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Osborne M, Fubara A, Ó Cinnéide E, Coughlan AY, Wolfe KH. WHO elements - A new category of selfish genetic elements at the borderline between homing elements and transposable elements. Semin Cell Dev Biol 2024; 163:2-13. [PMID: 38664119 DOI: 10.1016/j.semcdb.2024.04.001] [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: 11/21/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 05/26/2024]
Abstract
Homing genetic elements are a form of selfish DNA that inserts into a specific target site in the genome and spreads through the population by a process of biased inheritance. Two well-known types of homing element, called inteins and homing introns, were discovered decades ago. In this review we describe WHO elements, a newly discovered type of homing element that constitutes a distinct third category but is rare, having been found only in a few yeast species so far. WHO elements are inferred to spread using the same molecular homing mechanism as inteins and introns: they encode a site-specific endonuclease that cleaves the genome at the target site, making a DNA break that is subsequently repaired by copying the element. For most WHO elements, the target site is in the glycolytic gene FBA1. WHO elements differ from inteins and homing introns in two fundamental ways: they do not interrupt their host gene (FBA1), and they occur in clusters. The clusters were formed by successive integrations of different WHO elements into the FBA1 locus, the result of an 'arms race' between the endonuclease and its target site. We also describe one family of WHO elements (WHO10) that is no longer specifically associated with the FBA1 locus and instead appears to have become transposable, inserting at random genomic sites in Torulaspora globosa with up to 26 copies per strain. The WHO family of elements is therefore at the borderline between homing genetic elements and transposable elements.
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Affiliation(s)
- Matthieu Osborne
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Athaliah Fubara
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Eoin Ó Cinnéide
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Aisling Y Coughlan
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
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Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, de Souza F, de Queiroz M, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, Santiago A, De Miccolis Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Álvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Mkhwanazi GM, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Silva-Filho A, Souza-Motta C, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. What are the 100 most cited fungal genera? Stud Mycol 2024; 108:1-411. [PMID: 39100921 PMCID: PMC11293126 DOI: 10.3114/sim.2024.108.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/17/2024] [Indexed: 08/06/2024] Open
Abstract
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.
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Affiliation(s)
- C.S. Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Y.J. Chen
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - C. Phukhamsakda
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- The Yeasts Foundation, Amsterdam, the Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - E.H.C. McKenzie
- Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand
| | - E.C. Francisco
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Laboratório Especial de Micologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - V. G. Hurdeal
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Luangsa-ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - G. Perrone
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Amendola 122/O, 70126 Bari, Italy
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F.Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - J. Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Słowackiego 17, PL-71434 Szczecin, Poland
| | - U. Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Neuwerk 21, 06099 Halle (Saale), Germany
| | - F.A. de Souza
- Núcleo de Biologia Aplicada, Embrapa Milho e Sorgo, Empresa Brasileira de Pesquisa Agropecuária, Rodovia MG 424 km 45, 35701–970, Sete Lagoas, MG, Brazil
| | - M.B. de Queiroz
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - A.K. Dutta
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - D. Gonkhom
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B.T. Goto
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - V. Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - M.A. Lachance
- Department of Biology, University of Western Ontario London, Ontario, Canada N6A 5B7
| | - J.J. Li
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - K.Y. Luo
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - F. Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - S. Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - N. Roy
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - S. Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
| | - D.N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - D.Q. Wang
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - D.P. Wei
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
| | - C.L. Zhao
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - W. Aiphuk
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - O. Ajayi-Oyetunde
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
| | - T.D. Arantes
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - J.C. Araujo
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
| | - D. Begerow
- Organismic Botany and Mycology, Institute of Plant Sciences and Microbiology, Ohnhorststraße 18, 22609 Hamburg, Germany
| | - M. Bakhshi
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - R.N. Barbosa
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - F.H. Behrens
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - J.D.P. Bezerra
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - P. Bilański
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - C.A. Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA
| | - B. Bubner
- Johan Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Institut für Forstgenetik, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany
| | - T.I. Burgess
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
| | - B. Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39, 75231, Paris cedex 05, France
| | - N. Čadež
- University of Ljubljana, Biotechnical Faculty, Food Science and Technology Department Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.J.S. Calaça
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
- Laboratório de Pesquisa em Ensino de Ciências (LabPEC), Centro de Pesquisas e Educação Científica, Universidade Estadual de Goiás, Campus Central (CEPEC/UEG), Anápolis, GO, 75132-903, Brazil
| | - L.J. Campbell
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - P. Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, U.S.A
| | - Y.Y. Chen
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - K.W.T. Chethana
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B. Coetzee
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, University of Stellenbosch, South Africa
| | - M.M. Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.A. Custódio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Y.C. Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - A.L.C.M.A. Santiago
- Post-graduate course in the Biology of Fungi, Department of Mycology, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, 50740-465, Recife, PE, Brazil
| | | | - J. Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A.J. Dissanayake
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - M. Doilom
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - W. Dong
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - E. Álvarez-Duarte
- Mycology Unit, Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile, Chile
| | - M. Fischer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - A.J. Gajanayake
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - D. Gomdola
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.A.M. Gomes
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife-PE, Brazil
| | - G. Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 5N6
| | - M.Q. He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - I. Iturrieta-González
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - F. Jami
- Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - R. Jankowiak
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - R.S. Jayawardena
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, South Korea
| | - H. Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - L. Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
- Centre for Research and Development, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - N. Kobmoo
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - T. Kowalski
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - L. Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - C.G. Lin
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - J.K. Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - X.B. Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | | | - T. Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S.S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - G.J. Makhathini Mkhwanazi
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - I.S. Manawasinghe
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - Y. Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - A.R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park 4102, Queensland, Australia
| | - P.A. Moreau
- Univ. Lille, ULR 4515 - LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - O.V. Morozova
- Komarov Botanical Institute of the Russian Academy of Sciences, 2, Prof. Popov Str., 197376 Saint Petersburg, Russia
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - H.D. Osiewacz
- Faculty for Biosciences, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - D. Pem
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - R. Phookamsak
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - S. Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - A. Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - C. Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - A.J.L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - M. Phonemany
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - I. Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - A.R. Rathnayaka
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - G. Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - L. Rothmann
- Plant Pathology, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - C. Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), 10300 Baltimore Avenue, Beltsville MD, 20705, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - S.J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux cedex, France
| | - M. Scholler
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - P. Scott
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth WA 6000, Australia
| | - R.G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
| | - P. Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris Cité, 75205 Paris Cedex, France
| | - A.G.S. Silva-Filho
- IFungiLab, Departamento de Ciências e Matemática (DCM), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, BraziI
| | - C.M. Souza-Motta
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - C.F.J. Spies
- Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - A.M. Stchigel
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - K. Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Augasse 2–6, 1090, Vienna, Austria
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T.Y. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - S. Takamatsu
- Mie University, Graduate School, Department of Bioresources, 1577 Kurima-Machiya, Tsu 514-8507, Japan
| | - B. Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.C. Theodoro
- Laboratório de Micologia Médica, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, 59078-900, Natal, RN, Brazil
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt Am Main, Germany
| | - N. Thongklang
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - R. Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Agrobiotech de Lleida, Parc de Gardeny, 25003, Lleida, Catalonia, Spain
| | - B. Turchetti
- Department of Agricultural, Food and Environmental Sciences and DBVPG Industrial Yeasts Collection, University of Perugia, Italy
| | - T. van den Brule
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- TIFN, P.O. Box 557, 6700 AN Wageningen, the Netherlands
| | - X.W. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F. Wartchow
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Paraiba, João Pessoa, Brazil
| | - S. Welti
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - S.N. Wijesinghe
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - F. Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - R. Xu
- School of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
| | - Z.L. Yang
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - L. Zhao
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.L. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - N. Zhou
- Department of Biological Sciences and Biotechnology, Botswana University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht
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3
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Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, Čadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science 2024; 384:eadj4503. [PMID: 38662846 PMCID: PMC11298794 DOI: 10.1126/science.adj4503] [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: 06/28/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
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Affiliation(s)
- Dana A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Biology Department Villanova University, Villanova, PA 19085, USA
| | - Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 Research Campus Drive, Kannapolis, NC 28081, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - John F. Wolters
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Chao Liu
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | - Yonglin Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Jacek Kominek
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hayley R. Stoneman
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- University of Colorado - Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jenna VanDenAvond
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Caroline R. Miller
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Margarida Silva
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Emily J. Ubbelohde
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Kelly V. Buh
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Max A. B. Haase
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
- Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Neža Čadež
- Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina
| | - Jeremy H. DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Cletus P. Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
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4
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Mielecki D, Detman A, Aleksandrzak-Piekarczyk T, Widomska M, Chojnacka A, Stachurska-Skrodzka A, Walczak P, Grzesiuk E, Sikora A. Unlocking the genome of the non-sourdough Kazachstania humilis MAW1: insights into inhibitory factors and phenotypic properties. Microb Cell Fact 2024; 23:111. [PMID: 38622625 PMCID: PMC11017505 DOI: 10.1186/s12934-024-02380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Ascomycetous budding yeasts are ubiquitous environmental microorganisms important in food production and medicine. Due to recent intensive genomic research, the taxonomy of yeast is becoming more organized based on the identification of monophyletic taxa. This includes genera important to humans, such as Kazachstania. Until now, Kazachstania humilis (previously Candida humilis) was regarded as a sourdough-specific yeast. In addition, any antibacterial activity has not been associated with this species. RESULTS Previously, we isolated a yeast strain that impaired bio-hydrogen production in a dark fermentation bioreactor and inhibited the growth of Gram-positive and Gram-negative bacteria. Here, using next generation sequencing technologies, we sequenced the genome of this strain named K. humilis MAW1. This is the first genome of a K. humilis isolate not originating from a fermented food. We used novel phylogenetic approach employing the 18 S-ITS-D1-D2 region to show the placement of the K. humilis MAW1 among other members of the Kazachstania genus. This strain was examined by global phenotypic profiling, including carbon sources utilized and the influence of stress conditions on growth. Using the well-recognized bacterial model Escherichia coli AB1157, we show that K. humilis MAW1 cultivated in an acidic medium inhibits bacterial growth by the disturbance of cell division, manifested by filament formation. To gain a greater understanding of the inhibitory effect of K. humilis MAW1, we selected 23 yeast proteins with recognized toxic activity against bacteria and used them for Blast searches of the K. humilis MAW1 genome assembly. The resulting panel of genes present in the K. humilis MAW1 genome included those encoding the 1,3-β-glucan glycosidase and the 1,3-β-glucan synthesis inhibitor that might disturb the bacterial cell envelope structures. CONCLUSIONS We characterized a non-sourdough-derived strain of K. humilis, including its genome sequence and physiological aspects. The MAW1, together with other K. humilis strains, shows the new organization of the mating-type locus. The revealed here pH-dependent ability to inhibit bacterial growth has not been previously recognized in this species. Our study contributes to the building of genome sequence-based classification systems; better understanding of K.humilis as a cell factory in fermentation processes and exploring bacteria-yeast interactions in microbial communities.
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Affiliation(s)
- Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
- Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, Warsaw, 02-106, Poland
| | - Anna Detman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | | | - Małgorzata Widomska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Aleksandra Chojnacka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
- Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, 02-776, Poland
| | | | - Paulina Walczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland
| | - Anna Sikora
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland.
