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Maxwell PH. Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. Mob DNA 2020; 11:16. [PMID: 32336995 PMCID: PMC7175516 DOI: 10.1186/s13100-020-00215-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022] Open
Abstract
Genomics and other large-scale analyses have drawn increasing attention to the potential impacts of transposable elements (TEs) on their host genomes. However, it remains challenging to transition from identifying potential roles to clearly demonstrating the level of impact TEs have on genome evolution and possible functions that they contribute to their host organisms. I summarize TE content and distribution in four well-characterized yeast model systems in this review: the pathogens Candida albicans and Cryptococcus neoformans, and the nonpathogenic species Saccharomyces cerevisiae and Schizosaccharomyces pombe. I compare and contrast their TE landscapes to their lifecycles, genomic features, as well as the presence and nature of RNA interference pathways in each species to highlight the valuable diversity represented by these models for functional studies of TEs. I then review the regulation and impacts of the Ty1 and Ty3 retrotransposons from Saccharomyces cerevisiae and Tf1 and Tf2 retrotransposons from Schizosaccharomyces pombe to emphasize parallels and distinctions between these well-studied elements. I propose that further characterization of TEs in the pathogenic yeasts would enable this set of four yeast species to become an excellent set of models for comparative functional studies to address outstanding questions about TE-host relationships.
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2
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Sarilar V, Bleykasten-Grosshans C, Neuvéglise C. Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae. Genome Biol Evol 2014; 7:172-90. [PMID: 25532815 PMCID: PMC4316626 DOI: 10.1093/gbe/evu273] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences.
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Affiliation(s)
- Véronique Sarilar
- INRA, UMR 1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Claudine Bleykasten-Grosshans
- CNRS, UMR 7156, Laboratoire de Génétique Moléculaire, Génomique et Microbiologie, Université de Strasbourg, Strasbourg, France
| | - Cécile Neuvéglise
- INRA, UMR 1319 Micalis, Jouy-en-Josas, France AgroParisTech, UMR Micalis, Jouy-en-Josas, France
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3
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Zhang L, Yan L, Jiang J, Wang Y, Jiang Y, Yan T, Cao Y. The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans. Virulence 2014; 5:655-64. [PMID: 25101670 PMCID: PMC4139406 DOI: 10.4161/viru.32180] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons constitute a major part of the genome in a number of eukaryotes. Long-terminal repeat (LTR) retrotransposons are one type of the retrotransposons. Candida albicans have 34 distinct LTR-retrotransposon families. They respectively belong to the Ty1/copia and Ty3/gypsy groups which have been extensively studied in the model yeast Saccharomyces cerevisiae. LTR-retrotransposons carry two LTRs flanking a long internal protein-coding domain, open reading frames. LTR-retrotransposons use RNA as intermediate to synthesize double-stranded DNA copies. In this article, we describe the structure feature, retrotransposition mechanism and the influence on organism diversity of LTR retrotransposons in C. albicans. We also discuss the relationship between pathogenicity and LTR retrotransposons in C. albicans.
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Affiliation(s)
- Lulu Zhang
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Lan Yan
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Jingchen Jiang
- Department of Pharmacology; School of Pharmacy; China Pharmaceutical University; Nanjing, PR China
| | - Yan Wang
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Yuanying Jiang
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Tianhua Yan
- Department of Pharmacology; School of Pharmacy; China Pharmaceutical University; Nanjing, PR China
| | - Yongbing Cao
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
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4
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Bleykasten-Grosshans C, Neuvéglise C. Transposable elements in yeasts. C R Biol 2011; 334:679-86. [PMID: 21819950 DOI: 10.1016/j.crvi.2011.05.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/31/2011] [Indexed: 11/19/2022]
Abstract
With the development of new sequencing technologies in the past decade, yeast genomes have been extensively sequenced and their structures investigated. Transposable elements (TEs) are ubiquitous in eukaryotes and constitute a limited part of yeast genomes. However, due to their ability to move in genomes and generate dispersed repeated sequences, they contribute to modeling yeast genomes and thereby induce plasticity. This review assesses the TE contents of yeast genomes investigated so far. Their diversity and abundance at the inter- and intraspecific levels are presented, and their effects on gene expression and genome stability is considered. Recent results concerning TE-host interactions are also analyzed.
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Affiliation(s)
- Claudine Bleykasten-Grosshans
- CNRS UMR 7156, Laboratoire Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg, 28 rue Goethe, 67083 Strasbourg cedex, France.
