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Arruda MFC, da Silva Ramos RCP, de Oliveira NS, Rosa RT, Stuelp-Campelo PM, Bianchini LF, Villas-Bôas SG, Rosa EAR. Central Carbon Metabolism in Candida albicans Biofilms Is Altered by Dimethyl Sulfoxide. J Fungi (Basel) 2024; 10:337. [PMID: 38786692 PMCID: PMC11121877 DOI: 10.3390/jof10050337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 05/25/2024] Open
Abstract
The effect of dimethyl sulfoxide (DMSO) on fungal metabolism has not been well studied. This study aimed to evaluate, by metabolomics, the impact of DMSO on the central carbon metabolism of Candida albicans. Biofilms of C. albicans SC5314 were grown on paper discs, using minimum mineral (MM) medium, in a dynamic continuous flow system. The two experimental conditions were control and 0.03% DMSO (v/v). After 72 h of incubation (37 °C), the biofilms were collected and the metabolites were extracted. The extracted metabolites were subjected to gas chromatography-mass spectrometry (GC/MS). The experiment was conducted using five replicates on three independent occasions. The GC/MS analysis identified 88 compounds. Among the 88 compounds, the levels of 27 compounds were markedly different between the two groups. The DMSO group exhibited enhanced levels of putrescine and glutathione and decreased levels of methionine and lysine. Additionally, the DMSO group exhibited alterations in 13 metabolic pathways involved in primary and secondary cellular metabolism. Among the 13 altered pathways, seven were downregulated and six were upregulated in the DMSO group. These results indicated a differential intracellular metabolic profile between the untreated and DMSO-treated biofilms. Hence, DMSO was demonstrated to affect the metabolic pathways of C. albicans. These results suggest that DMSO may influence the results of laboratory tests when it is used as a solvent. Hence, the use of DMSO as a solvent must be carefully considered in drug research, as the effect of the researched drugs may not be reliably translated into clinical practice.
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Affiliation(s)
- Maria Fernanda Cordeiro Arruda
- Graduate Program on Dentistry, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (M.F.C.A.); (R.C.P.d.S.R.)
| | - Romeu Cassiano Pucci da Silva Ramos
- Graduate Program on Dentistry, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (M.F.C.A.); (R.C.P.d.S.R.)
| | - Nicoly Subtil de Oliveira
- Graduate Program on Animal Sciences, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil;
| | - Rosimeire Takaki Rosa
- Xenobiotics Research Unit, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (R.T.R.); (P.M.S.-C.); (L.F.B.)
| | - Patrícia Maria Stuelp-Campelo
- Xenobiotics Research Unit, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (R.T.R.); (P.M.S.-C.); (L.F.B.)
| | - Luiz Fernando Bianchini
- Xenobiotics Research Unit, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (R.T.R.); (P.M.S.-C.); (L.F.B.)
| | | | - Edvaldo Antonio Ribeiro Rosa
- Graduate Program on Dentistry, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (M.F.C.A.); (R.C.P.d.S.R.)
- Graduate Program on Animal Sciences, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil;
- Xenobiotics Research Unit, School of Medicine and Life Sciences, Pontifical Catholic University of Paraná, Curitiba 80215-901, Brazil; (R.T.R.); (P.M.S.-C.); (L.F.B.)
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2
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Yu JSL, Heineike BM, Hartl J, Aulakh SK, Correia-Melo C, Lehmann A, Lemke O, Agostini F, Lee CT, Demichev V, Messner CB, Mülleder M, Ralser M. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy. PLoS Biol 2022; 20:e3001912. [PMID: 36455053 PMCID: PMC9757880 DOI: 10.1371/journal.pbio.3001912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/16/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.
