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Farofonova V, Andreeva N, Kulakovskaya E, Karginov A, Agaphonov M, Kulakovskaya T. Multiple effects of the PHO91 gene knockout in Ogataea parapolymorpha. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01039-x. [PMID: 36753030 DOI: 10.1007/s12223-023-01039-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
Pho91 is a vacuolar phosphate transporter that exports phosphate from the vacuolar lumen to the cytosol in yeast cells. In this study, we have demonstrated the pleiotropic effects of the PHO91 gene knockout in the methylotrophic yeast Ogataea parapolymorpha (Hansenula polymorpha, Ogataea angusta). The content of both acid-soluble and acid-insoluble inorganic polyphosphate (polyP) in the ∆pho91 cells was slightly higher compared to the strain with wild-type PHO91, when the cells were cultivated on glucose. The pho91-Δ mutations both in O. parapolymorpha and in Saccharomyces cerevisiae diminished resistance to cadmium and increased resistance to manganese and peroxide stresses. The cells of the mutant strain of O. parapolymorpha were unable to consume methanol due to the lack of methanol oxidase activity. We speculate that these effects are associated with the inability of mutant cells to mobilize phosphate from the vacuolar pool and/or defects in the signaling pathways involving phosphate, polyP, and inositol polyphosphates.
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Affiliation(s)
- Vasilina Farofonova
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russian Federation.,Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Russian Federation
| | - Nadeshda Andreeva
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russian Federation
| | - Ekaterina Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russian Federation
| | - Azamat Karginov
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Michael Agaphonov
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Tatiana Kulakovskaya
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Russian Federation.
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Kulakova MV, Karginov AV, Alexandrov AI, Agaphonov MO. The GEM-GECO Calcium Indicator Is Useable in Ogataea parapolymorpha Yeast, but Aggravates Effects of Increased Cytosolic Calcium Levels. Int J Mol Sci 2022; 23:ijms231710004. [PMID: 36077401 PMCID: PMC9456557 DOI: 10.3390/ijms231710004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
Ca2+ is a ubiquitous second messenger, which allows eukaryotic cells to respond to external stimuli. The use of genetically encoded Ca2+ indicators allows real-time monitoring of cytosolic Ca2+ levels to study such responses. Here we explored the possibility of using the ratiometric Ca2+ indicator GEM-GECO for monitoring cytosolic Ca2+ concentration ([Ca2+]cyt) in the yeast Ogataea parapolymorpha. High-level production of GEM-GECO led to a severe growth defect in cells lacking the vacuolar Ca2+ ATPase Pmc1, which is involved in [Ca2+]cyt control, and prompted a phenotype resembling that of Pmc1 deficiency, in a strain with wild-type PMC1. This was likely due to the presence of the calmodulin domain in GEM-GECO. In contrast to previous studies of genetically-encoded calcium indicators in neuronal cells, our results suggest that physiological effects of GEM-GECO expression in yeast cells are due not to Ca2+ depletion, but to excessive Ca2+ signaling. Despite these drawbacks, study of fluorescence in individual cells revealed switching of GEM-GECO from the Ca2+-free to Ca2+-bound state minutes after external addition of CaCl2. This was followed by gradual return of GEM-GECO to a Ca2+-free-state that was impaired in the pmc1-Δ mutant. These results demonstrate GEM-GECO usability for [Ca2+]cyt monitoring in budding yeast.
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Manfrão-Netto JHC, Gomes AMV, Parachin NS. Advances in Using Hansenula polymorpha as Chassis for Recombinant Protein Production. Front Bioeng Biotechnol 2019; 7:94. [PMID: 31119131 PMCID: PMC6504786 DOI: 10.3389/fbioe.2019.00094] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/16/2019] [Indexed: 11/13/2022] Open
Abstract
The methylotrophic yeast Hansenula polymorpha, known as a non-conventional yeast, is used for the last 30 years for the production of recombinant proteins, including enzymes, vaccines, and biopharmaceuticals. Although a large number of reviews have been published elucidating the applications of this yeast as a cell factory, the latest was released about 10 years ago. Therefore, this review aimed at summarizing available information on the use of H. polymorpha as a host for recombinant protein production in the last decade. Examples of chemicals and virus-like particles produced using this yeast also are discussed. Firstly, the aspects that feature this yeast as a host for recombinant protein production are highlighted including the techniques available for its genetic manipulation as well as strategies for cultivation in bioreactors. Special attention is given to the novel genomic editing tools, mainly CRISPR/Cas9 that was recently established in this yeast. Finally, recent examples of using H. polymorpha as an expression platform are presented and discussed. The production of human Parathyroid Hormone (PTH) and Staphylokinase (SAK) in H. polymorpha are described as case studies for process establishment in this yeast. Altogether, this review is a guideline for this yeast utilization as an expression platform bringing a thorough analysis of the genetic aspects and fermentation protocols used up to date, thus encouraging the production of novel biomolecules in H. polymorpha.