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5
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Schön I, Martens K. Are ancient asexuals less burdened? Selfish DNA, transposons and reproductive mode. J NAT HIST 2010. [DOI: 10.1080/00222930110089148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Nie X, Liu X, Wang H, Chen J. Deletion of EFG1 promotes Candida albicans opaque formation responding to pH via Rim101. Acta Biochim Biophys Sin (Shanghai) 2010; 42:735-44. [PMID: 20870932 DOI: 10.1093/abbs/gmq076] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phenotypic switching in Candida albicans spontaneously generates different cellular morphologies. The reversible switching between white and opaque phenotypes is regulated by multiple regulators including Efg1 and Wor1. In mating-type-like locus (MTL) homozygous cells, the Efg1 functions as a repressor, whereas the Wor1 acts as an activator in white-opaque switching. We presented evidence that switching between white and opaque in efg1/efg1 mutant is regulated by ambient pH. In pH 6.8 media, the efg1/efg1 mutant cells exhibited opaque form, but shifted to white form in pH 4.5 media. The pH-dependent morphological switching is not blocked by further deletion of WOR1 in the efg1/efg1 mutant. Correlated with the phenotype, the opaque-phase-specific gene OP4 was induced in efg1/efg1 mutant cells when cultured in pH 6.8 media, and was repressed in pH 4.5 media. Consistently, the MTLa efg1/efg1 mutant cells could mate efficiently with MTLα cells in pH 6.8 media, but poorly in pH 4.5 media. Ectopic expression of the Rim101-405 allele in the efg1/efg1 mutant helped to bypass the pH restriction on white-opaque switching and show opaque form in both neutral and acidic media. We proposed that relief of the Efg1 repression enables C. albicans to undergo white-opaque switching in pH-dependent regulation mediated by Rim101-signaling pathway.
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Affiliation(s)
- Xinyi Nie
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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7
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Abstract
The unicellular eukaryotic organisms represent the popular model systems to understand aging in eukaryotes. Candida albicans, a polymorphic fungus, appears to be another distinctive unicellular aging model in addition to the budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe. The two types of Candida cells, yeast (blastospore) form and hyphal (filamentous) form, have similar replicative lifespan. Taking the advantage of morphologic changes, we are able to obtain cells of different ages. Old Candida cells tend to accumulate glycogen and oxidatively damaged proteins. Deletion of the SIR2 gene causes a decrease of lifespan, while insertion of an extra copy of SIR2 extends lifespan, indicating that like in S. cerevisiae, Sir2 regulates cellular aging in C. albicans. Interestingly, Sir2 deletion does not result in the accumulation of extra-chromosomal rDNA molecules, but influences the retention of oxidized proteins in mother cells, suggesting that the extra-chromosomal rDNA molecules may not be associated with cellular aging in C. albicans. This novel aging model, which allows efficient large-scale isolation of old cells, may facilitate biochemical characterizations and genomics/proteomics studies of cellular aging, and help to verify the aging pathways observed in other organisms including S. cerevisiae.
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Affiliation(s)
- Xiao-Hong Fu
- Max-Planck Junior Research Group in the State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Graduate School of Chinese Academy of Sciences, Shanghai, China
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8
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Cantero PD, Lengsfeld C, Prill SKH, Subanović M, Román E, Pla J, Ernst JF. Transcriptional and physiological adaptation to defective protein-O-mannosylation in Candida albicans. Mol Microbiol 2007; 64:1115-28. [PMID: 17501932 DOI: 10.1111/j.1365-2958.2007.05723.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Five Pmt isoforms O-mannosylate secretory proteins in Candida albicans. Comparisons of genome-wide transcript patterns of each pmt mutant revealed commonly downregulated genes involved in glycolysis and glycerol production. Increased phosphorylation of the Cek1p- but not the Mkc1p-MAP kinase, as well as increased transcript levels for some stress-related genes were detected in the pmt1 strain but not in the other pmt mutants. The transcriptomal pattern after short-term inhibition of Pmt1p activity confirmed stress responses, but did not indicate an alteration of glycolytic flow. Short- but not long-term adaptation to Pmt1p inhibition required signalling components Cek1p, Mkc1p, Efg1p and Tpk1p. Cna1p (calcineurin) but not its downstream effectors Crz1p and Crz2p was generally essential to allow growth during Pmt1p inhibition; accordingly, cyclosporin A strongly inhibited growth of the pmt1 mutant. The lack of Pmt isoforms influenced transcript levels for the remaining isoforms both positively and negatively, suggesting complex cross-regulation among PMT genes. These results confirm individual functions of Pmt isoforms but suggest a common biphasic adaptation response to Pmt deficiency. While known signalling pathways modulate adaptation for a short-term, long-term adaptation requires calcineurin, adjustments of remaining Pmt activities and of glycolytic flow.