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Affiliation(s)
- Jason S. L. Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Benjamin M. Heineike
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Johannes Hartl
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Simran K. Aulakh
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Clara Correia-Melo
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Lehmann
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Oliver Lemke
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Federica Agostini
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Cory T. Lee
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Vadim Demichev
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
| | - Christoph B. Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Mülleder
- Core Facility—High Throughput Mass Spectrometry, Charité Universitätsmedizin, Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin, Berlin, Germany
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3
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Kuplińska A, Rząd K, Wojciechowski M, Milewski S, Gabriel I. Antifungal Effect of Penicillamine Due to the Selective Targeting of L-Homoserine O-Acetyltransferase. Int J Mol Sci 2022; 23:ijms23147763. [PMID: 35887110 PMCID: PMC9317633 DOI: 10.3390/ijms23147763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/16/2022] Open
Abstract
Due to the apparent similarity of fungal and mammalian metabolic pathways, the number of established antifungal targets is low, and the identification of novel ones is highly desirable. The results of our studies, presented in this work, indicate that the fungal biosynthetic pathway of L-methionine, an amino acid essential for humans, seems to be an attractive perspective. The MET2 gene from Candida albicans encoding L-homoserine O-acetyltransferase (CaMet2p), an enzyme catalyzing the first step in that pathway, was cloned and expressed as the native or the oligo-His-tagged fusion protein in Escherichia coli. The recombinant enzymes were purified and characterized for their basic molecular properties and substrate specificities. The purified MET2 gene product revealed the appropriate activity, catalyzed the conversion of L-homoserine (L-Hom) to O-acetyl-L-homoserine (OALH), and exhibited differential sensitivity to several L-Hom or OALH analogues, including penicillamine. Surprisingly, both penicillamine enantiomers (L- and D-Pen) displayed comparable inhibitory effects. The results of the docking of L- and D-Pen to the model of CaMet2p confirmed that both enantiomeric forms of the inhibitor are able to bind to the catalytic site of the enzyme with similar affinities and a similar binding mode. The sensitivity of some fungal cells to L-Pen, depending on the presence or absence of L-Met in the medium, clearly indicate Met2p targeting. Moreover, C. glabrata clinical strains that are resistant to fluconazole displayed a similar susceptibility to L-Pen as the wild-type strains. Our results prove the potential usefulness of Met2p as a molecular target for antifungal chemotherapy.
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Affiliation(s)
| | | | | | | | - Iwona Gabriel
- Correspondence: ; Tel.: +48-58-348-6078; Fax: +48-58-347-1144
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4
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Shrivastava M, Feng J, Coles M, Clark B, Islam A, Dumeaux V, Whiteway M. Modulation of the complex regulatory network for methionine biosynthesis in fungi. Genetics 2021; 217:6078591. [PMID: 33724418 DOI: 10.1093/genetics/iyaa049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/07/2020] [Indexed: 01/19/2023] Open
Abstract
The assimilation of inorganic sulfate and the synthesis of the sulfur-containing amino acids methionine and cysteine is mediated by a multibranched biosynthetic pathway. We have investigated this circuitry in the fungal pathogen Candida albicans, which is phylogenetically intermediate between the filamentous fungi and Saccharomyces cerevisiae. In S. cerevisiae, this pathway is regulated by a collection of five transcription factors (Met4, Cbf1, Met28, and Met31/Met32), while in the filamentous fungi the pathway is controlled by a single Met4-like factor. We found that in C. albicans, the Met4 ortholog is also a core regulator of methionine biosynthesis, where it functions together with Cbf1. While C. albicans encodes this Met4 protein, a Met4 paralog designated Met28 (Orf19.7046), and a Met31 protein, deletion, and activation constructs suggest that of these proteins only Met4 is actually involved in the regulation of methionine biosynthesis. Both Met28 and Met31 are linked to other functions; Met28 appears essential, and Met32 appears implicated in the regulation of genes of central metabolism. Therefore, while S. cerevisiae and C. albicans share Cbf1 and Met4 as central elements of the methionine biosynthesis control, the other proteins that make up the circuit in S. cerevisiae are not members of the C. albicans control network, and so the S. cerevisiae circuit likely represents a recently evolved arrangement.