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5
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Tengölics R, Szappanos B, Mülleder M, Kalapis D, Grézal G, Sajben C, Agostini F, Mokochinski JB, Bálint B, Nagy LG, Ralser M, Papp B. The metabolic domestication syndrome of budding yeast. Proc Natl Acad Sci U S A 2024; 121:e2313354121. [PMID: 38457520 PMCID: PMC10945815 DOI: 10.1073/pnas.2313354121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 03/10/2024] Open
Abstract
Cellular metabolism evolves through changes in the structure and quantitative states of metabolic networks. Here, we explore the evolutionary dynamics of metabolic states by focusing on the collection of metabolite levels, the metabolome, which captures key aspects of cellular physiology. Using a phylogenetic framework, we profiled metabolites in 27 populations of nine budding yeast species, providing a graduated view of metabolic variation across multiple evolutionary time scales. Metabolite levels evolve more rapidly and independently of changes in the metabolic network's structure, providing complementary information to enzyme repertoire. Although metabolome variation accumulates mainly gradually over time, it is profoundly affected by domestication. We found pervasive signatures of convergent evolution in the metabolomes of independently domesticated clades of Saccharomyces cerevisiae. Such recurring metabolite differences between wild and domesticated populations affect a substantial part of the metabolome, including rewiring of the TCA cycle and several amino acids that influence aroma production, likely reflecting adaptation to human niches. Overall, our work reveals previously unrecognized diversity in central metabolism and the pervasive influence of human-driven selection on metabolite levels in yeasts.
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Affiliation(s)
- Roland Tengölics
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Szappanos
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- Department of Biotechnology, University of Szeged, Szeged6726, Hungary
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility High-Throughput Mass Spectrometry, Berlin10117, Germany
| | - Dorottya Kalapis
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Gábor Grézal
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Csilla Sajben
- Metabolomics Lab, Core facilities, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
| | - João Benhur Mokochinski
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Balázs Bálint
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - László G. Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
| | - Markus Ralser
- Department of Biochemistry, Charité Universitätsmedizin, Berlin10117, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, LondonNW11AT, United Kingdom
| | - Balázs Papp
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre Metabolic Systems Biology Lab, Szeged6726, Hungary
- Synthetic and System Biology Unit, National Laboratory of Biotechnology, Institute of Biochemistry, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
- National Laboratory for Health Security, Biological Research Centre, Hungarian Research Network, Szeged6726, Hungary
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6
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Balarezo-Cisneros LN, Timouma S, Hanak A, Currin A, Valle F, Delneri D. High quality de novo genome assembly of the non-conventional yeast Kazachstania bulderi describes a potential low pH production host for biorefineries. Commun Biol 2023; 6:918. [PMID: 37679437 PMCID: PMC10484914 DOI: 10.1038/s42003-023-05285-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Kazachstania bulderi is a non-conventional yeast species able to grow efficiently on glucose and δ-gluconolactone at low pH. These unique traits make K. bulderi an ideal candidate for use in sustainable biotechnology processes including low pH fermentations and the production of green chemicals including organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing long read sequencing we report a high-quality phased genome assembly for three strains of K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14 Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array and mating type locus. This high-quality reference genome provides a resource to advance our fundamental knowledge of biotechnologically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts in biotechnological processes.
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Affiliation(s)
| | - Soukaina Timouma
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Alistair Hanak
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew Currin
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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7
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Siddiqui M, Conant GC. POInT browse: orthology prediction and synteny exploration for paleopolyploid genomes. BMC Bioinformatics 2023; 24:174. [PMID: 37106333 PMCID: PMC10134530 DOI: 10.1186/s12859-023-05298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
We describe POInTbrowse, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool. Ancient, or paleo-, polyploidy events are widely distributed across the eukaryotic phylogeny, and the combination of duplicated and lost duplicated genes that these polyploidies produce can confound the identification of orthologous genes between genomes. POInT uses conserved synteny and phylogenetic models to infer orthologous genes between genomes with a shared polyploidy. It also gives confidence estimates for those orthology inferences. POInTbrowse gives both graphical and query-based access to these inferences from 12 different polyploidy events, allowing users to visualize genomic regions produced by polyploidies and perform batch queries for each polyploidy event, downloading genes trees and coding sequences for orthologous genes meeting user-specified criteria. POInTbrowse and the associated data are online at https://wgd.statgen.ncsu.edu .
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Affiliation(s)
- Mustafa Siddiqui
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Gavin C Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.
- Program in Genetics, North Carolina State University, Raleigh, NC, USA.
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8
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Smoak RA, Snyder LF, Fassler JS, He BZ. Parallel expansion and divergence of an adhesin family in pathogenic yeasts. Genetics 2023; 223:iyad024. [PMID: 36794645 PMCID: PMC10319987 DOI: 10.1093/genetics/iyad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Opportunistic yeast pathogens arose multiple times in the Saccharomycetes class, including the recently emerged, multidrug-resistant (MDR) Candida auris. We show that homologs of a known yeast adhesin family in Candida albicans, the Hyr/Iff-like (Hil) family, are enriched in distinct clades of Candida species as a result of multiple, independent expansions. Following gene duplication, the tandem repeat-rich region in these proteins diverged extremely rapidly and generated large variations in length and β-aggregation potential, both of which are known to directly affect adhesion. The conserved N-terminal effector domain was predicted to adopt a β-helical fold followed by an α-crystallin domain, making it structurally similar to a group of unrelated bacterial adhesins. Evolutionary analyses of the effector domain in C. auris revealed relaxed selective constraint combined with signatures of positive selection, suggesting functional diversification after gene duplication. Lastly, we found the Hil family genes to be enriched at chromosomal ends, which likely contributed to their expansion via ectopic recombination and break-induced replication. Combined, these results suggest that the expansion and diversification of adhesin families generate variation in adhesion and virulence within and between species and are a key step toward the emergence of fungal pathogens.
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Affiliation(s)
- Rachel A Smoak
- Civil and Environmental Engineering, The University of Iowa, Iowa City, IA 52242, USA
| | - Lindsey F Snyder
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
| | - Jan S Fassler
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Bin Z He
- Interdisciplinary Graduate Program in Genetics, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biology, The University of Iowa, Iowa City, IA 52242, USA
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9
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Fujiwara T, Matsura A, Fukuda M, Kuroki K, Ogata T. Isolation and characterization of Zygosaccharomyces sp. yeast strains from miso. J GEN APPL MICROBIOL 2023; 68:295-302. [PMID: 35934805 DOI: 10.2323/jgam.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
There is currently great interest in the salt-tolerant yeast strains used to produce miso and soy sauce. Since the isolation of Zygosaccharomyces sp. strain from Japanese miso more than 60 years, several hybrid strains have been identified in fermented foods. Studies have shown that the active mating-type locus of the original Zygosaccharomyces sp. yeast strain is located between the T-subgenome sequence and the P-subgenome sequence. In this study, 32 salt-tolerant Zygosaccharomyces sp. yeast strains were isolated from five miso factories in Hiroshima Prefecture, Japan. Analysis by flow cytometry revealed that 27 strains were diploid and five strains were haploid. PCR analysis indicated that the 27 diploid strains had the same chromosomal structure of the active mating-type (MAT) locus as the original yeast strain isolated from miso 60 years ago. In addition, the 27 diploid strains were allodiploid, namely, natural hybrids of Z. rouxii and a related species, while the five haploid strains were all Z. rouxii. We found that cells of yeast strains isolated from miso changed morphologically when co-cultured with a yeast strain of opposite mating-type under nitrogen starvation conditions. The DNA sequence of the active mating-type locus and the results of cell morphology changes by co-culture were consistent with the mating type of each strain shown in the mating experiments. These findings will be useful for the future production of miso and soy sauce.
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Affiliation(s)
- Tomoko Fujiwara
- Food Technology Research Center, Hiroshima Prefectural Technology Research Institute
| | - Atsuko Matsura
- Department of Life Engineering, Maebashi Institute of Technology
| | - Momoka Fukuda
- Department of Life Engineering, Maebashi Institute of Technology
| | - Katsuaki Kuroki
- Department of Life Engineering, Maebashi Institute of Technology
| | - Tomoo Ogata
- Department of Life Engineering, Maebashi Institute of Technology
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10
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Maria H, Rusche LN. The DNA replication protein Orc1 from the yeast Torulaspora delbrueckii is required for heterochromatin formation but not as a silencer-binding protein. Genetics 2022; 222:6650695. [PMID: 35894940 PMCID: PMC9434157 DOI: 10.1093/genetics/iyac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
To understand the process by which new protein functions emerge, we examined how the yeast heterochromatin protein Sir3 arose through gene duplication from the conserved DNA replication protein Orc1. Orc1 is a subunit of the origin recognition complex (ORC), which marks origins of DNA replication. In Saccharomyces cerevisiae, Orc1 also promotes heterochromatin assembly by recruiting the structural proteins Sir1-4 to silencer DNA. In contrast, the paralog of Orc1, Sir3, is a nucleosome-binding protein that spreads across heterochromatic loci in conjunction with other Sir proteins. We previously found that a non-duplicated Orc1 from the yeast Kluyveromyces lactis behaved like ScSir3 but did not have a silencer-binding function like ScOrc1. Moreover, K. lactis lacks Sir1, the protein that interacts directly with ScOrc1 at the silencer. Here, we examined whether the emergence of Sir1 coincided with Orc1 acting as a silencer-binding protein. In the non-duplicated species Torulaspora delbrueckii, which has an ortholog of Sir1 (TdKos3), we found that TdOrc1 spreads across heterochromatic loci independently of ORC, as ScSir3 and KlOrc1 do. This spreading is dependent on the nucleosome binding BAH domain of Orc1 and on Sir2 and Kos3. However, TdOrc1 does not have a silencer-binding function: T. delbrueckii silencers do not require ORC binding sites to function, and Orc1 and Kos3 do not appear to interact. Instead, Orc1 and Kos3 both spread across heterochromatic loci with other Sir proteins. Thus, Orc1 and Sir1/Kos3 originally had different roles in heterochromatin formation than they do now in S. cerevisiae.
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Affiliation(s)
- Haniam Maria
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY, 14260, USA
| | - Laura N Rusche
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY, 14260, USA
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11
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Mating-Type Switching in Budding Yeasts, from Flip/Flop Inversion to Cassette Mechanisms. Microbiol Mol Biol Rev 2022; 86:e0000721. [PMID: 35195440 PMCID: PMC8941940 DOI: 10.1128/mmbr.00007-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mating-type switching is a natural but unusual genetic control process that regulates cell identity in ascomycete yeasts. It involves physically replacing one small piece of genomic DNA by another, resulting in replacement of the master regulatory genes in the mating pathway and hence a switch of cell type and mating behavior. In this review, we concentrate on recent progress that has been made on understanding the origins and evolution of mating-type switching systems in budding yeasts (subphylum Saccharomycotina). Because of the unusual nature and the complexity of the mechanism in Saccharomyces cerevisiae, mating-type switching was assumed until recently to have originated only once or twice during yeast evolution. However, comparative genomics analysis now shows that switching mechanisms arose many times independently-at least 11 times in budding yeasts and once in fission yeasts-a dramatic example of convergent evolution. Most of these lineages switch mating types by a flip/flop mechanism that inverts a section of a chromosome and is simpler than the well-characterized 3-locus cassette mechanism (MAT/HML/HMR) used by S. cerevisiae. Mating-type switching (secondary homothallism) is one of the two possible mechanisms by which a yeast species can become self-fertile. The other mechanism (primary homothallism) has also emerged independently in multiple evolutionary lineages of budding yeasts, indicating that homothallism has been favored strongly by natural selection. Recent work shows that HO endonuclease, which makes the double-strand DNA break that initiates switching at the S. cerevisiae MAT locus, evolved from an unusual mobile genetic element that originally targeted a glycolytic gene, FBA1.
