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Knight A, Piskacek M. Cryptic inhibitory regions nearby activation domains. Biochimie 2022; 200:19-26. [PMID: 35561946 DOI: 10.1016/j.biochi.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
Previously, the Nine amino acid TransActivation Domain (9aaTAD) was identified in the Gal4 region 862-870 (DDVYNYLFD). Here, we identified 9aaTADs in the distal Gal4 orthologs by our prediction algorithm and found their conservation in the family. The 9aaTAD function as strong activators was demonstrated. We identified adjacent Gal4 region 871-811 (DEDTPPNPKKE) as a natural 9aaTAD inhibitory domain located at the extreme Gal4 terminus. Moreover, we identified conserved Gal4 region 172-185 (FDWSEEDDMSDGLP), which was capable to reverse the 9aaTAD inhibition. In conclusion, our results uncover the existence of the cryptic inhibitory domains, which need to be carefully implemented in all functional studies with transcription factors to avoid incorrect conclusions.
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Affiliation(s)
- Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.
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Choi JY, Hwang HJ, Cho WY, Choi JI, Lee PC. Differences in the Fatty Acid Profile, Morphology, and Tetraacetylphytosphingosine-Forming Capability Between Wild-Type and Mutant Wickerhamomyces ciferrii. Front Bioeng Biotechnol 2021; 9:662979. [PMID: 34178960 PMCID: PMC8220092 DOI: 10.3389/fbioe.2021.662979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
One tetraacetylphytosphingosine (TAPS)-producing Wickerhamomyces ciferrii mutant was obtained by exposing wild-type W. ciferrii to γ-ray irradiation. The mutant named 736 produced up to 9.1 g/L of TAPS (218.7 mg-TAPS/g-DCW) during batch fermentation in comparison with 1.7 g/L of TAPS (52.2 mg-TAPS/g-DCW) for the wild type. The highest production, 17.7 g/L of TAPS (259.6 mg-TAPS/g-DCW), was obtained during fed-batch fermentation by mutant 736. Fatty acid (FA) analysis revealed an altered cellular FA profile of mutant 736: decrease in C16:0 and C16:1 FA levels, and increase in C18:1 and C18:2 FA levels. Although a significant change in the cellular FA profile was observed, scanning electron micrographs showed that morphology of wild-type and mutant 736 cells was similar. Genetic alteration analysis of eight TAPS biosynthesis-related genes revealed that there are no mutations in these genes in mutant 736; however, mRNA expression analysis indicated 30% higher mRNA expression of TCS10 among the eight genes in mutant 736 than that in the wild-type. Collectively, these results imply that the enhancement of TAPS biosynthesis in mutant 736 may be a consequence of system-level genetic and physiological alterations of a complicated metabolic network. Reverse metabolic engineering based on system-level omics analysis of mutant 736 can make the mutant more suitable for commercial production of TAPS.
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Affiliation(s)
- Jun Young Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Hee Jin Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Woo Yeon Cho
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, South Korea
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea.,Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
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Sousa-Silva M, Vieira D, Soares P, Casal M, Soares-Silva I. Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii. J Fungi (Basel) 2021; 7:36. [PMID: 33435379 PMCID: PMC7827542 DOI: 10.3390/jof7010036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.
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Affiliation(s)
- Maria Sousa-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Daniel Vieira
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Margarida Casal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
| | - Isabel Soares-Silva
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (M.S.-S.); (D.V.); (P.S.); (M.C.)
