151
|
Koufopanou V, Burt A. Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis. Mol Biol Evol 2005; 22:1535-8. [PMID: 15843599 DOI: 10.1093/molbev/msi149] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.
Collapse
|
152
|
Abstract
Ashbya gossypii is a riboflavin-overproducing filamentous fungus that is closely related to unicellular yeasts such as Saccharomyces cerevisiae. With its close ties to yeast and the ease of genetic manipulation in this fungal species, A. gossypii is well suited as a model to elucidate the regulatory networks that govern the functional differences between filamentous growth and yeast growth, especially now that the A. gossypii genome sequence has been completed. Understanding these networks could be relevant to related dimorphic yeasts such as the human fungal pathogen Candida albicans, in which a switch in morphology from the yeast to the filamentous form in response to specific environmental stimuli is important for virulence.
Collapse
Affiliation(s)
- Jürgen Wendland
- Junior Research Group, Growth-control of Fungal Pathogens, Hans-Knöll Institute for Natural Products Research, Department of Microbiology, Friedrich-Schiller University, Hans-Knöll Strasse 2, D-07745 Jena, Germany.
| | | |
Collapse
|
153
|
Ren P, Roncaglia P, Springer DJ, Fan J, Chaturvedi V. Genomic organization and expression of 23 new genes from MATalpha locus of Cryptococcus neoformans var. gattii. Biochem Biophys Res Commun 2005; 326:233-41. [PMID: 15567176 DOI: 10.1016/j.bbrc.2004.11.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2004] [Indexed: 11/22/2022]
Abstract
The pathogenic yeast Cryptococcus neoformans (Cn) causes cryptococcosis, a life-threatening disease of the brain. Molecular studies of Cn variety gattii have lagged behind other two varieties (var. grubii and var. neoformans) although they have distinct biology and disease patterns. We focused on gene discovery in MATalpha locus because it predominates in clinical strains. A var. gattii cosmid library was screened with DNA probes from other two varieties. Two positive clones were sequenced to identify ORFs based on similarities to known proteins, and to ESTs using bioinformatics, and manually by a curator. Approximately 76kb sequenced DNA revealed 23 genes and ORFs. The existence of predicted genes was verified by RT-PCR analyses designed to amplify spliced sequences. The results confirmed that the transcripts were expressed both at 30 and 37 degrees C. The var. gattii MATalpha locus genes showed rearrangements in order and orientation vis-a-vis other two varieties. Mating-specific genes showed higher nonsynonymous mutation rates, and gene trees showed var. gattii strains in a distinct clade. The identification of the largest number, thus far, of var. gattii structural genes should set the stage for future molecular pathogenesis studies.
Collapse
Affiliation(s)
- Ping Ren
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | | | | | | | | |
Collapse
|
154
|
Wu W, Pujol C, Lockhart SR, Soll DR. Chromosome loss followed by duplication is the major mechanism of spontaneous mating-type locus homozygosis in Candida albicans. Genetics 2005; 169:1311-27. [PMID: 15654090 PMCID: PMC1449533 DOI: 10.1534/genetics.104.033167] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Candida albicans, which is diploid, possesses a single mating-type (MTL) locus on chromosome 5, which is normally heterozygous (a/alpha). To mate, C. albicans must undergo MTL homozygosis to a/a or alpha/alpha. Three possible mechanisms may be used in this process, mitotic recombination, gene conversion, or loss of one chromosome 5 homolog, followed by duplication of the retained homolog. To distinguish among these mechanisms, 16 spontaneous a/a and alpha/alpha derivatives were cloned from four natural a/alpha strains, P37037, P37039, P75063, and P34048, grown on nutrient agar. Eighteen polymorphic (heterozygous) markers were identified on chromosome 5, 6 to the left and 12 to the right of the MTL locus. These markers were then analyzed in MTL-homozygous derivatives of the four natural a/alpha strains to distinguish among the three mechanisms of homozygosis. An analysis of polymorphisms on chromosomes 1, 2, and R excluded meiosis as a mechanism of MTL homozygosis. The results demonstrate that while mitotic recombination was the mechanism for homozygosis in one offspring, loss of one chromosome 5 homolog followed by duplication of the retained homolog was the mechanism in the remaining 15 offspring, indicating that the latter mechanism is the most common in the spontaneous generation of MTL homozygotes in natural strains of C. albicans in culture.
