Bioresources in China and Southeast Asia, Yunnan University, Kunming, 650091, China.,Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co., Ltd., Kunming, 650106, China
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8
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Singh RK, Jaishankar J, Muthamilarasan M, Shweta S, Dangi A, Prasad M. Genome-wide analysis of heat shock proteins in C4 model, foxtail millet identifies potential candidates for crop improvement under abiotic stress. Sci Rep 2016; 6:32641. [PMID: 27586959 PMCID: PMC5009299 DOI: 10.1038/srep32641] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/10/2016] [Indexed: 11/12/2022] Open
Abstract
Heat shock proteins (HSPs) perform significant roles in conferring abiotic stress tolerance to crop plants. In view of this, HSPs and their encoding genes were extensively characterized in several plant species; however, understanding their structure, organization, evolution and expression profiling in a naturally stress tolerant crop is necessary to delineate their precise roles in stress-responsive molecular machinery. In this context, the present study has been performed in C4 panicoid model, foxtail millet, which resulted in identification of 20, 9, 27, 20 and 37 genes belonging to SiHSP100, SiHSP90, SiHSP70, SiHSP60 and SisHSP families, respectively. Comprehensive in silico characterization of these genes followed by their expression profiling in response to dehydration, heat, salinity and cold stresses in foxtail millet cultivars contrastingly differing in stress tolerance revealed significant upregulation of several genes in tolerant cultivar. SisHSP-27 showed substantial higher expression in response to heat stress in tolerant cultivar, and its over-expression in yeast system conferred tolerance to several abiotic stresses. Methylation analysis of SiHSP genes suggested that, in susceptible cultivar, higher levels of methylation might be the reason for reduced expression of these genes during stress. Altogether, the study provides novel clues on the role of HSPs in conferring stress tolerance.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Jananee Jaishankar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | | | - Shweta Shweta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Anand Dangi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi - 110067, India
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9
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Palma-Guerrero J, Torriani SFF, Zala M, Carter D, Courbot M, Rudd JJ, McDonald BA, Croll D. Comparative transcriptomic analyses of Zymoseptoria tritici strains show complex lifestyle transitions and intraspecific variability in transcription profiles. MOLECULAR PLANT PATHOLOGY 2016; 17:845-59. [PMID: 26610174 PMCID: PMC6638511 DOI: 10.1111/mpp.12333] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 05/03/2023]
Abstract
Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. The disease interaction is characterized by clearly defined temporal phases of infection, ultimately resulting in the death of host tissue. Zymoseptoria tritici is a highly polymorphic species with significant intraspecific variation in virulence profiles. We generated a deep transcriptomic sequencing dataset spanning the entire time course of an infection using a previously uncharacterized, highly virulent Z. tritici strain isolated from a Swiss wheat field. We found that seven clusters of gene transcription profiles explained the progression of the infection. The earliest highly up-regulated genes included chloroperoxidases, which may help the fungus cope with plant defences. The onset of necrotrophy was characterized by a concerted up-regulation of proteases, plant cell wall-degrading enzymes and lipases. Functions related to nutrition and growth characterized late necrotrophy and the transition to saprotrophic growth on dead plant tissue. We found that the peak up-regulation of genes essential for mating coincided with the necrotrophic phase. We performed an intraspecies comparative transcriptomics analysis using a comparable time course infection experiment of the genome reference isolate IPO323. Major components of the fungal infection transcriptome were conserved between the two strains. However, individual small, secreted proteins, proteases and cell wall-degrading enzymes showed strongly differentiated transcriptional profiles between isolates. Our analyses illustrate that successful STB infections involve complex transcriptomic remodelling to up-regulate distinct gene functions. Heterogeneity in transcriptomes among isolates may explain some of the considerable variation in virulence and host specialization found within the species.