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12
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Tapia SM, Pérez-Torrado R, Adam AC, Macías LG, Barrio E, Querol A. Functional divergence in the proteins encoded by ARO80 from S. uvarum, S. kudriavzevii and S. cerevisiae explain differences in the aroma production during wine fermentation. Microb Biotechnol 2022; 15:2281-2291. [PMID: 35536034 PMCID: PMC9328738 DOI: 10.1111/1751-7915.14071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/19/2022] [Accepted: 04/24/2022] [Indexed: 11/27/2022] Open
Abstract
Phenylethanol (PE) and phenylethyl acetate (PEA) are commonly desired compounds in wine because of their rose‐like aroma. The yeast S. cerevisiae produces the PE either through de novo biosynthesis by shikimate pathway followed by the Ehrlich pathway or the direct phenylalanine catabolism via Ehrlich pathway, and then converted into PEA. Previous work demonstrated that, compared to S. cerevisiae, other Saccharomyces species, such as S. kudriavzevii and S. uvarum, produce higher concentrations of PE and PEA from the precursor phenylalanine, which indicates differential activities of the biosynthetic‐involved enzymes. A previous in‐silico analysis suggested that the transcriptional activator Aro80p is one of the best candidates to explain these differences. An improved functional analysis identified significant radical amino acid changes in the S. uvarum and S. kudriavzevii Aro80p that could impact the expression of the catabolic genes ARO9 and ARO10, and hence, the production of PE from phenylalanine. Indeed, wine S. cerevisiae strains carrying the S. uvarum and S. kudriavzevii ARO80 alleles increased the production of both compounds in the presence of phenylalanine by increasing the expression of ARO9 and ARO10. This study provides novel insights of the unidentified Aro80p regulatory region and the potential usage of alternatives ARO80 alleles to enhance the PE and PEA concentration in wine.
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Affiliation(s)
- Sebastián M Tapia
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Roberto Pérez-Torrado
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Ana Cristina Adam
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
| | - Laura G Macías
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain.,Departament de Genètica, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Departamento de Biotecnología de los Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Los Alimentos (IATA)-CSIC, 46980, Valencia, Spain
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13
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Devillers H, Sarilar V, Grondin C, Sterck L, Segond D, Jacques N, Sicard D, Casaregola S, Tinsley C. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519748. [PMID: 35106561 PMCID: PMC8825440 DOI: 10.1093/gbe/evac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2022] [Indexed: 11/23/2022] Open
Abstract
Recent studies have suggested that species of the Kazachstania genus may be interesting models of yeast domestication. Among these, Kazachstania barnettii has been isolated from various microbially transformed foodstuffs such as sourdough bread and kefir. In the present work, we sequence, assemble, and annotate the complete genomes of two K. barnettii strains: CLIB 433, being one of the two reference strains for K. barnettii that was isolated as a spoilage organism in soft drink, and CLIB 1767, recently isolated from artisan bread-making sourdough. Both assemblies are of high quality with N50 statistics greater than 1.3 Mb and BUSCO score greater than 99%. An extensive comparison of the two obtained genomes revealed very few differences between the two K. barnettii strains, considering both genome structure and gene content. The proposed genome assemblies will constitute valuable references for future comparative genomic, population genomic, or transcriptomic studies of the K. barnettii species.
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Affiliation(s)
- Hugo Devillers
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- Corresponding author: E-mail:
| | - Véronique Sarilar
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- French Armed Forces Biomedical Research Institute (IRBA), Department of Platforms and Technology Research, Molecular Biology Unit, Brétigny-sur-Orge, France
| | - Cécile Grondin
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Lieven Sterck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Diego Segond
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Noémie Jacques
- Université Paris-Saclay, INRAE, UMR BIOGER, Thiverval-Grignon, France
| | - Delphine Sicard
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Serge Casaregola
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Colin Tinsley
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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14
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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15
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Terán LC, Mortera P, Tubio G, Alarcón SH, Blancato VS, Espariz M, Esteban L, Magni C. Genomic analysis revealed conserved acid tolerance mechanisms from native micro-organisms in fermented feed. J Appl Microbiol 2021; 132:1152-1165. [PMID: 34487594 DOI: 10.1111/jam.15292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/28/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022]
Abstract
AIMS Fermented feed is an agricultural practice used in many regions of the world to improve the growth performance of farm animals. This study aimed to identify and evaluate the lactic acid bacteria and yeast involved in the production of fermented feed. METHODS AND RESULTS We isolated and described two micro-organisms from autochthonous microbiota origin present in a regional feed product, Lactobacillus paracasei IBR07 (Lacticaseibacillus paracasei) and Kazachstania unispora IBR014 (Saccharomyces unisporum). Genome sequence analyses were performed to characterize both micro-organisms. Potential pathways involved in the acid response, tolerance and persistence were predicted in both genomes. Although L. paracasei and K. unispora are considered safe for animal feed, we analysed the presence of virulence factors, antibiotic resistance and pathogenicity islands. Furthermore, the Galleria mellonella model was used to support the safety of both isolates. CONCLUSIONS We conclude that IBR07 and IBR014 strains are good candidates to be used as starter cultures for feed fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY The data presented here will be helpful to explore other biotechnological aspects and constitute a starting point for further studies to establish the consumption benefit of fermented feed in farm animal production.
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Affiliation(s)
- Lucrecia C Terán
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Centro de Referencia para Lactobacilos, CERELA-CONICET, San Miguel de Tucuman, Tucumán, Argentina
| | - Pablo Mortera
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Gisela Tubio
- Instituto de Procesos Biotecnológicos y Químicos Rosario, IPROByQ (CONICET-UNR), Rosario, Argentina
| | - Sergio H Alarcón
- Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Instituto de Química de Rosario, IQUIR (CONICET-UNR), Rosario, Argentina
| | - Victor S Blancato
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
| | - Martín Espariz
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina.,Área Estadística y Procesamiento de Datos, Departamento de Matemática y Estadística, FBioyF-UNR, Rosario, Argentina
| | - Luis Esteban
- Química Biológica, Facultad de Ciencias Médicas, UNR, Rosario, Argentina
| | - Christian Magni
- Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), sede Facultad de Ciencias Bioquímicas y Farmacéuticas (FBioyF), Universidad Nacional de Rosario (UNR), Consejo Nacional de Ciencia y Tecnología (CONICET), Rosario, Argentina.,Laboratorio de Biotecnología e Inocuidad de los Alimentos, Área de Biotecnología de los alimentos, FBioyF, UNR-Municipalidad de Granadero Baigorria, Rosario, Argentina
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16
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Fernandes T, Silva-Sousa F, Pereira F, Rito T, Soares P, Franco-Duarte R, Sousa MJ. Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight. J Fungi (Basel) 2021; 7:jof7090712. [PMID: 34575750 PMCID: PMC8467266 DOI: 10.3390/jof7090712] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/28/2022] Open
Abstract
Torulaspora delbrueckii has attracted interest in recent years, especially due to its biotechnological potential, arising from its flavor- and aroma-enhancing properties when used in wine, beer or bread dough fermentation, as well as from its remarkable resistance to osmotic and freezing stresses. In the present review, genomic, biochemical, and phenotypic features of T. delbrueckii are described, comparing them with other species, particularly with the biotechnologically well-established yeast, Saccharomyces cerevisiae. We conclude about the aspects that make this yeast a promising biotechnological model to be exploited in a wide range of industries, particularly in wine and bakery. A phylogenetic analysis was also performed, using the core proteome of T. delbrueckii, to compare the number of homologous proteins relative to the most closely related species, understanding the phylogenetic placement of this species with robust support. Lastly, the genetic tools available for T. delbrueckii improvement are discussed, focusing on adaptive laboratorial evolution and its potential.
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Affiliation(s)
- Ticiana Fernandes
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Flávia Silva-Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Fábio Pereira
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Teresa Rito
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
- Correspondence: or ; Tel.: +351-253-604-310; Fax: +351-253-678-980
| | - Maria João Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal; (T.F.); (F.S.-S.); (F.P.); (T.R.); (P.S.); (M.J.S.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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17
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Maria H, Kapoor S, Liu T, Rusche LN. Conservation of a DNA Replication Motif among Phylogenetically Distant Budding Yeast Species. Genome Biol Evol 2021; 13:6300524. [PMID: 34132803 PMCID: PMC8290112 DOI: 10.1093/gbe/evab137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 01/23/2023] Open
Abstract
Eukaryotic DNA replication begins at genomic loci termed origins, which are bound by the origin recognition complex (ORC). Although ORC is conserved across species, the sequence composition of origins is more varied. In the budding yeast Saccharomyces cerevisiae, the ORC-binding motif consists of an A/T-rich 17 bp “extended ACS” sequence adjacent to a B1 element composed of two 3-bp motifs. Similar sequences occur at origins in closely related species, but it is not clear when this type of replication origin arose and whether it predated a whole-genome duplication that occurred around 100 Ma in the budding yeast lineage. To address these questions, we identified the ORC-binding sequences in the nonduplicated species Torulaspora delbrueckii. We used chromatin immunoprecipitation followed by sequencing and identified 190 ORC-binding sites distributed across the eight T. delbrueckii chromosomes. Using these sites, we identified an ORC-binding motif that is nearly identical to the known motif in S. cerevisiae. We also found that the T. delbrueckii ORC-binding sites function as origins in T. delbrueckii when cloned onto a plasmid and that the motif is required for plasmid replication. Finally, we compared an S. cerevisiae origin with two T. delbrueckii ORC-binding sites and found that they conferred similar stabilities to a plasmid. These results reveal that the ORC-binding motif arose prior to the whole-genome duplication and has been maintained for over 100 Myr.
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Affiliation(s)
- Haniam Maria
- Department of Biological Sciences, State University of New York at Buffalo, New York, USA
| | - Shivali Kapoor
- Department of Biological Sciences, State University of New York at Buffalo, New York, USA
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Laura N Rusche
- Department of Biological Sciences, State University of New York at Buffalo, New York, USA
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18
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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19
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Pacheco A, Donzella L, Hernandez-Lopez MJ, Almeida MJ, Prieto JA, Randez-Gil F, Morrissey JP, Sousa MJ. Hexose transport in Torulaspora delbrueckii: identification of Igt1, a new dual-affinity transporter. FEMS Yeast Res 2021; 20:5715911. [PMID: 31981362 DOI: 10.1093/femsyr/foaa004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 01/24/2020] [Indexed: 01/23/2023] Open
Abstract
Torulaspora delbrueckii is a yeast species receiving increasing attention from the biotechnology industry, with particular relevance in the wine, beer and baking sectors. However, little is known about its sugar transporters and sugar transport capacity, frequently a rate-limiting step of sugar metabolism and efficient fermentation. Actually, only one glucose transporter, Lgt1, has been characterized so far. Here we report the identification and characterization of a second glucose transporter gene, IGT1, located in a cluster, upstream of LGT1 and downstream of two other putative hexose transporters. Functional characterization of IGT1 in a Saccharomyces cerevisiae hxt-null strain revealed that it encodes a transporter able to mediate uptake of glucose, fructose and mannose and established that its affinity, as measured by Km, could be modulated by glucose concentration in the medium. In fact, IGT1-transformed S. cerevisiae hxt-null cells, grown in 0.1% glucose displayed biphasic glucose uptake kinetics with an intermediate- (Km = 6.5 ± 2.0 mM) and a high-affinity (Km = 0.10 ± 0.01 mM) component, whereas cells grown in 2% glucose displayed monophasic kinetics with an intermediate-affinity (Km of 11.5 ± 1.5 mM). This work contributes to a better characterization of glucose transport in T. delbrueckii, with relevant implications for its exploitation in the food industry.
