1
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Wagner A, Schosserer M. The epitranscriptome in ageing and stress resistance: A systematic review. Ageing Res Rev 2022; 81:101700. [PMID: 35908668 DOI: 10.1016/j.arr.2022.101700] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/15/2022] [Accepted: 07/25/2022] [Indexed: 01/31/2023]
Abstract
Modifications of RNA, collectively called the "epitranscriptome", might provide novel biomarkers and innovative targets for interventions in geroscience but are just beginning to be studied in the context of ageing and stress resistance. RNA modifications modulate gene expression by affecting translation initiation and speed, miRNA binding, RNA stability, and RNA degradation. Nonetheless, the precise underlying molecular mechanisms and physiological consequences of most alterations of the epitranscriptome are still only poorly understood. We here systematically review different types of modifications of rRNA, tRNA and mRNA, the methodology to analyze them, current challenges in the field, and human disease associations. Furthermore, we compiled evidence for a connection between individual enzymes, which install RNA modifications, and lifespan in yeast, worm and fly. We also included resistance to different stressors and competitive fitness as search criteria for genes potentially relevant to ageing. Promising candidates identified by this approach include RCM1/NSUN5, RRP8, and F33A8.4/ZCCHC4 that introduce base methylations in rRNA, the methyltransferases DNMT2 and TRM9/ALKBH8, as well as factors involved in the thiolation or A to I editing in tRNA, and finally the m6A machinery for mRNA.
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Affiliation(s)
- Anja Wagner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Schosserer
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria; Austrian Cluster for Tissue Regeneration, Vienna, Austria.
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2
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Wu L, Lyu Y, Wu P, Luo T, Zeng J, Shi T, Zhou J, Yu Y, Lu H. Meiosis-Based Laboratory Evolution of the Thermal Tolerance in Kluyveromyces marxianus. Front Bioeng Biotechnol 2022; 9:799756. [PMID: 35087802 PMCID: PMC8786734 DOI: 10.3389/fbioe.2021.799756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
Kluyveromyces marxianus is the fastest-growing eukaryote and a promising host for producing bioethanol and heterologous proteins. To perform a laboratory evolution of thermal tolerance in K. marxianus, diploid, triploid and tetraploid strains were constructed, respectively. Considering the genetic diversity caused by genetic recombination in meiosis, we established an iterative cycle of “diploid/polyploid - meiosis - selection of spores at high temperature” to screen thermotolerant strains. Results showed that the evolution of thermal tolerance in diploid strain was more efficient than that in triploid and tetraploid strains. The thermal tolerance of the progenies of diploid and triploid strains after a two-round screen was significantly improved than that after a one-round screen, while the thermal tolerance of the progenies after the one-round screen was better than that of the initial strain. After a two-round screen, the maximum tolerable temperature of Dip2-8, a progeny of diploid strain, was 3°C higher than that of the original strain. Whole-genome sequencing revealed nonsense mutations of PSR1 and PDE2 in the thermotolerant progenies. Deletion of either PSR1 or PDE2 in the original strain improved thermotolerance and two deletions displayed additive effects, suggesting PSR1 and PDE2 negatively regulated the thermotolerance of K. marxianus in parallel pathways. Therefore, the iterative cycle of “meiosis - spore screening” developed in this study provides an efficient way to perform the laboratory evolution of heat resistance in yeast.