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Affiliation(s)
| | - Antônio Milton Vieira Gomes
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil
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Karginov AV, Fokina AV, Kang HA, Kalebina TS, Sabirzyanova TA, Ter-Avanesyan MD, Agaphonov MO. Dissection of differential vanadate sensitivity in two Ogataea species links protein glycosylation and phosphate transport regulation. Sci Rep 2018; 8:16428. [PMID: 30401924 PMCID: PMC6219546 DOI: 10.1038/s41598-018-34888-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/24/2018] [Indexed: 11/08/2022] Open
Abstract
The closely related yeasts Ogataea polymorpha and O. parapolymorpha differ drastically from each other by sensitivity to the toxic phosphate analog vanadate. Search for genes underlying this difference revealed two genes, one designated as ABV1 (Alcian Blue staining, Vanadate resistance), which encodes a homologue of Saccharomyces cerevisiae Mnn4 responsible for attachment of mannosylphosphate to glycoside chains of secretory proteins, and the other designated as its S. cerevisiae homologue PHO87, encoding the plasma membrane low affinity phosphate sensor/transporter. The effect of Pho87 on vanadate resistance was bidirectional, since it decreased the resistance on phosphate-depleted medium, but was required for pronounced protection against vanadate by external phosphate. This highlights the dual function of this protein as a low affinity phosphate transporter and an external phosphate sensor. Involvement of Pho87 in phosphate sensing was confirmed by its effects on regulation of the promoter of the PHO84 gene, encoding a high affinity phosphate transporter. The effect of Abv1 was also complex, since it influenced Pho87 level and enhanced repression of the PHO84 promoter via a Pho87-independent pathway. Role of the identified genes in the difference in vanadate resistance between O. polymorpha and O. parapolymorpha is discussed.
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Affiliation(s)
- Azamat V Karginov
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Anastasia V Fokina
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Tatyana S Kalebina
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Tatyana A Sabirzyanova
- Department of Molecular Biology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation
| | - Michael O Agaphonov
- Bach Institute of Biochemistry, Research Center of Biotechnology RAS, Moscow, Russian Federation.
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Unrestrained markerless trait stacking in Nannochloropsis gaditana through combined genome editing and marker recycling technologies. Proc Natl Acad Sci U S A 2018; 115:E7015-E7022. [PMID: 29987047 PMCID: PMC6065045 DOI: 10.1073/pnas.1718193115] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Stacking traits in microalgae is limited by a lack of robust genome modification tools and selectable marker availability. This presents a key hurdle in developing strains for renewable products including biofuels. Here, we overcome these limitations by combining inducible Cre recombinase with constitutive Cas9 nuclease expression in the industrial strain, Nannochloropsis gaditana. With this system, we demonstrate marker- and reporter-free recapitulation of an important lipid productivity trait. In addition, we generate a strain harboring seven-gene knockouts within the photosystem antennae encoding genes. The combined use of relatively mature (Cre) and emerging (CAS9) genome modification technologies can thus accelerate the pace of industrial strain development and facilitate basic research into functionally redundant gene families. Robust molecular tool kits in model and industrial microalgae are key to efficient targeted manipulation of endogenous and foreign genes in the nuclear genome for basic research and, as importantly, for the development of algal strains to produce renewable products such as biofuels. While Cas9-mediated gene knockout has been demonstrated in a small number of algal species with varying efficiency, the ability to stack traits or generate knockout mutations in two or more loci are often severely limited by selectable agent availability. This poses a critical hurdle in developing production strains, which require stacking of multiple traits, or in probing functionally redundant gene families. Here, we combine Cas9 genome editing with an inducible Cre recombinase in the industrial alga Nannochloropsis gaditana to generate a strain, NgCas9+Cre+, in which the potentially unlimited stacking of knockouts and addition of new genes is readily achievable. Cre-mediated marker recycling is first demonstrated in the removal of the selectable marker and GFP reporter transgenes associated with the Cas9/Cre construct in NgCas9+Cre+. Next, we show the proof-of-concept generation of a markerless knockout in a gene encoding an acyl-CoA oxidase (Aco1), as well as the markerless recapitulation of a 2-kb insert in the ZnCys gene 5′-UTR, which results in a doubling of wild-type lipid productivity. Finally, through an industrially oriented process, we generate mutants that exhibit up to ∼50% reduction in photosynthetic antennae size by markerless knockout of seven genes in the large light-harvesting complex gene family.