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Affiliation(s)
- Javier Palma-Guerrero
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Stefano F F Torriani
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
- Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, Switzerland
| | - Marcello Zala
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Dee Carter
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Mikaël Courbot
- Syngenta Crop Protection AG, Schaffhauserstrasse, 4332, Stein, Switzerland
| | - Jason J Rudd
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
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10
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Heat shock response of thermophilic fungi: membrane lipids and soluble carbohydrates under elevated temperatures. Microbiology (Reading) 2016; 162:989-999. [DOI: 10.1099/mic.0.000279] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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11
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Simões J, Bezerra AR, Moura GR, Araújo H, Gut I, Bayes M, Santos MAS. The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons. Front Microbiol 2016; 7:401. [PMID: 27065968 PMCID: PMC4814463 DOI: 10.3389/fmicb.2016.00401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.
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Affiliation(s)
- João Simões
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Ana R Bezerra
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Gabriela R Moura
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Hugo Araújo
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
| | - Ivo Gut
- Centro Nacional de Análises Genómico, Parc Científic Barcelona, Spain
| | - Mónica Bayes
- Centro Nacional de Análises Genómico, Parc Científic Barcelona, Spain
| | - Manuel A S Santos
- Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal
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12
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Schmoll M, Dattenböck C, Carreras-Villaseñor N, Mendoza-Mendoza A, Tisch D, Alemán MI, Baker SE, Brown C, Cervantes-Badillo MG, Cetz-Chel J, Cristobal-Mondragon GR, Delaye L, Esquivel-Naranjo EU, Frischmann A, Gallardo-Negrete JDJ, García-Esquivel M, Gomez-Rodriguez EY, Greenwood DR, Hernández-Oñate M, Kruszewska JS, Lawry R, Mora-Montes HM, Muñoz-Centeno T, Nieto-Jacobo MF, Nogueira Lopez G, Olmedo-Monfil V, Osorio-Concepcion M, Piłsyk S, Pomraning KR, Rodriguez-Iglesias A, Rosales-Saavedra MT, Sánchez-Arreguín JA, Seidl-Seiboth V, Stewart A, Uresti-Rivera EE, Wang CL, Wang TF, Zeilinger S, Casas-Flores S, Herrera-Estrella A. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. Microbiol Mol Biol Rev 2016; 80:205-327. [PMID: 26864432 PMCID: PMC4771370 DOI: 10.1128/mmbr.00040-15] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genus Trichoderma contains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for "hot topic" research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism in T. reesei, T. atroviride, and T. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of each Trichoderma species discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved in N-linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma, and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.
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Affiliation(s)
- Monika Schmoll
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | - Christoph Dattenböck
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Doris Tisch
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Mario Ivan Alemán
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | - Scott E Baker
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher Brown
- University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand
| | | | - José Cetz-Chel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - Luis Delaye
- Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico
| | | | - Alexa Frischmann
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | - Monica García-Esquivel
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | | | - David R Greenwood
- The University of Auckland, School of Biological Sciences, Auckland, New Zealand
| | - Miguel Hernández-Oñate
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
| | - Joanna S Kruszewska
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Robert Lawry
- Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand
| | | | | | | | | | | | | | - Sebastian Piłsyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland
| | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aroa Rodriguez-Iglesias
- Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria
| | | | | | - Verena Seidl-Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | | | | | - Chih-Li Wang
- National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan
| | - Ting-Fang Wang
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan