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Affiliation(s)
- Li Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yilin Lyu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Pingping Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Tongyu Luo
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Junyuan Zeng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- *Correspondence: Yao Yu, ; Hong Lu,
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
- *Correspondence: Yao Yu, ; Hong Lu,
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3
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Vallejo B, Peltier E, Garrigós V, Matallana E, Marullo P, Aranda A. Role of Saccharomyces cerevisiae Nutrient Signaling Pathways During Winemaking: A Phenomics Approach. Front Bioeng Biotechnol 2020; 8:853. [PMID: 32793580 PMCID: PMC7387434 DOI: 10.3389/fbioe.2020.00853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/02/2020] [Indexed: 02/03/2023] Open
Abstract
The ability of the yeast Saccharomyces cerevisiae to adapt to the changing environment of industrial processes lies in the activation and coordination of many molecular pathways. The most relevant ones are nutrient signaling pathways because they control growth and stress response mechanisms as a result of nutrient availability or scarcity and, therefore, leave an ample margin to improve yeast biotechnological performance. A standardized grape juice fermentation assay allowed the analysis of mutants for different elements of many nutrient signaling pathways under different conditions (low/high nitrogen and different oxygenation levels) to allow genetic-environment interactions to be analyzed. The results indicate that the cAMP-dependent PKA pathway is the most relevant regardless of fermentation conditions, while mutations on TOR pathways display an effect that depends on nitrogen availability. The production of metabolites of interest, such as glycerol, acetic acid and pyruvate, is controlled in a coordinated manner by the contribution of several components of different pathways. Ras GTPase Ras2, a stimulator of cAMP production, is a key factor for achieving fermentation, and is also relevant for sensing nitrogen availability. Increasing cAMP concentrations by deleting an enzyme used for its degradation, phosphodiesterase Pde2, proved a good way to increase fermentation kinetics, and offered keys for biotechnological improvement. Surprisingly glucose repression protein kinase Snf1 and Nitrogen Catabolite Repression transcription factor Gln3 are relevant in fermentation, even in the absence of starvation. Gln3 proved essential for respiration in several genetic backgrounds, and its presence is required to achieve full glucose de-repression. Therefore, most pathways sense different types of nutrients and only their coordinated action can ensure successful wine fermentation.
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Affiliation(s)
- Beatriz Vallejo
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Emilien Peltier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Strasbourg, France.,ISVV UR Oenology, INRAE, Bordeaux INP, University of Bordeaux, Bordeaux, France.,Biolaffort, Bordeaux, France
| | - Victor Garrigós
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Emilia Matallana
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Philippe Marullo
- ISVV UR Oenology, INRAE, Bordeaux INP, University of Bordeaux, Bordeaux, France.,Biolaffort, Bordeaux, France
| | - Agustín Aranda
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
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4
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Li X, Liu Y, Tan X, Li D, Yang X, Zhang X, Zhang D. The high-affinity phosphodiesterase PcPdeH is involved in the polarized growth and pathogenicity of Phytophthora capsici. Fungal Biol 2020; 124:164-173. [PMID: 32220377 DOI: 10.1016/j.funbio.2020.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 01/04/2023]
Abstract
The cAMP signaling pathway has been shown to be important in controlling morphological changes and pathogenicity in plant pathogens. In the present study, we identified PcPdeH, a gene encoding a high-affinity phosphodiesterase (PDE), which is a key regulator of the cAMP signaling pathway. To elucidate the function of PcPdeH, PcPdeH-knockout mutants were obtained using a type II CRISPR/Cas9 system in Phytophthora capsici. The knockout transformants of PcPdeH showed vegetative growth defects and abnormal cyst germination. Infection assays indicated that compared with the wild type, PcPdeH-knockout mutants showed significantly reduced virulence on pepper and tobacco leaves and exhibited increased (1.5-2-fold) cAMP levels relative to the wild-type and CK strains. Based on these phenotypic features, we propose that PcPdeH is crucial for vegetative growth, cyst germination and pathogenicity in P. capsici.
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Affiliation(s)
- X Li
- Longping Branch, Graduate College, Hunan University, Changsha, 410125, China; Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Yong Liu
- Longping Branch, Graduate College, Hunan University, Changsha, 410125, China; Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Xinqiu Tan
- Longping Branch, Graduate College, Hunan University, Changsha, 410125, China; Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Delong Li
- College of Plant Health and Medicine, The Key Laboratory of Integrated Crop Pest Management of Shandong Province, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Xinyu Yang
- Shenyang Agricultural University, Plant Protection College, Shenyang, 110866, China.
