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Kaur J, Tiwari N, Asif MH, Dharmesh V, Naseem M, Srivastava PK, Srivastava S. Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133954. [PMID: 38484657 DOI: 10.1016/j.jhazmat.2024.133954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 04/07/2024]
Abstract
Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.
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Affiliation(s)
- Jasvinder Kaur
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Nikita Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Mehar Hasan Asif
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Varsha Dharmesh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mariya Naseem
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Pankaj Kumar Srivastava
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suchi Srivastava
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Abstract
Hypersaline waters and glacial ice are inhospitable environments that have low water activity and high concentrations of osmolytes. They are inhabited by diverse microbial communities, of which extremotolerant and extremophilic fungi are essential components. Some fungi are specialized in only one of these two environments and can thrive in conditions that are lethal to most other life-forms. Others are generalists, highly adaptable species that occur in both environments and tolerate a wide range of extremes. Both groups efficiently balance cellular osmotic pressure and ion concentration, stabilize cell membranes, remodel cell walls, and neutralize intracellular oxidative stress. Some species use unusual reproductive strategies. Further investigation of these adaptations with new methods and carefully designed experiments under ecologically relevant conditions will help predict the role of fungi in hypersaline and glacial environments affected by climate change, decipher their stress resistance mechanisms and exploit their biotechnological potential.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ,
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3
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Ochoa-Gutiérrez D, Reyes-Torres AM, de la Fuente-Colmenares I, Escobar-Sánchez V, González J, Ortiz-Hernández R, Torres-Ramírez N, Segal-Kischinevzky C. Alternative CUG Codon Usage in the Halotolerant Yeast Debaryomyces hansenii: Gene Expression Profiles Provide New Insights into Ambiguous Translation. J Fungi (Basel) 2022; 8:jof8090970. [PMID: 36135695 PMCID: PMC9502446 DOI: 10.3390/jof8090970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 12/04/2022] Open
Abstract
The halotolerant yeast Debaryomyces hansenii belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine–serine ambiguity in cellular adaptations to extreme environments. Here, we examine sequences and structures of tRNACAG from the CTG-Ser1 clade yeasts, finding that D. hansenii conserves the elements to translate ambiguously. Then, we show that D. hansenii has tolerance to conditions of salinity, acidity, alkalinity, and oxidative stress associated with phenotypic and ultrastructural changes. In these conditions, we found differential expression in both the logarithmic and stationary growth phases of tRNASer, tRNALeu, tRNACAG, LeuRS, and SerRS genes that could be involved in the adaptive process of this yeast. Finally, we compare the proteomic isoelectric points and hydropathy profiles, detecting that the most important variations among the physicochemical characteristics of D. hansenii proteins are in their hydrophobic and hydrophilic interactions with the medium. We propose that the ambiguous translation, i.e., leucylation or serynation, on translation of the CUG-encoded residues, could be linked to adaptation processes in extreme environments.
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Affiliation(s)
- Daniel Ochoa-Gutiérrez
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Anya M. Reyes-Torres
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Ileana de la Fuente-Colmenares
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Viviana Escobar-Sánchez
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - James González
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Rosario Ortiz-Hernández
- Laboratorio de Microscopía Electrónica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Nayeli Torres-Ramírez
- Laboratorio de Microscopía Electrónica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Claudia Segal-Kischinevzky
- Laboratorio de Biología Molecular y Genómica, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad # 3000, Cd. Universitaria, Coyoacán, Mexico City 04510, Mexico
- Correspondence:
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4
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Ribeiro RA, Bourbon-Melo N, Sá-Correia I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front Microbiol 2022; 13:953479. [PMID: 35966694 PMCID: PMC9366716 DOI: 10.3389/fmicb.2022.953479] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.