| | - Susanne Zeilinger
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria
| | | | - Alfredo Herrera-Estrella
- LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico
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Fu L, Ding Z, Han B, Hu W, Li Y, Zhang J. Physiological Investigation and Transcriptome Analysis of Polyethylene Glycol (PEG)-Induced Dehydration Stress in Cassava. Int J Mol Sci 2016; 17:283. [PMID: 26927071 PMCID: PMC4813147 DOI: 10.3390/ijms17030283] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/28/2016] [Accepted: 02/15/2016] [Indexed: 12/02/2022] Open
Abstract
Cassava is an important tropical and sub-tropical root crop that is adapted to drought environment. However, severe drought stress significantly influences biomass accumulation and starchy root production. The mechanism underlying drought-tolerance remains obscure in cassava. In this study, changes of physiological characters and gene transcriptome profiles were investigated under dehydration stress simulated by polyethylene glycol (PEG) treatments. Five traits, including peroxidase (POD) activity, proline content, malondialdehyde (MDA), soluble sugar and soluble protein, were all dramatically induced in response to PEG treatment. RNA-seq analysis revealed a gradient decrease of differentially expressed (DE) gene number in tissues from bottom to top of a plant, suggesting that cassava root has a quicker response and more induced/depressed DE genes than leaves in response to drought. Overall, dynamic changes of gene expression profiles in cassava root and leaves were uncovered: genes related to glycolysis, abscisic acid and ethylene biosynthesis, lipid metabolism, protein degradation, and second metabolism of flavonoids were significantly induced, while genes associated with cell cycle/organization, cell wall synthesis and degradation, DNA synthesis and chromatin structure, protein synthesis, light reaction of photosynthesis, gibberelin pathways and abiotic stress were greatly depressed. Finally, novel pathways in ABA-dependent and ABA-independent regulatory networks underlying PEG-induced dehydration response in cassava were detected, and the RNA-Seq results of a subset of fifteen genes were confirmed by real-time PCR. The findings will improve our understanding of the mechanism related to dehydration stress-tolerance in cassava and will provide useful candidate genes for breeding of cassava varieties better adapted to drought environment.
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Affiliation(s)
- Lili Fu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Wei Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Yajun Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou 571101, China.
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Petti C, Nair M, DeBolt S. The involvement of J-protein AtDjC17 in root development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2014; 5:532. [PMID: 25339971 PMCID: PMC4189540 DOI: 10.3389/fpls.2014.00532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/18/2014] [Indexed: 05/29/2023]
Abstract
In a screen for root hair morphogenesis mutants in Arabidopsis thaliana L. we identified a T-DNA insertion within a type III J-protein AtDjC17 caused altered root hair development and reduced hair length. Root hairs were observed to develop from trichoblast and atrichoblast cell files in both Atdjc17 and 35S::AtDJC17. Localization of gene expression in the root using transgenic plants expressing proAtDjC17::GUS revealed constitutive expression in stele cells. No AtDJC17 expression was observed in epidermal, endodermal, or cortical layers. To explore the contrast between gene expression in the stele and epidermal phenotype, hand cut transverse sections of Atdjc17 roots were examined showing that the endodermal and cortical cell layers displayed increased anticlinal cell divisions. Aberrant cortical cell division in Atdjc17 is proposed as causal in ectopic root hair formation via the positional cue requirement that exists between cortical and epidermal cell in hair cell fate determination. Results indicate a requirement for AtDJC17 in position-dependent cell fate determination and illustrate an intriguing requirement for molecular co-chaperone activity during root development.
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Affiliation(s)
| | | | - Seth DeBolt
- Department of Horticulture, University of KentuckyLexington, KY, USA
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15
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Pradhan S, Bandhiwal N, Shah N, Kant C, Gaur R, Bhatia S. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds. FRONTIERS IN PLANT SCIENCE 2014; 5:698. [PMID: 25566273 PMCID: PMC4267183 DOI: 10.3389/fpls.2014.00698] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/24/2014] [Indexed: 05/20/2023]
Abstract
Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.