| | - Xin Zhang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Deyong Zhang
- Longping Branch, Graduate College, Hunan University, Changsha, 410125, China; Hunan Plant Protection Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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5
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Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis. Int J Mol Sci 2019; 20:ijms20133321. [PMID: 31284545 PMCID: PMC6651063 DOI: 10.3390/ijms20133321] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 06/30/2019] [Accepted: 07/04/2019] [Indexed: 01/08/2023] Open
Abstract
Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the related genes in response to heat stress. In this work, some physiological parameter changes of young leaves under short-term heat stress were detected. Furthermore, we acquired 1802 differentially expressed mRNAs (including encoding some heat shock proteins, heat shock factor and heat shock-related transcription factors), 169 differentially expressed lncRNAs and three differentially expressed circRNAs (novel_circ_0000265, novel_circ_0000325 and novel_circ_0000315) through strand-specific RNA sequencing technology. We also found 10 differentially expressed miRNAs (ath-miR159b-3p, athmiR159c, ath-miR398a-3p, athmiR398b-3p, ath-miR165a-5p, ath-miR169g-3p, novel_86, novel_107, novel_21 and ath-miR171b-3p) by small RNA sequencing technology. Through function prediction and enrichment analysis, our results suggested that the significantly possible pathways/complexes related to heat stress in radish leaves were circadian rhythm-plant, photosynthesis-antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, arginine and proline metabolism, oxidative phosphorylation, peroxisome and plant hormone signal transduction. Besides, we identified one lncRNA-miRNA-mRNAs combination responsive to heat stress. These results will be helpful for further illustration of molecular regulation networks of how radish responds to heat stress.
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6
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Liu PT, Yu KJ, Li YT, Duan CQ, Yan GL. The content of linoleic acid in grape must influences the aromatic effect of branched-chain amino acids addition on red wine. Food Res Int 2018; 114:214-222. [DOI: 10.1016/j.foodres.2018.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/26/2018] [Accepted: 08/03/2018] [Indexed: 11/28/2022]
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7
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Yao Z, Delorme-Axford E, Backues SK, Klionsky DJ. Atg41/Icy2 regulates autophagosome formation. Autophagy 2016; 11:2288-99. [PMID: 26565778 DOI: 10.1080/15548627.2015.1107692] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Macroautophagy (hereafter autophagy) is one of the major degradation systems in eukaryotic cells, and its dysfunction may result in diseases ranging from neurodegeneration to cancer. Although most of the autophagy-related (Atg) proteins that function in this pathway were first identified in yeast, many were subsequently shown to have homologs in higher eukaryotes including humans, and the overall mechanism of autophagy is highly conserved. The most prominent feature of autophagy is the formation of a double-membrane sequestering compartment, the phagophore; this transient organelle surrounds part of the cytoplasm and matures into an autophagosome, which subsequently fuses with the vacuole or lysosome to allow degradation of the cargo. Much attention has focused on the process involved in phagophore nucleation and expansion, but many questions remain. Here, we identified the yeast protein Icy2, which we now name Atg41, as playing a role in autophagosome formation. Atg41 interacts with the transmembrane protein Atg9, a key component involved in autophagosome biogenesis, and both proteins display a similar localization profile. Under autophagy-inducing conditions the expression level of Atg41 increases dramatically and is regulated by the transcription factor Gcn4. This work provides further insight into the mechanism of Atg9 function and the dynamics of sequestering membrane formation during autophagy.
