1
|
Fiamenghi MB, Prodonoff JS, Borelli G, Carazzolle MF, Pereira GAG, José J. Comparative genomics reveals probable adaptations for xylose use in Thermoanaerobacterium saccharolyticum. Extremophiles 2024; 28:9. [PMID: 38190047 DOI: 10.1007/s00792-023-01327-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Second-generation ethanol, a promising biofuel for reducing greenhouse gas emissions, faces challenges due to the inefficient metabolism of xylose, a pentose sugar. Overcoming this hurdle requires exploration of genes, pathways, and organisms capable of fermenting xylose. Thermoanaerobacterium saccharolyticum is an organism capable of naturally fermenting compounds of industrial interest, such as xylose, and understanding evolutionary adaptations may help to bring novel genes and information that can be used for industrial yeast, increasing production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations in Thermoanaerobacterium saccharolyticum that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose-binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improve Thermoanaerobacterium saccharolyticum as a new microbial cell factory, which may help to solve current problems found in the biofuels' industry.
Collapse
Affiliation(s)
- Mateus Bernabe Fiamenghi
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Juliana Silveira Prodonoff
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Guilherme Borelli
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimaraes Pereira
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil.
| | - Juliana José
- Laboratory of Genomics and bioEnergy (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, UNICAMP, Campinas, São Paulo, Brazil
| |
Collapse
|
2
|
Coradini ALV, da Silveira Bezerra de Mello F, Furlan M, Maneira C, Carazzolle MF, Pereira GAG, Teixeira GS. QTL mapping of a Brazilian bioethanol strain links the cell wall protein-encoding gene GAS1 to low pH tolerance in S. cerevisiae. Biotechnol Biofuels 2021; 14:239. [PMID: 34915919 PMCID: PMC8675505 DOI: 10.1186/s13068-021-02079-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae is largely applied in many biotechnological processes, from traditional food and beverage industries to modern biofuel and biochemicals factories. During the fermentation process, yeast cells are usually challenged in different harsh conditions, which often impact productivity. Regarding bioethanol production, cell exposure to acidic environments is related to productivity loss on both first- and second-generation ethanol. In this scenario, indigenous strains traditionally used in fermentation stand out as a source of complex genetic architecture, mainly due to their highly robust background-including low pH tolerance. RESULTS In this work, we pioneer the use of QTL mapping to uncover the genetic basis that confers to the industrial strain Pedra-2 (PE-2) acidic tolerance during growth at low pH. First, we developed a fluorescence-based high-throughput approach to collect a large number of haploid cells using flow cytometry. Then, we were able to apply a bulk segregant analysis to solve the genetic basis of low pH resistance in PE-2, which uncovered a region in chromosome X as the major QTL associated with the evaluated phenotype. A reciprocal hemizygosity analysis revealed the allele GAS1, encoding a β-1,3-glucanosyltransferase, as the casual variant in this region. The GAS1 sequence alignment of distinct S. cerevisiae strains pointed out a non-synonymous mutation (A631G) prevalence in wild-type isolates, which is absent in laboratory strains. We further showcase that GAS1 allele swap between PE-2 and a low pH-susceptible strain can improve cell viability on the latter of up to 12% after a sulfuric acid wash process. CONCLUSION This work revealed GAS1 as one of the main causative genes associated with tolerance to growth at low pH in PE-2. We also showcase how GAS1PE-2 can improve acid resistance of a susceptible strain, suggesting that these findings can be a powerful foundation for the development of more robust and acid-tolerant strains. Our results collectively show the importance of tailored industrial isolated strains in discovering the genetic architecture of relevant traits and its implications over productivity.
Collapse
Affiliation(s)
- Alessandro L V Coradini
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Fellipe da Silveira Bezerra de Mello
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Monique Furlan
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Marcelo F Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Gonçalo Amarante Guimaraes Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil.