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Li D, Zhang B, Li S, Zhou J, Cao H, Huang Y, Cui Z. A Novel Vector for Construction of Markerless Multicopy Overexpression Transformants in Pichia pastoris. Front Microbiol 2017; 8:1698. [PMID: 28955309 PMCID: PMC5601908 DOI: 10.3389/fmicb.2017.01698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/23/2017] [Indexed: 01/08/2023] Open
Abstract
Pichia pastoris is widely used as a platform for heterologous protein expression because of its high volumetric productivity. Multicopy integration of the target gene is commonly used to improve the production of the target protein. Cre/lox recombination system is a powerful tool for the marker rescue during multiple integrations with one selection marker. Here we reported a novel expression vector based on the Cre/lox recombination system for multiple integrations of target gene to construct multicopy expression strain of P. pastoris. PAOX1 promoter was fused to cre to construct a methanol inducible Cre recombinase. The leakage expression of Cre recombinase in Escherichia coli was blocked by introducing the operator gene lacO. The expression vector designed pMCO-AOXα was stable in E. coli and could effectively rescue the Zeocin resistance gene for next round of integration in P. pastoris. Phytase AppA from E. coli was chosen as a reporter gene. Transformants with 2-16 copies of appA were constructed by using a single antibiotic. Expression of appA was gene dosage dependent when <12 copies were integrated. The protein yield increased 4.45-folds when 12 copies of appA were integrated comparing with the single copy integration. Our results showed that pMCO-AOXα was highly effective for rational construction of multicopy transformat in P. pastoris.
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Affiliation(s)
- Ding Li
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Bo Zhang
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Shuting Li
- College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Jie Zhou
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
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Fokina AV, Chechenova MB, Karginov AV, Ter-Avanesyan MD, Agaphonov MO. Genetic Evidence for the Role of the Vacuole in Supplying Secretory Organelles with Ca2+ in Hansenula polymorpha. PLoS One 2015; 10:e0145915. [PMID: 26717478 PMCID: PMC4696657 DOI: 10.1371/journal.pone.0145915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/10/2015] [Indexed: 11/18/2022] Open
Abstract
Processes taking place in the secretory organelles require Ca2+ and Mn2+, which in yeast are supplied by the Pmr1 ion pump. Here we observed that in the yeast Hansenula polymorpha Ca2+ deficiency in the secretory pathway caused by Pmr1 inactivation is exacerbated by (i) the ret1-27 mutation affecting COPI-mediated vesicular transport, (ii) inactivation of the vacuolar Ca2+ ATPase Pmc1 and (iii) inactivation of Vps35, which is a component of the retromer complex responsible for protein transport between the vacuole and secretory organelles. The ret1-27 mutation also exerted phenotypes indicating alterations in transport between the vacuole and secretory organelles. These data indicate that ret1-27, pmc1 and vps35 affect a previously unknown Pmr1-independent route of the Ca2+ delivery to the secretory pathway. We also observed that the vacuolar protein carboxypeptidase Y receives additional modifications of its glycoside chains if it escapes the Vps10-dependent sorting to the vacuole.
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Affiliation(s)
- Anastasia V. Fokina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria B. Chechenova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Azamat V. Karginov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Michael D. Ter-Avanesyan
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Michael O. Agaphonov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Serpionov GV, Alexandrov AI, Antonenko YN, Ter-Avanesyan MD. A protein polymerization cascade mediates toxicity of non-pathological human huntingtin in yeast. Sci Rep 2015; 5:18407. [PMID: 26673834 PMCID: PMC4682096 DOI: 10.1038/srep18407] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022] Open
Abstract
Several neurodegenerative amyloidoses, including Huntington disease, are caused by expansion of polyglutamine (polyQ) stretches in otherwise unrelated proteins. In a yeast model, an N-terminal fragment of mutant huntingtin with a stretch of 103 glutamine residues aggregates and causes toxicity, while its non-toxic wild type variant with a sequence of 25 glutamines (Htt25Q) does not aggregate. Here, we observed that non-toxic polymers of various proteins with glutamine-rich domains could seed polymerization of Htt25Q, which caused toxicity by seeding polymerization of the glutamine/asparagine-rich Sup35 protein thus depleting the soluble pools of this protein and its interacting partner, Sup45. Importantly, only polymers of Htt25Q, but not of the initial benign polymers, induced Sup35 polymerization, indicating an intermediary role of Htt25Q in cross-seeding Sup35 polymerization. These data provide a novel insight into interactions between amyloidogenic proteins and suggest a possible role for these interactions in the pathogenesis of Huntington and other polyQ diseases.
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Affiliation(s)
- Genrikh V Serpionov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Alexander I Alexandrov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gori, 1, bldg. 40, Moscow 119991, Russia
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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