Collapse
Affiliation(s)
- Wei Wu
- Department of Biological Sciences, University of Iowa, Iowa City, 52242, USA
| | | | | | | |
Collapse
|
155
|
Dyer PS, Paoletti M. Reproduction inAspergillus fumigatus: sexuality in a supposedly asexual species? Med Mycol 2005; 43 Suppl 1:S7-14. [PMID: 16110786 DOI: 10.1080/13693780400029015] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Aspergillus fumigatus has long been considered to reproduce only by asexual means. However, accumulating evidence suggest that a sexual stage for A. fumigatus may yet be identified. We describe results from published and ongoing studies involving population genetic analyses, genome analysis, studies of mating-type gene presence and distribution, expression of sex-related genes, and taxonomic work which support the assertion that A. fumigatus has the potential to reproduce by sexual means. The consequences of sexual reproduction for the population biology and disease management of the species are discussed. The possible mechanisms of evolution of asexuality are then considered. It is proposed that asexual species may arise in one step by mutation or loss of a key gene(s), and/or there may be a 'slow decline' in sexual fertility within the species as a whole. Thus, it is argued that species should not be considered simply as sexual or asexual, but rather as individual isolates being present on a continuum of sexual fertility, with the implications for understanding sexuality/asexuality in A. fumigatus discussed.
Collapse
Affiliation(s)
- P S Dyer
- School of Biology, University of Nottingham, Nottingham, UK.
| | | |
Collapse
|
156
|
Fabre E, Muller H, Therizols P, Lafontaine I, Dujon B, Fairhead C. Comparative genomics in hemiascomycete yeasts: evolution of sex, silencing, and subtelomeres. Mol Biol Evol 2004; 22:856-73. [PMID: 15616141 DOI: 10.1093/molbev/msi070] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The recent release of sequences of several unexplored yeast species that cover an evolutionary range comparable to the entire phylum of chordates offers us a unique opportunity to investigate how genes involved in adaptation have been shaped by evolution. We have examined how three different sets of genes, all related to adaptative processes at the genomic level, have evolved in hemiascomycetes: (1) the mating-type genes that govern sexuality, (2) the silencing genes that are connected to regulation of mating-type cassettes and to telomere position effect, and (3) the gene families found repeated in subtelomeric regions. We report new combinations of mating-type genes and cassettes in hemiascomycetous species; we show that silencing proteins diverge rapidly. We have also found that in all species studied, subtelomeric gene families exist and are specific to each species.
Collapse
Affiliation(s)
- Emmanuelle Fabre
- Unité de Génétique Moléculaire des Levures, URA2171 CNRS, UFR Université Pierre et Marie Curie, Département Structure et Dynamique des Génomes, Institut Pasteur, 75724 Cedex Paris, France.
| | | | | | | | | | | |
Collapse
|
157
|
Burt A, Koufopanou V. Homing endonuclease genes: the rise and fall and rise again of a selfish element. Curr Opin Genet Dev 2004; 14:609-15. [PMID: 15531154 DOI: 10.1016/j.gde.2004.09.010] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Homing endonuclease genes (HEGs) are selfish genetic elements that spread by first cleaving chromosomes that do not contain them and then getting copied across to the broken chromosome as a byproduct of the repair process. The success of this strategy will depend on the opportunities for homing--in other words, the frequency with which HEG(+) and HEG(-) chromosomes come into contact--which varies widely among host taxa. HEGs are also unusual in that the selection pressure for endonuclease function disappears if they become fixed in a population, which makes them susceptible to degeneration and imposes a need for regular horizontal transmission between species. HEGs will be selected to reduce the harm done to the host organism, and this is expected to influence the evolution of their sequence specificity and maturase functions. HEGs may also be domesticated by their hosts, and are currently being put to human uses.
Collapse
Affiliation(s)
- Austin Burt
- Department of Biological Sciences, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK.
