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Sambles C, Middelhaufe S, Soanes D, Kolak D, Lux T, Moore K, Matoušková P, Parker D, Lee R, Love J, Aves SJ. Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609. GENOMICS DATA 2017; 13:1-2. [PMID: 28560168 PMCID: PMC5440251 DOI: 10.1016/j.gdata.2017.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 05/09/2017] [Accepted: 05/12/2017] [Indexed: 01/25/2023]
Abstract
Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula (Rhodosporidium) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).
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Affiliation(s)
- Christine Sambles
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Sabine Middelhaufe
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Darren Soanes
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Dagmara Kolak
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Thomas Lux
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Karen Moore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Petra Matoušková
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - David Parker
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rob Lee
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - John Love
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Stephen J Aves
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Schmoll M, Seibel C, Tisch D, Dorrer M, Kubicek CP. A novel class of peptide pheromone precursors in ascomycetous fungi. Mol Microbiol 2010; 77:1483-501. [PMID: 20735770 PMCID: PMC3068285 DOI: 10.1111/j.1365-2958.2010.07295.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2010] [Indexed: 11/30/2022]
Abstract
Recently, sexual development in the heterothallic ascomycete Trichoderma reesei (anamorph of Hypocrea jecorina) has been achieved and thus initiated attempts to elucidate regulation and determinants of this process. While the α-type pheromone of this fungus fits the consensus known from other fungi, the assumed a-type peptide pheromone precursor shows remarkably unusual characteristics: it comprises three copies of the motif (LI)GC(TS)VM thus constituting a CAAX domain at the C-terminus and two Kex2-protease sites. This structure shares characteristics of both a- and α-type peptide pheromone precursors. Presence of hybrid-type peptide pheromone precursor 1 (hpp1) is essential for male fertility, thus indicating its functionality as a peptide pheromone precursor, while its phosphorylation site is not relevant for this process. However, sexual development in a female fertile background is not perturbed in the absence of hpp1, which rules out a higher order function in this process. Open reading frames encoding proteins with similar characteristics to HPP1 were also found in Fusarium spp., of which Fusarium solani still retains a putative a-factor-like protein, but so far in no other fungal genome available. We therefore propose the novel class of h-type (hybrid) peptide pheromone precursors with H. jecorina HPP1 as the first member of this class.
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Affiliation(s)
- Monika Schmoll
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/1665, Vienna 1060, Austria.
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Kothe E. Sexual attraction: on the role of fungal pheromone/receptor systems (A review). Acta Microbiol Immunol Hung 2008; 55:125-43. [PMID: 18595318 DOI: 10.1556/amicr.55.2008.2.5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pheromones have been detected in all fungal phylogenetic lineages. This came as a surprise, as the general role of pheromones in mate attraction was not envisioned for some fungi. Pheromones and pheromone receptor genes have been identified, however, in members of all true fungal lineages, and even for mycelia forming organisms of plant and amoeba lineages, like oomycetes and myxomycetes. The mating systems and genes governing the mating type are different in fungi, ranging from bipolar with two opposite mating types to tetrapolar mating systems (with four possible mating outcomes, only one of which leads to fertile sexual development) in homobasidioymcetes with more than 23,000 mating types occurring in nature. Pheromones and receptors specifically recognizing these pheromones have evolved with slightly different functions in these different systems. This review is dedicated to follow the evolution of pheromone/receptor systems from simple, biallelic bipolar systems to multiallelic, tetrapolar versions and to explain the slightly different functions the pheromone recognition and subsequent signal transduction cascades within the fungal kingdom. The biotechnological implications of a detailed understanding of mating systems for biological control and plant protection, in medicine, and in mushroom breeding are discussed.
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Affiliation(s)
- Erika Kothe
- Institute of Microbiology, Friedrich-Schiller-Universität, Neugasse 25, D-07743 Jena, Germany.
