1
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Wendegatz EC, Lettow J, Wierzbicka W, Schüller HJ. Transcriptional activation and coactivator binding by yeast Ino2 and human proto-oncoprotein c-Myc. Curr Genet 2025; 71:2. [PMID: 39820713 PMCID: PMC11739200 DOI: 10.1007/s00294-025-01309-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Revised: 12/20/2024] [Accepted: 01/06/2025] [Indexed: 01/30/2025]
Abstract
Basic helix-loop-helix domains in yeast regulatory proteins Ino2 and Ino4 mediate formation of a heterodimer which binds to and activates expression of phospholipid biosynthetic genes. The human proto-oncoprotein c-Myc (Myc) and its binding partner Max activate genes important for cellular proliferation and contain functional domains structure and position of which strongly resembles Ino2 and Ino4. Since Ino2-Myc and Ino4-Max may be considered as orthologs we performed functional comparisons in yeast. We demonstrate that Myc and Max could be stably synthesized in S. cerevisiae and together significantly activated a target gene of Ino2/Ino4 but nevertheless were unable to functionally complement an ino2 ino4 double mutant. We also map two efficient transcriptional activation domains in the N-terminus of Myc (TAD1: aa 1-41 and TAD2: aa 91-140), corresponding to TAD positions in Ino2. We finally show that coactivators such as TFIID subunits Taf1, Taf4, Taf6, Taf10 and Taf12 as well as ATPase subunits of chromatin remodelling complexes Swi2, Sth1 and Ino80 previously shown to interact with TADs of Ino2 were also able to bind TADs of Myc, supporting the view that heterodimers Ino2/Ino4 and Myc/Max are evolutionary related but have undergone transcriptional rewiring of target genes.
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Affiliation(s)
- Eva-Carina Wendegatz
- Center for Functional Genomics of Microbes, Institut Für Genetik Und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Julia Lettow
- Center for Functional Genomics of Microbes, Institut Für Genetik Und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Wiktoria Wierzbicka
- Center for Functional Genomics of Microbes, Institut Für Genetik Und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Institut Für Genetik Und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany.
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2
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Wang JJT, Steenwyk JL, Brem RB. Natural trait variation across Saccharomycotina species. FEMS Yeast Res 2024; 24:foae002. [PMID: 38218591 PMCID: PMC10833146 DOI: 10.1093/femsyr/foae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024] Open
Abstract
Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.
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Affiliation(s)
- Johnson J -T Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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3
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Rokas A, Wisecaver JH, Lind AL. The birth, evolution and death of metabolic gene clusters in fungi. Nat Rev Microbiol 2019; 16:731-744. [PMID: 30194403 DOI: 10.1038/s41579-018-0075-3] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fungi contain a remarkable diversity of both primary and secondary metabolic pathways involved in ecologically specialized or accessory functions. Genes in these pathways are frequently physically linked on fungal chromosomes, forming metabolic gene clusters (MGCs). In this Review, we describe the diversity in the structure and content of fungal MGCs, their population-level and species-level variation, the evolutionary mechanisms that underlie their formation, maintenance and decay, and their ecological and evolutionary impact on fungal populations. We also discuss MGCs from other eukaryotes and the reasons for their preponderance in fungi. Improved knowledge of the evolutionary life cycle of MGCs will advance our understanding of the ecology of specialized metabolism and of the interplay between the lifestyle of an organism and genome architecture.