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Affiliation(s)
- Ricardo A. Ribeiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Rodríguez-Pupo EC, Pérez-Llano Y, Tinoco-Valencia JR, Sánchez NS, Padilla-Garfias F, Calahorra M, Sánchez NDC, Sánchez-Reyes A, Rodríguez-Hernández MDR, Peña A, Sánchez O, Aguirre J, Batista-García RA, Folch-Mallol JL, Sánchez-Carbente MDR. Osmolyte Signatures for the Protection of Aspergillus sydowii Cells under Halophilic Conditions and Osmotic Shock. J Fungi (Basel) 2021; 7:414. [PMID: 34073303 PMCID: PMC8228332 DOI: 10.3390/jof7060414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus sydowii is a moderate halophile fungus extensively studied for its biotechnological potential and halophile responses, which has also been reported as a coral reef pathogen. In a recent publication, the transcriptomic analysis of this fungus, when growing on wheat straw, showed that genes related to cell wall modification and cation transporters were upregulated under hypersaline conditions but not under 0.5 M NaCl, the optimal salinity for growth in this strain. This led us to study osmolyte accumulation as a mechanism to withstand moderate salinity. In this work, we show that A. sydowii accumulates trehalose, arabitol, mannitol, and glycerol with different temporal dynamics, which depend on whether the fungus is exposed to hypo- or hyperosmotic stress. The transcripts coding for enzymes responsible for polyalcohol synthesis were regulated in a stress-dependent manner. Interestingly, A. sydowii contains three homologs (Hog1, Hog2 and MpkC) of the Hog1 MAPK, the master regulator of hyperosmotic stress response in S. cerevisiae and other fungi. We show a differential regulation of these MAPKs under different salinity conditions, including sustained basal Hog1/Hog2 phosphorylation levels in the absence of NaCl or in the presence of 2.0 M NaCl, in contrast to what is observed in S. cerevisiae. These findings indicate that halophilic fungi such as A. sydowii utilize different osmoadaptation mechanisms to hypersaline conditions.
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Affiliation(s)
- Eya Caridad Rodríguez-Pupo
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
- Centro de Investigación en Dinámica Celular, IICBA, UAEM, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico;
| | - Yordanis Pérez-Llano
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
- Centro de Investigación en Dinámica Celular, IICBA, UAEM, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico;
| | - José Raunel Tinoco-Valencia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Campus Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico;
| | - Norma Silvia Sánchez
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Francisco Padilla-Garfias
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Martha Calahorra
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Nilda del C. Sánchez
- Centro de Ciencias Genómicas, UNAM, Campus Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico;
| | - Ayixón Sánchez-Reyes
- Catedras Conacyt-Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Campus Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico;
| | - María del Rocío Rodríguez-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
| | - Antonio Peña
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Olivia Sánchez
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Jesús Aguirre
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, UAEM, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico;
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
| | - María del Rayo Sánchez-Carbente
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
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6
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González J, Castillo R, García-Campos MA, Noriega-Samaniego D, Escobar-Sánchez V, Romero-Aguilar L, Alba-Lois L, Segal-Kischinevzky C. Tolerance to Oxidative Stress in Budding Yeast by Heterologous Expression of Catalases A and T from Debaryomyces hansenii. Curr Microbiol 2020; 77:4000-4015. [PMID: 33064189 DOI: 10.1007/s00284-020-02237-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/01/2020] [Indexed: 01/24/2023]
Abstract
The function of catalases A and T from the budding yeast Saccharomyces cerevisiae (ScCta1 and ScCtt1) is to decompose hydrogen peroxide (H2O2) to mitigate oxidative stress. Catalase orthologs are widely found in yeast, suggesting that scavenging H2O2 is crucial to avoid the oxidative damage caused by reactive oxygen species (ROS). However, the function of catalase orthologs has not yet been experimentally characterized in vivo. Here, we heterologously expressed Debaryomyces hansenii DhCTA1 and DhCTT1 genes, encoding ScCta1 and ScCtt1 orthologs, respectively, in a S. cerevisiae acatalasemic strain (cta1Δ ctt1Δ). We performed a physiological analysis evaluating growth, catalase activity, and H2O2 tolerance of the strains grown with glucose or ethanol as carbon source, as well as under NaCl stress. We found that both genes complement the catalase function in S. cerevisiae. Particularly, the strain harboring DhCTT1 showed improved growth when ethanol was used as carbon source both in the absence or presence of salt stress. This phenotype is attributed to the high catalase activity of DhCtt1 detected at the exponential growth phase, which prevents intracellular ROS accumulation and confers oxidative stress resistance.
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Affiliation(s)
- James González
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Román Castillo
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Miguel Angel García-Campos
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Diego Noriega-Samaniego
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Viviana Escobar-Sánchez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Lucero Romero-Aguilar
- Departamento de Bioquímica, Facultad de Medicina, Facultad de Medicina, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Luisa Alba-Lois
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Claudia Segal-Kischinevzky
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México.
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7
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Nurcholis M, Lertwattanasakul N, Rodrussamee N, Kosaka T, Murata M, Yamada M. Integration of comprehensive data and biotechnological tools for industrial applications of Kluyveromyces marxianus. Appl Microbiol Biotechnol 2019; 104:475-488. [PMID: 31781815 DOI: 10.1007/s00253-019-10224-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/17/2022]
Abstract
Among the so-called non-conventional yeasts, Kluyveromyces marxianus has extremely potent traits that are suitable for industrial applications. Indeed, it has been used for the production of various enzymes, chemicals, and macromolecules in addition to utilization of cell biomass as nutritional materials, feed and probiotics. The yeast is expected to be an efficient ethanol producer with advantages over Saccharomyces cerevisiae in terms of high growth rate, thermotolerance and a wide sugar assimilation spectrum. Results of comprehensive analyses of its genome and transcriptome may accelerate studies for applications of the yeast and may further increase its potential by combination with recent biotechnological tools including the CRISPR/Cas9 system. We thus review published studies by merging with information obtained from comprehensive data including genomic and transcriptomic data, which would be useful for future applications of K. marxianus.