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Affiliation(s)
- Pilar D Cantero
- Institut für Mikrobiologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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9
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Genome-wide transcriptional profiling of the cyclic AMP-dependent signaling pathway during morphogenic transitions of Candida albicans. EUKARYOTIC CELL 2007; 6:2376-90. [PMID: 17951520 DOI: 10.1128/ec.00318-07] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Candida albicans is an opportunistic human fungal pathogen that causes systemic candidiasis as well as superficial mucosal candidiasis. In response to the host environment, C. albicans transitions between yeast and hyphal forms. In particular, hyphal growth is important in facilitating adhesion and invasion of host tissues, concomitant with the expression of various hypha-specific virulence factors. In previous work, we showed that the cyclic AMP (cAMP) signaling pathway plays a crucial role in morphogenic transitions and virulence of C. albicans by studying genes encoding adenylate cyclase-associated protein (CAP1) and high-affinity phosphodiesterase (PDE2) (Y. S. Bahn, J. Staab, and P. Sundstrom, Mol. Microbiol. 50:391-409, 2003; and Y. S. Bahn and P. Sundstrom, J. Bacteriol. 183:3211-3223, 2001). However, little is known about the downstream targets of the cAMP signaling pathway that are responsible for morphological transitions and the expression of virulence factors. Here, microarrays were probed with RNA from strains with hypoactive (cap1/cap1 null mutant), hyperactive (pde2/pde2 null mutant), and wild-type cAMP signaling pathways to provide insight into the molecular mechanisms of virulence that are regulated by cAMP and that are related to the morphogenesis of C. albicans. Genes controlling metabolic specialization, cell wall structure, ergosterol/lipid biosynthesis, and stress responses were modulated by cAMP during hypha formation. Phenotypic traits predicted to be regulated by cAMP from the profiling results correlated with the relative strengths of the mutants when tested for resistance to azoles and subjected to heat shock stress and oxidative/nitrosative stress. The results from this study provide important insights into the role of the cAMP signaling pathway not only in morphogenic transitions of C. albicans but also for adaptation to stress and for survival during host infections.
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10
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Kameda T, Ikegami K, Liu Y, Terada K, Sugiyama T. A hypothermic-temperature-sensitive gene silencing by the mammalian RNAi. Biochem Biophys Res Commun 2004; 315:599-602. [PMID: 14975743 DOI: 10.1016/j.bbrc.2004.01.097] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2004] [Indexed: 11/25/2022]
Abstract
RNA interference (RNAi) has been attracting a great deal of attention. This pathway is highly conserved among most eukaryotes and believed to be important for antiviral reactions and epigenetic gene regulation. Because a temperature-sensitive RNAi was reported in both plant and insect systems, suggesting its evolutional conservation, we analyzed the effect of different temperatures on mammalian RNAi, targeting the ectopic gene expression, and detected suppression at hypothermic temperatures. This phenomenon could be critical and useful to control ectopic and internal gene expressions by RNAi.
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Affiliation(s)
- Takashi Kameda
- Department of Biochemistry, Akita University School of Medicine 1-1-1 Hondo, Akita 010-8543, Japan
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11
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Ni J, Gao Y, Liu H, Chen J. Candida albicansCdc37 interacts with the Crk1 kinase and is required for Crk1 production. FEBS Lett 2004; 561:223-30. [PMID: 15013782 DOI: 10.1016/s0014-5793(04)00172-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2003] [Revised: 12/11/2003] [Accepted: 12/15/2003] [Indexed: 11/29/2022]
Abstract
Crk1, a Cdc2-related protein kinase from the human pathogenic fungus Candida albicans, plays an important role in hyphal development and virulence. To address its regulatory mechanisms, we searched for Crk1 interacting proteins by two-hybrid screening. A CDC37 ortholog (CaCDC37) was cloned from the screening with the Crk1 kinase domain as the bait. The CaCdc37 interacted preferentially with the kinase domain of Crk1 (Crk1N) as shown by two-hybrid and immunoprecipitation experiments. CaCDC37 could complement a cdc37 thermosensitive mutant (cdc37-34) of Saccharomyces cerevisiae. Importantly, Crk1 protein was hardly detectable in the cdc37-34 mutant at restrictive temperature. However, upon expression of CaCdc37 in the cdc37 mutant, Crk1 protein was detected even at restrictive temperature. Our data suggested that CaCdc37 was required for the production of Crk1 kinase. Like Cdc37 proteins of S. cerevisiae and higher eukaryotes, CaCdc37 might function as a molecular chaperone that stabilized Crk1 and other protein kinases in C. albicans. In support of this, CaSTI1 was identified from a two-hybrid screen with the full-length Crk1 as the bait. CaSti1 showed two-hybrid interactions with both Crk1 and the CaCdc37.