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McClelland CM, Fu J, Woodlee GL, Seymour TS, Wickes BL. Isolation and characterization of the Cryptococcus neoformans MATa pheromone gene. Genetics 2002; 160:935-47. [PMID: 11901112 PMCID: PMC1462016 DOI: 10.1093/genetics/160.3.935] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cryptococcus neoformans is a heterothallic basidiomycete with two mating types, MATa and MATalpha. The mating pathway of this fungus has a number of conserved genes, including a MATalpha-specific pheromone (MFalpha1). A modified differential display strategy was used to identify a gene encoding the MATa pheromone. The gene, designated MFa1, is 42 amino acids in length and contains a conserved farnesylation motif. MFa1 is present in three linked copies that span a 20-kb fragment of MATa-specific DNA and maps to the MAT-containing chromosome. Transformation studies showed that MFa1 induced filament formation only in MATalpha cells, demonstrating that MFa1 is functionally conserved. Sequence analysis of the predicted Mfa1 and Mfalpha1 proteins revealed that, in contrast to other fungi such as Saccharomyces cerevisiae, the C. neoformans pheromone genes are structurally and functionally conserved. However, unlike the MFalpha1 gene, which is found in MATalpha strains of both varieties of C. neoformans, MFa1 is specific for the neoformans variety of C. neoformans.
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Affiliation(s)
- Carol M McClelland
- Department of Microbiology, University of Texas Health Science Center, San Antonio, Texas 78229-3900, USA
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6
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Schein CH, Nagle GT, Page JS, Sweedler JV, Xu Y, Painter SD, Braun W. Aplysia attractin: biophysical characterization and modeling of a water-borne pheromone. Biophys J 2001; 81:463-72. [PMID: 11423429 PMCID: PMC1301526 DOI: 10.1016/s0006-3495(01)75714-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Attractin, a 58-residue protein secreted by the mollusk Aplysia californica, stimulates sexually mature animals to approach egg cordons. Attractin from five different Aplysia species are approximately 40% identical in sequence. Recombinant attractin, expressed in insect cells and purified by reverse-phase high-performance liquid chromatography (RP-HPLC), is active in a bioassay using A. brasiliana; its circular dichroism (CD) spectrum indicates a predominantly alpha-helical structure. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) characterization of proteolytic fragments identified disulfide bonds between the six conserved cysteines (I-VI, II-V, III-IV, where the Roman numeral indicates the order of occurrence in the primary sequence). Attractin has no significant similarity to any other sequence in the database. The protozoan Euplotes pheromones were selected by fold recognition as possible templates. These diverse proteins have three alpha-helices, with six cysteine residues disulfide-bonded in a different pattern from attractin. Model structures with good stereochemical parameters were prepared using the EXDIS/DIAMOD/FANTOM program suite and constraints based on sequence alignments with the Euplotes templates and the attractin disulfide bonds. A potential receptor-binding site is suggested based on these data. Future structural characterization of attractin will be needed to confirm these models.
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Affiliation(s)
- C H Schein
- Sealy Center for Structural Biology, Department of Human Biological Chemistry and Genetics, Galveston, Texas 77555, USA
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Anderson CM, Willits DA, Kosted PJ, Ford EJ, Martinez-Espinoza AD, Sherwood JE. Molecular analysis of the pheromone and pheromone receptor genes of Ustilago hordei. Gene 1999; 240:89-97. [PMID: 10564815 DOI: 10.1016/s0378-1119(99)00428-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cell-cell signaling is an integral part of the sexual and disease cycles of the smut fungi, which must mate to be pathogenic. This study reports the cloning and characterization of the pheromone genes Uhmfa1 and Uhmfa2 from MAT-1 and MAT-2 mating types of U. hordei, respectively, and the pheromone receptor gene Uhpra2 from MAT-2 cells. Similar to other fungal pheromone genes, Uhmfa1 and Uhmfa2 encode precursor peptides. Uhpra2 encodes a protein with sequence similarity to the 7-transmembrane class of G-protein coupled receptors. Deletion of Uhmfa1 and Uhpra1, and their subsequent replacement, confirmed the role of these genes in initiation of the sexual cycle. Uhmfa1 and Uhmfa2 were differentially expressed in various cell types and when opposite mating-type cells were grown together. The predicted mature pheromones of each mating type were synthesized, and each specifically induced conjugation tube formation in cells of the opposite mating type.
