1
|
Konkel Z, Kubatko L, Slot JC. CLOCI: unveiling cryptic fungal gene clusters with generalized detection. Nucleic Acids Res 2024:gkae625. [PMID: 39016185 DOI: 10.1093/nar/gkae625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Gene clusters are genomic loci that contain multiple genes that are functionally and genetically linked. Gene clusters collectively encode diverse functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Current detection algorithms focus on canonical 'core' biosynthetic functions many gene clusters encode, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization. We present CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier), an algorithm that identifies gene clusters using multiple proxies of selection for coordinated gene evolution. Our approach generalizes gene cluster detection and gene cluster family circumscription, improves detection of multiple known functional classes, and unveils non-canonical gene clusters. CLOCI is suitable for genome-enabled small molecule mining, and presents an easily tunable approach for delineating gene cluster families and homologous loci.
Collapse
Affiliation(s)
- Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Laura Kubatko
- Department of Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
2
|
Josselin L, Proctor RH, Lippolis V, Cervellieri S, Hoylaerts J, De Clerck C, Fauconnier ML, Moretti A. Does alteration of fumonisin production in Fusarium verticillioides lead to volatolome variation? Food Chem 2024; 438:138004. [PMID: 37983995 DOI: 10.1016/j.foodchem.2023.138004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Fusarium verticillioides, a major fungal pathogen of maize, produces fumonisins, mycotoxins of global food safety concern. Control practices are needed to reduce the negative health and economic impacts of fumonisins. Therefore, we investigated volatile organic compounds (VOCs) emitted by fumonisin-producing (wild-type) and nonproducing (mutant) strains of F. verticillioides. VOC emissions were analyzed by gas chromatography-mass spectrometry following inoculation of maize kernels, and fumonisin accumulation was analyzed by high-performance liquid chromatography. Mutants emitted VOCs, including ethyl 3-methylbutanoate, that the wild type did not emit. In particular, ANOVA analysis showed significant differences between mutants and wild type for 4 VOCs which emission was correlated with absence of fumonisins. Exogenous ethyl 3-methylbutanoate reduced growth and fumonisin production in wild-type F. verticillioides, showing its potential in biocontrol. Together, our findings offer valuable insights into how mycotoxin production can impact VOC emissions from F. verticillioides and reveal a potential biocontrol strategy to reduce fumonisin contamination.
Collapse
Affiliation(s)
- Laurie Josselin
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, Liege University, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology Unit, United States Department of Agriculture (USDA), Agriculture Research Service, National Center for Agricultural Utilization Research, 1815 N. University St. Peoria, IL 61604, USA.
| | - Vincenzo Lippolis
- Institute of Sciences of Food Production, National Research Council of Italy, Via Amendola 122/o, 70126 Bari, Italy.
| | - Salvatore Cervellieri
- Institute of Sciences of Food Production, National Research Council of Italy, Via Amendola 122/o, 70126 Bari, Italy.
| | - Jeffrey Hoylaerts
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, Liege University, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech, Liege University, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Marie-Laure Fauconnier
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, Liege University, Passage des déportés 2, 5030 Gembloux, Belgium.
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research Council of Italy, Via Amendola 122/o, 70126 Bari, Italy.
| |
Collapse
|
3
|
Khatana MA, Jahangir MM, Amjad M, Shahid M. Assessment of agronomic crops-based residues for growth and nutritional profile of Pleurotus eryngii. BRAZ J BIOL 2024; 84:e261752. [DOI: 10.1590/1519-6984.261752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/05/2022] [Indexed: 11/22/2022] Open
Abstract
Abstract Among edible mushrooms, Pleurotus eryngii is unique due to its flavor, admirable medicinal and nutritional profiling. Pakistan is an agricultural country diverse in various crops. However, the residues of the horticultural and agronomic crops are wasted without utilization in the food chain. Hence, a study was performed to assess the performance of relatively low-cost, easily available crops residues i.e. cotton, rice, wheat, mustard and water chestnut for yield and nutrition enhancement of Pleurotus eryngii strains P9 (China) and P10 (PSU-USA). The results revealed that morphological attributes i.e. mycelium run, fruit development, yield and biological efficiency were significantly higher by using cotton waste as compared to other substrates. Regarding biochemical attributes i.e. total soluble solids (12.67 °Brix), phenolics (259.6 mg/100g), moisture (92.3%) and ascorbic acid contents (2.9 mg/100ml) were also significantly higher by using cotton waste. Whereas, acidity (0.30%), reducing sugar (7.67%), non-reducing (4.33%) and total sugars contents (12%) were found highest by using mustard straw. Nutrient analysis of substrates showed that nutrient levels were increased after harvesting of crop as compared to before harvesting levels. Overall results revealed that cotton waste and mustard straw are promising substrates for Pleurotus eryngii better growth and have potential in yield and nutrition enhancement. Moreover, P10 strain performed better as compared to P9.
Collapse
Affiliation(s)
| | | | - M. Amjad
- University of Agriculture, Pakistan
| | | |
Collapse
|
4
|
Hibbard T, McLellan RM, Stevenson LJ, Richardson AT, Nicholson MJ, Parker EJ. Functional Crosstalk between Discrete Indole Terpenoid Gene Clusters in Tolypocladium album. Org Lett 2023; 25:7470-7475. [PMID: 37797949 PMCID: PMC10595974 DOI: 10.1021/acs.orglett.3c02412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Indexed: 10/07/2023]
Abstract
Indole terpenoids make up a large group of secondary metabolites that display an enticing array of bioactivities. While indole diterpene (IDT) and rarely indole sesquiterpene (IST) pathways have been found individually in filamentous fungi, here we show that both cluster types are encoded within the genome of Tolypocladium album. Through heterologous reconstruction, we demonstrate the SES cluster encodes for IST biosynthesis and can tailor IDT substrates produced by the TER cluster.
Collapse
Affiliation(s)
- Taylor
R. Hibbard
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Rose M. McLellan
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Luke J. Stevenson
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Alistair T. Richardson
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Matthew J. Nicholson
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Wellington
UniVentures, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Emily J. Parker
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| |
Collapse
|
5
|
Nickles GR, Oestereicher B, Keller NP, Drott M. Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters. Nucleic Acids Res 2023; 51:7220-7235. [PMID: 37427794 PMCID: PMC10415135 DOI: 10.1093/nar/gkad573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023] Open
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.
Collapse
Affiliation(s)
- Grant R Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Milton T Drott
- USDA-ARS Cereal Disease Lab (CDL), St. Paul, MN 55108, USA
| |
Collapse
|
6
|
Meyer M, Slot J. The evolution and ecology of psilocybin in nature. Fungal Genet Biol 2023; 167:103812. [PMID: 37210028 DOI: 10.1016/j.fgb.2023.103812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
Fungi produce diverse metabolites that can have antimicrobial, antifungal, antifeedant, or psychoactive properties. Among these metabolites are the tryptamine-derived compounds psilocybin, its precursors, and natural derivatives (collectively referred to as psiloids), which have played significant roles in human society and culture. The high allocation of nitrogen to psiloids in mushrooms, along with evidence of convergent evolution and horizontal transfer of psilocybin genes, suggest they provide a selective benefit to some fungi. However, no precise ecological roles of psilocybin have been experimentally determined. The structural and functional similarities of psiloids to serotonin, an essential neurotransmitter in animals, suggest that they may enhance the fitness of fungi through interference with serotonergic processes. However, other ecological mechanisms of psiloids have been proposed. Here, we review the literature pertinent to psilocybin ecology and propose potential adaptive advantages psiloids may confer to fungi.
Collapse
Affiliation(s)
- Matthew Meyer
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA; Environmental Science Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH 43210, USA.
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA; Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
7
|
Cittadino GM, Andrews J, Purewal H, Estanislao Acuña Avila P, Arnone JT. Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya. J Fungi (Basel) 2023; 9:jof9050523. [PMID: 37233234 DOI: 10.3390/jof9050523] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.
