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Hung PH, Liao CW, Ko FH, Tsai HK, Leu JY. Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains. iScience 2023; 26:106635. [PMID: 37138775 PMCID: PMC10149407 DOI: 10.1016/j.isci.2023.106635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/21/2023] [Accepted: 04/05/2023] [Indexed: 05/05/2023] Open
Abstract
Enhanced phenotypic diversity increases a population's likelihood of surviving catastrophic conditions. Hsp90, an essential molecular chaperone and a central network hub in eukaryotes, has been observed to suppress or enhance the effects of genetic variation on phenotypic diversity in response to environmental cues. Because many Hsp90-interacting genes are involved in signaling transduction pathways and transcriptional regulation, we tested how common Hsp90-dependent differential gene expression is in natural populations. Many genes exhibited Hsp90-dependent strain-specific differential expression in five diverse yeast strains. We further identified transcription factors (TFs) potentially contributing to variable expression. We found that on Hsp90 inhibition or environmental stress, activities or abundances of Hsp90-dependent TFs varied among strains, resulting in differential strain-specific expression of their target genes, which consequently led to phenotypic diversity. We provide evidence that individual strains can readily display specific Hsp90-dependent gene expression, suggesting that the evolutionary impacts of Hsp90 are widespread in nature.
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Affiliation(s)
- Po-Hsiang Hung
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Fu-Hsuan Ko
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Huai-Kuang Tsai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
- Corresponding author
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Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLoS Genet 2017; 13:e1006867. [PMID: 28704372 PMCID: PMC5509106 DOI: 10.1371/journal.pgen.1006867] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/13/2017] [Indexed: 12/29/2022] Open
Abstract
Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.
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Affiliation(s)
- Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States of America
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Kayla Stefanko
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Caitlyn Cubba
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States of America
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States of America
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3
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Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D. The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion. G3 (BETHESDA, MD.) 2017; 7:129-142. [PMID: 27856696 PMCID: PMC5217103 DOI: 10.1534/g3.116.034298] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/01/2016] [Indexed: 12/20/2022]
Abstract
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Toward understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light- and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion. We show that ADV-1 is necessary for transducing light and/or temporal information to its immediate downstream targets, including controlling rhythms in genes critical to somatic cell fusion. However, while ADV-1 targets are altered in predictable ways in Δadv-1 cells in response to light, this is not always the case for rhythmic target gene expression. These data suggest that a complex regulatory network downstream of ADV-1 functions to generate distinct temporal dynamics of target gene expression relative to the central clock mechanism.
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Affiliation(s)
- Rigzin Dekhang
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Kristina M Smith
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Teresa M Lamb
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | | | - Erin L Bredeweg
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Oneida Ibarra
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Jillian M Emerson
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | | | | | - Elham Azizi
- Bioinformatics Program, Boston University, Massachusetts 02215
| | - Jennifer M Hurley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jay C Dunlap
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - James E Galagan
- Bioinformatics Program, Boston University, Massachusetts 02215
- National Emerging Infectious Diseases Laboratories, Boston University, Massachusetts 02118
- Department of Microbiology, Boston University, Massachusetts 02215
- Department of Biomedical Engineering, Boston University, Massachusetts 02215
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, Texas 77843
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Hrdlickova R, Toloue M, Tian B. RNA-Seq methods for transcriptome analysis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27198714 DOI: 10.1002/wrna.1364] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/17/2022]
Abstract
Deep sequencing has been revolutionizing biology and medicine in recent years, providing single base-level precision for our understanding of nucleic acid sequences in high throughput fashion. Sequencing of RNA, or RNA-Seq, is now a common method to analyze gene expression and to uncover novel RNA species. Aspects of RNA biogenesis and metabolism can be interrogated with specialized methods for cDNA library preparation. In this study, we review current RNA-Seq methods for general analysis of gene expression and several specific applications, including isoform and gene fusion detection, digital gene expression profiling, targeted sequencing and single-cell analysis. In addition, we discuss approaches to examine aspects of RNA in the cell, technical challenges of existing RNA-Seq methods, and future directions. WIREs RNA 2017, 8:e1364. doi: 10.1002/wrna.1364 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
| | | | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