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Affiliation(s)
- Andreia Pacheco
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Lorena Donzella
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, T12YT20 Cork, Ireland
| | - Maria Jose Hernandez-Lopez
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - Maria Judite Almeida
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
| | - Jose Antonio Prieto
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroqumica y Tecnologia de los Alimentos, Consejo Superior de Investigaciones Cientficas, Avda. Agustn Escardino, 7. 46980-Paterna, Valencia, Spain
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Institute, University College Cork, T12YT20 Cork, Ireland
| | - Maria João Sousa
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, 4710-057 Braga, Portugal
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20
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Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast. J Fungi (Basel) 2021; 7:jof7040287. [PMID: 33920164 PMCID: PMC8070057 DOI: 10.3390/jof7040287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/15/2022] Open
Abstract
Saccharomyces cerevisiae is the most commonly used yeast in wine, beer, and bread fermentations. However, Torulaspora delbrueckii has attracted interest in recent years due to its properties, ranging from its ability to produce flavor- and aroma-enhanced wine to its ability to survive longer in frozen dough. In this work, publicly available genomes of T. delbrueckii were explored and their annotation was improved. A total of 32 proteins were additionally annotated for the first time in the type strain CBS1146, in comparison with the previous annotation available. In addition, the annotation of the remaining three T. delbrueckii strains was performed for the first time. eggNOG-mapper was used to perform the functional annotation of the deduced T. delbrueckii coding genes, offering insights into its biological significance, and revealing 24 clusters of orthologous groups (COGs), which were gathered in three main functional categories: information storage and processing (28% of the proteins), cellular processing and signaling (27%), and metabolism (23%). Small intraspecies variability was found when considering the functional annotation of the four available T. delbrueckii genomes. A comparative study was also conducted between the T. delbrueckii genome and those from 386 fungal species, revealing a high number of homologous genes with species from the Zygotorulaspora and Zygosaccharomyces genera, but also with Lachancea and S. cerevisiae. Lastly, the phylogenetic placement of T. delbrueckii was clarified using the core homologs that were found across 204 common protein sequences of 386 fungal species and strains.
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21
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Ogata T, Kuroki K. Regulation of mating and mating-type-specific genes in Zygosaccharomyces sp. yeast. Yeast 2021; 38:471-479. [PMID: 33811363 DOI: 10.1002/yea.3561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 11/11/2022] Open
Abstract
Zygosaccharomyces sp. is an industrially important yeast for the production traditional fermented foods in Japan. At present, however, there is no easy method for mating Zygosaccharomyces sp. strains in the laboratory; furthermore, little is known about the expression of mating-type-specific genes in this yeast. Here, mating was observed when Zygosaccharomyces sp. was subjected to nitrogen-starvation conditions. The expression of mating-type-specific genes, Zygo STE6 and Zygo MFα1, was induced under nitrogen-starvation conditions, as confirmed by lacZ reporter assay. This expression was mating-type-specific: Zygo STE6 was expressed specifically for mating-type a, whereas and Zygo MFα1 was expressed specifically for mating-type α. Yeast strains Zygosaccharomyces rouxii DL2 and DA2, derived from type strain Z. rouxii CBS732, did not show mating even under nitrogen-starvation conditions. Gene sequencing revealed that the Zygo STE12 in Z. rouxii CBS732 has a frameshift mutation. Under nitrogen starvation, mating was observed in both DL2 and DA2 transformed with the wild-type Zygo STE12. The expression of Zygo STE6 in Z. rouxii DL2 transformed with wild-type Zygo STE12 under nitrogen-starvation conditions was confirmed by lacZ reporter assay. Collectively, these results revealed that, under nitrogen-starvation conditions, Zygosaccharomyces sp. can mate and mating-type-specific genes are expressed. Furthermore, Zygo Ste12 is essential for both mating and the expression of mating-type-specific genes in Zygosaccharomyces sp.
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Affiliation(s)
- Tomoo Ogata
- Department of Biotechnology, Maebashi Institute of Technology, Maebashi, Japan
| | - Katsuaki Kuroki
- Department of Biotechnology, Maebashi Institute of Technology, Maebashi, Japan
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22
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Toyomura K, Hisatomi T, Yokoyama N, Miyamoto A. Identification of a novel gene controlling homothallism in the yeast Kazachstania naganishii isolated in Japan. Yeast 2020; 38:72-80. [PMID: 33047808 DOI: 10.1002/yea.3525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 11/08/2022] Open
Abstract
A novel gene controlling homothallic life cycle was identified in the yeast Kazachstania naganishii isolated in Japan. This gene was isolated by means of complementing a mutation, mti1, which had led to heterothallism from original homothallism in the yeast. The configuration of original mutation in MTI1 gene revealed that a truncated product is formed due to occurrence of a stop codon by a nucleotide insertion. When the gene was disrupted with a marker, the disruptant spore clone was haploid and stably heterothallic. Disfunction of the gene caused inability to self-diploidize due to defect of mating-type interconversion. The gene MTI1 (for Mating Type Interconversion) is a weak homolog of the Saccharomyces cerevisiae VID22/ENV11, which has been reported to function in vacuolar protein processing. K. naganishii has a gene representing significant homology with the HO gene of S. cerevisiae on chromosome V, which has not been clarified to be involved in regulation of life cycle in K. naganishii. The MTI1 gene defined in this study is located on K. naganishii chromosome IV and does not represent significant homology to the above ScHO-like gene and any other genes concerning life cycles of yeasts. From the viewpoint of gene evolution, it is extremely interesting that the MTI1 gene is a new type of gene controlling homothallism in addition to an HO-type gene, leading to discovery of an unknown mechanism regulating life cycles in yeasts.
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Affiliation(s)
- Kousuke Toyomura
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
| | - Taisuke Hisatomi
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
| | - Nanami Yokoyama
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
| | - Akira Miyamoto
- Department of Biotechnology, Faculty of Life Sciences and Biotechnology, Fukuyama University, Gakuen-cho, Fukuyama, Hiroshima, 729-0292, Japan
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23
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Zhou Li Y, Boisnard S, Enache-Angoulvant A, Fairhead C. Genome editing in the yeast Nakaseomyces delphensis and description of its complete sexual cycle. Yeast 2020; 38:57-71. [PMID: 32941662 DOI: 10.1002/yea.3522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/07/2020] [Accepted: 09/14/2020] [Indexed: 11/06/2022] Open
Abstract
The environmental yeast Nakaseomyces delphensis is, phylogenetically, the closest known species to Candida glabrata, a major fungal pathogen of humans. C. glabrata is haploid and described as asexual, while N. delphensis is also haploid, but has been described as competent for mating and meiosis. Both genomes contain homologues of all the genes necessary for sexual reproduction and also the genes for Ho-dependent mating-type switching, like Saccharomyces cerevisiae. We first report the construction of genetically engineered strains of N. delphensis, including by CRISPR-Cas 9 gene editing. We also report the description of the sexual cycle of N. delphensis. We show that it undergoes Ho-dependent mating-type switching in culture and that deletion of the HO gene prevents such switching and allows maintenance of stable, separate, MATa and MATalpha haploid strains. Rare, genetically selected diploids can be obtained through mating of haploid strains, mutated or not for the HO gene. In contrast to HO/HO diploids, which behave as expected, Δho/Δho diploids exhibit unusual profiles in flow cytometry. Both types of diploids can produce recombined haploid cells, which grow like the original haploid-type strain. Our experiments thus allow the genetic manipulation of N. delphensis and the reconstruction, in the laboratory, of its entire life cycle.
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Affiliation(s)
- Youfang Zhou Li
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
| | - Stéphanie Boisnard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | | | - Cécile Fairhead
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France
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24
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Matos TTS, Teixeira JF, Macías LG, Santos ARO, Suh SO, Barrio E, Lachance MA, Rosa CA. Kluyveromyces osmophilus is not a synonym of Zygosaccharomyces mellis; reinstatement as Zygosaccharomyces osmophilus comb. nov. Int J Syst Evol Microbiol 2020; 70:3374-3378. [PMID: 32375978 DOI: 10.1099/ijsem.0.004182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kluyveromyces osmophilus, a single-strain species isolated from Mozambique sugar, has been treated a synonym of Zygosaccharomyces mellis. Analyses of D1/D2 LSU rRNA gene sequences confirmed that the species belongs to the genus Zygosaccharomyces but showed it to be distinct from strains of Z. mellis. During studies of yeasts associated with stingless bees in Brazil, nine additional isolates of the species were obtained from unripe and ripe honey and pollen of Scaptotrigona cfr. bipunctata, as well as ripe honey of Tetragonisca angustula. The D1/D2 sequences of the Brazilian isolates were identical to those of the type strain of K. osmophilus CBS 5499 (=ATCC 22027), indicating that they represent the same species. Phylogenomic analyses using 4038 orthologous genes support the reinstatement of K. osmophilus as a member of the genus Zygosaccharomyces. We, therefore, propose the name Zygosaccharomyces osmophilus comb. nov. (lectotype ATCC 22027; MycoBank no. MB 833739).