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Affiliation(s)
- Zhiyuan Yao
- a Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology ; University of Michigan ; Ann Arbor , MI USA
| | - Elizabeth Delorme-Axford
- a Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology ; University of Michigan ; Ann Arbor , MI USA
| | - Steven K Backues
- b Department of Chemistry ; Eastern Michigan University ; Ypsilanti , MI USA
| | - Daniel J Klionsky
- a Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology ; University of Michigan ; Ann Arbor , MI USA
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8
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Wallace-Salinas V, Brink DP, Ahrén D, Gorwa-Grauslund MF. Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. BMC Genomics 2015; 16:514. [PMID: 26156140 PMCID: PMC4496855 DOI: 10.1186/s12864-015-1737-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/29/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved industrial Saccharomyces cerevisiae strain ISO12 that had acquired improved tolerance to grow and ferment in the presence of lignocellulose-derived inhibitors at high temperature (39 °C). In the current study, we used comparative genomics to uncover the extent of the genomic alterations that occurred during the evolution process and investigated possible associations between the mutations and the phenotypic traits in ISO12. RESULTS Through whole-genome sequencing and variant calling we identified a high number of strain-unique SNPs and INDELs in both ISO12 and the parental strain Ethanol Red. The variants were predicted to have 760 non-synonymous effects in both strains combined and were significantly enriched in Gene Ontology terms related to cell periphery, membranes and cell wall. Eleven genes, including MTL1, FLO9/FLO11, and CYC3 were found to be under positive selection in ISO12. Additionally, the FLO genes exhibited changes in copy number, and the alterations to this gene family were correlated with experimental results of multicellularity and invasive growth in the adapted strain. An independent lipidomic analysis revealed further differences between the strains in the content of nine lipid species. Finally, ISO12 displayed improved viability in undiluted spruce hydrolysate that was unrelated to reduction of inhibitors and changes in cell wall integrity, as shown by HPLC and lyticase assays. CONCLUSIONS Together, the results of the sequence comparison and the physiological characterisations indicate that cell-periphery proteins (e.g. extracellular sensors such as MTL1) and peripheral lipids/membranes are important evolutionary targets in the process of adaptation to the combined stresses. The capacity of ISO12 to develop complex colony formation also revealed multicellularity as a possible evolutionary strategy to improve competitiveness and tolerance to environmental stresses (also reflected by the FLO genes). Although a panel of altered genes with high relevance to the novel phenotype was detected, this study also demonstrates that the observed long-term molecular effects of thermal and inhibitor stress have polygenetic basis.
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Affiliation(s)
- Valeria Wallace-Salinas
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, Lund, SE-22100, Sweden.
| | - Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, Lund, SE-22100, Sweden.
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, Lund, Sweden.
| | - Marie F Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, Lund, SE-22100, Sweden.
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9
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MacGurn JA. Garbage on, garbage off: new insights into plasma membrane protein quality control. Curr Opin Cell Biol 2014; 29:92-8. [PMID: 24908345 DOI: 10.1016/j.ceb.2014.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 04/10/2014] [Accepted: 05/10/2014] [Indexed: 01/22/2023]
Abstract
Maintenance of cellular protein quality - by restoring misfolded proteins to their native state and by targeting terminally misfolded or damaged proteins for degradation - is a critical function of all cells. To ensure protein quality, cells have evolved various organelle-specific quality control mechanisms responsible for recognizing and responding to misfolded proteins at different subcellular locations of the cell. Recently, several publications have begun to elucidate mechanisms of quality control that operate at the plasma membrane (PM), recognizing misfolded PM proteins and targeting their endocytic trafficking and lysosomal degradation. Here, I discuss these recent developments in our understanding of PM quality control mechanisms and how they relate to global protein quality control strategies in the cell.
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Affiliation(s)
- Jason A MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232-8240, USA.
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10
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Zakrzewska A, van Eikenhorst G, Burggraaff JEC, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ. Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness. Mol Biol Cell 2011; 22:4435-46. [PMID: 21965291 PMCID: PMC3216668 DOI: 10.1091/mbc.e10-08-0721] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A genome-wide analysis of the acquisition of stress cross-tolerance shows that reduction of growth rate is an important determinant of severe stress survival. Cellular functions important for the coupling of growth rate to stress resistance are identified, as are those required for cross-tolerance acquisition independent of growth rate reduction. All organisms have evolved to cope with changes in environmental conditions, ensuring the optimal combination of proliferation and survival. In yeast, exposure to a mild stress leads to an increased tolerance for other stresses. This suggests that yeast uses information from the environment to prepare for future threats. We used the yeast knockout collection to systematically investigate the genes and functions involved in severe stress survival and in the acquisition of stress (cross-) tolerance. Besides genes and functions relevant for survival of heat, acid, and oxidative stress, we found an inverse correlation between mutant growth rate and stress survival. Using chemostat cultures, we confirmed that growth rate governs stress tolerance, with higher growth efficiency at low growth rates liberating the energy for these investments. Cellular functions required for stress tolerance acquisition, independent of the reduction in growth rate, were involved in vesicular transport, the Rpd3 histone deacetylase complex, and the mitotic cell cycle. Stress resistance and acquired stress tolerance in Saccharomyces cerevisiae are governed by a combination of stress-specific and general processes. The reduction of growth rate, irrespective of the cause of this reduction, leads to redistribution of resources toward stress tolerance functions, thus preparing the cells for impending change.