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Sistrom M, Park D, O’Brien HE, Wang Z, Guttman DS, Townsend JP, Turner PE. Genomic and Gene-Expression Comparisons among Phage-Resistant Type-IV Pilus Mutants of Pseudomonas syringae pathovar phaseolicola. PLoS One 2015; 10:e0144514. [PMID: 26670219 PMCID: PMC4687649 DOI: 10.1371/journal.pone.0144514] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/19/2015] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas syringae pv. phaseolicola (Pph) is a significant bacterial pathogen of agricultural crops, and phage Φ6 and other members of the dsRNA virus family Cystoviridae undergo lytic (virulent) infection of Pph, using the type IV pilus as the initial site of cellular attachment. Despite the popularity of Pph/phage Φ6 as a model system in evolutionary biology, Pph resistance to phage Φ6 remains poorly characterized. To investigate differences between phage Φ6 resistant Pph strains, we examined genomic and gene expression variation among three bacterial genotypes that differ in the number of type IV pili expressed per cell: ordinary (wild-type), non-piliated, and super-piliated. Genome sequencing of non-piliated and super-piliated Pph identified few mutations that separate these genotypes from wild type Pph--and none present in genes known to be directly involved in type IV pilus expression. Expression analysis revealed that 81.1% of gene ontology (GO) terms up-regulated in the non-piliated strain were down-regulated in the super-piliated strain. This differential expression is particularly prevalent in genes associated with respiration--specifically genes in the tricarboxylic acid cycle (TCA) cycle, aerobic respiration, and acetyl-CoA metabolism. The expression patterns of the TCA pathway appear to be generally up and down-regulated, in non-piliated and super-piliated Pph respectively. As pilus retraction is mediated by an ATP motor, loss of retraction ability might lead to a lower energy draw on the bacterial cell, leading to a different energy balance than wild type. The lower metabolic rate of the super-piliated strain is potentially a result of its loss of ability to retract.
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Affiliation(s)
- Mark Sistrom
- School of Natural Sciences, University of California Merced, Merced, 95343, CA, United States of America
- * E-mail:
| | - Derek Park
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
| | - Heath E. O’Brien
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Ontario, M5S 3B2, Canada
| | - Jeffrey P. Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, United States of America
- Program in Microbiology, Yale University, New Haven, CT 06520, United States of America
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, United States of America
- Program in Microbiology, Yale University, New Haven, CT 06520, United States of America
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Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa. EUKARYOTIC CELL 2013; 13:154-69. [PMID: 24243796 DOI: 10.1128/ec.00248-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fungi can serve as highly tractable models for understanding genetic basis of sexual development in multicellular organisms. Applying a reverse-genetic approach to advance such a model, we used random and multitargeted primers to assay gene expression across perithecial development in Neurospora crassa. We found that functionally unclassified proteins accounted for most upregulated genes, whereas downregulated genes were enriched for diverse functions. Moreover, genes associated with developmental traits exhibited stage-specific peaks of expression. Expression increased significantly across sexual development for mating type gene mat a-1 and for mat A-1 specific pheromone precursor ccg-4. In addition, expression of a gene encoding a protein similar to zinc finger, stc1, was highly upregulated early in perithecial development, and a strain with a knockout of this gene exhibited arrest at the same developmental stage. A similar expression pattern was observed for genes in RNA silencing and signaling pathways, and strains with knockouts of these genes were also arrested at stages of perithecial development that paralleled their peak in expression. The observed stage specificity allowed us to correlate expression upregulation and developmental progression and to identify regulators of sexual development. Bayesian networks inferred from our expression data revealed previously known and new putative interactions between RNA silencing genes and pathways. Overall, our analysis provides a fine-scale transcriptomic landscape and novel inferences regarding the control of the multistage development process of sexual crossing and fruiting body development in N. crassa.
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Nygren K, Wallberg A, Samils N, Stajich JE, Townsend JP, Karlsson M, Johannesson H. Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Evol Biol 2012. [PMID: 23186325 PMCID: PMC3571971 DOI: 10.1186/1471-2148-12-229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Background The broadly accepted pattern of rapid evolution of reproductive genes is primarily based on studies of animal systems, although several examples of rapidly evolving genes involved in reproduction are found in diverse additional taxa. In fungi, genes involved in mate recognition have been found to evolve rapidly. However, the examples are too few to draw conclusions on a genome scale. Results In this study, we performed microarray hybridizations between RNA from sexual and vegetative tissues of two strains of the heterothallic (self-sterile) filamentous ascomycete Neurospora intermedia, to identify a set of sex-associated genes in this species. We aligned Expressed Sequence Tags (ESTs) from sexual and vegetative tissue of N. intermedia to orthologs from three closely related species: N. crassa, N. discreta and N. tetrasperma. The resulting four-species alignments provided a dataset for molecular evolutionary analyses. Our results confirm a general pattern of rapid evolution of fungal sex-associated genes, compared to control genes with constitutive expression or a high relative expression during vegetative growth. Among the rapidly evolving sex-associated genes, we identified candidates that could be of importance for mating or fruiting-body development. Analyses of five of these candidate genes from additional species of heterothallic Neurospora revealed that three of them evolve under positive selection. Conclusions Taken together, our study represents a novel finding of a genome-wide pattern of rapid evolution of sex-associated genes in the fungal kingdom, and provides a list of candidate genes important for reproductive isolation in Neurospora.