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Affiliation(s)
- C M Anderson
- Department of Plant Sciences, Montana State University, Bozeman, MT, USA
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Hiscock SJ, Kües U. Cellular and molecular mechanisms of sexual incompatibility in plants and fungi. INTERNATIONAL REVIEW OF CYTOLOGY 1999; 193:165-295. [PMID: 10494623 DOI: 10.1016/s0074-7696(08)61781-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Plants and fungi show an astonishing diversity of mechanisms to promote outbreeding, the most widespread of which is sexual incompatibility. Sexual incompatibility involves molecular recognition between mating partners. In fungi and algae, highly polymorphic mating-type loci mediate mating through complementary interactions between molecules encoded or regulated by different mating-type haplotypes, whereas in flowering plants polymorphic self-incompatibility loci regulate mate recognition through oppositional interactions between molecules encoded by the same self-incompatibility haplotypes. This subtle mechanistic difference is a consequence of the different life cycles of fungi, algae, and flowering plants. Recent molecular and biochemical studies have provided fascinating insights into the mechanisms of mate recognition and are beginning to shed light on evolution and population genetics of these extraordinarily polymorphic genetic systems of incompatibility.
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Affiliation(s)
- S J Hiscock
- Department of Plant Sciences, University of Oxford, United Kingdom
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Raudaskoski M. The relationship between B-mating-type genes and nuclear migration in schizophyllum commune. Fungal Genet Biol 1998; 24:207-27. [PMID: 9742202 DOI: 10.1006/fgbi.1998.1069] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Raudaskoski, M. 1998. The relationship between B-mating-type genes and nuclear migration in Schizophyllum commune. Copyright 1998 Academic Press.
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Affiliation(s)
- M Raudaskoski
- Division of Plant Physiology, University of Helsinki, Viikinkaari 9, FIN-00014, Finland
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Chen P, Sapperstein SK, Choi JD, Michaelis S. Biogenesis of the Saccharomyces cerevisiae mating pheromone a-factor. J Cell Biol 1997; 136:251-69. [PMID: 9015298 PMCID: PMC2134810 DOI: 10.1083/jcb.136.2.251] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/1996] [Revised: 11/06/1996] [Indexed: 02/03/2023] Open
Abstract
The Saccharomyces cerevisiae mating pheromone a-factor is a prenylated and carboxyl methylated extracellular peptide signaling molecule. Biogenesis of the a-factor precursor proceeds via a distinctive multistep pathway that involves COOH-terminal modification. NH2-terminal proteolysis, and a nonclassical export mechanism. In this study, we examine the formation and fate of a-factor biosynthetic intermediates to more precisely define the events that occur during a-factor biogenesis. We have identified four distinct a-factor biosynthetic intermediates (P0, P1, P2, and M) by metabolic labeling, immunoprecipitation, and SDS-PAGE. We determined the biochemical composition of each by defining their NH2-terminal amino acid and COOH-terminal modification status. Unexpectedly, we discovered that not one, but two NH2-terminal cleavage steps occur during the biogenesis of a-factor. In addition, we have shown that COOH-terminal prenylation is required for the NH2-terminal processing of a-factor and that all the prenylated a-factor intermediates (P1, P2, and M) are membrane bound, suggesting that many steps of a-factor biogenesis occur in association with membranes. We also observed that although the biogenesis of a-factor is a rapid process, it is inherently inefficient, perhaps reflecting the potential for regulation. Previous studies have identified gene products that participate in the COOH-terminal modification (Ram1p, Ram2p, Ste14p), NH2-terminal processing (Ste24p, Axl1p), and export (Ste6p) of a-factor. The intermediates defined in the present study are discussed in the context of these biogenesis components to formulate an overall model for the pathway of a-factor biogenesis.