Collapse
Affiliation(s)
- Gina M Cittadino
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Johnathan Andrews
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Harpreet Purewal
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | | | - James T Arnone
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| |
Collapse
|
8
|
Nickles GR, Oestereicher B, Keller NP, Drott MT. Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537281. [PMID: 37131656 PMCID: PMC10153163 DOI: 10.1101/2023.04.17.537281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1 / 2 gene cluster family (GCF), which was thought to only exist in yeast, is present in ∼30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or horizontal gene transfers have shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website ( www.isocyanides.fungi.wisc.edu ) that facilitates the exploration, filtering, and downloading of all identified fungal ICS BGCs and GCFs.
Collapse
Affiliation(s)
- Grant R. Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | |
Collapse
|
9
|
Llewellyn T, Nowell RW, Aptroot A, Temina M, Prescott TAK, Barraclough TG, Gaya E. Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota). Genome Biol Evol 2023; 15:6986375. [PMID: 36634008 PMCID: PMC9907504 DOI: 10.1093/gbe/evad002] [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: 09/26/2022] [Revised: 11/25/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.
Collapse
Affiliation(s)
| | - Reuben W Nowell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Andre Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070-900, Brazil
| | - Marina Temina
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa, 3498838, Israel
| | - Thomas A K Prescott
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, SL5 7PY, UK,Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, TW9 3DS, UK
| |
Collapse
|
10
|
Li Y, Liu H, Steenwyk JL, LaBella AL, Harrison MC, Groenewald M, Zhou X, Shen XX, Zhao T, Hittinger CT, Rokas A. Contrasting modes of macro and microsynteny evolution in a eukaryotic subphylum. Curr Biol 2022; 32:5335-5343.e4. [PMID: 36334587 PMCID: PMC10615371 DOI: 10.1016/j.cub.2022.10.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
Examination of the changes in order and arrangement of homologous genes is key for understanding the mechanisms of genome evolution in eukaryotes. Previous comparisons between eukaryotic genomes have revealed considerable conservation across species that diverged hundreds of millions of years ago (e.g., vertebrates,1,2,3 bilaterian animals,4,5 and filamentous fungi6). However, understanding how genome organization evolves within and between eukaryotic major lineages remains underexplored. We analyzed high-quality genomes of 120 representative budding yeast species (subphylum Saccharomycotina) spanning ∼400 million years of eukaryotic evolution to examine how their genome organization evolved and to compare it with the evolution of animal and plant genome organization.7 We found that the decay of both macrosynteny (the conservation of homologous chromosomes) and microsynteny (the conservation of local gene content and order) was strongly associated with evolutionary divergence across budding yeast major clades. However, although macrosynteny decayed very fast, within ∼100 million years, the microsynteny of many genes-especially genes in metabolic clusters (e.g., in the GAL gene cluster8)-was much more deeply conserved both within major clades and across the subphylum. We further found that when genomes with similar evolutionary divergence times were compared, budding yeasts had lower macrosynteny conservation than animals and filamentous fungi but higher conservation than angiosperms. In contrast, budding yeasts had levels of microsynteny conservation on par with mammals, whereas angiosperms exhibited very low conservation. Our results provide new insight into the tempo and mode of the evolution of gene and genome organization across an entire eukaryotic subphylum.
Collapse
Affiliation(s)
- Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China.
| | - Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA
| | - Marizeth Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, 483 Wushan Road, Guangzhou 520643, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Taicheng Road 3, Yangling 712100, China
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, 1552 University Avenue, University of Wisconsin-Madison, Madison, WI 53726-4084, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, VU Station B#35-1634, Nashville, TN 37235, USA; Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.
| |
Collapse
|
11
|
Gong J, Peng Y, Yu J, Pei W, Zhang Z, Fan D, Liu L, Xiao X, Liu R, Lu Q, Li P, Shang H, Shi Y, Li J, Ge Q, Liu A, Deng X, Fan S, Pan J, Chen Q, Yuan Y, Gong W. Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in upland cotton. Comput Struct Biotechnol J 2022; 20:1841-1859. [PMID: 35521543 PMCID: PMC9046884 DOI: 10.1016/j.csbj.2022.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022] Open
Abstract
Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In ‘CCRI70′ RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In ‘0-153′ RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, LtnD, PGK, LPLAT1, and PAH2, formed hub genes and two of them, FER and RAV1, formed the key genes in the interaction network. Sequence variations in the coding regions of LtnD, FER, PGK, LPLAT1, and PAH2 genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds.
Collapse
Affiliation(s)
- Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yan Peng
- Third Division of the Xinjiang Production and Construction Corps Agricultural Research Institute, Tumushuke, Xijiang 843900, China
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Daoran Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Linjie Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Xianghui Xiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Ruixian Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Quanwei Lu
- College of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Pengtao Li
- College of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, Xinjiang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| |
Collapse
|
12
|
The evolution of the GALactose utilization pathway in budding yeasts. Trends Genet 2022; 38:97-106. [PMID: 34538504 PMCID: PMC8678326 DOI: 10.1016/j.tig.2021.08.013] [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: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 01/03/2023]
Abstract
The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker's yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the sugar galactose for energy and biomass production. The GAL pathway has long served as a model system for understanding how eukaryotic metabolic pathways, including their modes of regulation, evolve. More recently, the physical linkage of the structural genes GAL1, GAL7, and GAL10 in diverse budding yeast genomes has been used as a model for understanding the evolution of gene clustering. In this review, we summarize exciting recent work on three different aspects of this iconic pathway's evolution: gene cluster organization, GAL gene regulation, and the population genetics of the GAL pathway.
Collapse
|
13
|
Zinani OQH, Keseroğlu K, Özbudak EM. Regulatory mechanisms ensuring coordinated expression of functionally related genes. Trends Genet 2022; 38:73-81. [PMID: 34376301 PMCID: PMC8678166 DOI: 10.1016/j.tig.2021.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/03/2023]
Abstract
Coordinated spatiotemporal expression of large sets of genes is required for the development and homeostasis of organisms. To achieve this goal, organisms use myriad strategies where they form operons, utilize bidirectional promoters, cluster genes, share enhancers among genes by DNA looping, and form topologically associated domains and transcriptional condensates. Coexpression achieved by these different strategies is hypothesized to have functional importance in minimizing gene expression variability, establishing dosage balance to ensure stoichiometry of protein complexes, and minimizing accumulation of toxic intermediate metabolites. By combining gene-editing tools with computational modeling, recent studies tested the advantages of adjacent genes located in pairs and clusters. We propose that with the advancement of gene editing, single-cell sequencing, and imaging tools, one could readily test the functional importance of different coexpression strategies in a variety of biological processes.
Collapse
Affiliation(s)
- Oriana Q H Zinani
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kemal Keseroğlu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M Özbudak
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| |
Collapse
|
14
|
Nagel JH, Wingfield MJ, Slippers B. Next-generation sequencing provides important insights into the biology and evolution of the Botryosphaeriaceae. FUNGAL BIOL REV 2021. [DOI: 10.1016/j.fbr.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
15
|
Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
Collapse
Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
16
|
Bokor E, Flipphi M, Kocsubé S, Ámon J, Vágvölgyi C, Scazzocchio C, Hamari Z. Genome organization and evolution of a eukaryotic nicotinate co-inducible pathway. Open Biol 2021; 11:210099. [PMID: 34582709 PMCID: PMC8478523 DOI: 10.1098/rsob.210099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In Aspergillus nidulans a regulon including 11 hxn genes (hxnS, T, R, P, Y, Z, X, W, V, M and N) is inducible by a nicotinate metabolic derivative, repressible by ammonium and under stringent control of the nitrogen-state-sensitive GATA factor AreA and the specific transcription factor HxnR. This is the first report in a eukaryote of the genomic organization of a possibly complete pathway of nicotinate utilization. In A. nidulans the regulon is organized in three distinct clusters, this organization is variable in the Ascomycota. In some Pezizomycotina species all 11 genes map in a single cluster; in others they map in two clusters. This variable organization sheds light on cluster evolution. Instances of gene duplication followed by or simultaneous with integration in the cluster, partial or total cluster loss, and horizontal gene transfer of several genes (including an example of whole cluster re-acquisition in Aspergillus of section Flavi) were detected, together with the incorporation in some clusters of genes not found in the A. nidulans co-regulated regulon, which underlie both the plasticity and the reticulate character of metabolic cluster evolution. This study provides a comprehensive phylogeny of six members of the cluster across representatives of all Ascomycota classes.