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Affiliation(s)
- Kristiina Nygren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36, Uppsala, Sweden
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Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genet Biol 2012; 49:533-43. [PMID: 22626843 DOI: 10.1016/j.fgb.2012.05.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 05/08/2012] [Accepted: 05/09/2012] [Indexed: 12/18/2022]
Abstract
The impact of loci that determine sexual identity upon the asexual, dominant stage of fungal life history has been well studied. To investigate their impact, expression differences between strains of different mating type during asexual development were assayed, with RNA sampled from otherwise largely isogenic mat A and mat a strains of Neurospora crassa at early, middle, and late clonal stages of development. We observed significant differences in overall gene expression between mating types across clonal development, especially at late development stages. The expression levels of mating-type genes and pheromone genes were assayed by reverse transcription and quantitative PCR, revealing expression of pheromone and receptor genes in strains of both mating types in all development stages, and revealing that mating type (mat) genes were increasingly expressed over the course of asexual development. Interestingly, among differentially expressed genes, the mat A genotype more frequently exhibited a higher expression level than mat a, and demonstrated greater transcriptional regulatory dynamism. Significant up-regulation of expression was observed for many late light-responsive genes at late asexual development stages. Further investigation of the impact of light and the roles of light response genes in asexual development of both mating types are warranted.
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Wang Z, Lehr N, Trail F, Townsend JP. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genet Biol 2012; 49:405-13. [PMID: 22469835 DOI: 10.1016/j.fgb.2012.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/09/2012] [Accepted: 03/13/2012] [Indexed: 02/04/2023]
Abstract
Fungal fruiting body size and form are influenced by the ecology of the species, including diverse environmental stimuli. Accordingly, nutritional resources available to the fungus during development can be vital to successful production of fruiting bodies. To investigate the effect of nutrition, perithecial development of Neurospora crassa was induced on two different media, a chemically sparsely nutritive Synthetic Crossing Medium (SCM) and a natural Carrot Agar (CA). Protoperithecia were collected before crossing, and perithecia were collected at 2, 24, 48, 72, 96, 120, and at full maturity 144 h after crossing. No differences in fruiting body morphology were observed between the two media at any time point. A circuit of microarray hybridizations comparing cDNA from all neighboring stages was performed. For a majority of differentially expressed genes, expression was higher in SCM than in CA, and expression of core metabolic genes was particularly affected. Effects of nutrition were highest in magnitude before crossing, lowering in magnitude during early perithecial development. Interestingly, metabolic effects of the media were also large in magnitude during late perithecial development, at which stage the lower expression in CA presumably reflected the continued intake of diverse complex initial compounds, diminishing the need for expression of anabolic pathways. However, for genes with key regulatory roles in sexual development, including pheromone precursor ccg-4 and poi2, expression patterns were similar between treatments. When possible, a common nutritional environment is ideal for comparing transcriptional profiles between different fungi. Nevertheless, the observed consistency of the developmental program across media, despite considerable metabolic differentiation is reassuring. This result facilitates comparative studies that will require different nutritional resources for sexual development in different fungi.
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Affiliation(s)
- Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
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Hodgins-Davis A, Townsend JP. Evolving gene expression: from G to E to GxE. Trends Ecol Evol 2009; 24:649-58. [PMID: 19699549 PMCID: PMC2805859 DOI: 10.1016/j.tree.2009.06.011] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 06/05/2009] [Accepted: 06/08/2009] [Indexed: 12/21/2022]
Abstract
Analyses of gene expression data sets for multiple individuals and species promise to shed light on the mode of evolution of gene expression. However, complementary complexities challenge this goal. Characterization of the genetic variation underlying gene expression can easily be compromised by lack of environmental control. Conversely, the breadth of conclusions from studies of environmental effects has been limited by the use of single strains. Controlled studies have hinted at extensive genexenvironment interaction. Thus, both genetics and environment are key components in models of the evolution of gene expression. We review the literature on the evolution of gene expression in terms of genetics (G), environmental response (E) and GxE interactions to make this conceptual point.
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Affiliation(s)
- Andrea Hodgins-Davis
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA.
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