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Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. .,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Abigail L Lind
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA.,Gladstone Institutes, San Francisco, CA, USA
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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5
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White RR, Ponsford AH, Weekes MP, Rodrigues RB, Ascher DB, Mol M, Selkirk ME, Gygi SP, Sanderson CM, Artavanis-Tsakonas K. Ubiquitin-Dependent Modification of Skeletal Muscle by the Parasitic Nematode, Trichinella spiralis. PLoS Pathog 2016; 12:e1005977. [PMID: 27870901 PMCID: PMC5117777 DOI: 10.1371/journal.ppat.1005977] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022] Open
Abstract
Trichinella spiralis is a muscle-specific parasitic worm that is uniquely intracellular. T. spiralis reprograms terminally differentiated skeletal muscle cells causing them to de-differentiate and re-enter the cell cycle, a process that cannot occur naturally in mammalian skeletal muscle cells, but one that holds great therapeutic potential. Although the host ubiquitin pathway is a common target for viruses and bacteria during infection, its role in parasite pathogenesis has been largely overlooked. Here we demonstrate that the secreted proteins of T. spiralis contain E2 Ub-conjugating and E3 Ub-ligase activity. The E2 activity is attributed to TsUBE2L3, a novel and conserved T. spiralis enzyme located in the secretory organ of the parasite during the muscle stages of infection. TsUBE2L3 cannot function with any T.spiralis secreted E3, but specifically binds to a panel of human RING E3 ligases, including the RBR E3 ARIH2 with which it interacts with a higher affinity than the mammalian ortholog UbcH7/UBE2L3. Expression of TsUBE2L3 in skeletal muscle cells causes a global downregulation in protein ubiquitination, most predominantly affecting motor, sarcomeric and extracellular matrix proteins, thus mediating their stabilization with regards to proteasomal degradation. This effect is not observed in the presence of the mammalian ortholog, suggesting functional divergence in the evolution of the parasite protein. These findings demonstrate the first example of host-parasite interactions via a parasite-derived Ub conjugating enzyme; an E2 that demonstrates a novel muscle protein stabilization function. Parasitic worms often establish long-lasting infections in their hosts; tightly regulating their surroundings to strike a delicate balance between host cell modulation and protection that will ensure their replication. This is accomplished via the active secretion of parasite glycolipids and glycoproteins into the host. Trichinella spiralis, a parasitic nematode that infects skeletal muscle of mammals, birds and reptiles, is the only parasitic worm with a true intracellular stage. T. spiralis invade terminally differentiated myotubes, reprogramming them to de-differentiate and re-enter the cell cycle, a process that cannot occur naturally in mammalian skeletal muscle cells, but one that holds great therapeutic potential. We have identified and characterized a novel T. spiralis secreted protein that, despite a high level of sequence identity, appears to have evolved a different function to its host ortholog. This protein is an active Ub conjugating enzyme that binds to a panel of human E3 Ub ligases with higher affinity than the host ortholog. Furthermore, when expressed in skeletal muscle cells in culture, its presence uniquely leads to the stabilization of muscle-specific proteins via the downregulation of their ubiquitination.
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Affiliation(s)
- Rhiannon R. White
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Amy H. Ponsford
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Department of Cell Biology, Harvard Medical School, Boston, United States of America
| | - Rachel B. Rodrigues
- Department of Cell Biology, Harvard Medical School, Boston, United States of America
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Melbourne, Melbourne, Australia
| | - Marco Mol
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Murray E. Selkirk
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States of America
| | - Christopher M. Sanderson
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Katerina Artavanis-Tsakonas
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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6
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Das Adhikari AK, Bhat PJ. The binary response of the GAL/MEL genetic switch of Saccharomyces cerevisiae is critically dependent on Gal80p-Gal4p interaction. FEMS Yeast Res 2016; 16:fow069. [PMID: 27573383 DOI: 10.1093/femsyr/fow069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2016] [Indexed: 11/13/2022] Open
Abstract
Studies on the Saccharomyces cerevisiae GAL/MEL genetic switch have revealed that its bistability is dependent on ultrasensitivity that can be altered or abolished by disabling different combinations of nested feedback loops. In contrast, we have previously demonstrated that weakening of the interaction between Gal80p and Gal4p alone is sufficient to abolish the ultrasensitivity (Das Adhikari et al. 2014). Here, we demonstrate that altering the epistatic interaction between Gal80p and Gal4p also abolishes the bistability, and the switch response to galactose becomes graded instead of binary. However, the GAL/MEL switch of wild-type and epistatically altered strains responded in a graded fashion to melibiose. The properties of the epistatically altered strain resemble Kluyveromyces lactis, which separated from the Saccharomyces lineage 100 mya before whole-genome duplication (WGD). Based on the results reported here, we propose that epistatic interactions played a crucial role in the evolution of the fine regulation of S. cerevisiae GAL/MEL switch following WGD.