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Affiliation(s)
- Anna Zakrzewska
- Molecular Biology and Microbial Food Safety, University of Amsterdam, 1098 XH Amsterdam, Netherlands
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11
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A shift to 50°C provokes death in distinct ways for glucose- and oleate-grown cells of Yarrowia lipolytica. Appl Microbiol Biotechnol 2011; 93:2125-34. [DOI: 10.1007/s00253-011-3537-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 07/22/2011] [Accepted: 08/05/2011] [Indexed: 01/04/2023]
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12
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Albrecht D, Kniemeyer O, Mech F, Gunzer M, Brakhage A, Guthke R. On the way toward systems biology of Aspergillus fumigatus infection. Int J Med Microbiol 2011; 301:453-9. [DOI: 10.1016/j.ijmm.2011.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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13
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Zhang H, Liu K, Zhang X, Tang W, Wang J, Guo M, Zhao Q, Zheng X, Wang P, Zhang Z. Two phosphodiesterase genes, PDEL and PDEH, regulate development and pathogenicity by modulating intracellular cyclic AMP levels in Magnaporthe oryzae. PLoS One 2011; 6:e17241. [PMID: 21386978 PMCID: PMC3046207 DOI: 10.1371/journal.pone.0017241] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Accepted: 01/22/2011] [Indexed: 01/02/2023] Open
Abstract
Cyclic AMP (cAMP) signaling plays an important role in regulating multiple cellular responses, such as growth, morphogenesis, and/or pathogenicity of eukaryotic organisms such as fungi. As a second messenger, cAMP is important in the activation of downstream effector molecules. The balance of intracellular cAMP levels depends on biosynthesis by adenylyl cyclases (ACs) and hydrolysis by cAMP phosphodiesterases (PDEases). The rice blast fungus Magnaporthe oryzae contains a high-affinity (PdeH/Pde2) and a low-affinity (PdeL/Pde1) PDEases, and a previous study showed that PdeH has a major role in asexual differentiation and pathogenicity. Here, we show that PdeL is required for asexual development and conidial morphology, and it also plays a minor role in regulating cAMP signaling. This is in contrast to PdeH whose mutation resulted in major defects in conidial morphology, cell wall integrity, and surface hydrophobicity, as well as a significant reduction in pathogenicity. Consistent with both PdeH and PdeL functioning in cAMP signaling, disruption of PDEH only partially rescued the mutant phenotype of ΔmagB and Δpka1. Further studies suggest that PdeH might function through a feedback mechanism to regulate the expression of pathogenicity factor Mpg1 during surface hydrophobicity and pathogenic development. Moreover, microarray data revealed new insights into the underlying cAMP regulatory mechanisms that may help to identify potential pathogenicity factors for the development of new disease management strategies.