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Affiliation(s)
| | - Jinrong Feng
- Medical School, Nantong University, Nangtong, Jiangsu, China
| | - Mark Coles
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Benjamin Clark
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Amjad Islam
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Vanessa Dumeaux
- Depatment of Biology, Concordia University, Montreal, QC, Canada
| | - Malcolm Whiteway
- Depatment of Biology, Concordia University, Montreal, QC, Canada
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5
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Ohtsuka H, Shimasaki T, Aiba H. Response to sulfur in Schizosaccharomyces pombe. FEMS Yeast Res 2021; 21:6324000. [PMID: 34279603 PMCID: PMC8310684 DOI: 10.1093/femsyr/foab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
Sulfur is an essential component of various biologically important molecules, including methionine, cysteine and glutathione, and it is also involved in coping with oxidative and heavy metal stress. Studies using model organisms, including budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe), have contributed not only to understanding various cellular processes but also to understanding the utilization and response mechanisms of each nutrient, including sulfur. Although fission yeast can use sulfate as a sulfur source, its sulfur metabolism pathway is slightly different from that of budding yeast because it does not have a trans-sulfuration pathway. In recent years, it has been found that sulfur starvation causes various cellular responses in S. pombe, including sporulation, cell cycle arrest at G2, chronological lifespan extension, autophagy induction and reduced translation. This MiniReview identifies two sulfate transporters in S. pombe, Sul1 (encoded by SPBC3H7.02) and Sul2 (encoded by SPAC869.05c), and summarizes the metabolic pathways of sulfur assimilation and cellular response to sulfur starvation. Understanding these responses, including metabolism and adaptation, will contribute to a better understanding of the various stress and nutrient starvation responses and chronological lifespan regulation caused by sulfur starvation.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
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6
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Molecular targets for antifungals in amino acid and protein biosynthetic pathways. Amino Acids 2021; 53:961-991. [PMID: 34081205 PMCID: PMC8241756 DOI: 10.1007/s00726-021-03007-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 01/22/2023]
Abstract
Fungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increasing importance is attached to the health and economic problems caused by fungal pathogens. There is a growing need for improvement of the availability of antifungal drugs, decreasing their prices and reducing side effects. Searching for novel approaches in this respect, amino acid and protein biosynthesis pathways appear to be competitive. The route that leads from amino acid biosynthesis to protein folding and its activation is rich in enzymes that are descriptive of fungi. Blocking the action of those enzymes often leads to avirulence or growth inhibition. In this review, we want to trace the principal processes of fungi vitality. We present the data of genes encoding enzymes involved in amino acid and protein biosynthesis, potential molecular targets in antifungal chemotherapy, and describe the impact of inhibitors on fungal organisms.
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Mardanov AV, Eldarov MA, Beletsky AV, Tanashchuk TN, Kishkovskaya SA, Ravin NV. Transcriptome Profile of Yeast Strain Used for Biological Wine Aging Revealed Dynamic Changes of Gene Expression in Course of Flor Development. Front Microbiol 2020; 11:538. [PMID: 32308650 PMCID: PMC7145950 DOI: 10.3389/fmicb.2020.00538] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/12/2020] [Indexed: 01/08/2023] Open
Abstract
Flor strains of Saccharomyces cerevisiae are principal microbial agents responsible for biological wine aging used for production of sherry-like wines. The flor yeast velum formed on the surface of fortified fermented must is a major adaptive and technological characteristic of flor yeasts that helps them to withstanding stressful winemaking conditions and ensures specific biochemical and sensory oxidative alterations typical for sherry wines. We have applied RNAseq technology for transcriptome analysis of an industrial flor yeast strain at different steps of velum development over 71 days under experimental winemaking conditions. Velum growth and maturation was accompanied by accumulation of aldehydes and acetales. We have identified 1490 differentially expressed genes including 816 genes upregulated and 674 downregulated more than 2-fold at mature biofilm stage as compared to the early biofilm. Distinct expression patterns of genes involved in carbon and nitrogen metabolism, respiration, cell cycle, DNA repair, cell adhesion, response to various stresses were observed. Many genes involved in response to different stresses, oxidative carbon metabolism, high affinity transport of sugars, glycerol utilization, sulfur metabolism, protein quality control and recycling, cell wall biogenesis, apoptosis were induced at the mature biofilm stage. Strong upregulation was observed for FLO11 flocculin while expression of other flocculins remained unaltered or moderately downregulated. Downregulated genes included those for proteins involved in glycolysis, transportation of ions, metals, aminoacids, sugars, indicating repression of some major transport and metabolic process at the mature biofilm stage. Presented results are important for in-depth understanding of cell response elicited by velum formation and sherry wine manufacturing conditions, and for the comprehension of relevant regulatory mechanisms. Such knowledge may help to better understand the molecular mechanisms that flor yeasts use to adapt to winemaking environments, establish the functions of previously uncharacterized genes, improve the technology of sherry- wine production, and find target genes for strain improvement.