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Affiliation(s)
- Thelma T S Matos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Juliana F Teixeira
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Laura G Macías
- Departament de Genètica, Universitat de València, València, Spain.,Departamento de Biotecnología de Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Alimentos (IATA)-CSIC, Valencia, Spain
| | - Ana Raquel O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Sung-Oui Suh
- Manufacturing Science and Technology Program, ATCC, 10801 University Boulevard, Manassas, VA 20110-2209, USA
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, València, Spain.,Departamento de Biotecnología de Alimentos, Grupo de Biología de Sistemas en Levaduras de Interés Biotecnológico, Instituto de Agroquímica y Tecnología de Alimentos (IATA)-CSIC, Valencia, Spain
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, N6A 5B7, London, Ontario, Canada
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
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25
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Non-tandem repeat polymorphisms at microsatellite loci in wine yeast species. Mol Genet Genomics 2020; 295:685-693. [DOI: 10.1007/s00438-020-01652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/07/2020] [Indexed: 10/24/2022]
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26
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Coughlan AY, Lombardi L, Braun-Galleani S, Martos AA, Galeote V, Bigey F, Dequin S, Byrne KP, Wolfe KH. The yeast mating-type switching endonuclease HO is a domesticated member of an unorthodox homing genetic element family. eLife 2020; 9:55336. [PMID: 32338594 PMCID: PMC7282813 DOI: 10.7554/elife.55336] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023] Open
Abstract
The mating-type switching endonuclease HO plays a central role in the natural life cycle of Saccharomyces cerevisiae, but its evolutionary origin is unknown. HO is a recent addition to yeast genomes, present in only a few genera close to Saccharomyces. Here we show that HO is structurally and phylogenetically related to a family of unorthodox homing genetic elements found in Torulaspora and Lachancea yeasts. These WHO elements home into the aldolase gene FBA1, replacing its 3' end each time they integrate. They resemble inteins but they operate by a different mechanism that does not require protein splicing. We show that a WHO protein cleaves Torulaspora delbrueckii FBA1 efficiently and in an allele-specific manner, leading to DNA repair by gene conversion or NHEJ. The DNA rearrangement steps during WHO element homing are very similar to those during mating-type switching, and indicate that HO is a domesticated WHO-like element. In the same way as a sperm from a male and an egg from a female join together to form an embryo in most animals, yeast cells have two sexes that coordinate how they reproduce. These are called “mating types” and, rather than male or female, an individual yeast cell can either be mating type “a” or “alpha”. Every yeast cell contains the genes for both mating types, and each cell’s mating type is determined by which of those genes it has active. Only one mating type gene can be ‘on’ at a time, but some yeast species can swap mating type on demand by switching the corresponding genes ‘on’ or ‘off’. This switch is unusual. Rather than simply activate one of the genes it already has, the yeast cell keeps an inactive version of each mating type gene tucked away, makes a copy of the gene it wants to be active and pastes that copy into a different location in its genome. To do all of this yeast need another gene called HO. This gene codes for an enzyme that cuts the DNA at the location of the active mating type gene. This makes an opening that allows the cell to replace the ‘a’ gene with the ‘alpha’ gene, or vice versa. This system allows yeast cells to continue mating even if all the cells in a colony start off as the same mating type. But, cutting into the DNA is risky, and can damage the health of the cell. So, why did yeast cells evolve a system that could cause them harm? To find out where the HO gene came from, Coughlan et al. searched through all the available genomes from yeast species for other genes with similar sequences and identified a cluster which they nicknamed “weird HO” genes, or WHO genes for short. Testing these genes revealed that they also code for enzymes that make cuts in the yeast genome, but the way the cell repairs the cuts is different. The WHO genes are jumping genes. When the enzyme encoded by a WHO gene makes a cut in the genome, the yeast cell copies the gene into the gap, allowing the gene to ‘jump’ from one part of the genome to another. It is possible that this was the starting point for the evolution of the HO gene. Changes to a WHO gene could have allowed it to cut into the mating type region of the yeast genome, giving the yeast an opportunity to ‘domesticate’ it. Over time, the yeast cell stopped the WHO gene from jumping into the gap and started using the cut to change its mating type. Understanding how cells adapt genes for different purposes is a key question in evolutionary biology. There are many other examples of domesticated jumping genes in other organisms, including in the human immune system. Understanding the evolution of HO not only sheds light on how yeast mating type switching evolved, but on how other species might harness and adapt their genes.
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Affiliation(s)
- Aisling Y Coughlan
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Lisa Lombardi
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | | | - Alexandre Ar Martos
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Virginie Galeote
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Frédéric Bigey
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Sylvie Dequin
- SPO, INRAE, Université Montpellier, Montpellier SupAgro, Montpellier, France
| | - Kevin P Byrne
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth H Wolfe
- UCD Conway Institute and School of Medicine, University College Dublin, Dublin, Ireland
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27
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Alternative Lengthening of Telomeres in the Budding Yeast Naumovozyma castellii. G3-GENES GENOMES GENETICS 2019; 9:3345-3358. [PMID: 31427453 PMCID: PMC6778800 DOI: 10.1534/g3.119.400428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The enzyme telomerase ensures the integrity of linear chromosomes by maintaining telomere length. As a hallmark of cancer, cell immortalization and unlimited proliferation is gained by reactivation of telomerase. However, a significant fraction of cancer cells instead uses alternative telomere lengthening mechanisms to ensure telomere function, collectively known as Alternative Lengthening of Telomeres (ALT). Although the budding yeast Naumovozyma castellii (Saccharomyces castellii) has a proficient telomerase activity, we demonstrate here that telomeres in N. castellii are efficiently maintained by a novel ALT mechanism after telomerase knockout. Remarkably, telomerase-negative cells proliferate indefinitely without any major growth crisis and display wild-type colony morphology. Moreover, ALT cells maintain linear chromosomes and preserve a wild-type DNA organization at the chromosome termini, including a short stretch of terminal telomeric sequence. Notably, ALT telomeres are elongated by the addition of ∼275 bp repeats containing a short telomeric sequence and the subtelomeric DNA located just internally (TelKO element). Although telomeres may be elongated by several TelKO repeats, no dramatic genome-wide amplification occurs, thus indicating that the repeat addition may be regulated. Intriguingly, a short interstitial telomeric sequence (ITS) functions as the initiation point for the addition of the TelKO element. This implies that N. castellii telomeres are structurally predisposed to efficiently switch to the ALT mechanism as a response to telomerase dysfunction.
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28
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Krassowski T, Kominek J, Shen XX, Opulente DA, Zhou X, Rokas A, Hittinger CT, Wolfe KH. Multiple Reinventions of Mating-type Switching during Budding Yeast Evolution. Curr Biol 2019; 29:2555-2562.e8. [PMID: 31353182 PMCID: PMC6692504 DOI: 10.1016/j.cub.2019.06.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/08/2019] [Accepted: 06/20/2019] [Indexed: 11/25/2022]
Abstract
Cell type in budding yeasts is determined by the genotype at the mating-type (MAT) locus, but yeast species differ widely in their mating compatibility systems and life cycles. Among sexual yeasts, heterothallic species are those in which haploid strains fall into two distinct and stable mating types (MATa and MATα), whereas homothallic species are those that can switch mating types or that appear not to have distinct mating types [1, 2]. The evolutionary history of these mating compatibility systems is uncertain, particularly regarding the number and direction of transitions between homothallism and heterothallism, and regarding whether the process of mating-type switching had a single origin [3, 4, 5]. Here, we inferred the mating compatibility systems of 332 budding yeast species from their genome sequences. By reference to a robust phylogenomic tree [6], we detected evolutionary transitions between heterothallism and homothallism, and among different forms of homothallism. We find that mating-type switching has arisen independently at least 11 times during yeast evolution and that transitions from heterothallism to homothallism greatly outnumber transitions in the opposite direction (31 versus 3). Although the 3-locus MAT-HML-HMR mechanism of mating-type switching as seen in Saccharomyces cerevisiae had a single evolutionary origin in budding yeasts, simpler “flip/flop” mechanisms of switching evolved separately in at least 10 other groups of yeasts. These results point to the adaptive value of homothallism and mating-type switching to unicellular fungi. Mating-type switching by flip-flopping arose at least 10 separate times Mating-type switching by copy-and-paste arose only once in budding yeasts Transitions toward homothallism outnumber transitions away from homothallism Heterothallic species can become homothallic by DNA introgression
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Affiliation(s)
- Tadeusz Krassowski
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland; Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland.
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29
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Borelli G, Fiamenghi MB, dos Santos LV, Carazzolle MF, Pereira GAG, José J. Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts' Fermentation in Industry. Genome Biol Evol 2019; 11:1923-1938. [PMID: 31070742 PMCID: PMC6637916 DOI: 10.1093/gbe/evz036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Xylose assimilation and fermentation are important traits for second generation ethanol production. However, some genomic features associated with this pentose sugar's metabolism remain unknown in yeasts. Comparative genomics studies have led to important insights in this field, but we are still far from completely understanding endogenous yeasts' xylose metabolism. In this work, we carried out a deep evolutionary analysis suited for comparative genomics of xylose-consuming yeasts, searching for of positive selection on genes associated with glucose and xylose metabolism in the xylose-fermenters' clade. Our investigation detected positive selection fingerprints at this clade not only among sequences of important genes for xylose metabolism, such as xylose reductase and xylitol dehydrogenase, but also in genes expected to undergo neutral evolution, such as the glycolytic gene phosphoglycerate mutase. In addition, we present expansion, positive selection marks, and convergence as evidence supporting the hypothesis that natural selection is shaping the evolution of the little studied methylglyoxal reductases. We propose a metabolic model suggesting that selected codons among these proteins caused a putative change in cofactor preference from NADPH to NADH that alleviates cellular redox imbalance. These findings provide a wider look into pentose metabolism of yeasts and add this previously overlooked piece into the intricate puzzle of oxidative imbalance. Although being extensively discussed in evolutionary works the awareness of selection patterns is recent in biotechnology researches, rendering insights to surpass the reached status quo in many of its subareas.
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Affiliation(s)
- Guilherme Borelli
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Mateus Bernabe Fiamenghi
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Juliana José
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
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30
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Braun-Galleani S, Ortiz-Merino RA, Wu Q, Xu Y, Wolfe KH. Zygosaccharomyces pseudobailii, another yeast interspecies hybrid that regained fertility by damaging one of its MAT loci. FEMS Yeast Res 2019; 18:5056719. [PMID: 30052970 PMCID: PMC6093378 DOI: 10.1093/femsyr/foy079] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/19/2018] [Indexed: 12/30/2022] Open
Abstract
Interspecies hybridization is an important evolutionary mechanism in yeasts. The genus Zygosaccharomyces in particular contains numerous hybrid strains and/or species. Here, we investigated the genome of Zygosaccharomyces strain MT15, an isolate from Maotai-flavor Chinese liquor fermentation. We found that it is an interspecies hybrid and identified it as Zygosaccharomyces pseudobailii. The Z. bailii species complex consists of three species: Z. bailii, which is not a hybrid and whose 10 Mb genome is designated 'A', and two hybrid species Z. parabailii ('AB' genome, 20 Mb) and Z. pseudobailii ('AC' genome, 20 Mb). The A, B and C subgenomes are all approximately 7%-10% different from one another in nucleotide sequence, and are derived from three different parental species. Despite being hybrids, Z. pseudobailii and Z. parabailii are capable of mating and sporulating. We previously showed that Z. parabailii regained fertility when one copy of its MAT locus became broken into two parts, causing the allodiploid hybrid to behave as a haploid gamete. In Z. pseudobailii, we find that a very similar process occurred after hybridization, when a deletion of 1.5 kb inactivated one of the two copies of its MAT locus. The half-sibling species Z. parabailii and Z. pseudobailii therefore went through remarkably parallel but independent steps to regain fertility after they were formed by separate interspecies hybridizations.