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Affiliation(s)
- Jian Ni
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai 200031, PR China
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12
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Holton NJ, Goodwin TJ, Butler MI, Poulter RT. An active retrotransposon in Candida albicans. Nucleic Acids Res 2001; 29:4014-24. [PMID: 11574684 PMCID: PMC60234 DOI: 10.1093/nar/29.19.4014] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2001] [Revised: 08/06/2001] [Accepted: 08/06/2001] [Indexed: 11/13/2022] Open
Abstract
Tca2 is a Ty1/copia-type retrotransposon from the pathogenic yeast Candida albicans. It was originally identified as an abundant, linear, extrachromosomal, double-stranded DNA molecule. Here we show that Tca2 is widespread in C.albicans, but that the abundance of extrachromosomal Tca2 DNA varies greatly among different strains and is strongly dependent on the growth temperature. The relative levels of Tca2 RNA vary in a similar pattern to the extrachromosomal DNA, raising the possibility that the variations in extrachromosomal DNA levels are introduced predominantly at the level of transcription. We have also analysed the retrotranspositional activity of the element by developing a transposition assay involving a cloned Tca2 element tagged with a selectable marker gene that is activated by passage through an RNA intermediate. We show that the marked Tca2 is transpositionally active as transposed copies of the marked element became integrated at a variety of new positions in the genome and an intron in the donor element was precisely removed in the newly transposed copies. This is the first report of transposition in C.albicans.
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Affiliation(s)
- N J Holton
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
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13
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Abstract
This report describes the identification and characterization of a retrotransposon, termed Tca5, from the pathogenic yeast Candida albicans. Tca5 has identical 685 bp LTRs flanking 4218 bp of internal sequence within which lies a single long ORF. Immediately internal to the left LTR is a primer binding site complementary to an internal portion of the initiator methionine tRNA and upstream of the right LTR is a polypurine tract. The ORF predicts a protein containing all the conserved motifs characteristic of Gag, protease, integrase, reverse transcriptase and RNaseH. Genomic Southern blots probed with Tca5 sequences show that it is a low copy number element and is present at different loci in different strains. This, together with the apparently intact structure of Tca5, suggests that it has transposed very recently. Potentially full-length Tca5 transcripts were detected in some strains raising the possibility that some copies of Tca5 may still be active. Phylogenetic analyses and other sequence comparisons suggest that Tca5 is most closely related to the Ty5 element of Saccharomyces cerevisiae and S. paradoxus. The nucleotide sequence of Tca5 has been submitted to GenBank under Accession No. AF093417.
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Affiliation(s)
- E P Plant
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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14
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Chen J, Zhou S, Wang Q, Chen X, Pan T, Liu H. Crk1, a novel Cdc2-related protein kinase, is required for hyphal development and virulence in Candida albicans. Mol Cell Biol 2000; 20:8696-708. [PMID: 11073971 PMCID: PMC86484 DOI: 10.1128/mcb.20.23.8696-8708.2000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Both mitogen-activated protein kinases and cyclin-dependent kinases play a role in hyphal development in Candida albicans. Using an oligonucleotide probe-based screen, we have isolated a new member of the Cdc2 kinase subfamily, designated Crk1 (Cdc2-related kinase). The protein sequence of Crk1 is most similar to those of Saccharomyces cerevisiae Sgv1 and human Pkl1/Cdk9. In S. cerevisiae, CRK1 suppresses some, but not all, of the defects associated with an sgv1 mutant. Deleting both copies of CRK1 in C. albicans slows growth slightly but leads to a profound defect in hyphal development under all conditions examined. crk1/crk1 mutants are impaired in the induction of hypha-specific genes and are avirulent in mice. Consistent with this, ectopic expression of the Crk1 kinase domain (CRK1N) promotes filamentous or invasive growth in S. cerevisiae and hyphal development in C. albicans. The activity of Crk1 in S. cerevisiae requires Flo8 but is independent of Ste12 and Phd1. Similarly, Crk1 promotes filamentation through a route independent of Cph1 and Efg1 in C. albicans. RAS1(V13) can also activate filamentation in a cph1/cph1 efg1/efg1 double mutant. Interestingly, CRK1N produces florid hyphae in ras1/ras1 strains, while RAS1(V13) generates feeble hyphae in crk1/crk1 strains.