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Affiliation(s)
- Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Mikhail A Eldarov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Tatiana N Tanashchuk
- Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - Svetlana A Kishkovskaya
- Research Institute of Viticulture and Winemaking "Magarach" of the Russian Academy of Sciences, Yalta, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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8
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Yoo SJ, Sohn MJ, Jeong DM, Kang HA. Short bZIP homologue of sulfur regulator Met4 from Ogataea parapolymorpha does not depend on DNA-binding cofactors for activating genes in sulfur starvation. Environ Microbiol 2019; 22:310-328. [PMID: 31680403 DOI: 10.1111/1462-2920.14849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/28/2022]
Abstract
The acquisition of sulfur from environment and its assimilation is essential for fungal growth and activities. Here, we describe novel features of the regulatory network of sulfur metabolism in Ogataea parapolymorpha, a thermotolerant methylotrophic yeast with high resistance to harsh environmental conditions. A short bZIP protein (OpMet4p) of O. parapolymorpha, displaying the combined structural characteristics of yeast and filamentous fungal Met4 homologues, plays a key role as a master regulator of cell homeostasis during sulfur limitation, but also its function is required for the tolerance of various stresses. Domain swapping analysis, combined with deletion analysis of the regulatory domains and genes encoding OpCbf1p, OpMet28p, and OpMet32p, indicated that OpMet4p does not require the interaction with these DNA-binding cofactors to induce the expression of sulfur genes, unlike the Saccharomyces cerevisiae Met4p. ChIP analysis confirmed the notion that OpMet4p, which contains a canonical bZIP domain, can bind the target DNA in the absence of cofactors, similar to homologues in other filamentous fungi. Collectively, the identified unique features of the O. parapolymorpha regulatory network, as the first report on the sulfur regulation by a short yeast Met4 homologue, provide insights into conservation and divergence of the sulfur regulatory networks among diverse ascomycetous fungi.
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Affiliation(s)
- Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Min Jeong Sohn
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Da Min Jeong
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
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9
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How does the addition of antioxidants and other sulfur compounds affect the metabolism of polyfunctional mercaptan precursors in model fermentations? Food Res Int 2019; 122:1-9. [DOI: 10.1016/j.foodres.2019.03.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/18/2022]
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10
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Pracharova P, Lieben P, Pollet B, Beckerich JM, Bonnarme P, Landaud S, Swennen D. Geotrichum candidum gene expression and metabolite accumulation inside the cells reflect the strain oxidative stress sensitivity and ability to produce flavour compounds. FEMS Yeast Res 2019; 19:5116167. [PMID: 30295727 PMCID: PMC6211236 DOI: 10.1093/femsyr/foy111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/04/2018] [Indexed: 12/02/2022] Open
Abstract
Geotrichum candidum is a fungus-like yeast widely used as a starter culture for cheese ripening for its proteolytic and lipolytic activities and its contribution to the cheese flavours. The sequenced strain G. candidum CLIB 918 was isolated from cheese Pont-L’Evêque. This strain's ability to produce volatile compounds was compared to the ability of a known strong sulphur compound producer G. candidum strain (Gc203). The aminotransferase-coding genes BAT2 and ARO8 were identified to be involved in methionine catabolism. The production of volatile compounds indicated that the sequenced strain was a moderate producer compared to the strong producer strain. The major volatile compounds were produced from sulphur amino acid, branched-chain amino acid and fatty acid metabolisms. Metabolite content of the cells showed that the ability of the strain to produce volatile compounds was inversely proportional to its ability to store amino acids inside the cells. Reduced glutathione, hypotaurine and taurine intracellular concentrations and volatile fatty aldehyde production indicated the role of oxidative stress sensitivity in flavour production. The increase in expression of several genes in a Reblochon-type cheese at the end of ripening confirmed that oxygen and iron were key factors regulating cheese flavour production.