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Affiliation(s)
- P Chen
- Department of Cell Biology and Anatomy, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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11
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Urban M, Kahmann R, Bölker M. The biallelic a mating type locus of Ustilago maydis: remnants of an additional pheromone gene indicate evolution from a multiallelic ancestor. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:414-20. [PMID: 8602158 DOI: 10.1007/bf02174029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The a mating type locus of Ustilago maydis contains the structural genes for a pheromone-based cell recognition system that governs fusion of haploid cells. The locus exists in two alleles, termed a1 and a2. We have completed the analysis of the nucleotide sequences unique to a1 and a2. Within these dissimilar regions we find two short patches of DNA sequence similarity. Interestingly, one of these segments corresponds to the transcribed region of the a1 pheromone precursor. As a result of multiple nucleotide exchanges this sequence does not code for a functional product. The existence of a second pheromone gene in the a2 allele suggests that the present locus had a multiallelic ancestor. In addition, we describe the presence of two additional genes in the a2 allele. We have investigated the role of these genes during mating and pathogenic development and speculate that they might affect mitochondrial inheritance.
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Affiliation(s)
- M Urban
- Institut für Genetik und Mikrobiologie der Universität München, München, Germany
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Vaillancourt LJ, Raper CA. Pheromones and pheromone receptors as mating-type determinants in basidiomycetes. GENETIC ENGINEERING 1996; 18:219-47. [PMID: 8785123 DOI: 10.1007/978-1-4899-1766-9_13] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- L J Vaillancourt
- Markey Center for Molecular Genetics, Department of Microbiology and Molecular Genetics, University of Vermont, Burlington 05405, USA
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13
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Bölker M, Kahmann R. Sexual pheromones and mating responses in fungi. THE PLANT CELL 1993; 5:1461-1469. [PMID: 8281042 PMCID: PMC160376 DOI: 10.1105/tpc.5.10.1461] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- M Bölker
- Institut für Genetik und Mikrobiologie, Universität München, Germany
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Newman CM, Magee AI. Posttranslational processing of the ras superfamily of small GTP-binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1155:79-96. [PMID: 8504132 DOI: 10.1016/0304-419x(93)90023-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- C M Newman
- Laboratory of Eukaryotic Molecular Genetics, National Institute for Medical Research, Mill Hill, London, UK
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Affiliation(s)
- G W Gooday
- Department of Molecular and Cell Biology, University of Aberdeen, UK
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17
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Abstract
The a mating type locus of the phytopathogenic fungus U. maydis controls fusion of haploid cells and filamentous growth of the dikaryotic mycelium. The a locus exists in two alleles, termed a1 and a2, which are defined by nonhomologous DNA regions comprising 4.5 kb for a1 and 8 kb for a2, flanked by identical sequences. Based on functional assays, mutants, and sequencing, we demonstrate that the mating type in each allele is determined by a set of two genes. One encodes a precursor for a lipopeptide mating factor, and the other specifies the receptor for the pheromone secreted by cells of opposite mating type. Thus, U. maydis employs a novel strategy to determine its mating type by providing the primary determinants of cell-cell recognition directly from the mating type locus.
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Affiliation(s)
- M Bölker
- Institut für Genbiologische Forschung Berlin GmbH, Federal Republic of Germany
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18
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Maltese WA, Sheridan KM, Repko EM, Erdman RA. Post-translational modification of low molecular mass GTP-binding proteins by isoprenoid. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39953-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Genomic organization of multiple genes coding for rhodotorucine A, a lipopeptide mating pheromone of the basidiomycetous yeast Rhodosporidium toruloides. Arch Microbiol 1989. [DOI: 10.1007/bf00446934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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