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Affiliation(s)
| | - Raúl A Ortiz-Merino
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Qun Wu
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology, Ministry of Education, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yan Xu
- State Key Laboratory of Food Science and Technology, Key Laboratory of Industrial Biotechnology, Ministry of Education, Synergetic Innovation Center of Food Safety and Nutrition, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland
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31
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Faure G, Jézéquel K, Roisné-Hamelin F, Bitard-Feildel T, Lamiable A, Marcand S, Callebaut I. Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1. Genome Biol Evol 2019; 11:572-585. [PMID: 30668669 PMCID: PMC6394760 DOI: 10.1093/gbe/evz010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2019] [Indexed: 12/22/2022] Open
Abstract
Sir4 is a core component of heterochromatin found in yeasts of the Saccharomycetaceae family, whose general hallmark is to harbor a three-loci mating-type system with two silent loci. However, a large part of the Sir4 amino acid sequences has remained unexplored, belonging to the dark proteome. Here, we analyzed the phylogenetic profile of yet undescribed foldable regions present in Sir4 as well as in Esc1, an Sir4-interacting perinuclear anchoring protein. Within Sir4, we identified a new conserved motif (TOC) adjacent to the N-terminal KU-binding motif. We also found that the Esc1-interacting region of Sir4 is a Dbf4-related H-BRCT domain, only present in species possessing the HO endonuclease and in Kluveryomyces lactis. In addition, we found new motifs within Esc1 including a motif (Esc1-F) that is unique to species where Sir4 possesses an H-BRCT domain. Mutagenesis of conserved amino acids of the Sir4 H-BRCT domain, known to play a critical role in the Dbf4 function, shows that the function of this domain is separable from the essential role of Sir4 in transcriptional silencing and the protection from HO-induced cutting in Saccharomyces cerevisiae. In the more distant methylotrophic clade of yeasts, which often harbor a two-loci mating-type system with one silent locus, we also found a yet undescribed H-BRCT domain in a distinct protein, the ISWI2 chromatin-remodeling factor subunit Itc1. This study provides new insights on yeast heterochromatin evolution and emphasizes the interest of using sensitive methods of sequence analysis for identifying hitherto ignored functional regions within the dark proteome.
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Affiliation(s)
- Guilhem Faure
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Kévin Jézéquel
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Florian Roisné-Hamelin
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - Tristan Bitard-Feildel
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Alexis Lamiable
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Stéphane Marcand
- Institut de Biologie François Jacob, IRCM/SIGRR/LTR, INSERM U1274, Université Paris-Saclay, CEA Paris-Saclay, Paris, France.,Sorbonne Université, UMR CNRS 7238, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France.,Sorbonne Université, UMR CNRS 7238, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
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32
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Macías LG, Morard M, Toft C, Barrio E. Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation. Front Genet 2019; 10:187. [PMID: 30930934 PMCID: PMC6425871 DOI: 10.3389/fgene.2019.00187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/21/2019] [Indexed: 12/02/2022] Open
Abstract
Yeasts belonging to the Saccharomyces genus play an important role in human-driven fermentations. The species S. cerevisiae has been widely studied because it is the dominant yeast in most fermentations and it has been widely used as a model eukaryotic organism. Recently, other species of the Saccharomyces genus are gaining interest to solve the new challenges that the fermentation industry are facing. One of these species is S. kudriavzevii, which exhibits interesting physiological properties compared to S. cerevisiae, such as a better adaptation to grow at low temperatures, a higher glycerol synthesis and lower ethanol production. The aim of this study is to understand the molecular basis behind these phenotypic differences of biotechnological interest by using a species-based comparative genomics approach. In this work, we sequenced, assembled and annotated two new genomes of S. kudriavzevii. We used a combination of different statistical methods to identify functional divergence, signatures of positive selection and acceleration of substitution rates at specific amino acid sites of proteins in S. kudriavzevii when compared to S. cerevisiae, and vice versa. We provide a list of candidate genes in which positive selection could be acting during the evolution of both S. cerevisiae and S. kudriavzevii clades. Some of them could be related to certain important differences in metabolism previously reported by other authors such us DAL3 and ARO4, involved in nitrogen assimilation and amino acid biosynthesis. In addition, three of those genes (FBA1, ZIP1, and RQC2) showed accelerated evolutionary rates in Sk branch. Finally, genes of the riboflavin biosynthesis were also among those genes with a significant higher rate of nucleotide substitution and those proteins have amino acid positions contributing to functional divergence.
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Affiliation(s)
- Laura G Macías
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Miguel Morard
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Christina Toft
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
| | - Eladio Barrio
- Departament de Genètica, Universitat de València, Valencia, Spain.,Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos IATA, CSIC, Valencia, Spain
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33
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Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies. G3-GENES GENOMES GENETICS 2019; 9:879-887. [PMID: 30674538 PMCID: PMC6404606 DOI: 10.1534/g3.118.200745] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Illumina sequencing has revolutionized yeast genomics, with prices for commercial draft genome sequencing now below $200. The popular SPAdes assembler makes it simple to generate a de novo genome assembly for any yeast species. However, whereas making genome assemblies has become routine, understanding what they contain is still challenging. Here, we show how graphing the information that SPAdes provides about the length and coverage of each scaffold can be used to investigate the nature of an assembly, and to diagnose possible problems. Scaffolds derived from mitochondrial DNA, ribosomal DNA, and yeast plasmids can be identified by their high coverage. Contaminating data, such as cross-contamination from other samples in a multiplex sequencing run, can be identified by its low coverage. Scaffolds derived from the bacteriophage PhiX174 and Lambda DNAs that are frequently used as molecular standards in Illumina protocols can also be detected. Assemblies of yeast genomes with high heterozygosity, such as interspecies hybrids, often contain two types of scaffold: regions of the genome where the two alleles assembled into two separate scaffolds and each has a coverage level C, and regions where the two alleles co-assembled (collapsed) into a single scaffold that has a coverage level 2C. Visualizing the data with Coverage-vs.-Length (CVL) plots, which can be done using Microsoft Excel or Google Sheets, provides a simple method to understand the structure of a genome assembly and detect aberrant scaffolds or contigs. We provide a Python script that allows assemblies to be filtered to remove contaminants identified in CVL plots.
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34
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Bizzarri M, Cassanelli S, Bartolini L, Pryszcz LP, Dušková M, Sychrová H, Solieri L. Interplay of Chimeric Mating-Type Loci Impairs Fertility Rescue and Accounts for Intra-Strain Variability in Zygosaccharomyces rouxii Interspecies Hybrid ATCC42981. Front Genet 2019; 10:137. [PMID: 30881382 PMCID: PMC6405483 DOI: 10.3389/fgene.2019.00137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
The pre-whole genome duplication (WGD) Zygosaccharomyces clade comprises several allodiploid strain/species with industrially interesting traits. The salt-tolerant yeast ATCC42981 is a sterile and allodiploid strain which contains two subgenomes, one of them resembling the haploid parental species Z. rouxii. Recently, different mating-type-like (MTL) loci repertoires were reported for ATCC42981 and the Japanese strain JCM22060, which are considered two stocks of the same strain. MTL reconstruction by direct sequencing approach is challenging due to gene redundancy, structure complexities, and allodiploid nature of ATCC42981. Here, DBG2OLC and MaSuRCA hybrid de novo assemblies of ONT and Illumina reads were combined with in vitro long PCR to definitively solve these incongruences. ATCC42981 exhibits several chimeric MTL loci resulting from reciprocal translocation between parental haplotypes and retains two MATa/MATα expression loci, in contrast to MATα in JCM22060. Consistently to these reconstructions, JCM22060, but not ATCC42981, undergoes mating and meiosis. To ascertain whether the damage of one allele at the MAT locus regains the complete sexual cycle in ATCC42981, we removed the MATα expressed locus by gene deletion. The resulting MATa/- hemizygous mutants did not show any evidence of sporulation, as well as of self- and out-crossing fertility, probably because incomplete silencing at the chimeric HMLα cassette masks the loss of heterozygosity at the MAT locus. We also found that MATα deletion switched off a2 transcription, an activator of a-specific genes in pre-WGD species. These findings suggest that regulatory scheme of cell identity needs to be further investigated in Z. rouxii protoploid yeast.
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Affiliation(s)
- Melissa Bizzarri
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Laura Bartolini
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Leszek P. Pryszcz
- Laboratory of Zebrafish Developmental Genomics, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michala Dušková
- Department of Membrane Transport, Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Hana Sychrová
- Department of Membrane Transport, Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
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35
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Tondini F, Lang T, Chen L, Herderich M, Jiranek V. Linking gene expression and oenological traits: Comparison between Torulaspora delbrueckii and Saccharomyces cerevisiae strains. Int J Food Microbiol 2019; 294:42-49. [PMID: 30763906 DOI: 10.1016/j.ijfoodmicro.2019.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 11/16/2022]
Abstract
Wine fermentations typically involve the yeast Saccharomyces cerevisiae. However, many other yeast species participate to the fermentation process, some with interesting oenological traits. In this study the species Torulaspora delbrueckii, used occasionally in mixed or sequential fermentation with S. cerevisiae to improve wine sensory profile, was investigated to understand the physiological differences between the two. Next generation sequencing was used to characterize the transcriptome of T. delbrueckii and highlight the different genomic response of these yeasts during growth under wine-like conditions. Of particular interest were the basic differences in the glucose fermentation pathway and the formation of aromatic and flavour compounds such as glycerol, esters and acetic acid. Paralog genes were missing in glycolysis and glycerol biosynthesis in T. delbrueckii. Results indicate the tendency of T. delbrueckii to produce less acetic acid relied on a higher expression of alcoholic fermentation related genes, whereas acetate esters were influenced by the absence of esterases, ATF1-2. Additionally, in the Δbap2 S. cerevisiae strain, the final concentration of short branched chain ethyl esters (SBCEEs) was related to branched chain amino acid (BCAA) uptake. In conclusion, different adaption strategies are apparent for T. delbrueckii and S. cerevisiae yeasts, an understanding of which will allow winemakers to make better use of such microbial tools to achieve a desired wine sensory outcome.
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Affiliation(s)
- Federico Tondini
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia; Australian Research Council Industrial Transformation Training Centre for Innovative Wine Production, Glen Osmond, South Australia 5064, Australia
| | - Tom Lang
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Liang Chen
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Markus Herderich
- Australian Research Council Industrial Transformation Training Centre for Innovative Wine Production, Glen Osmond, South Australia 5064, Australia; The Australian Wine Research Institute, Glen Osmond, South Australia 5064, Australia
| | - Vladimir Jiranek
- Department of Wine & Food Science, University of Adelaide, Glen Osmond, South Australia 5064, Australia; Australian Research Council Industrial Transformation Training Centre for Innovative Wine Production, Glen Osmond, South Australia 5064, Australia.
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36
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Makeeva DS, Lando AS, Anisimova A, Egorov AA, Logacheva MD, Penin AA, Andreev DE, Sinitcyn PG, Terenin IM, Shatsky IN, Kulakovskiy IV, Dmitriev SE. Translatome and transcriptome analysis of TMA20 (MCT-1) and TMA64 (eIF2D) knockout yeast strains. Data Brief 2019; 23:103701. [PMID: 30815525 PMCID: PMC6378902 DOI: 10.1016/j.dib.2019.103701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/15/2018] [Accepted: 01/21/2019] [Indexed: 02/05/2023] Open
Abstract
TMA20 (MCT-1), TMA22 (DENR) and TMA64 (eIF2D) are eukaryotic translation factors involved in ribosome recycling and re-initiation. They operate with P-site bound tRNA in post-termination or (re-)initiation translation complexes, thus participating in the removal of 40S ribosomal subunit from mRNA stop codons after termination and controlling translation re-initiation on mRNAs with upstream open reading frames (uORFs), as well as de novo initiation on some specific mRNAs. Here we report ribosomal profiling data of S.cerevisiae strains with individual deletions of TMA20, TMA64 or both TMA20 and TMA64 genes. We provide RNA-Seq and Ribo-Seq data from yeast strains grown in the rich YPD or minimal SD medium. We illustrate our data by plotting differential distribution of ribosomal-bound mRNA fragments throughout uORFs in 5'-untranslated region (5' UTR) of GCN4 mRNA and on mRNA transcripts encoded in MAT locus in the mutant and wild-type strains, thus providing a basis for investigation of the role of these factors in the stress response, mating and sporulation. We also document a shift of transcription start site of the APC4 gene which occurs when the neighboring TMA64 gene is replaced by the standard G418-resistance cassette used for the creation of the Yeast Deletion Library. This shift results in dramatic deregulation of the APC4 gene expression, as revealed by our Ribo-Seq data, which can be probably used to explain strong genetic interactions of TMA64 with genes involved in the cell cycle and mitotic checkpoints. Raw RNA-Seq and Ribo-Seq data as well as all gene counts are available in NCBI Gene Expression Omnibus (GEO) repository under GEO accession GSE122039 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122039).