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Affiliation(s)
- Akshay Kumar Das Adhikari
- Laboratory of Molecular Genetics, Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Paike Jayadeva Bhat
- Laboratory of Molecular Genetics, Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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7
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Sarda S, Hannenhalli S. High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. Mol Biol Evol 2015; 32:3047-63. [PMID: 26399482 DOI: 10.1093/molbev/msv203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A coregulated module of genes ("regulon") can have evolutionarily conserved expression patterns and yet have diverged upstream regulators across species. For instance, the ribosomal genes regulon is regulated by the transcription factor (TF) TBF1 in Candida albicans, while in Saccharomyces cerevisiae it is regulated by RAP1. Only a handful of such rewiring events have been established, and the prevalence or conditions conducive to such events are not well known. Here, we develop a novel probabilistic scoring method to comprehensively screen for regulatory rewiring within regulons across 23 yeast species. Investigation of 1,713 regulons and 176 TFs yielded 5,353 significant rewiring events at 5% false discovery rate (FDR). Besides successfully recapitulating known rewiring events, our analyses also suggest TF candidates for certain processes reported to be under distinct regulatory controls in S. cerevisiae and C. albicans, for which the implied regulators are not known: 1) Oxidative stress response (Sc-MSN2 to Ca-FKH2) and 2) nutrient modulation (Sc-RTG1 to Ca-GCN4/Ca-UME6). Furthermore, a stringent screen to detect TF rewiring at individual genes identified 1,446 events at 10% FDR. Overall, these events are supported by strong coexpression between the predicted regulator and its target gene(s) in a species-specific fashion (>50-fold). Independent functional analyses of rewiring TF pairs revealed greater functional interactions and shared biological processes between them (P = 1 × 10(-3)).Our study represents the first comprehensive assessment of regulatory rewiring; with a novel approach that has generated a unique high-confidence resource of several specific events, suggesting that evolutionary rewiring is relatively frequent and may be a significant mechanism of regulatory innovation.
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Affiliation(s)
- Shrutii Sarda
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park
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8
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Amorim-Vaz S, Delarze E, Ischer F, Sanglard D, Coste AT. Examining the virulence of Candida albicans transcription factor mutants using Galleria mellonella and mouse infection models. Front Microbiol 2015; 6:367. [PMID: 25999923 PMCID: PMC4419840 DOI: 10.3389/fmicb.2015.00367] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/10/2015] [Indexed: 01/08/2023] Open
Abstract
The aim of the present study was to identify Candida albicans transcription factors (TFs) involved in virulence. Although mice are considered the gold-standard model to study fungal virulence, mini-host infection models have been increasingly used. Here, barcoded TF mutants were first screened in mice by pools of strains and fungal burdens (FBs) quantified in kidneys. Mutants of unannotated genes which generated a kidney FB significantly different from that of wild-type were selected and individually examined in Galleria mellonella. In addition, mutants that could not be detected in mice were also tested in G. mellonella. Only 25% of these mutants displayed matching phenotypes in both hosts, highlighting a significant discrepancy between the two models. To address the basis of this difference (pool or host effects), a set of 19 mutants tested in G. mellonella were also injected individually into mice. Matching FB phenotypes were observed in 50% of the cases, highlighting the bias due to host effects. In contrast, 33.4% concordance was observed between pool and single strain infections in mice, thereby highlighting the bias introduced by the "pool effect." After filtering the results obtained from the two infection models, mutants for MBF1 and ZCF6 were selected. Independent marker-free mutants were subsequently tested in both hosts to validate previous results. The MBF1 mutant showed impaired infection in both models, while the ZCF6 mutant was only significant in mice infections. The two mutants showed no obvious in vitro phenotypes compared with the wild-type, indicating that these genes might be specifically involved in in vivo adapt.