Collapse
Affiliation(s)
- Eszter Bokor
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Michel Flipphi
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Sándor Kocsubé
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Judit Ámon
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, UK,Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Zsuzsanna Hamari
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary
| |
Collapse
|
17
|
Abstract
Historically, it has been understood that for gene expression in eukaryotes, each messenger RNA encodes a single protein. With the recent development of technologies to sequence full-length transcripts en masse, we have discovered hundreds of examples in two species of green algae where two, three, or more proteins are translated from a single transcript. These “polycistronic” transcripts are found in diverse species throughout the green algal lineage, which highlights their biological importance. We have leveraged these findings to coexpress pairs of genes on polycistronic transcripts in vitro, which should facilitate efforts to engineer algae for research and industrial applications. Polycistronic gene expression, common in prokaryotes, was thought to be extremely rare in eukaryotes. The development of long-read sequencing of full-length transcript isomers (Iso-Seq) has facilitated a reexamination of that dogma. Using Iso-Seq, we discovered hundreds of examples of polycistronic expression of nuclear genes in two divergent species of green algae: Chlamydomonas reinhardtii and Chromochloris zofingiensis. Here, we employ a range of independent approaches to validate that multiple proteins are translated from a common transcript for hundreds of loci. A chromatin immunoprecipitation analysis using trimethylation of lysine 4 on histone H3 marks confirmed that transcription begins exclusively at the upstream gene. Quantification of polyadenylated [poly(A)] tails and poly(A) signal sequences confirmed that transcription ends exclusively after the downstream gene. Coexpression analysis found nearly perfect correlation for open reading frames (ORFs) within polycistronic loci, consistent with expression in a shared transcript. For many polycistronic loci, terminal peptides from both ORFs were identified from proteomics datasets, consistent with independent translation. Synthetic polycistronic gene pairs were transcribed and translated in vitro to recapitulate the production of two distinct proteins from a common transcript. The relative abundance of these two proteins can be modified by altering the Kozak-like sequence of the upstream gene. Replacement of the ORFs with selectable markers or reporters allows production of such heterologous proteins, speaking to utility in synthetic biology approaches. Conservation of a significant number of polycistronic gene pairs between C. reinhardtii, C. zofingiensis, and five other species suggests that this mechanism may be evolutionarily ancient and biologically important in the green algal lineage.
Collapse
|
18
|
Acyltransferase AniI, a Tailoring Enzyme with Broad Substrate Tolerance for High-Level Production of Anisomycin. Appl Environ Microbiol 2021; 87:e0017221. [PMID: 33931417 DOI: 10.1128/aem.00172-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anisomycin (compound 1), a pyrrolidine antibiotic, exhibits diverse biological and pharmacologic activities. The biosynthetic gene cluster of compound 1 has been identified previously, and the multistep assembly of the core benzylpyrrolidine scaffold was characterized. However, enzymatic modifications, such as acylation, involved in compound 1 biosynthesis are unknown. In this study, the genetic manipulation of aniI proved that it encoded an indispensable acetyltransferase for compound 1 biosynthesis. Bioinformatics analysis suggested AniI as a member of maltose (MAT) and galactoside O-acetyltransferases (GAT) with C-terminal left-handed parallel beta-helix (LbH) subdomain, which were referred to as LbH-MAT-GAT sugar O-acetyltransferases. However, the biochemical assay identified that its target site was the hydroxyl group of the pyrrolidine ring. AniI was found to be tolerant of acyl donors with different chain lengths for the biosynthesis of compound 1 and derivatives 12 and 13 with butyryl and isovaleryl groups, respectively. Meanwhile, it showed comparable activity toward biosynthetic intermediates and synthesized analogues, suggesting promiscuity to the pyrrolidine ring structure of compound 1. These data may inspire new viable synthetic routes for the construction of more complex pyrrolidine ring scaffolds in compound 1. Finally, the overexpression of aniI under the control of strong promoters contributed to the higher productivities of compound 1 and its analogues. These findings reported here not only improve the understanding of anisomycin biosynthesis but also expand the substrate scope of O-acetyltransferase working on the pyrrolidine ring and pave the way for future metabolic engineering construction of high-yield strains. IMPORTANCE Acylation is an important tailoring reaction during natural product biosynthesis. Acylation could increase the structural diversity and affect the chemical stability, volatility, biological activity, and even the cellular localization of specialized compounds. Many acetyltransferases have been reported in natural product biosynthesis. The typical example of the LbH-MAT-GAT sugar O-acetyltransferase subfamily was reported to catalyze the coenzyme A (CoA)-dependent acetylation of the 6-hydroxyl group of sugars. However, no protein of this family has been characterized to acetylate a nonsugar secondary metabolic product. Here, AniI was found to catalyze the acylation of the hydroxyl group of the pyrrolidine ring and be tolerant of diverse acyl donors and acceptors, which made the biosynthesis more efficient and exclusive for biosynthesis of compound 1 and its derivatives. Moreover, the overexpression of aniI serves as a successful example of genetic manipulation of a modification gene for the high production of final products and might set the stage for future metabolic engineering.
Collapse
|
19
|
Foflonker F, Blaby-Haas CE. Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery. Mol Biol Evol 2021; 38:650-662. [PMID: 32886760 PMCID: PMC7826186 DOI: 10.1093/molbev/msaa221] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.
Collapse
|
20
|
Venkatesh A, Murray AL, Coughlan AY, Wolfe KH. Giant GAL gene clusters for the melibiose-galactose pathway in Torulaspora. Yeast 2021; 38:117-126. [PMID: 33141945 PMCID: PMC7898345 DOI: 10.1002/yea.3532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/19/2022] Open
Abstract
In many yeast species, the three genes at the centre of the galactose catabolism pathway, GAL1, GAL10 and GAL7, are neighbours in the genome and form a metabolic gene cluster. We report here that some yeast strains in the genus Torulaspora have much larger GAL clusters that include genes for melibiase (MEL1), galactose permease (GAL2), glucose transporter (HGT1), phosphoglucomutase (PGM1) and the transcription factor GAL4, in addition to GAL1, GAL10, and GAL7. Together, these eight genes encode almost all the steps in the pathway for catabolism of extracellular melibiose (a disaccharide of galactose and glucose). We show that a progenitor 5-gene cluster containing GAL 7-1-10-4-2 was likely present in the common ancestor of Torulaspora and Zygotorulaspora. It added PGM1 and MEL1 in the ancestor of most Torulaspora species. It underwent further expansion in the T. pretoriensis clade, involving the fusion of three progenitor clusters in tandem and the gain of HGT1. These giant GAL clusters are highly polymorphic in structure, and subject to horizontal transfers, pseudogenization and gene losses. We identify recent horizontal transfers of complete GAL clusters from T. franciscae into one strain of T. delbrueckii, and from a relative of T. maleeae into one strain of T. globosa. The variability and dynamic evolution of GAL clusters in Torulaspora indicates that there is strong natural selection on the GAL pathway in this genus.
Collapse
Affiliation(s)
- Anjan Venkatesh
- UCD Conway Institute and School of MedicineUniversity College DublinDublinIreland
| | - Anthony L. Murray
- UCD Conway Institute and School of MedicineUniversity College DublinDublinIreland
| | - Aisling Y. Coughlan
- UCD Conway Institute and School of MedicineUniversity College DublinDublinIreland
| | - Kenneth H. Wolfe
- UCD Conway Institute and School of MedicineUniversity College DublinDublinIreland
| |
Collapse
|
21
|
Hagee D, Abu Hardan A, Botero J, Arnone JT. Genomic clustering within functionally related gene families in Ascomycota fungi. Comput Struct Biotechnol J 2020; 18:3267-3277. [PMID: 33209211 PMCID: PMC7653285 DOI: 10.1016/j.csbj.2020.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022] Open
Abstract
Multiple mechanisms collaborate for proper regulation of gene expression. One layer of this regulation is through the clustering of functionally related genes at discrete loci throughout the genome. This phenomenon occurs extensively throughout Ascomycota fungi and is an organizing principle for many gene families whose proteins participate in diverse molecular functions throughout the cell. Members of this phylum include organisms that serve as model systems and those of interest medically, pharmaceutically, and for industrial and biotechnological applications. In this review, we discuss the prevalence of functional clustering through a broad range of organisms within the phylum. Position effects on transcription, genomic locations of clusters, transcriptional regulation of clusters, and selective pressures contributing to the formation and maintenance of clusters are addressed, as are common methods to identify and characterize clusters.