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Affiliation(s)
- Desislava S Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Andrey S Lando
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia
| | - Aleksandra Anisimova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Artyom A Egorov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,Department of Medical Physics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991 Russia
| | - Maria D Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - Alexey A Penin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991 Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Pavel G Sinitcyn
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991 Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - Ivan V Kulakovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991 Russia.,Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234 Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234 Russia
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37
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Carbonetto B, Ramsayer J, Nidelet T, Legrand J, Sicard D. Bakery yeasts, a new model for studies in ecology and evolution. Yeast 2018; 35:591-603. [DOI: 10.1002/yea.3350] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Belén Carbonetto
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
- Instituto Gulbenkian de Ciência; Bioinformatics and Computational Biology Unit; Oeiras Portugal
| | - Johan Ramsayer
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
| | - Thibault Nidelet
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
| | - Judith Legrand
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; Gif-sur-Yvette France
| | - Delphine Sicard
- SPO, Univ Montpellier, INRA; Montpellier SupAgro; Montpellier France
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38
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Sorrells TR, Johnson AN, Howard CJ, Britton CS, Fowler KR, Feigerle JT, Weil PA, Johnson AD. Intrinsic cooperativity potentiates parallel cis-regulatory evolution. eLife 2018; 7:37563. [PMID: 30198843 PMCID: PMC6173580 DOI: 10.7554/elife.37563] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/09/2018] [Indexed: 12/27/2022] Open
Abstract
Convergent evolutionary events in independent lineages provide an opportunity to understand why evolution favors certain outcomes over others. We studied such a case where a large set of genes-those coding for the ribosomal proteins-gained cis-regulatory sequences for a particular transcription regulator (Mcm1) in independent fungal lineages. We present evidence that these gains occurred because Mcm1 shares a mechanism of transcriptional activation with an ancestral regulator of the ribosomal protein genes, Rap1. Specifically, we show that Mcm1 and Rap1 have the inherent ability to cooperatively activate transcription through contacts with the general transcription factor TFIID. Because the two regulatory proteins share a common interaction partner, the presence of one ancestral cis-regulatory sequence can 'channel' random mutations into functional sites for the second regulator. At a genomic scale, this type of intrinsic cooperativity can account for a pattern of parallel evolution involving the fixation of hundreds of substitutions.
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Affiliation(s)
- Trevor R Sorrells
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Amanda N Johnson
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conor J Howard
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Candace S Britton
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Kyle R Fowler
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
| | - Jordan T Feigerle
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - P Anthony Weil
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Alexander D Johnson
- Department of Biochemistry and Biophysics, Tetrad Graduate Program, University of California, San Francisco, United States.,Department of Microbiology and Immunology, University of California, San Francisco, United States
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39
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Ye Z, Pan Y, Zhang Y, Cui H, Jin G, McHardy AC, Fan L, Yu X. Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome. DNA Res 2018; 24:635-648. [PMID: 28992048 PMCID: PMC5726479 DOI: 10.1093/dnares/dsx031] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 07/06/2017] [Indexed: 12/31/2022] Open
Abstract
Ustilago esculenta, infects Zizania latifolia, and induced host stem swollen to be a popular vegetable called Jiaobai in China. It is the long-standing artificial selection that maximizes the occurrence of favourable Jiaobai, and thus maintaining the plant-fungi interaction and modulating the fungus evolving from plant pathogen to entophyte. In this study, whole genome of U. esculenta was sequenced and transcriptomes of the fungi and its host were analysed. The 20.2 Mb U. esculenta draft genome of 6,654 predicted genes including mating, primary metabolism, secreted proteins, shared a high similarity to related Smut fungi. But U. esculenta prefers RNA silencing not repeat-induced point in defence and has more introns per gene, indicating relatively slow evolution rate. The fungus also lacks some genes in amino acid biosynthesis pathway which were filled by up-regulated host genes and developed distinct amino acid response mechanism to balance the infection-resistance interaction. Besides, U. esculenta lost some surface sensors, important virulence factors and host range-related effectors to maintain the economic endophytic life. The elucidation of the U. esculenta genomic information as well as expression profiles can not only contribute to more comprehensive insights into the molecular mechanism underlying artificial selection but also into smut fungi-host interactions.
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Affiliation(s)
- Zihong Ye
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
| | - Yao Pan
- Department of Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Yafen Zhang
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
| | - Haifeng Cui
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
| | - Gulei Jin
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, China
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Longjiang Fan
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, China
| | - Xiaoping Yu
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
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40
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Viigand K, Põšnograjeva K, Visnapuu T, Alamäe T. Genome Mining of Non-Conventional Yeasts: Search and Analysis of MAL Clusters and Proteins. Genes (Basel) 2018; 9:E354. [PMID: 30013016 PMCID: PMC6070925 DOI: 10.3390/genes9070354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic clustering of functionally related genes is rare in yeasts and other eukaryotes with only few examples available. Here, we summarize our data on a nontelomeric MAL cluster of a non-conventional methylotrophic yeast Ogataea (Hansenula) polymorpha containing genes for α-glucosidase MAL1, α-glucoside permease MAL2 and two hypothetical transcriptional activators. Using genome mining, we detected MAL clusters of varied number, position and composition in many other maltose-assimilating non-conventional yeasts from different phylogenetic groups. The highest number of MAL clusters was detected in Lipomyces starkeyi while no MAL clusters were found in Schizosaccharomyces pombe and Blastobotrys adeninivorans. Phylograms of α-glucosidases and α-glucoside transporters of yeasts agreed with phylogenesis of the respective yeast species. Substrate specificity of unstudied α-glucosidases was predicted from protein sequence analysis. Specific activities of Scheffersomycesstipitis α-glucosidases MAL7, MAL8, and MAL9 heterologously expressed in Escherichia coli confirmed the correctness of the prediction-these proteins were verified promiscuous maltase-isomaltases. α-Glucosidases of earlier diverged yeasts L. starkeyi, B. adeninivorans and S. pombe showed sequence relatedness with α-glucosidases of filamentous fungi and bacilli.
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Affiliation(s)
- Katrin Viigand
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Kristina Põšnograjeva
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Triinu Visnapuu
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
| | - Tiina Alamäe
- Department of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
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41
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Abstract
We report here the genome sequence of the ascomycetous yeast Torulaspora microellipsoides CLIB 830T. A reference genome for this species, which has been found as a donor of genetic material in wine strains of Saccharomyces cerevisiae, will undoubtedly give clues to our understanding of horizontal transfer mechanisms between species in the wine environment. We report here the genome sequence of the ascomycetous yeast Torulaspora microellipsoides CLIB 830T. A reference genome for this species, which has been found as a donor of genetic material in wine strains of Saccharomyces cerevisiae, will undoubtedly give clues to our understanding of horizontal transfer mechanisms between species in the wine environment.
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42
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Szabóová D, Hapala I, Sulo P. The complete mitochondrial DNA sequence from Kazachstania sinensis reveals a general +1C frameshift mechanism in CTGY codons. FEMS Yeast Res 2018. [PMID: 29528462 DOI: 10.1093/femsyr/foy028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complete mitochondrial DNA (mtDNA) sequence from Kazachstania sinensis was analysed and compared to mtDNA from related yeasts. It contained the same set of genes; however, it only contained 23 tRNAs, as the trnR2 gene was absent. Most of the 12 introns within cox1, cob and rnl genes were inserted in the same sites as in other yeasts; however, two introns in rnl were in unusual positions. Traits such as gene order and GC cluster number were more related to Saccharomyces than to the other Kazachstania or linked clades. The most exceptional feature was the +1 frameshift in cox3, atp6 and cob open reading frames that was also found in other Kazachstania, Nakaseomyces delphensis and Candida glabrata. Comparison of DNA and protein sequences revealed the universal sites of +1C frameshifts were either CTGT or CTGC sequences. Moreover, an A→G substitution was found at position 37 in the anticodon stem loop tRNA gene for cysteine in all species with frameshifts but not in other sibling yeasts. This substitution allowed strong Watson-Crick base-pairing between an unmodified G (ACG) and the skipped C in the CTGY, leading to this quadruplet being read as cysteine.
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Affiliation(s)
- Dana Szabóová
- Department of Biochemistry, Comenius University, Faculty of Natural Sciences, Ilkovicova ulica 6, Bratislava 84215, Slovakia
| | - Ivan Hapala
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences SAS, Dúbravská 9, Bratislava 840 05, Slovakia
| | - Pavol Sulo
- Department of Biochemistry, Comenius University, Faculty of Natural Sciences, Ilkovicova ulica 6, Bratislava 84215, Slovakia
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43
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Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing. GENOME ANNOUNCEMENTS 2018; 6:6/17/e00321-18. [PMID: 29700153 PMCID: PMC5920178 DOI: 10.1128/genomea.00321-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here, we report the first sequenced genome of an indigenous Australian wine isolate of Torulaspora delbrueckii using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes.
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44
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Stavrou AA, Mixão V, Boekhout T, Gabaldón T. Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications. Yeast 2018; 35:425-429. [PMID: 29320804 PMCID: PMC6001429 DOI: 10.1002/yea.3303] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/30/2017] [Accepted: 12/21/2017] [Indexed: 11/05/2022] Open
Abstract
Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, which once entered in the database can be propagated and mislead downstream analyses. Here we present an illustrating case of misidentification of Candida albicans from a clinical sample as Naumovozyma dairenensis based on whole-genome shotgun data. Analyses of phylogenetic markers, read mapping and single nucleotide polymorphisms served to correct the identification. We propose that the routine use of such analyses could help to detect misidentifications arising from unsupervised analyses and correct them before they enter the databases. Finally, we discuss broader implications of such misidentifications and the difficulty of correcting them once they are in the records.