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Affiliation(s)
- Sara Amorim-Vaz
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne Lausanne, Switzerland
| | - Eric Delarze
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne Lausanne, Switzerland
| | - Françoise Ischer
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne Lausanne, Switzerland
| | - Alix T Coste
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne Lausanne, Switzerland
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9
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Lind AL, Wisecaver JH, Smith TD, Feng X, Calvo AM, Rokas A. Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PLoS Genet 2015; 11:e1005096. [PMID: 25786130 PMCID: PMC4364702 DOI: 10.1371/journal.pgen.1005096] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/23/2015] [Indexed: 01/07/2023] Open
Abstract
Filamentous fungi produce diverse secondary metabolites (SMs) essential to their ecology and adaptation. Although each SM is typically produced by only a handful of species, global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes, such as development. We examined the interplay between the taxonomic narrowness of SM distribution and the broad conservation of global regulation of SM and development in Aspergillus, a diverse fungal genus whose members produce well-known SMs such as penicillin and gliotoxin. Evolutionary analysis of the 2,124 genes comprising the 262 SM pathways in four Aspergillus species showed that most SM pathways were species-specific, that the number of SM gene orthologs was significantly lower than that of orthologs in primary metabolism, and that the few conserved SM orthologs typically belonged to non-homologous SM pathways. RNA sequencing of two master transcriptional regulators of SM and development, veA and mtfA, showed that the effects of deletion of each gene, especially veA, on SM pathway regulation were similar in A. fumigatus and A. nidulans, even though the underlying genes and pathways regulated in each species differed. In contrast, examination of the role of these two regulators in development, where 94% of the underlying genes are conserved in both species showed that whereas the role of veA is conserved, mtfA regulates development in the homothallic A. nidulans but not in the heterothallic A. fumigatus. Thus, the regulation of these highly conserved developmental genes is divergent, whereas-despite minimal conservation of target genes and pathways-the global regulation of SM production is largely conserved. We suggest that the evolution of the transcriptional regulation of secondary metabolism in Aspergillus represents a novel type of regulatory circuit rewiring and hypothesize that it has been largely driven by the dramatic turnover of the target genes involved in the process.
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Affiliation(s)
- Abigail L. Lind
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jennifer H. Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Timothy D. Smith
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Xuehuan Feng
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Ana M. Calvo
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
| | - Antonis Rokas
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America,* E-mail:
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10
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Das Adhikari AK, Qureshi MT, Kar RK, Bhat PJ. Perturbation of the interaction between Gal4p and Gal80p of the Saccharomyces cerevisiae GAL switch results in altered responses to galactose and glucose. Mol Microbiol 2014; 94:202-17. [PMID: 25135592 DOI: 10.1111/mmi.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2014] [Indexed: 11/30/2022]
Abstract
In S. cerevisiae, following the Whole Genome Duplication (WGD), GAL1-encoded galactokinase retained its signal transduction function but lost basal expression. On the other hand, its paralogue GAL3, lost kinase activity but retained its signalling function and basal expression, thus making it indispensable for the rapid induction of the S. cerevisiae GAL switch. However, a gal3Δ strain exhibits delayed growth kinetics due to the redundant signalling function of GAL1. The subfunctionalization between the paralogues GAL1 and GAL3 is due to expression divergence and is proposed to be due to the alteration in the Upstream Activating Sequences (UASG ). We demonstrate that the GAL switch becomes independent of GAL3 by altering the interaction between Gal4p and Gal80p without altering the configuration of UASG . In addition to the above, the altered switch of S. cerevisiae loses ultrasensitivity and stringent glucose repression. These changes caused an increase in fitness in the disaccharide melibiose at the expense of a decrease in fitness in galactose. The above altered features of the ScGAL switch are similar to the features of the GAL switch of K. lactis that diverged from S. cerevisiae before the WGD.