| | - Gleidson Silva Teixeira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| |
Collapse
|
3
|
Moretti-Almeida G, Thomazella DPT, Pereira GAG, Monteiro G. Heterologous expression of an alternative oxidase from Moniliophthora perniciosa in Saccharomyces cerevisiae: Antioxidant function and in vivo platform for the study of new drugs against witches' broom disease. Fungal Genet Biol 2019; 126:50-55. [PMID: 30794952 DOI: 10.1016/j.fgb.2019.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 01/22/2019] [Accepted: 02/17/2019] [Indexed: 11/24/2022]
Abstract
The fungus Moniliophthora perniciosa is the causal agent of witches' broom disease (WBD), one of the most devastating diseases of cacao, the chocolate tree. Many strategies to control WBD have been tested so far, including the use of agrochemicals such as the strobilurins. Strobilurins are fungicides of the QoI family, and they are used in the control of a wide array of fungal diseases in many different crops, including cereals, field crops, fruits, tree nuts, and vegetables. These drugs act by specifically inhibiting fungal respiration at the Qo site of complex III, which is a component of the main mitochondrial respiratory chain. However, M. perniciosa is resistant to this family of chemicals. It has been postulated that this resistant phenotype is, at least in part, a result of the strong ability of this fungus to counteract the oxidative stress generated by the impairment of the main mitochondrial respiratory chain, through the activation of an alternative oxidase (Mp-AOX). To test this hypothesis, we expressed functional mitochondria-localized Mp-AOX in the model yeast Saccharomyces cerevisiae. We demonstrated that heterologous expression of Mp-AOX strongly inhibits hydrogen peroxide production by mitochondria. It also diminishes the total cell amount of oxidized glutathione (GSSG), resulting in a fifty-fold higher GSH/GSSG ratio in cells expressing Mp-AOX than in wild type cells. In addition, Mp-AOX activity decreases yeast growth rate and leads to low biomass production. Therefore, we propose the use of this heterologous expression system to direct the development of new inhibitors of fungal AOX by comparing the differences in optical density of Mp-AOX-expressing cells in the presence and absence of potential AOX inhibitors. Together, our results confirm the antioxidant role of Mp-AOX and provide an in vivo platform to be used in the screening of new fungicides based on Mp-AOX inhibition.
Collapse
Affiliation(s)
- G Moretti-Almeida
- Laboratório de Biologia Molecular e Biotecnologia Industrial de Microrganismos, Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil
| | - D P T Thomazella
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-970, Brazil; Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - G A G Pereira
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP 13083-970, Brazil
| | - G Monteiro
- Laboratório de Biologia Molecular e Biotecnologia Industrial de Microrganismos, Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP 05508-000, Brazil.
| |
Collapse
|
4
|
Salazar MM, Nascimento LC, Camargo ELO, Vidal RO, Lepikson-Neto J, Goncalves DC, Marques WL, Teixeira PJSL, Pereira GAG. Comparative transcriptome analysis of tree Eucalyptusspecies using RNAseq technology: analysis of genes interfering in wood quality aspects. BMC Proc 2011. [PMCID: PMC3240025 DOI: 10.1186/1753-6561-5-s7-p175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
5
|
Judice CC, Carazzole MF, Festa F, Sogayar MC, Hartfelder K, Pereira GAG. Gene expression profiles underlying alternative caste phenotypes in a highly eusocial bee, Melipona quadrifasciata. Insect Mol Biol 2006; 15:33-44. [PMID: 16469066 DOI: 10.1111/j.1365-2583.2005.00605.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
To evaluate caste-biased gene expression in Melipona quadrifasciata, a stingless bee, we generated 1278 ESTs using Representational Difference Analysis. Most annotated sequences were similar to honey bee genes of unknown function. Only few queen-biased sequences had their putative function assigned by sequence comparison, contrasting with the worker-biased ESTs. The expression of six annotated genes connected to caste specificity was validated by real time PCR. Interestingly, queens that were developmentally induced by treatment with a juvenile hormone analogue displayed an expression profile clearly different from natural queens for this set of genes. In summary, this study represents an important first step in applying a comparative genomic approach to queen/worker polyphenism in the bee.
Collapse
Affiliation(s)
- C C Judice
- Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas-Campinas, Brazil
| | | | | | | | | | | |
Collapse
|
6
|
Scarpari LM, Meinhardt LW, Mazzafera P, Pomella AWV, Schiavinato MA, Cascardo JCM, Pereira GAG. Biochemical changes during the development of witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa. J Exp Bot 2005; 56:865-77. [PMID: 15642708 DOI: 10.1093/jxb/eri079] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Witches' broom disease (WBD) is caused by the hemibiotrophic basidiomycete fungus Crinipellis perniciosa, which is one of the most important diseases of cocoa in the western hemisphere. In this study, the contents of soluble sugars, amino acids, alkaloids, ethylene, phenolics, tannins, flavonoids, pigments, malondialdehyde (MDA), glycerol, and fatty acids were analysed in cocoa (Theobroma cacao) shoots during the infection and development of WBD. Alterations were observed in the content of soluble sugars (sucrose, glucose, and fructose), asparagine and alkaloids (caffeine and theobromine), ethylene, and tannins. Ethylene and tannins increased prior to symptom development and declined with the death of the infected tissues. Furthermore, MDA and glycerol concentrations were higher in infected tissue than in the controls, while fatty acid composition changed in the infected tissues. Chlorophylls a and b were lower throughout the development of the disease while carotenoids and xanthophylls dropped in the infected tissue by the time of symptom development. These results show co-ordinated biochemical alterations in the infected tissues, indicating major stress responses with the production of ethylene. Ethylene levels are hypothesized to play a key role in broom development. Some of the other biochemical alterations are directly associated with ethylene synthesis and may be important for the modification of its effect on the infected tissues.
Collapse
Affiliation(s)
- L M Scarpari
- Departamento de Genética e Evolução, IB/UNICAMP, CP 6109, 13083-970, Campinas-SP, Brazil
| | | | | | | | | | | | | |
Collapse
|