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Affiliation(s)
- Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Kaiyue Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Xing Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Wei Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Jiansheng Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Min Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Qian Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
| | - Ping Wang
- Department of Pediatrics and the Research Institute for Children, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing, China
- * E-mail:
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Aloisi G, Silvano E, Rossi M, Millan MJ, Maggio R. Differential induction of adenylyl cyclase supersensitivity by antiparkinson drugs acting as agonists at dopamine D1/D2/D3 receptors vs D2/D3 receptors only: parallel observations from co-transfected human and native cerebral receptors. Neuropharmacology 2010; 60:439-45. [PMID: 21035472 DOI: 10.1016/j.neuropharm.2010.10.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/14/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
Abstract
Though there is evidence that sustained exposure of dopamine (DA) receptors to agonists can elicit a supersensitivity of adenylyl cyclase (AC), little is known about the pharmacological characteristics of this phenomenon, and possible interrelationships amongst DA receptor subtypes have not been examined. In cells co-transfected with D(1) plus D(2), or D(1) plus D(3), receptors, which are known to physically and functionally interact, long-term exposure to quinpirole, pramipexole and ropinirole (which possess negligible affinities for D(1) sites) elicited supersensitivity of D(1) receptor-activated AC. By contrast, D(2)/D(3) receptor agonists that also act as D(1) receptor agonists, bromocriptine, lisuride, cabergoline, apomorphine and DA itself, did not elicit supersensitivity. Interestingly, AC supersensitivity was also observed in the nucleus accumbens of mice pretreated with twice-daily pramipexole and quinpirole, whereas no change was seen either with lisuride or with the DA precursor, L-DOPA. Thus, AC supersensitivity is elicited by the sustained exposure of cloned human and native mouse populations of dopaminergic receptors, to D(2)/D(3) but not D(1)/D(2)/D(3) agonists. These observations may be related to the exacerbation of gambling in Parkinson's disease that is provoked by antiparkinson agents acting as selective D(2)/D(3) receptor agonists, notably pramipexole.
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Affiliation(s)
- Gabriella Aloisi
- Department of Experimental Medicine, University of L'Aquila, Via Vetoio Coppito 2, 67100 L'Aquila, Italy
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Morsy MR, Oswald J, He J, Tang Y, Roossinck MJ. Teasing apart a three-way symbiosis: transcriptome analyses of Curvularia protuberata in response to viral infection and heat stress. Biochem Biophys Res Commun 2010; 401:225-30. [PMID: 20849822 DOI: 10.1016/j.bbrc.2010.09.034] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 09/08/2010] [Indexed: 11/26/2022]
Abstract
The fungus Curvularia protuberata carries a dsRNA virus, Curvularia thermal tolerance virus, and develops a three-way symbiotic relationship with plants to enable their survival in extreme soil temperatures. To learn about the genome of C. protuberata and possible mechanisms of heat tolerance a collection of expressed sequence tags (ESTs) were developed from two subtracted cDNA libraries from mycelial cultures grown under control and heat stress conditions. We analyzed 4207 ESTs that were assembled into 1926 unique transcripts. Of the unique transcripts, 1347 (70%) had sequence similarity with GenBank entries using BLASTX while the rest represented unknown proteins with no matches in the databases. The majority of ESTs with known similarities were homologues to fungal genes. The EST collection presents a rich source of heat stress and viral induced genes of a fungal endophyte that is involved in a symbiotic relationship with plants. Expression profile analyses of some candidate genes suggest possible involvement of osmoprotectants such as trehalose, glycine betaine, and taurine in the heat stress response. The fungal pigment melanin, and heat shock proteins also may be involved in the thermotolerance of C. protuberata in culture. The results assist in understanding the molecular basis of thermotolerance of the three-way symbiosis. Further studies will confirm or refute the involvement of these pathways in stress tolerance.
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Affiliation(s)
- Mustafa R Morsy
- The Samuel Robert Noble Foundation, Plant Biology Division, Ardmore, OK 73402, United States.