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
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Bae JH, Kim IH, Lee KT, Hou CT, Kim HR. Molecular cloning and characterization of a novel cold-active lipase from Pichia lynferdii NRRL Y-7723. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Pryszcz LP, Gabaldón T. Redundans: an assembly pipeline for highly heterozygous genomes. Nucleic Acids Res 2016; 44:e113. [PMID: 27131372 PMCID: PMC4937319 DOI: 10.1093/nar/gkw294] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/06/2016] [Indexed: 11/14/2022] Open
Abstract
Many genomes display high levels of heterozygosity (i.e. presence of different alleles at the same loci in homologous chromosomes), being those of hybrid organisms an extreme such case. The assembly of highly heterozygous genomes from short sequencing reads is a challenging task because it is difficult to accurately recover the different haplotypes. When confronted with highly heterozygous genomes, the standard assembly process tends to collapse homozygous regions and reports heterozygous regions in alternative contigs. The boundaries between homozygous and heterozygous regions result in multiple assembly paths that are hard to resolve, which leads to highly fragmented assemblies with a total size larger than expected. This, in turn, causes numerous problems in downstream analyses such as fragmented gene models, wrong gene copy number, or broken synteny. To circumvent these caveats we have developed a pipeline that specifically deals with the assembly of heterozygous genomes by introducing a step to recognise and selectively remove alternative heterozygous contigs. We tested our pipeline on simulated and naturally-occurring heterozygous genomes and compared its accuracy to other existing tools. Our method is freely available at https://github.com/Gabaldonlab/redundans.
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Affiliation(s)
- Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Genomics and the making of yeast biodiversity. Curr Opin Genet Dev 2015; 35:100-9. [PMID: 26649756 DOI: 10.1016/j.gde.2015.10.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 12/22/2022]
Abstract
Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies.
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Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP. Clade- and species-specific features of genome evolution in the Saccharomycetaceae. FEMS Yeast Res 2015; 15:fov035. [PMID: 26066552 PMCID: PMC4629796 DOI: 10.1093/femsyr/fov035] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 12/12/2022] Open
Abstract
Many aspects of the genomes of yeast species in the family Saccharomycetaceae have been well conserved during evolution. They have similar genome sizes, genome contents, and extensive collinearity of gene order along chromosomes. Gene functions can often be inferred reliably by using information from Saccharomyces cerevisiae. Beyond this conservative picture however, there are many instances where a species or a clade diverges substantially from the S. cerevisiae paradigm—for example, by the amplification of a gene family, or by the absence of a biochemical pathway or a protein complex. Here, we review clade-specific features, focusing on genomes sequenced in our laboratory from the post-WGD genera Naumovozyma, Kazachstania and Tetrapisispora, and from the non-WGD species Torulaspora delbrueckii. Examples include the loss of the pathway for histidine synthesis in the cockroach-associated species Tetrapisispora blattae; the presence of a large telomeric GAL gene cluster in To. delbrueckii; losses of the dynein and dynactin complexes in several independent yeast lineages; fragmentation of the MAT locus and loss of the HO gene in Kazachstania africana; and the patchy phylogenetic distribution of RNAi pathway components. The authors review species-specific evolutionary attributes of yeast genomes.
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Affiliation(s)
- Kenneth H Wolfe
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - David Armisén
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Institut de Génomique Fonctionnelle de Lyon, ENS de Lyon - CNRS UMR 5242 - INRA USC 1370, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Estelle Proux-Wera
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Science for Life Laboratory, Dept. of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Seán S ÓhÉigeartaigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Centre for the Study of Existential Risk, University of Cambridge, CRASSH, Alison Richard Building, 7 West Road, Cambridge, CB3 9DT, UK
| | - Haleema Azam
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jonathan L Gordon
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland CIRAD, UMR CMAEE, Site de Duclos, Prise d'eau, F-97170, Petit-Bourg, Guadeloupe, France
| | - Kevin P Byrne
- UCD Conway Institute, School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
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Genome Sequence of the Yeast Cyberlindnera fabianii (Hansenula fabianii). GENOME ANNOUNCEMENTS 2014; 2:2/4/e00638-14. [PMID: 25103752 PMCID: PMC4125763 DOI: 10.1128/genomea.00638-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The yeast Cyberlindnera fabianii is used in wastewater treatment, fermentation of alcoholic beverages, and has caused blood infections. To assist in the accurate identification of this species, and to determine the genetic basis for properties involved in fermentation and water treatment, we sequenced and annotated the genome of C. fabianii (YJS4271).