Collapse
Affiliation(s)
- Danielle Hagee
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Ahmad Abu Hardan
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Juan Botero
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - James T. Arnone
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| |
Collapse
|
22
|
Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
Collapse
Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
| |
Collapse
|
23
|
Rokas A, Mead ME, Steenwyk JL, Raja HA, Oberlies NH. Biosynthetic gene clusters and the evolution of fungal chemodiversity. Nat Prod Rep 2020; 37:868-878. [PMID: 31898704 PMCID: PMC7332410 DOI: 10.1039/c9np00045c] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: up to 2019Fungi produce a remarkable diversity of secondary metabolites: small, bioactive molecules not required for growth but which are essential to their ecological interactions with other organisms. Genes that participate in the same secondary metabolic pathway typically reside next to each other in fungal genomes and form biosynthetic gene clusters (BGCs). By synthesizing state-of-the-art knowledge on the evolution of BGCs in fungi, we propose that fungal chemodiversity stems from three molecular evolutionary processes involving BGCs: functional divergence, horizontal transfer, and de novo assembly. We provide examples of how these processes have contributed to the generation of fungal chemodiversity, discuss their relative importance, and outline major, outstanding questions in the field.
Collapse
Affiliation(s)
- Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
| | | | | | | | | |
Collapse
|
24
|
Khan RAA, Najeeb S, Hussain S, Xie B, Li Y. Bioactive Secondary Metabolites from Trichoderma spp. against Phytopathogenic Fungi. Microorganisms 2020; 8:E817. [PMID: 32486107 PMCID: PMC7356054 DOI: 10.3390/microorganisms8060817] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/05/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023] Open
Abstract
Phytopathogenic fungi, causing significant economic and production losses, are becoming a serious threat to global food security. Due to an increase in fungal resistance and the hazardous effects of chemical fungicides to human and environmental health, scientists are now engaged to explore alternate non-chemical and ecofriendly management strategies. The use of biocontrol agents and their secondary metabolites (SMs) is one of the potential approaches used today. Trichoderma spp. are well known biocontrol agents used globally. Many Trichoderma species are the most prominent producers of SMs with antimicrobial activity against phytopathogenic fungi. Detailed information about these secondary metabolites, when grouped together, enhances the understanding of their efficient utilization and further exploration of new bioactive compounds for the management of plant pathogenic fungi. The current literature provides the information about SMs of Trichoderma spp. in a different context. In this review, we summarize and group different antifungal SMs of Trichoderma spp. against phytopathogenic fungi along with a comprehensive overview of some aspects related to their chemistry and biosynthesis. Moreover, a brief overview of the biosynthesis pathway, action mechanism, and different approaches for the analysis of SMs and the factors affecting the regulation of SMs in Trichoderma is also discussed.
Collapse
Affiliation(s)
- Raja Asad Ali Khan
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| | - Saba Najeeb
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| | - Shaukat Hussain
- Department of Plant Pathology, The University of Agriculture Peshawar, Peshawar 25130, Pakistan;
| | - Bingyan Xie
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| | - Yan Li
- Institute of Vegetables and Flowers (Plant Pathology Lab), Chinese Academy of Agricultural Sciences, Beijing 100081, China; (R.A.A.K.); (S.N.)
| |
Collapse
|
25
|
Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis. Microorganisms 2020; 8:microorganisms8030321. [PMID: 32110897 PMCID: PMC7143498 DOI: 10.3390/microorganisms8030321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/02/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022] Open
Abstract
The growing global population and developing world has put a strain on non-renewable natural resources, such as fuels. The shift to renewable sources will, thus, help meet demands, often through the modification of existing biosynthetic pathways or the introduction of novel pathways into non-native species. There are several useful biosynthetic pathways endogenous to organisms that are not conducive for the scale-up necessary for industrial use. The use of genetic and synthetic biological approaches to engineer these pathways in non-native organisms can help ameliorate these challenges. The budding yeast Saccharomyces cerevisiae offers several advantages for genetic engineering for this purpose due to its widespread use as a model system studied by many researchers. The focus of this review is to present a primer on understanding genomic considerations prior to genetic modification and manipulation of S. cerevisiae. The choice of a site for genetic manipulation can have broad implications on transcription throughout a region and this review will present the current understanding of position effects on transcription.
Collapse
|
26
|
Xu H, Liu JJ, Liu Z, Li Y, Jin YS, Zhang J. Synchronization of stochastic expressions drives the clustering of functionally related genes. SCIENCE ADVANCES 2019; 5:eaax6525. [PMID: 31633028 PMCID: PMC6785257 DOI: 10.1126/sciadv.aax6525] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 05/18/2023]
Abstract
Functionally related genes tend to be chromosomally clustered in eukaryotic genomes even after the exclusion of tandem duplicates, but the biological significance of this widespread phenomenon is unclear. We propose that stochastic expression fluctuations of neighboring genes resulting from chromatin dynamics are more or less synchronized such that their expression ratio is more stable than that for unlinked genes. Consequently, chromosomal clustering could be advantageous when the expression ratio of the clustered genes needs to stay constant, for example, because of the accumulation of toxic compounds when this ratio is altered. Evidence from manipulative experiments on the yeast GAL cluster, comprising three chromosomally adjacent genes encoding enzymes catalyzing consecutive reactions in galactose catabolism, unequivocally supports this hypothesis and elucidates how disorder in one biological phenomenon-gene expression noise-could prompt the emergence of order in another-genome organization.
Collapse
Affiliation(s)
- Haiqing Xu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhen Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ying Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
27
|
Sun M, Zhang J. Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PLoS Genet 2019; 15:e1008389. [PMID: 31525198 PMCID: PMC6762216 DOI: 10.1371/journal.pgen.1008389] [Citation(s) in RCA: 14] [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: 06/06/2019] [Revised: 09/26/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Gene expression is subject to stochastic noise, but to what extent and by which means such stochastic variations are coordinated among different genes are unclear. We hypothesize that neighboring genes on the same chromosome co-fluctuate in expression because of their common chromatin dynamics, and verify it at the genomic scale using allele-specific single-cell RNA-sequencing data of mouse cells. Unexpectedly, the co-fluctuation extends to genes that are over 60 million bases apart. We provide evidence that this long-range effect arises in part from chromatin co-accessibilities of linked loci attributable to three-dimensional proximity, which is much closer intra-chromosomally than inter-chromosomally. We further show that genes encoding components of the same protein complex tend to be chromosomally linked, likely resulting from natural selection for intracellular among-component dosage balance. These findings have implications for both the evolution of genome organization and optimal design of synthetic genomes in the face of gene expression noise.
Collapse
Affiliation(s)
- Mengyi Sun
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| |
Collapse
|
28
|
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: 111] [Impact Index Per Article: 22.2] [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.
Collapse
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
| |
Collapse
|
29
|
Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
Collapse
Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
30
|
Yi X, Gao Q, Zhang L, Wang X, He Y, Hu F, Zhang J, Zou G, Yang S, Zhou Z, Bao J. Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn stover. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:126. [PMID: 31139256 PMCID: PMC6528196 DOI: 10.1186/s13068-019-1466-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 05/10/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Fast, complete, and ultimate removal of inhibitory compounds derived from lignocellulose pretreatment is the prerequisite for efficient production of cellulosic ethanol and biochemicals. Biodetoxification is the most promising method for inhibitor removal by its unique advantages. The biodetoxification mechanisms of a unique diploid fungus responsible for highly efficient biodetoxification in solid-state culture was extensively investigated in the aspects of cellular structure, genome sequencing, transcriptome analysis, and practical biodetoxification. RESULTS The inborn heterozygous diploid structure of A. resinae ZN1 uniquely contributed to the enhancement of inhibitor tolerance and conversion. The co-expression of gene pairs contributed to the enhancement of the degradation of lignocellulose-derived model inhibitors. The ultimate inhibitors degradation pathways and sugar conservation were elucidated by microbial degradation experimentation as well as the genomic and transcriptomic sequencing analysis. CONCLUSIONS The finding of the heterozygous diploid structure in A. resinae ZN1 on biodetoxification took the first insight into the global overview of biodetoxification mechanism of lignocellulose-derived inhibitors. This study provided a unique and practical biodetoxification biocatalyst of inhibitor compounds for lignocellulose biorefinery processing, as well as the synthetic biology tools on biodetoxification of biorefinery fermenting strains.