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16
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Ramanujam R, Naqvi NI. PdeH, a high-affinity cAMP phosphodiesterase, is a key regulator of asexual and pathogenic differentiation in Magnaporthe oryzae. PLoS Pathog 2010; 6:e1000897. [PMID: 20463817 PMCID: PMC2865543 DOI: 10.1371/journal.ppat.1000897] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 04/05/2010] [Indexed: 02/07/2023] Open
Abstract
Cyclic AMP-dependent pathways mediate the communication between external stimuli and the intracellular signaling machinery, thereby influencing important aspects of cellular growth, morphogenesis and differentiation. Crucial to proper function and robustness of these signaling cascades is the strict regulation and maintenance of intracellular levels of cAMP through a fine balance between biosynthesis (by adenylate cyclases) and hydrolysis (by cAMP phosphodiesterases). We functionally characterized gene-deletion mutants of a high-affinity (PdeH) and a low-affinity (PdeL) cAMP phosphodiesterase in order to gain insights into the spatial and temporal regulation of cAMP signaling in the rice-blast fungus Magnaporthe oryzae. In contrast to the expendable PdeL function, the PdeH activity was found to be a key regulator of asexual and pathogenic development in M. oryzae. Loss of PdeH led to increased accumulation of intracellular cAMP during vegetative and infectious growth. Furthermore, the pdeHDelta showed enhanced conidiation (2-3 fold), precocious appressorial development, loss of surface dependency during pathogenesis, and highly reduced in planta growth and host colonization. A pdeHDelta pdeLDelta mutant showed reduced conidiation, exhibited dramatically increased (approximately 10 fold) cAMP levels relative to the wild type, and was completely defective in virulence. Exogenous addition of 8-Br-cAMP to the wild type simulated the pdeHDelta defects in conidiation as well as in planta growth and development. While a fully functional GFP-PdeH was cytosolic but associated dynamically with the plasma membrane and vesicular compartments, the GFP-PdeL localized predominantly to the nucleus. Based on data from cAMP measurements and Real-Time RTPCR, we uncover a PdeH-dependent biphasic regulation of cAMP levels during early and late stages of appressorial development in M. oryzae. We propose that PdeH-mediated sustenance and dynamic regulation of cAMP signaling during M. oryzae development is crucial for successful establishment and spread of the blast disease in rice.
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Affiliation(s)
- Ravikrishna Ramanujam
- Fungal Patho-Biology Group, Temasek Life Sciences Laboratory, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Naweed I. Naqvi
- Fungal Patho-Biology Group, Temasek Life Sciences Laboratory, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail:
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Albrecht D, Guthke R, Brakhage AA, Kniemeyer O. Integrative analysis of the heat shock response in Aspergillus fumigatus. BMC Genomics 2010; 11:32. [PMID: 20074381 PMCID: PMC2820008 DOI: 10.1186/1471-2164-11-32] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 01/15/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Aspergillus fumigatus is a thermotolerant human-pathogenic mold and the most common cause of invasive aspergillosis (IA) in immunocompromised patients. Its predominance is based on several factors most of which are still unknown. The thermotolerance of A. fumigatus is one of the traits which have been assigned to pathogenicity. It allows the fungus to grow at temperatures up to and above that of a fevered human host. To elucidate the mechanisms of heat resistance, we analyzed the change of the A. fumigatus proteome during a temperature shift from 30 degrees C to 48 degrees C by 2D-fluorescence difference gel electrophoresis (DIGE). To improve 2D gel image analysis results, protein spot quantitation was optimized by missing value imputation and normalization. Differentially regulated proteins were compared to previously published transcriptome data of A. fumigatus. The study was augmented by bioinformatical analysis of transcription factor binding sites (TFBSs) in the promoter region of genes whose corresponding proteins were differentially regulated upon heat shock. RESULTS 91 differentially regulated protein spots, representing 64 different proteins, were identified by mass spectrometry (MS). They showed a continuous up-, down- or an oscillating regulation. Many of the identified proteins were involved in protein folding (chaperones), oxidative stress response, signal transduction, transcription, translation, carbohydrate and nitrogen metabolism. A correlation between alteration of transcript levels and corresponding proteins was detected for half of the differentially regulated proteins. Interestingly, some previously undescribed putative targets for the heat shock regulator Hsf1 were identified. This provides evidence for Hsf1-dependent regulation of mannitol biosynthesis, translation, cytoskeletal dynamics and cell division in A. fumigatus. Furthermore, computational analysis of promoters revealed putative binding sites for an AP-2alpha-like transcription factor upstream of some heat shock induced genes. Until now, this factor has only been found in vertebrates. CONCLUSIONS Our newly established DIGE data analysis workflow yields improved data quality and is widely applicable for other DIGE datasets. Our findings suggest that the heat shock response in A. fumigatus differs from already well-studied yeasts and other filamentous fungi.