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Affiliation(s)
- Akshay Kumar Das Adhikari
- Laboratory of Molecular Genetics, Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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11
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Campbell MA, Staats M, van Kan JAL, Rokas A, Slot JC. Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 2013; 105:1126-34. [PMID: 23921237 DOI: 10.3852/12-390] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
At least five of the six genes of the bikaverin secondary metabolic gene cluster were shown to have undergone horizontal transfer (HGT) from a Fusarium donor to the Botrytis lineage. Of these five, two enzyme-encoding genes are found as pseudogenes in B. cinerea whereas two regulatory genes and the transporter remain intact. To reconstruct the evolutionary events leading to decay of this gene cluster and infer a more precise timing of its transfer, we examined the genomes of nine additional broadly sampled Botrytis species. We found evidence that a Botrytis ancestor acquired the entire gene cluster through an ancient HGT that occurred before the diversification of the genus. During the subsequent evolution and diversification of the genus, four of the 10 genomes appear to have lost the gene cluster, while in the other six the cluster is in various stages of degeneration. Across the Botrytis genomes, the modes of gene decay in the cluster differed between enzyme-encoding genes, which had higher rates of transition to or retention of pseudogenes and were universally inactivated, and regulatory genes (particularly the non-pathway-specific regulator bik4), which more frequently appeared intact. Consistent with these results, the regulatory genes bik4 and bik5 showed stronger evidence of transcriptional expression than other bikaverin genes under multiple conditions in B. cinerea. These results could be explained by pleiotropy in the bikaverin regulatory genes either through rewiring or their interaction with more central pathways or by constraints on the order of gene loss driven by the intrinsic toxicity of the pathway. Our finding that most of the bikaverin pathway genes have been lost or pseudogenized in these Botrytis genomes suggests that the incidence of HGT of gene cluster-encoded metabolic pathways might be higher than what is possible to be inferred from isolated genome analyses.
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Affiliation(s)
- Matthew A Campbell
- Vanderbilt University, Department of Biological Sciences, VU Station B 351364, Nashville, Tennessee 37235, and University of Hawaii at Mânoa, Botany Department, 3190 Maile Way, Room 101, Honolulu, Hawaii 96822
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12
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Kamthan M, Kamthan A, Ruhela D, Maiti P, Bhavesh NS, Datta A. Upregulation of galactose metabolic pathway by N-acetylglucosamine induced endogenous synthesis of galactose in Candida albicans. Fungal Genet Biol 2013; 54:15-24. [PMID: 23454545 DOI: 10.1016/j.fgb.2013.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 02/04/2013] [Accepted: 02/09/2013] [Indexed: 12/28/2022]
Abstract
N-Acetylglucosamine (GlcNAc) is an important signaling molecule that plays multiple roles in Candida albicans. Induction of galactose metabolic pathway by GlcNAc is an intriguing aspect of C. albicans biology. In order to investigate the role of galactose metabolic genes (GAL genes) in presence of GlcNAc, we created knockouts of galactokinase (GAL1) and UDP galactose epimerase (GAL10) genes. These mutants failed to grow on galactose and also showed lower growth rate in presence of GlcNAc. Interestingly, expression of GAL genes in presence of GlcNAc was higher in gal1Δ strain relative to that of wild type strain. Moreover, no GlcNAc induced upregulation of GAL genes was observed in the gal10Δ strain suggesting that UDP galactose epimerase is essential for GlcNAc induced activation of GAL genes. GlcNAc induced expression of GAL genes was also investigated in GlcNAc metabolic pathway triple mutant N216 (hxk1Δ nag1Δ dac1Δ). Interestingly, in this mutant the GAL genes are neither induced nor repressed and remain derepressed as found on a neutral carbon source such as glycerol, suggesting that catabolism of GlcNAc play an important role in the expression of GAL genes. GC/MS analysis of derivatized metabolites revealed a significant accumulation of galactose in the gal1Δ strain while no galactose was detected in gal10Δ and N216 strain. Solution-state NMR spectroscopy using N-acetyl-¹³C₁-glucosamine confirmed the flow of ¹³C label from GlcNAc to galactose. Thus, internal galactose synthesized via UDP galactose pathway from GlcNAc metabolites acts as the inducer of GAL genes in presence of GlcNAc.