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Affiliation(s)
- J Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry, Chinese Academy of Sciences, Shanghai 200031, China
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15
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Goodwin TJ, Poulter RT. Multiple LTR-retrotransposon families in the asexual yeast Candida albicans. Genome Res 2000; 10:174-91. [PMID: 10673276 DOI: 10.1101/gr.10.2.174] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have begun a characterization of the long terminal repeat (LTR) retrotransposons in the asexual yeast Candida albicans. A database of assembled C. albicans genomic sequence at Stanford University, which represents 14.9 Mb of the 16-Mb haploid genome, was screened and >350 distinct retrotransposon insertions were identified. The majority of these insertions represent previously unrecognized retrotransposons. The various elements were classified into 34 distinct families, each family being similar, in terms of the range of sequences that it represents, to a typical Ty element family of the related yeast Saccharomyces cerevisiae. These C. albicans retrotransposon families are generally of low copy number and vary widely in coding capacity. For only three families, was a full-length and apparently intact retrotransposon identified. For many families, only solo LTRs and LTR fragments remain. Several families of highly degenerate elements appear to be still capable of transposition, presumably via trans-activation. The overall structure of the retrotransposon population in C. albicans differs considerably from that of S. cerevisiae. In that species, retrotransposon insertions can be assigned to just five families. Most of these families still retain functional examples, and they generally appear at higher copy numbers than the C. albicans families. The possibility that these differences between the two species are attributable to the nonstandard genetic code of C. albicans or the asexual nature of its genome is discussed. A region rich in retrotransposon fragments, that lies adjacent to many of the CARE-2/Rel-2 sub-telomeric repeats, and which appears to have arisen through multiple rounds of duplication and recombination, is also described.
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Affiliation(s)
- T J Goodwin
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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16
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Goodwin TJ, Poulter RT. The CARE-2 and rel-2 repetitive elements of Candida albicans contain LTR fragments of a new retrotransposon. Gene X 1998; 218:85-93. [PMID: 9751806 DOI: 10.1016/s0378-1119(98)00362-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
CARE-2 and Rel-2 are dispersed, repetitive elements of Candida albicans. Hybridisation experiments suggest that they are present at 10-20 copies per genome and appear on most, if not all, of the chromosomes. A high degree of interstrain variation has been demonstrated for CARE-2, making it of use for strain typing. Until now, however, the nature of the repetitive elements within CARE-2 and Rel-2 was unknown. We show here that CARE-2 and Rel-2 contain long terminal repeat (LTR) fragments of a new retrotransposon. These LTRs, which we designate kappa, are partially responsible for the repetitive nature of CARE-2 and Rel-2. Complete copies of the kappa elements are present elsewhere in the genome and adjacent to some are sequences characteristic of the internal regions of retrotransposons. An apparently high degree of scrambling of the kappa elements suggests that they may represent a hotspot for mutation and recombination in C. albicans.
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Affiliation(s)
- T J Goodwin
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand
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17
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Vieira C, Aubry P, Lepetit D, Biémont C. A temperature cline in copy number for 412 but not roo/B104 retrotransposons in populations of Drosophila simulans. Proc Biol Sci 1998; 265:1161-5. [PMID: 9699309 PMCID: PMC1689186 DOI: 10.1098/rspb.1998.0413] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The copy number of the retrotransposable element 412 of Drosophila simulans from populations collected worldwide shows a negative correlation with minimum temperature. No association was detected for the roo/B104 element. The possibility that selective pressures might regulate the 412 copy number in these natural populations is supported by detection of selection against the detrimental effects of 412 insertions (estimated by the proportion of insertions on the X chromosome in comparison with the autosomes) but not roo/B104. These data reveal different spatial patterns for two element families, and strongly suggest that some factors in the environment, such as temperature, may interfere with the control of retrotransposition, thus affecting important aspects of genomic evolution.
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Affiliation(s)
- C Vieira
- Laboratoire de Biométrie, Génétique, Biologie des populations, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France.
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18
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Chen JY, Wang Q, Fu Z, Zhou S, Fonzi WA. Tca1, the retrotransposon-like element of Candida albicans, is a degenerate and inactive element. J Bacteriol 1998; 180:3657-62. [PMID: 9658011 PMCID: PMC107336 DOI: 10.1128/jb.180.14.3657-3662.1998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Candida albicans is an asexual fungus and as such must rely on mechanisms other than sexual recombination to generate genetic diversity. Retrotransposons are ubiquitous genetic elements known to generate multiple types of genomic alterations. We have further investigated the nature of the retrotransposon-like element Tca1 in C. albicans. Tca1 is present at two loci in strain SC5314. Both loci have now been cloned, and one element was sequenced in its entirety. This element was flanked by alpha elements, or long terminal repeats (LTRs), and contained an intervening region of 5,614 bp. The intervening region was highly degenerate and contained no extended open reading frames, indicating that Tca1 is not a functional element. Partial sequence determination demonstrated that the elements from the two loci were nearly identical. Genetic manipulation of the elements showed that both loci were heterozygous for Tca1, that both were transcriptionally active, and that deletion of both had no effect on growth rate or germ tube formation. Thus, it is unclear why this nonfunctional, highly degenerate element has been maintained in many clinical isolates.