| | | |
Collapse
|
158
|
Fraser JA, Diezmann S, Subaran RL, Allen A, Lengeler KB, Dietrich FS, Heitman J. Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. PLoS Biol 2004; 2:e384. [PMID: 15538538 PMCID: PMC526376 DOI: 10.1371/journal.pbio.0020384] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 09/10/2004] [Indexed: 02/03/2023] Open
Abstract
Sexual identity is governed by sex chromosomes in plants and animals, and by mating type (MAT) loci in fungi. Comparative analysis of the MAT locus from a species cluster of the human fungal pathogen Cryptococcus revealed sequential evolutionary events that fashioned this large, highly unusual region. We hypothesize that MAT evolved via four main steps, beginning with acquisition of genes into two unlinked sex-determining regions, forming independent gene clusters that then fused via chromosomal translocation. A transitional tripolar intermediate state then converted to a bipolar system via gene conversion or recombination between the linked and unlinked sex-determining regions. MAT was subsequently subjected to intra- and interallelic gene conversion and inversions that suppress recombination. These events resemble those that shaped mammalian sex chromosomes, illustrating convergent evolution in sex-determining structures in the animal and fungal kingdoms. A comparative genomic analysis of the sex determining region in fungi reveals a remarkable similarity between its evolution and the events which shaped mammalian sex chromosomes
Collapse
MESH Headings
- Alleles
- Animals
- Biodiversity
- Chromosomes
- Chromosomes, Artificial, Bacterial
- Chromosomes, Fungal
- Cryptococcus/genetics
- Cryptococcus neoformans/genetics
- Evolution, Molecular
- Fungi/physiology
- Gene Conversion
- Gene Library
- Genes, Mating Type, Fungal
- Genome
- Genome, Fungal
- Humans
- Models, Genetic
- Molecular Sequence Data
- Phylogeny
- Recombination, Genetic
- Sex Chromosomes
- Sex Determination Processes
- Translocation, Genetic
Collapse
Affiliation(s)
- James A Fraser
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 2Howard Hughes Medical Institute, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Stephanie Diezmann
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 3Duke Institute for Genomics Sciences and Policy, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Ryan L Subaran
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Andria Allen
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 3Duke Institute for Genomics Sciences and Policy, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Klaus B Lengeler
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 2Howard Hughes Medical Institute, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Fred S Dietrich
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 3Duke Institute for Genomics Sciences and Policy, Duke University Medical CenterDurham, North CarolinaUnited States of America
| | - Joseph Heitman
- 1Department of Molecular Genetics and Microbiology, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 2Howard Hughes Medical Institute, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 4Department of Medicine, Duke University Medical CenterDurham, North CarolinaUnited States of America
- 5Department of Pharmacology and Cancer Biology, Duke University Medical CenterDurham, North CarolinaUnited States of America
| |
Collapse
|
159
|
O'Donnell K, Ward TJ, Geiser DM, Corby Kistler H, Aoki T. Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade. Fungal Genet Biol 2004; 41:600-23. [PMID: 15121083 DOI: 10.1016/j.fgb.2004.03.003] [Citation(s) in RCA: 425] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 03/05/2004] [Indexed: 10/26/2022]
Abstract
Species limits were investigated within the Fusarium graminearum clade (Fg clade) through phylogenetic analyses of DNA sequences from portions of 11 nuclear genes including the mating-type (MAT) locus. Nine phylogenetically distinct species were resolved within the Fg clade, and they all possess contiguous MAT1-1 and MAT1-2 idiomorphs consistent with a homothallic reproductive mode. In contrast, only one of the two MAT idiomorphs was found in five other species, four of which were putatively asexual, and the other was heterothallic. Molecular evolutionary analyses indicate the MAT genes are under strong purifying selection and that they are functionally constrained, even in species for which a sexual state is unknown. The phylogeny supports a monophyletic and apomorphic origin of homothallism within this clade. Morphological analyses demonstrate that a combination of conidial characters could be used to differentiate three species and three species pairs. Species rank is formally proposed for the eight unnamed species within the Fg clade using fixed nucleotide characters.
Collapse
Affiliation(s)
- Kerry O'Donnell
- National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA.
| | | | | | | | | |
Collapse
|
160
|
Abstract
For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide the background to use more yeast species in model studies, to combat pathogens and for efficient manipulation of industrial strains.
Collapse
Affiliation(s)
- Jure Piskur
- BioCentrum-DTU, Building 301, Technical University of Denmark, DK-2800 Kgl. Lyngby, Denmark.
| | | |
Collapse
|
161
|
Abstract
Two new genome sequences confirm that a whole genome duplication occurred in an ancestor of Saccharomyces cerevisiae. This left a legacy of about 500 pairs of duplicated genes, many of which contribute to this yeast's ability to ferment glucose anaerobically; a few have been evolving so quickly they retain almost no sequence similarity to each other.
Collapse
Affiliation(s)
- Ken Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland.
| |
Collapse
|
162
|
Abstract
New data from yeast species show that both changing the cis-acting DNA elements in promoters, and replacing the trans-acting regulatory proteins can regulate gene expression. The molecular mechanisms that regulate gene expression can evolve either by changing the cis-acting DNA elements in promoters, or by replacing the trans-acting regulatory proteins. New data from yeast species show that both processes can happen.
Collapse
Affiliation(s)
- Devin R Scannell
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Ken Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
| |
Collapse
|