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Affiliation(s)
- Mohan Kamthan
- National Institute of Plant Genome Research, New Delhi, India
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13
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Altwasser R, Linde J, Buyko E, Hahn U, Guthke R. Genome-Wide Scale-Free Network Inference for Candida albicans. Front Microbiol 2012; 3:51. [PMID: 22355294 PMCID: PMC3280432 DOI: 10.3389/fmicb.2012.00051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/31/2012] [Indexed: 11/13/2022] Open
Abstract
Discovery of essential genes in pathogenic organisms is an important step in the development of new medication. Despite a growing number of genome data available, little is known about C. albicans, a major fungal pathogen. Most of the human population carries C. albicans as commensal, but it can cause systemic infection that may lead to the death of the host if the immune system has deteriorated. In many organisms central nodes in the interaction network (hubs) play a crucial role for information and energy transport. Knock-outs of such hubs often lead to lethal phenotypes making them interesting drug targets. To identify these central genes via topological analysis, we inferred gene regulatory networks that are sparse and scale-free. We collected information from various sources to complement the limited expression data available. We utilized a linear regression algorithm to infer genome-wide gene regulatory interaction networks. To evaluate the predictive power of our approach, we used an automated text-mining system that scanned full-text research papers for known interactions. With the help of the compendium of known interactions, we also optimize the influence of the prior knowledge and the sparseness of the model to achieve the best results. We compare the results of our approach with those of other state-of-the-art network inference methods and show that we outperform those methods. Finally we identify a number of hubs in the genome of the fungus and investigate their biological relevance.
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Affiliation(s)
- Robert Altwasser
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell InstituteJena, Germany
| | - Jörg Linde
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell InstituteJena, Germany
| | - Ekaterina Buyko
- Jena University Language and Information Engineering Lab, Friedrich Schiller UniversityJena, Germany
| | - Udo Hahn
- Jena University Language and Information Engineering Lab, Friedrich Schiller UniversityJena, Germany
| | - Reinhard Guthke
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell InstituteJena, Germany
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Campbell MA, Rokas A, Slot JC. Horizontal transfer and death of a fungal secondary metabolic gene cluster. Genome Biol Evol 2012; 4:289-93. [PMID: 22294497 PMCID: PMC3318441 DOI: 10.1093/gbe/evs011] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A cluster composed of four structural and two regulatory genes found in several species of the fungal genus Fusarium (class Sordariomycetes) is responsible for the production of the red pigment bikaverin. We discovered that the unrelated fungus Botrytis cinerea (class Leotiomycetes) contains a cluster of five genes that is highly similar in sequence and gene order to the Fusarium bikaverin cluster. Synteny conservation, nucleotide composition, and phylogenetic analyses of the cluster genes indicate that the B. cinerea cluster was acquired via horizontal transfer from a Fusarium donor. Upon or subsequent to the transfer, the B. cinerea gene cluster became inactivated; one of the four structural genes is missing, two others are pseudogenes, and the fourth structural gene shows an accelerated rate of nonsynonymous substitutions along the B. cinerea lineage, consistent with relaxation of selective constraints. Interestingly, the bik4 regulatory gene is still intact and presumably functional, whereas bik5, which is a pathway-specific regulator, also shows a mild but significant acceleration of evolutionary rate along the B. cinerea lineage. This selective preservation of the bik4 regulator suggests that its conservation is due to its likely involvement in other non-bikaverin-related biological processes in B. cinerea. Thus, in addition to novel metabolism, horizontal transfer of wholesale metabolic gene clusters might also be contributing novel regulation.