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Affiliation(s)
| | | | | | | | | | - Sabhyata Bhatia
- *Correspondence: Sabhyata Bhatia, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India e-mail:
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Behr M, Serchi T, Cocco E, Guignard C, Sergeant K, Renaut J, Evers D. Description of the mechanisms underlying geosmin production in Penicillium expansum using proteomics. J Proteomics 2013; 96:13-28. [PMID: 24189443 DOI: 10.1016/j.jprot.2013.10.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 09/30/2013] [Accepted: 10/24/2013] [Indexed: 11/25/2022]
Abstract
UNLABELLED A 2D-DIGE proteomics experiment was performed to describe the mechanism underlying the production of geosmin, an earthy-smelling sesquiterpene which spoils wine, produced by Penicillium expansum. The strains were identified by sequencing of the ITS and beta-tubulin regions. This study was based on a selection of four strains showing different levels of geosmin production, assessed by GC-MS/MS. The proteomics study revealed the differential abundance of 107 spots between the different strains; these were picked and submitted to MALDI-TOF-TOF MS analysis for identification. They belonged to the functional categories of protein metabolism, redox homeostasis, metabolic processes (glycolysis, ATP production), cell cycle and cell signalling pathways. From these data, an implication of oxidative stress in geosmin production may be hypothesized. Moreover, the differential abundance of some glycolytic enzymes may explain the different patterns of geosmin biosynthesis. This study provides data for the characterisation of the mechanism and the regulation of the production of this off-flavour, which are so far not described in filamentous fungi. BIOLOGICAL SIGNIFICANCE Green mould on grapes, caused by P. expansum may be at the origin of off-flavours in wine. These are characterized by earthy-mouldy smells and are due to the presence of the compound geosmin. This work aims at describing how geosmin is produced by P. expansum. This knowledge is of use for the research community on grapes for understanding why these off-flavours occasionally occur in vintages.
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Affiliation(s)
- Marc Behr
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Tommaso Serchi
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Emmanuelle Cocco
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Cédric Guignard
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Kjell Sergeant
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Jenny Renaut
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Danièle Evers
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
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Vosloo D, Vosloo A, Morillion EJ, Samuels JN, Sommer P. Metabolic readjustment in juvenile South African abalone (Haliotis midae) acclimated to combinations of temperature and dissolved oxygen levels. J Therm Biol 2013. [DOI: 10.1016/j.jtherbio.2013.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Al-Whaibi MH. Plant heat-shock proteins: A mini review. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2011. [PMID: 0 DOI: 10.1016/j.jksus.2010.06.022] [Citation(s) in RCA: 229] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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Vosloo D, Vosloo A. Response of cold-acclimated, farmed South African abalone (Haliotis midae) to short-term and long-term changes in temperature. J Therm Biol 2010. [DOI: 10.1016/j.jtherbio.2010.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Nicholls S, Leach MD, Priest CL, Brown AJP. Role of the heat shock transcription factor, Hsf1, in a major fungal pathogen that is obligately associated with warm-blooded animals. Mol Microbiol 2009; 74:844-61. [PMID: 19818013 PMCID: PMC3675641 DOI: 10.1111/j.1365-2958.2009.06883.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
All organisms have evolved mechanisms that protect them against environmental stress. The major fungal pathogen of humans, Candida albicans, has evolved robust stress responses that protect it against human immune defences and promote its pathogenicity. However, C. albicans is unlikely to be exposed to heat shock as it is obligatorily associated with warm-blooded animals. Therefore, we examined the role of the heat shock transcription factor (Hsf1) in this pathogen. We show that C. albicans expresses an evolutionarily conserved Hsf1 (orf19.4775) that is phosphorylated in response to heat shock, induces transcription via the heat shock element (HSE), contributes to the global transcriptional response to heat shock, and is essential for viability. Why has Hsf1 been conserved in this obligate animal saprophyte? We reasoned that Hsf1 might contribute to medically relevant stress responses. However, this is not the case, as an Hsf1-specific HSE-lacZ reporter is not activated by oxidative, osmotic, weak acid or pH stress. Rather, Hsf1 is required for the expression of essential chaperones in the absence of heat shock (e.g. Hsp104, Hsp90, Hsp70). Furthermore, Hsf1 regulates the expression of HSE-containing genes in response to growth temperature in C. albicans. Therefore, the main role of Hsf1 in this pathogen might be the homeostatic modulation of chaperone levels in response to growth temperature, rather than the activation of acute responses to sudden thermal transitions.
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Affiliation(s)
- Susan Nicholls
- Aberdeen Fungal Group, School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Aberdeen AB25 2ZD, UK
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