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Affiliation(s)
- Mochamad Nurcholis
- Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan.,Department of Food Science and Technology, Faculty of Agricultural Technology, Brawijaya University, Malang, 65145, Indonesia
| | - Noppon Lertwattanasakul
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Nadchanok Rodrussamee
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tomoyuki Kosaka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Masayuki Murata
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan.,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Mamoru Yamada
- Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan. .,Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8515, Japan. .,Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, 753-8515, Japan.
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8
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Nagy LG, Riley R, Bergmann PJ, Krizsán K, Martin FM, Grigoriev IV, Cullen D, Hibbett DS. Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution. Mol Biol Evol 2016; 34:35-44. [DOI: 10.1093/molbev/msw238] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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9
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Gumá-Cintrón Y, Bandyopadhyay A, Rosado W, Shu-Hu W, Nadathur GS. Transcriptomic analysis of cobalt stress in the marine yeast Debaryomyces hansenii. FEMS Yeast Res 2015; 15:fov099. [PMID: 26546454 DOI: 10.1093/femsyr/fov099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2015] [Indexed: 12/11/2022] Open
Abstract
The yeast Debaryomyces hansenii overproduces riboflavin upon exposure to subtoxic levels of cobalt (Co(+2)). However, mechanisms for survival have yet to be studied and have been hindered by D. hansenii's high genetic heterogeneity among strains. In this study, we used transcriptomic analyses and RNA-seq in order to identify differentially expressed genes in D. hansenii in response to cobalt exposure. Highly upregulated genes under this condition were identified to primarily comprise DNA damage and repair genes, oxidative stress response genes, and genes for cell wall integrity and growth. The main response of D. hansenii to heavy metal stress is the activation of non-enzymatic oxidative stress response mechanisms and control of biological production of reactive oxygen species. Our results indicate that D. hansenii does not seem to be pre-adapted to survive high concentrations of heavy metals. These organisms appear to possess genetic survival and detoxification mechanisms that enable the cells to recover from heavy metal stress.
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Affiliation(s)
- Yariela Gumá-Cintrón
- Department of Marine Science, University of Puerto Rico at Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Arpan Bandyopadhyay
- Department of Chemical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - William Rosado
- Department of Marine Science, University of Puerto Rico at Mayagüez, Mayagüez, PR 00681, Puerto Rico
| | - Wei Shu-Hu
- Department of Chemical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - G S Nadathur
- Department of Marine Science, University of Puerto Rico at Mayagüez, Mayagüez, PR 00681, Puerto Rico
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Calderón-Torres M, Castro DE, Montero P, Peña A. DhARO4 induction and tyrosine nitration in response to reactive radicals generated by salt stress in Debaryomyces hansenii. Yeast 2011; 28:733-46. [PMID: 21905093 DOI: 10.1002/yea.1903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 08/09/2011] [Indexed: 11/11/2022] Open
Affiliation(s)
- Marissa Calderón-Torres
- Unidad de Biomedicina, Facultad de Estudios Superiores-Iztacala; Universidad Nacional Autónoma de México; Av. De los Barrios #1, Col. Los Reyes Iztacala; Tlalnepantla; Estado de México, CP; 54090; Mexico
| | - Daniela E. Castro
- Departamento de Genética Molecular, Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; Circuito Exterior s/n; Ciudad Universitaria; DF; 04510; Mexico
| | - Paloma Montero
- Departamento de Genética Molecular, Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; Circuito Exterior s/n; Ciudad Universitaria; DF; 04510; Mexico
| | - Antonio Peña
- Departamento de Genética Molecular, Instituto de Fisiología Celular; Universidad Nacional Autónoma de México; Circuito Exterior s/n; Ciudad Universitaria; DF; 04510; Mexico
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Dragosits M, Stadlmann J, Graf A, Gasser B, Maurer M, Sauer M, Kreil DP, Altmann F, Mattanovich D. The response to unfolded protein is involved in osmotolerance of Pichia pastoris. BMC Genomics 2010; 11:207. [PMID: 20346137 PMCID: PMC2867824 DOI: 10.1186/1471-2164-11-207] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 03/26/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The effect of osmolarity on cellular physiology has been subject of investigation in many different species. High osmolarity is of importance for biotechnological production processes, where high cell densities and product titers are aspired. Several studies indicated that increased osmolarity of the growth medium can have a beneficial effect on recombinant protein production in different host organisms. Thus, the effect of osmolarity on the cellular physiology of Pichia pastoris, a prominent host for recombinant protein production, was studied in carbon limited chemostat cultures at different osmolarities. Transcriptome and proteome analyses were applied to assess differences upon growth at different osmolarities in both, a wild type strain and an antibody fragment expressing strain. While our main intention was to analyze the effect of different osmolarities on P. pastoris in general, this was complemented by studying it in context with recombinant protein production. RESULTS In contrast to the model yeast Saccharomyces cerevisiae, the main osmolyte in P. pastoris was arabitol rather than glycerol, demonstrating differences in osmotic stress response as well as energy metabolism. 