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Affiliation(s)
- J y Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry, Academia Sinica, Shanghai 200031, People's Republic of China
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19
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De Bernardis F, Mühlschlegel FA, Cassone A, Fonzi WA. The pH of the host niche controls gene expression in and virulence of Candida albicans. Infect Immun 1998; 66:3317-25. [PMID: 9632601 PMCID: PMC108348 DOI: 10.1128/iai.66.7.3317-3325.1998] [Citation(s) in RCA: 191] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Little is known of the biological attributes conferring pathogenicity on the opportunistic fungal pathogen Candida albicans. Infection by this pathogen, as for bacterial pathogens, may rely upon environmental signals within the host niche to regulate the expression of virulence determinants. To determine if C. albicans responds to the pH of the host niche, we tested the virulence of strains with mutations in either of two pH-regulated genes, PHR1 and PHR2. In vitro, PHR1 is expressed when the ambient pH is at 5.5 or higher and deletion of the gene results in growth and morphological defects at neutral to alkaline pHs. Conversely, PHR2 is expressed at an ambient pH below 5.5, and the growth and morphology of the null mutant is compromised below this pH. A PHR1 null mutant was avirulent in a mouse model of systemic infection but uncompromised in its ability to cause vaginal infection in rats. Since systemic pH is near neutrality and vaginal pH is around 4.5, the virulence phenotype paralleled the pH dependence of the in vitro phenotypes. The virulence phenotype of a PHR2 null mutant was the inverse. The mutant was virulent in a systemic-infection model but avirulent in a vaginal-infection model. Heterozygous mutants exhibited partial reductions in their pathogenic potential, suggesting a gene dosage effect. Unexpectedly, deletion of PHR2 did not prevent hyphal development in vaginal tissue, suggesting that it is not essential for hyphal development in this host niche. The results suggest that the pH of the infection site regulates the expression of genes essential to survival within that niche. This implies that the study of environmentally regulated genes may provide a rationale for understanding the pathobiology of C. albicans.
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Affiliation(s)
- F De Bernardis
- Laboratory of Bacteriology and Medical Mycology, Instituto Superiore di Sanita, 00161 Rome, Italy
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20
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Cutler JE. The Candida albicans phosphomannan complex in Candida-host interactions. RESEARCH IN IMMUNOLOGY 1998; 149:299-308; discussion 507-9. [PMID: 9720948 DOI: 10.1016/s0923-2494(98)80754-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- J E Cutler
- Department of Microbiology, Montana State University, Bozeman 59717-3520, USA
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21
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Matthews GD, Goodwin TJ, Butler MI, Berryman TA, Poulter RT. pCal, a highly unusual Ty1/copia retrotransposon from the pathogenic yeast Candida albicans. J Bacteriol 1997; 179:7118-28. [PMID: 9371461 PMCID: PMC179655 DOI: 10.1128/jb.179.22.7118-7128.1997] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Retrotransposons are mobile genetic elements. They can transpose via the reverse transcription of mRNA into double-stranded DNA (dsDNA) followed by the insertion of this dsDNA into new sites within the host genome. The unintegrated, linear, dsDNA form of retrotransposons is usually very rare. We report here the isolation of a retrotransposon from Candida albicans which is unusual in this respect. This element, which we have named pCal, was first identified as a distinct band when uncut C. albicans DNA was examined on an agarose gel. Sequence analysis of the cloned element revealed that it is a retrotransposon belonging to the Ty1/copia group. It is estimated that pCal produces 50 to 100 free, linear, dsDNA copies of itself per cell. This is a much higher level of expression than even that of the system in which Ty1 is expressed behind the highly active GAL1 promoter on a high-copy-number plasmid (about 10 copies per cell). Another unusual feature of pCal is that its Pol enzymes are likely to be expressed via the pseudoknot-assisted suppression of an upstream, in-phase stop codon, as has been shown for Moloney murine leukemia virus.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Candida albicans/genetics
- Chromosome Mapping
- Cloning, Molecular
- Codon, Terminator
- DNA Transposable Elements/genetics
- DNA, Fungal/analysis
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- Endopeptidases/genetics
- Gene Expression Regulation, Fungal
- Gene Products, pol/genetics
- Gene Products, pol/metabolism
- Integrases/genetics
- Molecular Sequence Data
- Molecular Structure
- Open Reading Frames
- Phylogeny
- Plasmids
- Promoter Regions, Genetic
- RNA-Directed DNA Polymerase/genetics
- Retroelements
- Ribonucleases/genetics
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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Affiliation(s)
- G D Matthews
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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22
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Lauermann V, Hermankova M, Boeke JD. Increased length of long terminal repeats inhibits Ty1 transposition and leads to the formation of tandem multimers. Genetics 1997; 145:911-22. [PMID: 9093846 PMCID: PMC1207896 DOI: 10.1093/genetics/145.4.911] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Ty1 retrotransposon of Saccharomyces cerevisiae is bounded by long-terminal repeats (LTRs). We have constructed a variety of Ty1 elements in which the LTR length has been increased from the normal length of 334 bp to > 2 kb. Although small insertions in the LTR have minimal effects on transposition frequency, larger insertions dramatically reduce it. Nevertheless, elements with long LTRs are incorporated into the genome at a low frequency. Most of these rare insertion events represent Ty1 tandem (head to tail) multimers.