Collapse
Affiliation(s)
- Xia Yi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
- Jiangxi Provincial Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000 China
| | - Qiuqiang Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Lei Zhang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Xia Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
- Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yanqing He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Fengxian Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Jian Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Gen Zou
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Shihui Yang
- Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Zhihua Zhou
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| |
Collapse
|
31
|
Olarte RA, Menke J, Zhang Y, Sullivan S, Slot JC, Huang Y, Badalamenti JP, Quandt AC, Spatafora JW, Bushley KE. Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum. BMC Genomics 2019; 20:120. [PMID: 30732559 PMCID: PMC6367777 DOI: 10.1186/s12864-018-5399-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/19/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Genes involved in production of secondary metabolites (SMs) in fungi are exceptionally diverse. Even strains of the same species may exhibit differences in metabolite production, a finding that has important implications for drug discovery. Unlike in other eukaryotes, genes producing SMs are often clustered and co-expressed in fungal genomes, but the genetic mechanisms involved in the creation and maintenance of these secondary metabolite biosynthetic gene clusters (SMBGCs) remains poorly understood. RESULTS In order to address the role of genome architecture and chromosome scale structural variation in generating diversity of SMBGCs, we generated chromosome scale assemblies of six geographically diverse isolates of the insect pathogenic fungus Tolypocladium inflatum, producer of the multi-billion dollar lifesaving immunosuppressant drug cyclosporin, and utilized a Hi-C chromosome conformation capture approach to address the role of genome architecture and structural variation in generating intraspecific diversity in SMBGCs. Our results demonstrate that the exchange of DNA between heterologous chromosomes plays an important role in generating novelty in SMBGCs in fungi. In particular, we demonstrate movement of a polyketide synthase (PKS) and several adjacent genes by translocation to a new chromosome and genomic context, potentially generating a novel PKS cluster. We also provide evidence for inter-chromosomal recombination between nonribosomal peptide synthetases located within subtelomeres and uncover a polymorphic cluster present in only two strains that is closely related to the cluster responsible for biosynthesis of the mycotoxin aflatoxin (AF), a highly carcinogenic compound that is a major public health concern worldwide. In contrast, the cyclosporin cluster, located internally on chromosomes, was conserved across strains, suggesting selective maintenance of this important virulence factor for infection of insects. CONCLUSIONS This research places the evolution of SMBGCs within the context of whole genome evolution and suggests a role for recombination between chromosomes in generating novel SMBGCs in the medicinal fungus Tolypocladium inflatum.
Collapse
Affiliation(s)
- Rodrigo A. Olarte
- 0000000419368657grid.17635.36Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN USA
| | - Jon Menke
- 0000 0001 0703 5300grid.450240.7Cargill Inc., Wayzata, MN USA
| | - Ying Zhang
- 0000000419368657grid.17635.36Minnesota Supercomputing Institute, Minneapolis, MN USA
| | | | - Jason C. Slot
- 0000 0001 2285 7943grid.261331.4Department of Plant Pathology, Ohio State University, Columbus, OH USA
| | - Yinyin Huang
- 0000000419368657grid.17635.36Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN USA
| | - Jonathan P. Badalamenti
- 0000000419368657grid.17635.36University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN USA
| | - Alisha C. Quandt
- 0000000096214564grid.266190.aDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO USA
| | - Joseph W. Spatafora
- 0000 0001 2112 1969grid.4391.fDepartment of Botany and Plant Pathology, Oregon State University, Corvallis, OR USA
| | - Kathryn E. Bushley
- 0000000419368657grid.17635.36Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN USA
| |
Collapse
|
32
|
Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function. Toxins (Basel) 2019; 11:toxins11010036. [PMID: 30646506 PMCID: PMC6357111 DOI: 10.3390/toxins11010036] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/15/2018] [Accepted: 01/08/2019] [Indexed: 01/07/2023] Open
Abstract
Food security is a global concern. Fusarium are among the most economically important fungal pathogens because they are ubiquitous, disease management remains a challenge, they produce mycotoxins that affect food and feed safety, and trichothecene mycotoxin production can increase the pathogenicity of some Fusarium species depending on the host species. Although trichothecenes may differ in structure by their patterns of hydroxylation or acetylation, these small changes have a significant impact on toxicity and the biological activity of these compounds. Therefore, detecting and identifying which chemotype is present in a given population are important to predicting the specific toxins that may be produced and, therefore, to evaluating the risk of exposure. Due to the challenges of inducing trichothecene production by Fusarium isolates in vitro for subsequent chemical analysis, PCR assays using gene-specific primers, either singly or in combination, designed against specific genes of the trichothecene gene cluster of multiple species of Fusarium have been developed. The establishment of TRI genotypes that potentially correspond to a specific chemotype requires examination of an information and knowledge pipeline whose critical aspects in sequential order are: (i) understanding the TRI gene cluster organization which differs according to Fusarium species under study; (ii) knowledge of the re-arrangements to the core TRI gene cluster over evolutionary time, which also differs according to Fusarium species; (iii) the functions of the TRI genes in the biosynthesis of trichothecene analogs; and (iv) based on (i)⁻(iii), selection of appropriate target TRI gene(s) for primer design in PCR amplification for the Fusarium species under study. This review, therefore, explains this pipeline and its connection to utilizing TRI genotypes as a possible proxy to chemotype designation.
Collapse
|
33
|
Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. The renaissance of comparative biochemistry. AMERICAN JOURNAL OF BOTANY 2019; 106:3-13. [PMID: 30629738 DOI: 10.1002/ajb2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
34
|
Moreno LF, Vicente VA, de Hoog S. Black yeasts in the omics era: Achievements and challenges. Med Mycol 2018. [PMID: 29538737 DOI: 10.1093/mmy/myx129] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Black yeasts (BY) comprise a group of polyextremotolerant fungi, mainly belonging to the order Chaetothyriales, which are capable of colonizing a wide range of extreme environments. The tolerance to hostile habitats can be explained by their intrinsic ability to survive under acidic, alkaline, and toxic conditions, high temperature, low nutrient availability, and osmotic and mechanical stress. Occasionally, some species can cause human chromoblastomycosis, a chronic subcutaneous infection, as well as disseminated or cerebral phaeohyphomycosis. Three years after the release of the first black yeast genome, the number of projects for sequencing these organisms has significantly increased. Over 37 genomes of important opportunistic and saprobic black yeasts and relatives are now available in different databases. The whole-genome sequencing, as well as the analysis of differentially expressed mRNAs and the determination of protein expression profiles generated an unprecedented amount of data, requiring the development of a curated repository to provide easy accesses to this information. In the present article, we review various aspects of the impact of genomics, transcriptomics, and proteomics on black yeast studies. We discuss recent key findings achieved by the use of these technologies and further directions for medical mycology in this area. An important vehicle is the Working Groups on Black Yeasts and Chromoblastomycosis, under the umbrella of ISHAM, which unite the clinicians and a highly diverse population of fundamental scientists to exchange data for joint publications.
Collapse
Affiliation(s)
- Leandro Ferreira Moreno
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands.,Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazil
| | | | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands.,Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazil.,Center of Expertise in Mycology of Radboudumc / CWZ, Nijmegen, The Netherlands
| |
Collapse
|
35
|
Gluck‐Thaler E, Vijayakumar V, Slot JC. Fungal adaptation to plant defences through convergent assembly of metabolic modules. Mol Ecol 2018; 27:5120-5136. [DOI: 10.1111/mec.14943] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/14/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Emile Gluck‐Thaler
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences The Ohio State University Columbus Ohio
| | - Vinod Vijayakumar
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences The Ohio State University Columbus Ohio
| | - Jason C. Slot
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences The Ohio State University Columbus Ohio
| |
Collapse
|
36
|
Abstract
In bacteria, more than half of the genes in the genome are organized in operons. In contrast, in eukaryotes, functionally related genes are usually dispersed across the genome. There are, however, numerous examples of functional clusters of nonhomologous genes for metabolic pathways in fungi and plants. Despite superficial similarities with operons (physical clustering, coordinate regulation), these clusters have not usually originated by horizontal gene transfer from bacteria, and (unlike operons) the genes are typically transcribed separately rather than as a single polycistronic message. This clustering phenomenon raises intriguing questions about the origins of clustered metabolic pathways in eukaryotes and the significance of clustering for pathway function. Here we review metabolic gene clusters from fungi and plants, highlight commonalities and differences, and consider how these clusters form and are regulated. We also identify opportunities for future research in the areas of large-scale genomics, synthetic biology, and experimental evolution.