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Affiliation(s)
- Daniela Albrecht
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
- Friedrich Schiller University, Jena, Germany
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18
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The role of oxygen in yeast metabolism during high cell density brewery fermentations. Appl Microbiol Biotechnol 2009; 82:1143-56. [DOI: 10.1007/s00253-009-1909-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/03/2009] [Accepted: 02/03/2009] [Indexed: 12/27/2022]
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Wilson D, Tutulan-Cunita A, Jung W, Hauser NC, Hernandez R, Williamson T, Piekarska K, Rupp S, Young T, Stateva L. Deletion of the high-affinity cAMP phosphodiesterase encoded by PDE2 affects stress responses and virulence in Candida albicans. Mol Microbiol 2007; 65:841-56. [PMID: 17614954 DOI: 10.1111/j.1365-2958.2007.05788.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previously, we have shown that PDE2 is required for hyphal development and cell wall integrity in Candida albicans. In the present study, we have investigated the effects of its deletion by genome-wide transcriptome profiling. Changes in expression levels of genes involved in metabolism, transcription, protein and nucleic acids synthesis, as well as stress responses, cell wall and membrane biogenesis, adherence and virulence have been observed. By comparing these changes with previously reported transcriptome profiles of pde2Delta mutants of Saccharomyces cerevisiae, as well as cdc35Delta, ras1Delta and efg1Delta mutants of C. albicans, conserved and species-specific cAMP-regulated genes have been identified. The genes whose transcription is altered upon deletion of PDE2 in C. albicans has also allowed us to predict that the pde2Delta mutant would have a defective ability to adhere to, and invade host cells, and an impaired virulence as well as response to different stresses. Using appropriate assays, we have tested these predictions and compared the roles of the high- and low-affinity cAMP phosphodiesterases, Pde2p and Pde1p in stress, adhesion and virulence. We suggest that phosphodiesterases, and in particular the high-affinity cAMP phosphodiesterase encoded by PDE2, have real potential as targets for antifungal chemotherapy.
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Affiliation(s)
- Duncan Wilson
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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Current awareness on yeast. Yeast 2005; 22:71-8. [PMID: 15685779 DOI: 10.1002/yea.1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Jung WH, Warn P, Ragni E, Popolo L, Nunn CD, Turner MP, Stateva L. Deletion ofPDE2, the gene encoding the high-affinity cAMP phosphodiesterase, results in changes of the cell wall and membrane inCandida albicans. Yeast 2005; 22:285-94. [PMID: 15789349 DOI: 10.1002/yea.1199] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A role for the cAMP-dependent pathway in regulation of the cell wall in the model yeast Saccharomyces cerevisiae has recently been demonstrated. In this study we report the results of a phenotypic analysis of a Candida albicans mutant, characterized by a constitutive activation of the cAMP pathway due to deletion of PDE2, the gene encoding the high cAMP-affinity phosphodiesterase. Unlike wild-type strains, this mutant has an increased sensitivity to cell wall and membrane perturbing agents such as SDS and CFW, and antifungals such as amphotericin B and flucytosine. Moreover, the mutant is characterized by an altered sensitivity and a significantly reduced tolerance to fluconazole. The mutant's membrane has around 30% higher ergosterol content and the cell wall glucan was 22% lower than in the wild-type. These cell wall and membrane changes are manifested by a considerable reduction in the thickness of the cell wall, which in the mutant is on average 60-65 nm, compared to 80-85 nm in the wild-type strains as revealed by electron microscopy. These results suggest that constitutive activation of the cAMP pathway affects cell wall and membrane structure, and biosynthesis, not only in the model yeast S. cerevisiae but also in the human fungal pathogen C. albicans.
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Affiliation(s)
- Won Hee Jung
- Faculty of Life Sciences, Jackson's Mill, University of Manchester, PO Box 88, Sackville Street, Manchester M60 1QD, UK
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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