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Biotechnological production of sphingoid bases and their applications. Appl Microbiol Biotechnol 2013; 97:4301-8. [DOI: 10.1007/s00253-013-4878-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/22/2013] [Accepted: 03/22/2013] [Indexed: 12/14/2022]
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Wolff D, ter Veld F, Köhler T, Poetsch A. Combined application of targeted and untargeted proteomics identifies distinct metabolic alterations in the tetraacetylphytosphingosine (TAPS) producing yeast Wickerhamomyces ciferrii. J Proteomics 2013; 82:274-87. [PMID: 23500128 DOI: 10.1016/j.jprot.2013.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 02/26/2013] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
Abstract
UNLABELLED The Wickerhamomyces ciferrii strain NRRL Y-1031 F-60-10A is a well-known producer of tetraacetylphytosphingosine (TAPS) and used for the biotechnological production of sphingolipids and ceramides. It was our aim to gain new biological insights into the sphingolipid metabolism by employing a dual platform mass spectrometry strategy. The first step comprised metabolic (15)N-labeling in combination with label-free proteomics using high resolution LTQ Orbitrap mass spectrometry. Then selected reaction monitoring tandem mass spectrometry served for the targeted quantification of sphingoid base biosynthesis enzymes. The non-producer strain NRRL Y-1031-27 served as a reference strain. In total, 1697 proteins were identified, and 123 enzymes of main metabolic pathways were observed as differentially expressed. Major findings were: 1) the likely presence of higher carbon flux in NRRL Y-1031 F-60-10A, resulting in higher availability of pyruvate and acetyl-CoA; 2) indications of oleaginous yeast-like behavior in NRRL Y-1031 F-60-10A; and 3) approx. 2-fold higher abundance of eight sphingolipid biosynthesis enzymes in NRRL Y-1031 F-60-10A. Taken together, in NRRL Y-1031 F-60-10A, the levels of glycolytic enzymes apparently gear carbon flux towards higher acetyl-CoA synthesis rates, while simultaneously reducing protein biosynthesis in the process. Thereby, C2 building blocks for acyl-moieties and downstream sphingoid base acetylation are provided to maintain TAPS production. BIOLOGICAL SIGNIFICANCE First quantitative proteome study for a phytosphingosine-producing yeast.
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Affiliation(s)
- Daniel Wolff
- Dept. of Plant Biochemistry, Ruhr-University Bochum, D-44801 Bochum, Germany
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Production of tetraacetyl phytosphingosine (TAPS) in Wickerhamomyces ciferrii is catalyzed by acetyltransferases Sli1p and Atf2p. Appl Microbiol Biotechnol 2013; 97:8537-46. [PMID: 23318835 DOI: 10.1007/s00253-012-4670-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/03/2012] [Accepted: 12/19/2012] [Indexed: 10/27/2022]
Abstract
Wickerhamomyces ciferrii secretes tetraacetyl phytosphingosine (TAPS), and in this study, the catalyzing acetyltransferases were identified using mass spectrometry-based proteomics. The proteome of wild-type strain NRRL Y-1031 served as control and was compared to the tetraacetyl phytosphingosine defective mating type NRRL Y-1031-27. Acetylation of phytosphingosine in W. ciferrii is catalyzed by acetyltransferases Sli1p and Atf2p, encoded by genes similar to Saccharomyces cerevisiae YGR212W and YGR177C, respectively. Ablation of SLI1 resulted in an almost complete loss of tri- and tetraacetyl phytosphingosines, whereas the loss ATF2 resulted in an 15-fold increase in triacetyl phytosphingosine. Most likely, it is the concerted action of these two acetyltransferases that yields tetraacetyl phytosphingosine, in which Sli1p catalyzes initial O- and N-acetylation, producing triacetyl phytosphingosine. Finally, Atf2p catalyzes final O-acetylation to yield tetraacetyl phytosphingosine. The current study demonstrates that mass spectrometry-based proteomics can be employed to identify key steps in ill-explored metabolite biosynthesis pathways of nonconventional microorganisms. Furthermore, the identification of phytosphingosine as substrate for alcohol acetyltransferase Atf2p broadens the known substrate range of this enzyme. This interesting property of Atf2p may be exploited to enhance the secretion of heterologous compounds.
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