Collapse
Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom; .,Current affiliation: Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom;
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London SW7 2AZ, United Kingdom; .,Institute for Integrative Biology of the Cell, 91190 Gif-sur-Yvette, France
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom;
| |
Collapse
|
37
|
Ámon J, Fernández-Martín R, Bokor E, Cultrone A, Kelly JM, Flipphi M, Scazzocchio C, Hamari Z. A eukaryotic nicotinate-inducible gene cluster: convergent evolution in fungi and bacteria. Open Biol 2018; 7:rsob.170199. [PMID: 29212709 PMCID: PMC5746545 DOI: 10.1098/rsob.170199] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/09/2017] [Indexed: 12/23/2022] Open
Abstract
Nicotinate degradation has hitherto been elucidated only in bacteria. In the ascomycete Aspergillus nidulans, six loci, hxnS/AN9178 encoding the molybdenum cofactor-containing nicotinate hydroxylase, AN11197 encoding a Cys2/His2 zinc finger regulator HxnR, together with AN11196/hxnZ, AN11188/hxnY, AN11189/hxnP and AN9177/hxnT, are clustered and stringently co-induced by a nicotinate derivative and subject to nitrogen metabolite repression mediated by the GATA factor AreA. These genes are strictly co-regulated by HxnR. Within the hxnR gene, constitutive mutations map in two discrete regions. Aspergillus nidulans is capable of using nicotinate and its oxidation products 6-hydroxynicotinic acid and 2,5-dihydroxypyridine as sole nitrogen sources in an HxnR-dependent way. HxnS is highly similar to HxA, the canonical xanthine dehydrogenase (XDH), and has originated by gene duplication, preceding the origin of the Pezizomycotina. This cluster is conserved with some variations throughout the Aspergillaceae. Our results imply that a fungal pathway has arisen independently from bacterial ones. Significantly, the neo-functionalization of XDH into nicotinate hydroxylase has occurred independently from analogous events in bacteria. This work describes for the first time a gene cluster involved in nicotinate catabolism in a eukaryote and has relevance for the formation and evolution of co-regulated primary metabolic gene clusters and the microbial degradation of N-heterocyclic compounds.
Collapse
Affiliation(s)
- Judit Ámon
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH)
| | | | - Eszter Bokor
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH)
| | - Antonietta Cultrone
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Joan M Kelly
- Department of Biology, University of Essex, Colchester, UK
| | - Michel Flipphi
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| | - Claudio Scazzocchio
- Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France .,Department of Biology, University of Essex, Colchester, UK.,Department of Microbiology, Imperial College, London, UK (present address of CS).,Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France (present address of CS)
| | - Zsuzsanna Hamari
- Department of Microbiology, University of Szeged Faculty of Science and Informatics, Szeged, Hungary (present address of ZH) .,Institute de Génétique et Microbiologie, Université Paris-Sud, Orsay, France
| |
Collapse
|
38
|
Olsen KM, Small LL. Micro- and macroevolutionary adaptation through repeated loss of a complete metabolic pathway. THE NEW PHYTOLOGIST 2018; 219:757-766. [PMID: 29708583 DOI: 10.1111/nph.15184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/27/2018] [Indexed: 05/27/2023]
Abstract
There is growing evidence for the convergent evolution of physically linked gene clusters encoding chemical defense pathways. Metabolic clusters are proposed to evolve because they ensure co-inheritance of all required genes where the defense is favored, and prevent inheritance of toxic partial pathways where it is not. This hypothesis rests on the assumption that clusters evolve in species where selection favors intraspecific polymorphism for the defense; however, they have not been examined in polymorphic species. We examined metabolic cluster evolution in relation to an adaptive polymorphism for cyanogenic glucoside (CNglc) production in clover. Using 163 accessions, we performed CNglc assays, BAC sequencing, Southern hybridizations and molecular evolutionary analyses. We find that the CNglc pathway forms a 138-kb cluster in white clover, and that the adaptive polymorphism occurs through presence/absence of the complete cluster. Component genes are orthologous to those in the distantly related legume Lotus japonicus. These findings provide empirical support for the co-inheritance hypothesis, and they indicate that adaptive CNglc variation in white clover evolves through recurrent deletions of the entire pathway. They further indicate that the shared ancestor of many important legume crops was likely cyanogenic and that this defense was lost repeatedly over the last 50 Myr.
Collapse
Affiliation(s)
- Kenneth M Olsen
- Biology Department, Washington University, Campus Box 1137, St Louis, MO, 63130-4899, USA
| | - Linda L Small
- Biology Department, Washington University, Campus Box 1137, St Louis, MO, 63130-4899, USA
| |
Collapse
|
39
|
Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum. Proc Natl Acad Sci U S A 2018; 115:E5459-E5466. [PMID: 29844193 PMCID: PMC6004482 DOI: 10.1073/pnas.1712798115] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species in the fungal genus Cercospora cause diseases in many important crops worldwide. Their success as pathogens is largely due to the secretion of cercosporin during infection. We report that the cercosporin toxin biosynthesis (CTB) gene cluster is ancient and was horizontally transferred to diverse fungal plant pathogens. Because our analyses revealed genes adjacent to the established CTB cluster with similar evolutionary trajectories, we evaluated their role in Cercospora beticola to show that four are necessary for cercosporin biosynthesis. Lastly, we confirmed that the apple pathogen Colletotrichum fioriniae produces cercosporin, the first case outside the family Mycosphaerellaceae. Other Colletotrichum plant pathogens also harbor the CTB cluster, which points to a wider role that this toxin may play in virulence. Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean, and other major food crops. Here, we sequenced the genome of the sugar beet pathogen Cercospora beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide-host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to rely on an eight-gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein, previously shown to be involved with cercosporin autoresistance, and four additional genes required for cercosporin biosynthesis, including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Lastly, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.
Collapse
|
40
|
Schuler D, Höll C, Grün N, Ulrich J, Dillner B, Klebl F, Ammon A, Voll LM, Kämper J. Galactose metabolism and toxicity in Ustilago maydis. Fungal Genet Biol 2018; 114:42-52. [PMID: 29580862 DOI: 10.1016/j.fgb.2018.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/07/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
In most organisms, galactose is metabolized via the Leloir pathway, which is conserved from bacteria to mammals. Utilization of galactose requires a close interplay of the metabolic enzymes, as misregulation or malfunction of individual components can lead to the accumulation of toxic intermediate compounds. For the phytopathogenic basidiomycete Ustilago maydis, galactose is toxic for wildtype strains, i.e. leads to growth repression despite the presence of favorable carbon sources as sucrose. The galactose sensitivity can be relieved by two independent modifications: (1) by disruption of Hxt1, which we identify as the major transporter for galactose, and (2) by a point mutation in the gene encoding the galactokinase Gal1, the first enzyme of the Leloir pathway. The mutation in gal1(Y67F) leads to reduced enzymatic activity of Gal1 and thus may limit the formation of putatively toxic galactose-1-phosphate. However, systematic deletions and double deletions of different genes involved in galactose metabolism point to a minor role of galactose-1-phosphate in galactose toxicity. Our results show that molecular triggers for galactose toxicity in U. maydis differ from yeast and mammals.