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Josephides C, Moses AM. Modeling the evolution of a classic genetic switch. BMC SYSTEMS BIOLOGY 2011; 5:24. [PMID: 21294912 PMCID: PMC3048525 DOI: 10.1186/1752-0509-5-24] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 02/05/2011] [Indexed: 11/10/2022]
Abstract
Background The regulatory network underlying the yeast galactose-use pathway has emerged as a model system for the study of regulatory network evolution. Evidence has recently been provided for adaptive evolution in this network following a whole genome duplication event. An ancestral gene encoding a bi-functional galactokinase and co-inducer protein molecule has become subfunctionalized as paralogous genes (GAL1 and GAL3) in Saccharomyces cerevisiae, with most fitness gains being attributable to changes in cis-regulatory elements. However, the quantitative functional implications of the evolutionary changes in this regulatory network remain unexplored. Results We develop a modeling framework to examine the evolution of the GAL regulatory network. This enables us to translate molecular changes in the regulatory network to changes in quantitative network function. We computationally reconstruct an inferred ancestral version of the network and trace the evolutionary paths in the lineage leading to S. cerevisiae. We explore the evolutionary landscape of possible regulatory networks and find that the operation of intermediate networks leading to S. cerevisiae differs substantially depending on the order in which evolutionary changes accumulate; in particular, we systematically explore evolutionary paths and find that some network features cannot be optimized simultaneously. Conclusions We find that a computational modeling approach can be used to analyze the evolution of a well-studied regulatory network. Our results are consistent with several experimental studies of the evolutionary of the GAL regulatory network, including increased fitness in Saccharomyces due to duplication and adaptive regulatory divergence. The conceptual and computational tools that we have developed may be applicable in further studies of regulatory network evolution.
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Affiliation(s)
- Christos Josephides
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5 S 3B2, Canada
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Mansfield BE, Oltean HN, Oliver BG, Hoot SJ, Leyde SE, Hedstrom L, White TC. Azole drugs are imported by facilitated diffusion in Candida albicans and other pathogenic fungi. PLoS Pathog 2010; 6:e1001126. [PMID: 20941354 PMCID: PMC2947996 DOI: 10.1371/journal.ppat.1001126] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 09/01/2010] [Indexed: 12/21/2022] Open
Abstract
Despite the wealth of knowledge regarding the mechanisms of action and the mechanisms of resistance to azole antifungals, very little is known about how the azoles are imported into pathogenic fungal cells. Here the in-vitro accumulation and import of Fluconazole (FLC) was examined in the pathogenic fungus, Candida albicans. In energized cells, FLC accumulation correlates inversely with expression of ATP-dependent efflux pumps. In de-energized cells, all strains accumulate FLC, suggesting that FLC import is not ATP-dependent. The kinetics of import in de-energized cells displays saturation kinetics with a Km of 0.64 uM and Vmax of 0.0056 pmol/min/108 cells, demonstrating that FLC import proceeds via facilitated diffusion through a transporter rather than passive diffusion. Other azoles inhibit FLC import on a mole/mole basis, suggesting that all azoles utilize the same facilitated diffusion mechanism. An analysis of related compounds indicates that competition for azole import depends on an aromatic ring and an imidazole or triazole ring together in one molecule. Import of FLC by facilitated diffusion is observed in other fungi, including Cryptococcus neoformans, Saccharomyces cerevisiae, and Candida krusei, indicating that the mechanism of transport is conserved among fungal species. FLC import was shown to vary among Candida albicans resistant clinical isolates, suggesting that altered facilitated diffusion may be a previously uncharacterized mechanism of resistance to azole drugs. Azole antifungals are used to treat a wide variety of fungal infections of humans, animals and plants. A great deal is known about how the azoles interact with their target enzyme within fungal cells and how the azoles are exported from the fungal cell through various efflux pumps. Altered interactions with the target enzyme and altered efflux pump expression are common mechanisms of azole resistance in fungi. However, the mechanism by which azoles enter a fungal cell is not clear—many have assumed that azoles passively diffuse into the cell. This study demonstrates that azoles are not passively diffused, or actively pumped, into the cell. Instead, azoles are imported by facilitated diffusion, mediated by a transporter. Facilitated diffusion of azoles is saturable. All clinically important azoles, and many structurally related compounds, compete for FLC import, while structurally unrelated drugs do not compete. Azole import by facilitated diffusion is shown in four species of fungi, suggesting that it is common for most if not all fungi. Altered facilitated diffusion is observed in a collection of clinical isolates, suggesting that altered import is a previously uncharacterized mechanism of resistance.