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Affiliation(s)
- V Lauermann
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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23
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Niimi M, Niimi K, Cannon RD. Temperature-related expression of the vacuolar aspartic proteinase (APR1) gene and beta-N-acetylglucosaminidase (HEX1) gene during Candida albicans morphogenesis. FEMS Microbiol Lett 1997; 148:247-54. [PMID: 9084153 DOI: 10.1111/j.1574-6968.1997.tb10296.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Expression of the Candida albicans vacuolar aspartic proteinase (APR1) and beta-N-acetylglucosaminidase (HEX1) genes was studied when carbon-starved cells of strains ATCC 10261 and A72 were induced to grow as yeast or as germ tube-forming cells. Amounts of APR1 mRNA were similar under yeast or germ tube growth conditions. However, more APR1 mRNA was present in cells grown at 28 degrees C than in cells grown at 37 degrees C. The Apr1 enzyme activity of cell-free extracts was not affected by cellular morphology, culture pH or growth temperature. Amounts of HEX1 mRNA were also higher in N-acetylglucosamine (GlcNAc)-induced cells grown at 28 degrees C than in cells grown at 37 degrees C. There was slightly more HEX1 mRNA in cells grown at pH 4.5 than in cells grown at pH 6.7. The beta-N-acetylglucosaminidase activities of GlcNAc-grown cells correlated with the amounts of HEX1 mRNA and were higher when cells were grown at a lower temperature and at a lower pH. Although a similar temperature- and pH-dependent pattern of HEX1 mRNA expression was seen in cells grown on glucose, the enzyme activities in cell-free extracts were all very low. These data indicate that the APR1 and HEX1 genes play no direct role in the dimorphic transition of C. albicans and that transcription of both genes appears to be temperature regulated when the cells are released from carbon starvation. The expression of HEX1 mRNA is in part under the control of culture pH and translation of HEX1 mRNA seems to be regulated by glucose.
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Affiliation(s)
- M Niimi
- Department of Oral Biology and Oral Pathology, University of Otago, Dunedin, New Zealand.
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24
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25
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Affiliation(s)
- J Pla
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Spain
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26
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Neuveglise C, Sarfati J, Latge JP, Paris S. Afut1, a retrotransposon-like element from Aspergillus fumigatus. Nucleic Acids Res 1996; 24:1428-34. [PMID: 8628674 PMCID: PMC145799 DOI: 10.1093/nar/24.8.1428] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A repeated DNA sequence used for epidemiological studies of the human opportunistic pathogen Aspergillus fumigatus has been characterized. It is a retroelement of 6914 bp in length, bounded by long terminal repeats of 282 bp, with sequence and features characteristic of retroviruses and retrotransposons. A 5 bp duplication site was found at its borders. This element, designated Afut1, encodes amino acid sequences homologous to the reverse transcriptase, RNase H and endonuclease encoded by the pol genes of retroelements. Comparison of the peptidic sequences with other putative polypeptides of fungal LTR retrotransposons showed that Afut1 is a member of the gypsy group. This is the first report of a transposable element in A.fumigatus. Afut1 is a defective element: the putative coding domains contain multiple stop codons due exclusively to transitions from C:G to T:A.
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Affiliation(s)
- C Neuveglise
- Laboratoire des Aspergillus, Institut Pasteur, Paris, France
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27
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Hoyer LL, Scherer S, Shatzman AR, Livi GP. Candida albicans ALS1: domains related to a Saccharomyces cerevisiae sexual agglutinin separated by a repeating motif. Mol Microbiol 1995; 15:39-54. [PMID: 7752895 DOI: 10.1111/j.1365-2958.1995.tb02219.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Transfer of budding Candida albicans yeast cells from the rich, complex medium YEPD to the defined tissue culture medium RPMI 1640 (RPMI) at 37 degrees C and 5% CO2 causes rapid onset of hyphal induction. Among the genes induced under these conditions are hyphal-specific genes as well as genes expressed in response to changes in temperature, CO2 and specific media components. A cDNA library constructed from cells incubated for 20 min in RPMI was differentially screened with yeast (YEPD)- and hyphal (RPMI)-specific probes resulting in identification of a gene expressed in response to culture conditions but not regulated by the yeast-hyphal transition. The deduced gene product displays significant identity to Saccharomyces cerevisiae alpha-agglutinin, encoded by AG alpha 1, an adhesion glycoprotein that mediates mating of haploid cells. The presence of this gene in C. albicans is curious since the organism has not been observed to undergo meiosis. We designate the C. albicans gene ALS1 (for agglutinin-like sequence). While the N- and C-termini of the predicted 1260-amino-acid ALS1 protein resemble those of the 650-amino-acid AG alpha 1, ALS1 contains a central domain of tandem repeats consisting of a highly conserved 36-amino-acid sequence not present in AG alpha 1. These repeats are also present on the nucleotide level as a highly conserved 108 bp motif. Southern and Northern blot analyses indicate a family of C. albicans genes that contain the tandem repeat motif; at least one gene in addition to ALS1 is expressed under conditions similar to those for ALS1 expression. Genomic Southern blots from several C. albicans isolates indicate that the number of copies of the tandem repeat element in ALS1 differs across strains and, in some cases, between ALS1 alleles in the same strain, suggesting a strain-dependent variability in ALS1 protein size. Potential roles for the ALS1 protein are discussed.