Collapse
Affiliation(s)
- David Schuler
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Christina Höll
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Nathalie Grün
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Jonas Ulrich
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Bastian Dillner
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
| | - Franz Klebl
- FAU Erlangen-Nuremberg, Department of Biology, Molecular Plant Physiology, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alexandra Ammon
- Philips-University of Marburg, Department of Biology, Plant Physiology and Photo Biology, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Lars M Voll
- Philips-University of Marburg, Department of Biology, Plant Physiology and Photo Biology, Karl von Frisch Strasse 8, 35043 Marburg, Germany
| | - Jörg Kämper
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, Fritz Haber Weg 4, 76131 Karlsruhe, Germany.
| |
Collapse
|
41
|
Specialized plant biochemistry drives gene clustering in fungi. ISME JOURNAL 2018; 12:1694-1705. [PMID: 29463891 DOI: 10.1038/s41396-018-0075-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/18/2018] [Accepted: 01/26/2018] [Indexed: 01/31/2023]
Abstract
The fitness and evolution of prokaryotes and eukaryotes are affected by the organization of their genomes. In particular, the physical clustering of genes can coordinate gene expression and can prevent the breakup of co-adapted alleles. Although clustering may thus result from selection for phenotype optimization and persistence, the impact of environmental selection pressures on eukaryotic genome organization has rarely been systematically explored. Here, we investigated the organization of fungal genes involved in the degradation of phenylpropanoids, a class of plant-produced secondary metabolites that mediate many ecological interactions between plants and fungi. Using a novel gene cluster detection method, we identified 1110 gene clusters and many conserved combinations of clusters in a diverse set of fungi. We demonstrate that congruence in genome organization over small spatial scales is often associated with similarities in ecological lifestyle. Additionally, we find that while clusters are often structured as independent modules with little overlap in content, certain gene families merge multiple modules into a common network, suggesting they are important components of phenylpropanoid degradation strategies. Together, our results suggest that phenylpropanoids have repeatedly selected for gene clustering in fungi, and highlight the interplay between genome organization and ecological evolution in this ancient eukaryotic lineage.
Collapse
|
42
|
UDP-4-Keto-6-Deoxyglucose, a Transient Antifungal Metabolite, Weakens the Fungal Cell Wall Partly by Inhibition of UDP-Galactopyranose Mutase. mBio 2017; 8:mBio.01559-17. [PMID: 29162710 PMCID: PMC5698552 DOI: 10.1128/mbio.01559-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Can accumulation of a normally transient metabolite affect fungal biology? UDP-4-keto-6-deoxyglucose (UDP-KDG) represents an intermediate stage in conversion of UDP-glucose to UDP-rhamnose. Normally, UDP-KDG is not detected in living cells, because it is quickly converted to UDP-rhamnose by the enzyme UDP-4-keto-6-deoxyglucose-3,5-epimerase/-4-reductase (ER). We previously found that deletion of the er gene in Botrytis cinerea resulted in accumulation of UDP-KDG to levels that were toxic to the fungus due to destabilization of the cell wall. Here we show that these negative effects are at least partly due to inhibition by UDP-KDG of the enzyme UDP-galactopyranose mutase (UGM), which reversibly converts UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). An enzymatic activity assay showed that UDP-KDG inhibits the B. cinerea UGM enzyme with a Ki of 221.9 µM. Deletion of the ugm gene resulted in strains with weakened cell walls and phenotypes that were similar to those of the er deletion strain, which accumulates UDP-KDG. Galf residue levels were completely abolished in the Δugm strain and reduced in the Δer strain, while overexpression of the ugm gene in the background of a Δer strain restored Galf levels and alleviated the phenotypes. Collectively, our results show that the antifungal activity of UDP-KDG is due to inhibition of UGM and possibly other nucleotide sugar-modifying enzymes and that the rhamnose metabolic pathway serves as a shunt that prevents accumulation of UDP-KDG to toxic levels. These findings, together with the fact that there is no Galf in mammals, support the possibility of developing UDP-KDG or its derivatives as antifungal drugs.IMPORTANCE Nucleotide sugars are donors for the sugars in fungal wall polymers. We showed that production of the minor sugar rhamnose is used primarily to neutralize the toxic intermediate compound UDP-KDG. This surprising finding highlights a completely new role for minor sugars and other secondary metabolites with undetermined function. Furthermore, the toxic potential of predicted transition metabolites that never accumulate in cells under natural conditions are highlighted. We demonstrate that UDP-KDG inhibits the UDP-galactopyranose mutase enzyme, thereby affecting production of Galf, which is one of the components of cell wall glycans. Given the structural similarity, UDP-KDG likely inhibits additional nucleotide sugar-utilizing enzymes, a hypothesis that is also supported by our findings. Our results suggest that UDP-KDG could serve as a template to develop antifungal drugs.
Collapse
|
43
|
Abstract
Metabolic gene clusters (MGCs) have provided some of the earliest glimpses at the biochemical machinery of yeast and filamentous fungi. MGCs encode diverse genetic mechanisms for nutrient acquisition and the synthesis/degradation of essential and adaptive metabolites. Beyond encoding the enzymes performing these discrete anabolic or catabolic processes, MGCs may encode a range of mechanisms that enable their persistence as genetic consortia; these include enzymatic mechanisms to protect their host fungi from their inherent toxicities, and integrated regulatory machinery. This modular, self-contained nature of MGCs contributes to the metabolic and ecological adaptability of fungi. The phylogenetic and ecological patterns of MGC distribution reflect the broad diversity of fungal life cycles and nutritional modes. While the origins of most gene clusters are enigmatic, MGCs are thought to be born into a genome through gene duplication, relocation, or horizontal transfer, and analyzing the death and decay of gene clusters provides clues about the mechanisms selecting for their assembly. Gene clustering may provide inherent fitness advantages through metabolic efficiency and specialization, but experimental evidence for this is currently limited. The identification and characterization of gene clusters will continue to be powerful tools for elucidating fungal metabolism as well as understanding the physiology and ecology of fungi.
Collapse
Affiliation(s)
- Jason C Slot
- The Ohio State University, Columbus, OH, United States.
| |
Collapse
|
44
|
Reuß DR, Commichau FM, Stülke J. The contribution of bacterial genome engineering to sustainable development. Microb Biotechnol 2017; 10:1259-1263. [PMID: 28772004 PMCID: PMC5609340 DOI: 10.1111/1751-7915.12784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 11/30/2022] Open
Abstract
The United Nations’ Sustainable Development Goals define important challenges for the prosperous development of mankind. To reach several of these goals, among them the production of value‐added compounds, improved economic and ecologic balance of production processes, prevention of climate change and protection of ecosystems, the use of engineered bacteria can make valuable contributions. We discuss the strategies for genome engineering and how they can be applied to meet the United Nations’ goals for sustainable development.