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Affiliation(s)
- P Pracharova
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - P Lieben
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - B Pollet
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - J M Beckerich
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - P Bonnarme
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - S Landaud
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - D Swennen
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, 78850 Thiverval-Grignon, France
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Reeves TD, Warner DM, Ludlow LH, O'Connor CM. Pathways over Time: Functional Genomics Research in an Introductory Laboratory Course. CBE LIFE SCIENCES EDUCATION 2018; 17:ar1. [PMID: 29326101 PMCID: PMC6007769 DOI: 10.1187/cbe.17-01-0012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 07/28/2017] [Accepted: 10/04/2017] [Indexed: 05/30/2023]
Abstract
National reports have called for the introduction of research experiences throughout the undergraduate curriculum, but practical implementation at many institutions faces challenges associated with sustainability, cost, and large student populations. We describe a novel course-based undergraduate research experience (CURE) that introduces introductory-level students to research in functional genomics in a 3-credit, multisection laboratory class. In the Pathways over Time class project, students study the functional conservation of the methionine biosynthetic pathway between divergent yeast species. Over the five semesters described in this study, students (N = 793) showed statistically significant and sizable growth in content knowledge (d = 1.85) and in self-reported research methods skills (d = 0.65), experimental design, oral and written communication, database use, and collaboration. Statistical analyses indicated that content knowledge growth was larger for underrepresented minority students and that growth in content knowledge, but not research skills, varied by course section. Our findings add to the growing body of evidence that CUREs can support the scientific development of large numbers of students with diverse characteristics. The Pathways over Time project is designed to be sustainable and readily adapted to other institutional settings.
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Affiliation(s)
- Todd D Reeves
- Department of Measurement, Evaluation, Statistics, and Assessment, Boston College, Chestnut Hill, MA 02467
| | | | - Larry H Ludlow
- Department of Measurement, Evaluation, Statistics, and Assessment, Boston College, Chestnut Hill, MA 02467
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12
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Rząd K, Milewski S, Gabriel I. Versatility of putative aromatic aminotransferases from Candida albicans. Fungal Genet Biol 2017; 110:26-37. [PMID: 29199101 DOI: 10.1016/j.fgb.2017.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/28/2022]
Abstract
Amino acids constitute the key sources of nitrogen for growth of Candida albicans. In order to survive inside the host in different and rapidly changing environments, this fungus must be able to adapt via its expression of genes for amino acid metabolism. We analysed the ARO8, ARO9, YER152C, and BNA3 genes with regards to their role in the nutritional flexibility of C. albicans. CaAro8p is undoubtedly the most versatile enzyme among the aminotransferases investigated. It is involved in the catabolism of histidine, lysine, and aromatic amino acids as well as in l-Lys, Phe and Tyr biosynthesis. CaAro9p participates in the catabolism of aromatic amino acids and lysine at high concentrations of these compounds, with no biosynthetic role. Conversely, the CaYer152Cp catalytic potential for aromatic amino acid catabolism observed in vitro appears to be of little importance in vivo. Neither biosynthetic nor catabolic roles of CaBan3p were observed for any proteinogenic amino acid. Finally, none of the analysed aminotransferases was solely responsible for the catabolism of a single particular amino acid or its biosynthesis.
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Affiliation(s)
- Kamila Rząd
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland
| | - Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, 11/12 Narutowicza Str., 80-233 Gdańsk, Poland.
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13
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ATP Sulfurylase is Essential for the Utilization of Sulfamate as a Sulfur Source in the Yeast Komagataella pastoris (syn. Pichia pastoris). Curr Microbiol 2017; 74:1021-1025. [PMID: 28603806 PMCID: PMC5534208 DOI: 10.1007/s00284-017-1276-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/02/2017] [Indexed: 11/30/2022]
Abstract
The methylotrophic yeast Komagataella pastoris (syn. Pichia pastoris) is one of the few known yeasts that can utilize sulfamate (\documentclass[12pt]{minimal}
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\begin{document}$${\text{NH}}_{2} {\text{SO}}_{3}^{ - }$$\end{document}NH2SO3-) as a sulfur source. The biochemical pathway responsible for the catabolism of sulfamate has yet to be identified. The present study sought to investigate whether sulfamate catabolism proceeds through either of the inorganic sulfur intermediates sulfate (\documentclass[12pt]{minimal}
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\begin{document}$${\text{SO}}_{4}^{2 - }$$\end{document}SO42-) or sulfite (\documentclass[12pt]{minimal}
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\begin{document}$${\text{SO}}_{3}^{2 - }$$\end{document}SO32-) before its assimilation and subsequent incorporation into sulfur-containing amino acids and their derivatives. Two key genes in the K. pastoris inorganic sulfur assimilation pathway were deleted separately and the ability of each deletion mutant to utilize sulfamate and other selected sulfur sources was studied. Deletion of the MET3 gene (which encodes the enzyme ATP sulfurylase) did not affect growth on l-methionine, sulfite, methanesulfonate, or taurine but completely abolished growth on sulfate, methyl sulfate and sulfamate. Deletion of the MET5 gene (which encodes the β subunit of the enzyme sulfite reductase) abolished growth on all tested sulfur sources except l-methionine. These results suggest that the catabolism of sulfamate proceeds through a sulfate intermediate before its assimilation.