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Affiliation(s)
- Bryce E. Mansfield
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Hanna N. Oltean
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Brian G. Oliver
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Samantha J. Hoot
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Sarah E. Leyde
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Lizbeth Hedstrom
- Brandeis University Department of Biology and Chemistry, Waltham, Massachusetts, United States of America
| | - Theodore C. White
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- University of Washington Program in Pathobiology, Seattle, Washington, United States of America
- * E-mail:
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Wohlbach DJ, Thompson DA, Gasch AP, Regev A. From elements to modules: regulatory evolution in Ascomycota fungi. Curr Opin Genet Dev 2009; 19:571-8. [PMID: 19879128 DOI: 10.1016/j.gde.2009.09.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 09/03/2009] [Accepted: 09/11/2009] [Indexed: 12/13/2022]
Abstract
Regulatory divergence is likely a major driving force in evolution. Comparative transcriptomics provides a new glimpse into the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for studies of regulatory evolution, because of broad phylogenetic scope, many sequenced genomes, and facility of genomic analysis. Here we review the substantial divergence in gene expression in Ascomycota and how this is reconciled with the modular organization of transcriptional networks. We show that flexibility and redundancy in both cis-regulation and trans-regulation can lead to changes from altered expression of single genes to wholesale rewiring of regulatory modules. Redundancy thus emerges as a major driving force facilitating expression divergence while preserving the coherent functional organization of a transcriptional response.
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Affiliation(s)
- Dana J Wohlbach
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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An integrated approach to identifying cis-regulatory modules in the human genome. PLoS One 2009; 4:e5501. [PMID: 19434238 PMCID: PMC2677454 DOI: 10.1371/journal.pone.0005501] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Accepted: 04/21/2009] [Indexed: 11/21/2022] Open
Abstract
In eukaryotic genomes, it is challenging to accurately determine target sites of transcription factors (TFs) by only using sequence information. Previous efforts were made to tackle this task by considering the fact that TF binding sites tend to be more conserved than other functional sites and the binding sites of several TFs are often clustered. Recently, ChIP-chip and ChIP-sequencing experiments have been accumulated to identify TF binding sites as well as survey the chromatin modification patterns at the regulatory elements such as promoters and enhancers. We propose here a hidden Markov model (HMM) to incorporate sequence motif information, TF-DNA interaction data and chromatin modification patterns to precisely identify cis-regulatory modules (CRMs). We conducted ChIP-chip experiments on four TFs, CREB, E2F1, MAX, and YY1 in 1% of the human genome. We then trained a hidden Markov model (HMM) to identify the labels of the CRMs by incorporating the sequence motifs recognized by these TFs and the ChIP-chip ratio. Chromatin modification data was used to predict the functional sites and to further remove false positives. Cross-validation showed that our integrated HMM had a performance superior to other existing methods on predicting CRMs. Incorporating histone signature information successfully penalized false prediction and improved the whole performance. The dataset we used and the software are available at http://nash.ucsd.edu/CIS/.
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