2D Fluorescence Difference Gel electrophoresis and microarray analysis were applied and demonstrated that processes such as protein folding, ribosome biogenesis and cell wall organization were affected by increased osmolarity. These data indicated that upon increased osmolarity less adaptations on both the transcript and protein level occurred in a P. pastoris strain, secreting the Fab fragment, compared with the wild type strain. No transcriptional activation of the high osmolarity glycerol (HOG) pathway was observed at steady state conditions. Furthermore, no change of the specific productivity of recombinant Fab was observed at increased osmolarity. CONCLUSION These data point out that the physiological response to increased osmolarity is different to S. cerevisiae. Increased osmolarity resulted in an unfolded protein response (UPR) like response in P. pastoris and lead to pre-conditioning of the recombinant Fab producing strain of P. pastoris to growth at high osmolarity. The current data demonstrate a strong similarity of environmental stress response mechanisms and recombinant protein related stresses. Therefore, these results might be used in future strain and bioprocess engineering of this biotechnologically relevant yeast.
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Affiliation(s)
- Martin Dragosits
- Department of Biotechnology, BOKU-University of Natural Resources and Applied Life Sciences, Vienna, Austria
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van Zutphen T, Baerends RJS, Susanna KA, de Jong A, Kuipers OP, Veenhuis M, van der Klei IJ. Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis. BMC Genomics 2010; 11:1. [PMID: 20044946 PMCID: PMC2827406 DOI: 10.1186/1471-2164-11-1] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 01/04/2010] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Methylotrophic yeast species (e.g. Hansenula polymorpha, Pichia pastoris) can grow on methanol as sole source of carbon and energy. These organisms are important cell factories for the production of recombinant proteins, but are also used in fundamental research as model organisms to study peroxisome biology. During exponential growth on glucose, cells of H. polymorpha typically contain a single, small peroxisome that is redundant for growth while on methanol multiple, enlarged peroxisomes are present. These organelles are crucial to support growth on methanol, as they contain key enzymes of methanol metabolism.In this study, changes in the transcriptional profiles during adaptation of H. polymorpha cells from glucose- to methanol-containing media were investigated using DNA-microarray analyses. RESULTS Two hours after the shift of cells from glucose to methanol nearly 20% (1184 genes) of the approximately 6000 annotated H. polymorpha genes were significantly upregulated with at least a two-fold differential expression. Highest upregulation (> 300-fold) was observed for the genes encoding the transcription factor Mpp1 and formate dehydrogenase, an enzyme of the methanol dissimilation pathway. Upregulated genes also included genes encoding other enzymes of methanol metabolism as well as of peroxisomal beta-oxidation.A moderate increase in transcriptional levels (up to 4-fold) was observed for several PEX genes, which are involved in peroxisome biogenesis. Only PEX11 and PEX32 were higher upregulated. In addition, an increase was observed in expression of the several ATG genes, which encode proteins involved in autophagy and autophagy processes. The strongest upregulation was observed for ATG8 and ATG11.Approximately 20% (1246 genes) of the genes were downregulated. These included glycolytic genes as well as genes involved in transcription and translation. CONCLUSION Transcriptional profiling of H. polymorpha cells shifted from glucose to methanol showed the expected downregulation of glycolytic genes together with upregulation of the methanol utilisation pathway. This serves as a confirmation and validation of the array data obtained. Consistent with this, also various PEX genes were upregulated. The strong upregulation of ATG genes is possibly due to induction of autophagy processes related to remodeling of the cell architecture required to support growth on methanol. These processes may also be responsible for the enhanced peroxisomal beta-oxidation, as autophagy leads to recycling of membrane lipids. The prominent downregulation of transcription and translation may be explained by the reduced growth rate on methanol (td glucose 1 h vs td methanol 4.5 h).
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Affiliation(s)
- Tim van Zutphen
- Molecular Cell Biology, University of Groningen, Haren, the Netherlands
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