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Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K, Amselem J, Beckerich JM, Henrissat B, Van de Peer Y, Wincker P, Souciet JL, Gabaldón T, Tinsley CR, Casaregola S. Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep 2015; 5:11571. [PMID: 26108467 PMCID: PMC4479816 DOI: 10.1038/srep11571] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
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Affiliation(s)
- Guillaume Morel
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Lieven Sterck
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Dominique Swennen
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Djamila Onesime
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Anthony Levasseur
- INRA UMR1163, Biotechnologie des Champignons Filamenteux, Aix-Marseille Université, Polytech Marseille, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | - Noémie Jacques
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Sandrine Mallet
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Arnaux Couloux
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Karine Labadie
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
| | - Joëlle Amselem
- INRA UR1164, Unité de Recherche Génomique – Info, 78000 Versailles, France
| | - Jean-Marie Beckerich
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | | | - Yves Van de Peer
- Department of Plant Systems Biology VIB, Technologiepark 927, 9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Patrick Wincker
- CEA, Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, Évry F-91000, France
- CNRS UMR 8030, 2 Rue Gaston Crémieux, Évry, 91000, France
- Université d’Evry, Bd François Mitterand, Evry,91025, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, Strasbourg, 67000, France
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Colin R. Tinsley
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
| | - Serge Casaregola
- INRA UMR1319, Micalis Institute, CIRM-Levures, 78850 F-Thiverval-Grignon, France
- AgroParisTech UMR1319, Micalis Institute, 78850 F-Thiverval-Grignon, France
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Gomes D, Aguiar TQ, Dias O, Ferreira EC, Domingues L, Rocha I. Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. BMC Genomics 2014; 15:810. [PMID: 25253284 PMCID: PMC4190384 DOI: 10.1186/1471-2164-15-810] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/15/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ashbya gossypii is an industrially relevant microorganism traditionally used for riboflavin production. Despite the high gene homology and gene order conservation comparatively with Saccharomyces cerevisiae, it presents a lower level of genomic complexity. Its type of growth, placing it among filamentous fungi, questions how close it really is from the budding yeast, namely in terms of metabolism, therefore raising the need for an extensive and thorough study of its entire metabolism. This work reports the first manual enzymatic genome-wide re-annotation of A. gossypii as well as the first annotation of membrane transport proteins. RESULTS After applying a developed enzymatic re-annotation pipeline, 847 genes were assigned with metabolic functions. Comparatively to KEGG's annotation, these data corrected the function for 14% of the common genes and increased the information for 52 genes, either completing existing partial EC numbers or adding new ones. Furthermore, 22 unreported enzymatic functions were found, corresponding to a significant increase in the knowledge of the metabolism of this organism. The information retrieved from the metabolic re-annotation and transport annotation was used for a comprehensive analysis of A. gossypii's metabolism in comparison to the one of S. cerevisiae (post-WGD - whole genome duplication) and Kluyveromyces lactis (pre-WGD), suggesting some relevant differences in several parts of their metabolism, with the majority being found for the metabolism of purines, pyrimidines, nitrogen and lipids. A considerable number of enzymes were found exclusively in A. gossypii comparatively with K. lactis (90) and S. cerevisiae (13). In a similar way, 176 and 123 enzymatic functions were absent on A. gossypii comparatively to K. lactis and S. cerevisiae, respectively, confirming some of the well-known phenotypes of this organism. CONCLUSIONS This high quality metabolic re-annotation, together with the first membrane transporters annotation and the metabolic comparative analysis, represents a new important tool for the study and better understanding of A. gossypii's metabolism.