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Affiliation(s)
- L L Hoyer
- Human Genome Center, Lawrence Berkeley Laboratory, Berkeley, California 94720
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28
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Schmid-Berger N, Schmid B, Barth G. Ylt1, a highly repetitive retrotransposon in the genome of the dimorphic fungus Yarrowia lipolytica. J Bacteriol 1994; 176:2477-82. [PMID: 8169196 PMCID: PMC205382 DOI: 10.1128/jb.176.9.2477-2482.1994] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A highly repetitive composite element, Ylt1, was detected in the genome of the dimorphic fungus Yarrowia lipolytica. Ylt1 resembles retrotransposons found in other eukaryotes. It is about 9.4 kb long and can transpose in the genome. The Ylt1 element is bounded by a long terminal repeat (LTR), the zeta element. Several copies of zeta were isolated and sequenced. The sequence of this element is well conserved. It is 714 bp long and is bounded by nucleotides 5'-TG...CA-3', which are part of a short inverted repeat, a feature conserved in the LTRs of retroviruses and retrotransposons. Sequence analysis revealed motifs commonly found in LTR elements, like signals for the start and termination of transcription. The zeta element exists as part of retrotransposon Ylt1, as well as a solo element in the genome. Ylt1 and solo zeta elements are flanked by a 4-bp directly repeated genomic sequence. The copy numbers of Ylt1 and solo zeta are dependent on the strain examined, but at least 35 copies of the composite Ylt1 element and more than 30 copies of the solo zeta element per haploid genome have been observed.
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Affiliation(s)
- N Schmid-Berger
- Department of Microbiology, University of Basel, Switzerland
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29
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Abstract
Recent studies on transposable elements (TEs) have shed light on the mechanisms that have shaped their evolution. In addition to accumulating nucleotide substitutions over evolutionary time, TEs appear to be especially prone to genetic rearrangements and vertical transmissions across even distantly related species. As a consequence of replicating in host genomes, TEs have a significant mutational effect on their hosts. Although most TE-insertion mutations seem to exert a negative effect on host fitness, a growing body of evidence indicates that some TE-mediated genetic changes have become established features of host species genomes indicating that TEs can contribute significantly to organismic evolution.
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Affiliation(s)
- J F McDonald
- Department of Genetics, University of Georgia, Athens 30602
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30
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Coleman DC, Bennett DE, Sullivan DJ, Gallagher PJ, Henman MC, Shanley DB, Russell RJ. Oral Candida in HIV infection and AIDS: new perspectives/new approaches. Crit Rev Microbiol 1993; 19:61-82. [PMID: 8338619 DOI: 10.3109/10408419309113523] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Oral candidosis has become an increasingly important problem in HIV-infected individuals. At present, the small body of published literature on the characterization of the Candida strains and species found in HIV+ patients is full of confusion and contradictions. Some of these difficulties are the result of the methodological shortcomings of a number of the techniques that have been used. Examples of the problems that may be encountered on primary isolation and subculture are described and the drawbacks associated with the systems used to date for phenotyping Candida are quoted. While molecular characterization techniques would appear to offer a reliable and objective alternative, they too have their strengths and weaknesses. An attempt is made to summarize the progress that has been made recently in the detection and identification of Candida albicans and also the non-albicans species from HIV-infected individuals. What emerges is that the commensal Candida species that inhabit the oral cavities of HIV+ patients are subjected to a number of significant pressures that probably promote the selection of organisms with unusual phenotypes and genotypes. These Candida are more difficult to characterize and behave differently compared to their counterparts in HIV- individuals. It is clear that uncovering the factors that are important for the selection of treatment regimens and will be predictive of outcome will not be easy. Candida organisms are neither as benign nor as simple as once thought.
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Affiliation(s)
- D C Coleman
- University of Dublin, Moyne Institute, Department of Microbiology, Republic of Ireland
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