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Affiliation(s)
- Aimilia A Stavrou
- Westerdijk Fungal Biodiversity Institute, 3584, Utrecht, The Netherlands.,Institute for Biodiversity and ecosystem Dynamics, University of Amsterdam, 1012, WX, Amsterdam, The Netherlands
| | - Verónica Mixão
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584, Utrecht, The Netherlands.,Institute for Biodiversity and ecosystem Dynamics, University of Amsterdam, 1012, WX, Amsterdam, The Netherlands
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010, Barcelona, Spain
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45
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Ogata T, Kuroki K, Ito K, Kondo A, Nakamura K. Variations in mating-type-like ( MTL) loci direct PCR-based tracking of Zygosaccharomyces strains formed by mating. J GEN APPL MICROBIOL 2018; 64:127-135. [DOI: 10.2323/jgam.2017.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Tomoo Ogata
- Department of Biotechnology, Maebashi Institute of Technology
| | - Katsuaki Kuroki
- Department of Biotechnology, Maebashi Institute of Technology
| | - Koki Ito
- Department of Biotechnology, Maebashi Institute of Technology
| | - Akifumi Kondo
- Department of Biotechnology, Maebashi Institute of Technology
| | - Kensuke Nakamura
- Department of Life Science and Informatics, Maebashi Institute of Technology
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46
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Tsakraklides V, Kamineni A, Consiglio AL, MacEwen K, Friedlander J, Blitzblau HG, Hamilton MA, Crabtree DV, Su A, Afshar J, Sullivan JE, LaTouf WG, South CR, Greenhagen EH, Shaw AJ, Brevnova EE. High-oleate yeast oil without polyunsaturated fatty acids. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:131. [PMID: 29760773 PMCID: PMC5941336 DOI: 10.1186/s13068-018-1131-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/28/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Oleate-enriched triacylglycerides are well-suited for lubricant applications that require high oxidative stability. Fatty acid carbon chain length and degree of desaturation are key determinants of triacylglyceride properties and the ability to manipulate fatty acid composition in living organisms is critical to developing a source of bio-based oil tailored to meet specific application requirements. RESULTS We sought to engineer the oleaginous yeast Yarrowia lipolytica for production of high-oleate triacylglyceride oil. We studied the effect of deletions and overexpressions in the fatty acid and triacylglyceride synthesis pathways to identify modifications that increase oleate levels. Oleic acid accumulation in triacylglycerides was promoted by exchanging the native ∆9 fatty acid desaturase and glycerol-3-phosphate acyltransferase with heterologous enzymes, as well as deletion of the Δ12 fatty acid desaturase and expression of a fatty acid elongase. By combining these engineering steps, we eliminated polyunsaturated fatty acids and created a Y. lipolytica strain that accumulates triglycerides with > 90% oleate content. CONCLUSIONS High-oleate content and lack of polyunsaturates distinguish this triacylglyceride oil from plant and algal derived oils. Its composition renders the oil suitable for applications that require high oxidative stability and further demonstrates the potential of Y. lipolytica as a producer of tailored lipid profiles.
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Affiliation(s)
| | | | | | - Kyle MacEwen
- Novogy, Inc, 85 Bolton Street, Cambridge, MA 02140 USA
| | | | | | | | | | - Austin Su
- Novogy, Inc, 85 Bolton Street, Cambridge, MA 02140 USA
| | | | | | | | | | - Emily H. Greenhagen
- Novogy, Inc, 85 Bolton Street, Cambridge, MA 02140 USA
- Present Address: Ginkgo Bioworks, 27 Drydock Avenue, 8th Floor, Boston, MA 02210 USA
| | - A. Joe Shaw
- Novogy, Inc, 85 Bolton Street, Cambridge, MA 02140 USA
| | - Elena E. Brevnova
- Novogy, Inc, 85 Bolton Street, Cambridge, MA 02140 USA
- Present Address: Ginkgo Bioworks, 27 Drydock Avenue, 8th Floor, Boston, MA 02210 USA
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47
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Bizzarri M, Cassanelli S, Solieri L. Mating-type switching in CBS 732T derived subcultures unveils potential genetic and phenotypic novelties in haploid Zygosaccharomyces rouxii. FEMS Microbiol Lett 2017; 365:4693835. [DOI: 10.1093/femsle/fnx263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
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48
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Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data. Sci Rep 2017; 7:15209. [PMID: 29123238 PMCID: PMC5680185 DOI: 10.1038/s41598-017-15484-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022] Open
Abstract
Phylogenetic studies aim to discover evolutionary relationships and histories. These studies are based on similarities of morphological characters and molecular sequences. Currently, widely accepted phylogenetic approaches are based on multiple sequence alignments, which analyze shared gene datasets and concatenate/coalesce these results to a final phylogeny with maximum support. However, these approaches still have limitations, and often have conflicting results with each other. Reconstructing ancestral genomes helps us understand mechanisms and corresponding consequences of evolution. Most existing genome level phylogeny and ancestor reconstruction methods can only process simplified real genome datasets or simulated datasets with identical genome content, unique genome markers, and limited types of evolutionary events. Here, we provide an alternative way to resolve phylogenetic problems based on analyses of real genome data. We use phylogenetic signals from all types of genome level evolutionary events, and overcome the conflicting issues existing in traditional phylogenetic approaches. Further, we build an automated computational pipeline to reconstruct phylogenies and ancestral genomes for two high-resolution real yeast genome datasets. Comparison results with recent studies and publications show that we reconstruct very accurate and robust phylogenies and ancestors. Finally, we identify and analyze the conserved syntenic blocks among reconstructed ancestral genomes and present yeast species.
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49
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Mechanism for Restoration of Fertility in Hybrid Zygosaccharomyces rouxii Generated by Interspecies Hybridization. Appl Environ Microbiol 2017; 83:AEM.01187-17. [PMID: 28842546 DOI: 10.1128/aem.01187-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/18/2017] [Indexed: 11/20/2022] Open
Abstract
The mechanism of whole-genome duplication (WGD) in yeast has been intensively studied because it has a large impact on yeast evolution. WGD has shaped the genomic architecture of modern Saccharomyces cerevisiae; however, the mechanism for restoring fertility after interspecies hybridization, which would be involved in the process of WGD, has not been thoroughly elucidated. In this study, we obtained a draft genome sequence of the salt-tolerant yeast Zygosaccharomyces rouxii NBRC110957 and revealed that it is a hybrid lineage of Z. rouxii (allodiploid) with two subgenomes equivalent to NBRC1876. Because this allodiploid yeast can mate with other allodiploid strains and form spores, it can be a good model of restoring fertility after interspecies hybridization. We observed that NBRC110957 and NBRC1876 contain six mating-type-like (MTL) loci. There are no large deletions or deleterious mutations in MTL loci, except for several-base-pair deletions in the X region in certain MTL loci. We also assigned only one mating-type (MAT) locus that exclusively determines mating types from six MTL loci. These results suggest that it is possible to recover mating competence regardless of whether cells lose one MAT locus through random gene loss by mitotically dividing after interspecies hybridization. Moreover, we propose that perturbation of gene expression and substantial breakdown of MAT heterozygosity caused by chromosomal rearrangement at MTL loci play roles in restoring the mating competence of allodiploids. This scenario can provide a mechanism for restoring fertility after interspecies hybridization that is compatible with random gene loss models and suggests genomic plasticity during WGD in yeast.IMPORTANCE A whole-genome duplication occurred in an ancestor of the baker's yeast Saccharomyces cerevisiae The origins of this complex and multifaceted process, which requires intra- or interspecies hybridization followed by dysfunction of one mating-type (MAT) locus to regain mating competence, has not been thoroughly elucidated. In this study, we provide a mechanism for regaining fertility in an interspecies hybrid, Zygosaccharomyces rouxii The draft genome sequence analysis and mating test showed that the Z. rouxii strain used in this study is an intact interspecies hybrid, suggesting that it is possible to recover fertility regardless of whether cells lose one MAT locus.
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50
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Yun SH, Kim HK, Lee T, Turgeon BG. Self-fertility in Chromocrea spinulosa is a consequence of direct repeat-mediated loss of MAT1-2, subsequent imbalance of nuclei differing in mating type, and recognition between unlike nuclei in a common cytoplasm. PLoS Genet 2017; 13:e1006981. [PMID: 28892488 PMCID: PMC5608430 DOI: 10.1371/journal.pgen.1006981] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/21/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
The filamentous fungus Chromocrea spinulosa (Trichoderma spinulosum) exhibits both self-fertile (homothallic) and self-sterile (heterothallic) sexual reproductive behavior. Self-fertile strains produce progeny cohorts that are 50% homothallic, 50% heterothallic. Heterothallic progeny can mate only with homothallic strains, and progeny also segregate 50% homothallic, 50% heterothallic. Sequencing of the mating type (MAT) region of homothallic and heterothallic strains revealed that both carry an intact MAT1-1 locus with three MAT1-1 genes (MAT1-1-1, MAT1-1-2, MAT1-1-3), as previously described for the Sordariomycete group of filamentous fungi. Homothallic strains, however, have a second version of MAT with the MAT1-2 locus genetically linked to MAT1-1. In this version, the MAT1-1-1 open reading frame is split into a large and small fragment and the truncated ends are bordered by 115bp direct repeats (DR). The MAT1-2-1 gene and additional sequences are inserted between the repeats. To understand the mechanism whereby C. spinulosa can exhibit both homothallic and heterothallic behavior, we utilized molecular manipulation to delete one of the DRs from a homothallic strain and insert MAT1-2 into a heterothallic strain. Mating assays indicated that: i) the DRs are key to homothallic behavior, ii) looping out of MAT1-2-1 via intra-molecular homologous recombination between the DRs in self-fertile strains results in two nuclear types in an individual (one carrying both MAT1-1 and MAT1-2 and one carrying MAT1-1 only), iii) self-fertility is achieved by inter-nuclear recognition between these two nuclear types before meiosis, iv) the two types of nuclei are in unequal proportion, v) having both an intact MAT1-1-1 and MAT1-2-1 gene in a single nucleus is not sufficient for self-fertility, and vi) the large truncated MAT1-1-1 fragment is expressed. Comparisons with MAT regions of Trichoderma reesei and Trichoderma virens suggest that several crossovers between misaligned parental MAT chromosomes may have led to the MAT architecture of homothallic C. spinulosa. Fungi employ one of two mating tactics for sexual reproduction: self-sterile/heterothallic species can mate only with a genetically distinct partner while self-fertile/homothallic species do not require a partner. In ascomycetes, sexual reproduction is controlled by master regulators encoded by the mating-type (MAT) locus. The architecture of MAT differs in heterothallic versus homothallic species; heterothallics carry one of two forms (MAT1-1 or MAT1-2) per nucleus, whereas most homothallics carry both MAT forms in a single nucleus. There are intriguing exceptions. For example, the yeast models, Saccharomyces cerevisiae, and Schizosaccharomyces pombe undergo reversible MAT switching, not demonstrated in filamentous fungi. Here, we describe the mating mechanism in Chromocrea spinulosa (Trichoderma spinulosum), a filamentous ascomycete that exhibits both homothallic and heterothallic behavior. Self-fertile strains produce progeny cohorts that are 50% homothallic, 50% heterothallic. Self-sterile strains can mate only with homothallic strains, and when this occurs, homothallic and heterothallic progeny are also produced in a 1:1 ratio. By MAT sequencing and manipulation, we discovered unique MAT architecture and determined that self-fertility is achieved by deletion of MAT1-2 from most homothallic nuclei and subsequent inter-nuclear recognition between the resulting two, unevenly present, nuclear types in a common cytoplasm.
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Affiliation(s)
- Sung-Hwan Yun
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
- * E-mail: (SHY); (BGT)
| | - Hee-Kyoung Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Chungnam, Republic of Korea
| | - Theresa Lee
- Microbial Safety Team, National Institute of Agricultural Science, Rural Development Administration, Wanju, Jeonbuk, Republic of Korea
| | - B. Gillian Turgeon
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
- * E-mail: (SHY); (BGT)
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