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Affiliation(s)
- Daniel Gomes
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Tatiana Q Aguiar
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Oscar Dias
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eugénio C Ferreira
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Lucília Domingues
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Majtan T, Pey AL, Fernández R, Fernández JA, Martínez-Cruz LA, Kraus JP. Domain organization, catalysis and regulation of eukaryotic cystathionine beta-synthases. PLoS One 2014; 9:e105290. [PMID: 25122507 PMCID: PMC4133348 DOI: 10.1371/journal.pone.0105290] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/23/2014] [Indexed: 01/01/2023] Open
Abstract
Cystathionine beta-synthase (CBS) is a key regulator of sulfur amino acid metabolism diverting homocysteine, a toxic intermediate of the methionine cycle, via the transsulfuration pathway to the biosynthesis of cysteine. Although the pathway itself is well conserved among eukaryotes, properties of eukaryotic CBS enzymes vary greatly. Here we present a side-by-side biochemical and biophysical comparison of human (hCBS), fruit fly (dCBS) and yeast (yCBS) enzymes. Preparation and characterization of the full-length and truncated enzymes, lacking the regulatory domains, suggested that eukaryotic CBS exists in one of at least two significantly different conformations impacting the enzyme’s catalytic activity, oligomeric status and regulation. Truncation of hCBS and yCBS, but not dCBS, resulted in enzyme activation and formation of dimers compared to native tetramers. The dCBS and yCBS are not regulated by the allosteric activator of hCBS, S-adenosylmethionine (AdoMet); however, they have significantly higher specific activities in the canonical as well as alternative reactions compared to hCBS. Unlike yCBS, the heme-containing dCBS and hCBS showed increased thermal stability and retention of the enzyme’s catalytic activity. The mass-spectrometry analysis and isothermal titration calorimetry showed clear presence and binding of AdoMet to yCBS and hCBS, but not dCBS. However, the role of AdoMet binding to yCBS remains unclear, unlike its role in hCBS. This study provides valuable information for understanding the complexity of the domain organization, catalytic specificity and regulation among eukaryotic CBS enzymes.
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Affiliation(s)
- Tomas Majtan
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, Colorado, United States of America
| | - Angel L. Pey
- Department of Physical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain
| | - Roberto Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - José A. Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Jan P. Kraus
- Department of Pediatrics, University of Colorado, School of Medicine, Aurora, Colorado, United States of America
- * E-mail:
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Sohn MJ, Yoo SJ, Oh DB, Kwon O, Lee SY, Sibirny AA, Kang HA. Novel cysteine-centered sulfur metabolic pathway in the thermotolerant methylotrophic yeast Hansenula polymorpha. PLoS One 2014; 9:e100725. [PMID: 24959887 PMCID: PMC4069077 DOI: 10.1371/journal.pone.0100725] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/27/2014] [Indexed: 11/19/2022] Open
Abstract
In yeast and filamentous fungi, sulfide can be condensed either with O-acetylhomoserine to generate homocysteine, the precursor of methionine, or with O-acetylserine to directly generate cysteine. The resulting homocysteine and cysteine can be interconverted through transsulfuration pathway. Here, we systematically analyzed the sulfur metabolic pathway of the thermotolerant methylotrophic yeast Hansenula polymorpha, which has attracted much attention as an industrial yeast strain for various biotechnological applications. Quite interestingly, the detailed sulfur metabolic pathway of H. polymorpha, which was reconstructed based on combined analyses of the genome sequences and validation by systematic gene deletion experiments, revealed the absence of de novo synthesis of homocysteine from inorganic sulfur in this yeast. Thus, the direct biosynthesis of cysteine from sulfide is the only pathway of synthesizing sulfur amino acids from inorganic sulfur in H. polymorpha, despite the presence of both directions of transsulfuration pathway Moreover, only cysteine, but no other sulfur amino acid, was able to repress the expression of a subset of sulfur genes, suggesting its central and exclusive role in the control of H. polymorpha sulfur metabolism. 35S-Cys was more efficiently incorporated into intracellular sulfur compounds such as glutathione than 35S-Met in H. polymorpha, further supporting the cysteine-centered sulfur pathway. This is the first report on the novel features of H. polymorpha sulfur metabolic pathway, which are noticeably distinct from those of other yeast and filamentous fungal species.