Collapse
Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| |
Collapse
|
45
|
Reynolds HT, Slot JC, Divon HH, Lysøe E, Proctor RH, Brown DW. Differential Retention of Gene Functions in a Secondary Metabolite Cluster. Mol Biol Evol 2017; 34:2002-2015. [DOI: 10.1093/molbev/msx145] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
46
|
Teixeira M, Moreno L, Stielow B, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané J, Priest M, Souza R, Young S, Ferreira K, Zeng Q, da Cunha M, Gladki A, Barker B, Vicente V, de Souza E, Almeida S, Henrissat B, Vasconcelos A, Deng S, Voglmayr H, Moussa T, Gorbushina A, Felipe M, Cuomo C, de Hoog GS. Exploring the genomic diversity of black yeasts and relatives ( Chaetothyriales, Ascomycota). Stud Mycol 2017; 86:1-28. [PMID: 28348446 PMCID: PMC5358931 DOI: 10.1016/j.simyco.2017.01.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
Collapse
Affiliation(s)
- M.M. Teixeira
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - L.F. Moreno
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - B.J. Stielow
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - A. Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - M. Hainaut
- Université Aix-Marseille (CNRS), Marseille, France
| | - L. Gonzaga
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | | | - J.S.L. Patané
- Department of Biochemistry, University of São Paulo, Brazil
| | - M. Priest
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - R. Souza
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Young
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - K.S. Ferreira
- Department of Biological Sciences, Federal University of São Paulo, Diadema, SP, Brazil
| | - Q. Zeng
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - M.M.L. da Cunha
- Núcleo Multidisciplinar de Pesquisa em Biologia UFRJ-Xerém-NUMPEX-BIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A. Gladki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - B. Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - V.A. Vicente
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
| | - E.M. de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
| | - S. Almeida
- Department of Clinical and Toxicological Analysis, University of São Paulo, São Paulo, SP, Brazil
| | - B. Henrissat
- Université Aix-Marseille (CNRS), Marseille, France
| | - A.T.R. Vasconcelos
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Deng
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - H. Voglmayr
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - T.A.A. Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - A. Gorbushina
- Federal Institute for Material Research and Testing (BAM), Berlin, Germany
| | - M.S.S. Felipe
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - C.A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
47
|
Kuivanen J, Arvas M, Richard P. Clustered Genes Encoding 2-Keto-l-Gulonate Reductase and l-Idonate 5-Dehydrogenase in the Novel Fungal d-Glucuronic Acid Pathway. Front Microbiol 2017; 8:225. [PMID: 28261181 PMCID: PMC5306355 DOI: 10.3389/fmicb.2017.00225] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/31/2017] [Indexed: 12/03/2022] Open
Abstract
D-Glucuronic acid is a biomass component that occurs in plant cell wall polysaccharides and is catabolized by saprotrophic microorganisms including fungi. A pathway for D-glucuronic acid catabolism in fungal microorganisms is only partly known. In the filamentous fungus Aspergillus niger, the enzymes that are known to be part of the pathway are the NADPH requiring D-glucuronic acid reductase forming L-gulonate and the NADH requiring 2-keto-L-gulonate reductase that forms L-idonate. With the aid of RNA sequencing we identified two more enzymes of the pathway. The first is a NADPH requiring 2-keto-L-gulonate reductase that forms L-idonate, GluD. The second is a NAD+ requiring L-idonate 5-dehydrogenase forming 5-keto-gluconate, GluE. The genes coding for these two enzymes are clustered and share the same bidirectional promoter. The GluD is an enzyme with a strict requirement for NADP+/NADPH as cofactors. The kcat for 2-keto-L-gulonate and L-idonate is 21.4 and 1.1 s-1, and the Km 25.3 and 12.6 mM, respectively, when using the purified protein. In contrast, the GluE has a strict requirement for NAD+/NADH. The kcat for L-idonate and 5-keto-D-gluconate is 5.5 and 7.2 s-1, and the Km 30.9 and 8.4 mM, respectively. These values also refer to the purified protein. The gluD deletion resulted in accumulation of 2-keto-L-gulonate in the liquid cultivation while the gluE deletion resulted in reduced growth and cessation of the D-glucuronic acid catabolism.
Collapse
Affiliation(s)
- Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd Espoo, Finland
| | - Mikko Arvas
- VTT Technical Research Centre of Finland Ltd Espoo, Finland
| | - Peter Richard
- VTT Technical Research Centre of Finland Ltd Espoo, Finland
| |
Collapse
|
48
|
Darbani B, Motawia MS, Olsen CE, Nour-Eldin HH, Møller BL, Rook F. The biosynthetic gene cluster for the cyanogenic glucoside dhurrin in Sorghum bicolor contains its co-expressed vacuolar MATE transporter. Sci Rep 2016; 6:37079. [PMID: 27841372 PMCID: PMC5107947 DOI: 10.1038/srep37079] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/24/2016] [Indexed: 01/15/2023] Open
Abstract
Genomic gene clusters for the biosynthesis of chemical defence compounds are increasingly identified in plant genomes. We previously reported the independent evolution of biosynthetic gene clusters for cyanogenic glucoside biosynthesis in three plant lineages. Here we report that the gene cluster for the cyanogenic glucoside dhurrin in Sorghum bicolor additionally contains a gene, SbMATE2, encoding a transporter of the multidrug and toxic compound extrusion (MATE) family, which is co-expressed with the biosynthetic genes. The predicted localisation of SbMATE2 to the vacuolar membrane was demonstrated experimentally by transient expression of a SbMATE2-YFP fusion protein and confocal microscopy. Transport studies in Xenopus laevis oocytes demonstrate that SbMATE2 is able to transport dhurrin. In addition, SbMATE2 was able to transport non-endogenous cyanogenic glucosides, but not the anthocyanin cyanidin 3-O-glucoside or the glucosinolate indol-3-yl-methyl glucosinolate. The genomic co-localisation of a transporter gene with the biosynthetic genes producing the transported compound is discussed in relation to the role self-toxicity of chemical defence compounds may play in the formation of gene clusters.
Collapse
Affiliation(s)
- Behrooz Darbani
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.,VILLUM Research Center for Plant Plasticity, University of Copenhagen, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.,VILLUM Research Center for Plant Plasticity, University of Copenhagen, Denmark
| | - Carl Erik Olsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.,VILLUM Research Center for Plant Plasticity, University of Copenhagen, Denmark
| | - Hussam H Nour-Eldin
- Plant Molecular Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.,VILLUM Research Center for Plant Plasticity, University of Copenhagen, Denmark
| | - Fred Rook
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark.,VILLUM Research Center for Plant Plasticity, University of Copenhagen, Denmark
| |
Collapse
|
49
|
Nützmann HW, Huang A, Osbourn A. Plant metabolic clusters - from genetics to genomics. THE NEW PHYTOLOGIST 2016; 211:771-89. [PMID: 27112429 PMCID: PMC5449196 DOI: 10.1111/nph.13981] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/22/2016] [Indexed: 05/18/2023]
Abstract
Contents 771 I. 771 II. 772 III. 780 IV. 781 V. 786 786 References 786 SUMMARY: Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters - architecture, regulation and assembly - will be instrumental in expediting natural product discovery. This review summarizes progress in this area.
Collapse
Affiliation(s)
- Hans-Wilhelm Nützmann
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ancheng Huang
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| |
Collapse
|
50
|
Iosue CL, Attanasio N, Shaik NF, Neal EM, Leone SG, Cali BJ, Peel MT, Grannas AM, Wykoff DD. Partial Decay of Thiamine Signal Transduction Pathway Alters Growth Properties of Candida glabrata. PLoS One 2016; 11:e0152042. [PMID: 27015653 PMCID: PMC4807840 DOI: 10.1371/journal.pone.0152042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/21/2016] [Indexed: 12/31/2022] Open
Abstract
The phosphorylated form of thiamine (Vitamin B1), thiamine pyrophosphate (TPP) is essential for the metabolism of amino acids and carbohydrates in all organisms. Plants and microorganisms, such as yeast, synthesize thiamine de novo whereas animals do not. The thiamine signal transduction (THI) pathway in Saccharomyces cerevisiae is well characterized. The ~10 genes required for thiamine biosynthesis and uptake are transcriptionally upregulated during thiamine starvation by THI2, THI3, and PDC2. Candida glabrata, a human commensal and opportunistic pathogen, is closely related to S. cerevisiae but is missing half of the biosynthetic pathway, which limits its ability to make thiamine. We investigated the changes to the THI pathway in C. glabrata, confirming orthologous functions. We found that C. glabrata is unable to synthesize the pyrimidine subunit of thiamine as well as the thiamine precursor vitamin B6. In addition, THI2 (the gene encoding a transcription factor) is not present in C. glabrata, indicating a difference in the transcriptional regulation of the pathway. Although the pathway is upregulated by thiamine starvation in both species, C. glabrata appears to upregulate genes involved in thiamine uptake to a greater extent than S. cerevisiae. However, the altered regulation of the THI pathway does not alter the concentration of thiamine and its vitamers in the two species as measured by HPLC. Finally, we demonstrate potential consequences to having a partial decay of the THI biosynthetic and regulatory pathway. When the two species are co-cultured, the presence of thiamine allows C. glabrata to rapidly outcompete S. cerevisiae, while absence of thiamine allows S. cerevisiae to outcompete C. glabrata. This simplification of the THI pathway in C. glabrata suggests its environment provides thiamine and/or its precursors to cells, whereas S. cerevisiae is not as reliant on environmental sources of thiamine.
Collapse
Affiliation(s)
- Christine L. Iosue
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Nicholas Attanasio
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Noor F. Shaik
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Erin M. Neal
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Sarah G. Leone
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Brian J. Cali
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Michael T. Peel
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Amanda M. Grannas
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, United States of America
| | - Dennis D. Wykoff
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|