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Affiliation(s)
- Min Jeong Sohn
- Department of Life Science, Chung-Ang University, Seoul, Korea
- Department of Chemical & Biomolecular Engineering (BK21+ program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Su Jin Yoo
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Doo-Byoung Oh
- Biochemicals and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Ohsuk Kwon
- Biochemicals and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Sang Yup Lee
- Department of Chemical & Biomolecular Engineering (BK21+ program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Andriy A. Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Korea
- * E-mail:
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Xu F, Jerlström-Hultqvist J, Einarsson E, Ástvaldsson Á, Svärd SG, Andersson JO. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PLoS Genet 2014; 10:e1004053. [PMID: 24516394 PMCID: PMC3916229 DOI: 10.1371/journal.pgen.1004053] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/08/2013] [Indexed: 11/18/2022] Open
Abstract
Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host. Studies of model organisms are very powerful. However, to appreciate the enormous diversity of genetic and cell biological processes we need to extend the number of available model organisms. For example, there are very few model organisms for diverse microbial eukaryotes, a group of organisms which indeed represents the vast majority of the eukaryotic diversity. To this end, we have developed a system to do genetic modification on the Atlantic salmon pathogen Spironucleus salmonicida. Using this system we could show that the organism is capable of producing hydrogen within specialised compartments. Here we present the genome sequence of S. salmonicida together with a thorough annotation. We compare the results with the closest available model organism, the human intestinal parasite Giardia intestinalis. The fish parasite has a more elaborate system for regulation of gene expression, as well as a larger metabolic capacity. This indicates that S. salmonicida is a well-adapted pathogen that can deal with fluctuating environments, an important trait to be able to establish systemic infections in the host. The development of S. salmonicida into a model system will benefit the studies of fish infections, as well as cell biological processes.
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Affiliation(s)
- Feifei Xu
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, BMC, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, BMC, Uppsala, Sweden
| | - Elin Einarsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, BMC, Uppsala, Sweden
| | - Ásgeir Ástvaldsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, BMC, Uppsala, Sweden
| | - Staffan G. Svärd
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, BMC, Uppsala, Sweden
| | - Jan O. Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, BMC, Uppsala, Sweden
- * E-mail:
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New insights into sulfur metabolism in yeasts as revealed by studies of Yarrowia lipolytica. Appl Environ Microbiol 2012; 79:1200-11. [PMID: 23220962 DOI: 10.1128/aem.03259-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yarrowia lipolytica, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution.
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Abstract
Although observations from biochemistry and cell biology seemingly illustrate hundreds of examples of exquisite molecular adaptations, the fact that experimental manipulation can often result in improvements in cellular infrastructure raises the question as to what ultimately limits the level of molecular perfection achievable by natural selection. Here, it is argued that random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes. Moreover, although substantial improvements in fitness may sometimes be accomplished via the emergence of novel cellular features that improve on previously established mechanisms, such advances are expected to often be transient, with overall fitness eventually returning to the level before incorporation of the genetic novelty. As a consequence of such changes, increased molecular/cellular complexity can arise by Darwinian processes, while yielding no long-term increase in adaptation and imposing increased energetic and mutational costs.
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Sulfurous gases as biological messengers and toxins: comparative genetics of their metabolism in model organisms. J Toxicol 2011; 2011:394970. [PMID: 22131987 PMCID: PMC3216388 DOI: 10.1155/2011/394970] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 08/11/2011] [Indexed: 01/31/2023] Open
Abstract
Gasotransmitters are biologically produced gaseous signalling molecules. As gases with potent biological activities, they are toxic as air pollutants, and the sulfurous compounds are used as fumigants. Most investigations focus on medical aspects of gasotransmitter biology rather than toxicity toward invertebrate pests of agriculture. In fact, the pathways for the metabolism of sulfur containing gases in lower organisms have not yet been described. To address this deficit, we use protein sequences from Homo sapiens to query Genbank for homologous proteins in Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. In C. elegans, we find genes for all mammalian pathways for synthesis and catabolism of the three sulfur containing gasotransmitters, H2S, SO2 and COS. The genes for H2S synthesis have actually increased in number in C. elegans. Interestingly, D. melanogaster and Arthropoda in general, lack a gene for 3-mercaptopyruvate sulfurtransferase, an enzym for H2S synthesis under reducing conditions.
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Hébert A, Forquin-Gomez MP, Roux A, Aubert J, Junot C, Loux V, Heilier JF, Bonnarme P, Beckerich JM, Landaud S. Exploration of sulfur metabolism in the yeast Kluyveromyces lactis. Appl Microbiol Biotechnol 2011; 91:1409-23. [DOI: 10.1007/s00253-011-3481-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/29/2011] [Accepted: 07/13/2011] [Indexed: 10/17/2022]
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Uzunov ZG, Petrova VY, Ivanov SL, Kujumdzieva AV. In SilicoStudy of Aro Genes Involved in the Ehrlich Pathway: Comparison between Saccharomyces Cerevisiaeand Kluyveromyces Lactis. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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