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Herrera CRJ, Vieira VR, Benoliel T, Carneiro CVGC, De Marco JL, de Moraes LMP, de Almeida JRM, Torres FAG. Engineering Zymomonas mobilis for the Production of Xylonic Acid from Sugarcane Bagasse Hydrolysate. Microorganisms 2021; 9:1372. [PMID: 34202822 PMCID: PMC8304316 DOI: 10.3390/microorganisms9071372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Sugarcane bagasse is an agricultural residue rich in xylose, which may be used as a feedstock for the production of high-value-added chemicals, such as xylonic acid, an organic acid listed as one of the top 30 value-added chemicals on a NREL report. Here, Zymomonas mobilis was engineered for the first time to produce xylonic acid from sugarcane bagasse hydrolysate. Seven coding genes for xylose dehydrogenase (XDH) were tested. The expression of XDH gene from Paraburkholderia xenovorans allowed the highest production of xylonic acid (26.17 ± 0.58 g L-1) from 50 g L-1 xylose in shake flasks, with a productivity of 1.85 ± 0.06 g L-1 h-1 and a yield of 1.04 ± 0.04 gAX/gX. Deletion of the xylose reductase gene further increased the production of xylonic acid to 56.44 ± 1.93 g L-1 from 54.27 ± 0.26 g L-1 xylose in a bioreactor. Strain performance was also evaluated in sugarcane bagasse hydrolysate as a cheap feedstock, which resulted in the production of 11.13 g L-1 xylonic acid from 10 g L-1 xylose. The results show that Z. mobilis may be regarded as a potential platform for the production of organic acids from cheap lignocellulosic biomass in the context of biorefineries.
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Affiliation(s)
- Christiane Ribeiro Janner Herrera
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
| | - Vanessa Rodrigues Vieira
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
| | - Tiago Benoliel
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
| | - Clara Vida Galrão Corrêa Carneiro
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
- Laboratório de Genética e Biotecnologia, Parque Estação Biológica, Embrapa, Agroenergia, W3 Norte, Brasília 70770-901, DF, Brazil;
| | - Janice Lisboa De Marco
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
| | - Lídia Maria Pepe de Moraes
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
| | - João Ricardo Moreira de Almeida
- Laboratório de Genética e Biotecnologia, Parque Estação Biológica, Embrapa, Agroenergia, W3 Norte, Brasília 70770-901, DF, Brazil;
| | - Fernando Araripe Gonçalves Torres
- Departamento de Biologia Celular, Universidade de Brasília, Brasília 70910-900, DF, Brazil; (C.R.J.H.); (V.R.V.); (T.B.); (C.V.G.C.C.); (J.L.D.M.); (L.M.P.d.M.)
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Betancur MO, Reis VCB, Nicola AM, De Marco JL, de Moraes LMP, Torres FAG. Multicopy plasmid integration in Komagataella phaffii mediated by a defective auxotrophic marker. Microb Cell Fact 2017; 16:99. [PMID: 28595601 PMCID: PMC5465527 DOI: 10.1186/s12934-017-0715-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 06/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background A commonly used approach to improve recombinant protein production is to increase the levels of expression by providing extra-copies of a heterologous gene. In Komagataella phaffii (Pichia pastoris) this is usually accomplished by transforming cells with an expression vector carrying a drug-resistance marker following a screening for multicopy clones on plates with increasingly higher concentrations of an antibiotic. Alternatively, defective auxotrophic markers can be used for the same purpose. These markers are generally transcriptionally impaired genes lacking most of the promoter region. Among the defective markers commonly used in Saccharomyces cerevisiae is leu2-d, an allele of LEU2 which is involved in leucine metabolism. Cells transformed with this marker can recover prototrophy when they carry multiple copies of leu2-d in order to compensate the poor transcription from this defective allele. Results A K. phaffii strain auxotrophic for leucine (M12) was constructed by disrupting endogenous LEU2. The resulting strain was successfully transformed with a vector carrying leu2-d and an EGFP (enhanced green fluorescent protein) reporter gene. Vector copy numbers were determined from selected clones which grew to different colony sizes on transformation plates. A direct correlation was observed between colony size, number of integrated vectors and EGFP production. By using this approach we were able to isolate genetically stable clones bearing as many as 20 integrated copies of the vector and with no significant effects on cell growth. Conclusions In this work we have successfully developed a genetic system based on a defective auxotrophic which can be applied to improve heterologous protein production in K. phaffii. The system comprises a K. phaffii leu2 strain and an expression vector carrying the defective leu2-d marker which allowed the isolation of multicopy clones after a single transformation step. Because a linear correlation was observed between copy number and heterologous protein production, this system may provide a simple approach to improve recombinant protein productivity in K. phaffii. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0715-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maritza Ocampo Betancur
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Viviane Castelo Branco Reis
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - André Moraes Nicola
- Faculdade de Medicina, Laboratório de Imunologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Janice Lisboa De Marco
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Lídia Maria Pepe de Moraes
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Fernando Araripe Gonçalves Torres
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
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Galdino AS, Silva RN, Lottermann MT, Alvares ACM, de Moraes LMP, Torres FAG, de Freitas SM, Ulhoa CJ. Biochemical and Structural Characterization of Amy1: An Alpha-Amylase from Cryptococcus flavus Expressed in Saccharomyces cerevisiae. Enzyme Res 2011; 2011:157294. [PMID: 21490699 PMCID: PMC3068306 DOI: 10.4061/2011/157294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 12/18/2010] [Indexed: 11/20/2022] Open
Abstract
An extracellular alpha-amylase (Amy1) whose gene from Cryptococcus flavus was previously expressed in Saccharomyces cerevisiae was purified to homogeneity (67 kDa) by ion-exchange and molecular exclusion chromatography. The enzyme was activated by NH4+ and inhibited by Cu+2 and Hg+2. Significant biochemical and structural discrepancies between wild-type and recombinant α-amylase with respect to Km values, enzyme specificity, and secondary structure content were found. Far-UV CD spectra analysis at pH 7.0 revealed the high thermal stability of both proteins and the difference in folding pattern of Amy1 compared with wild-type amylase from C. flavus, which reflected in decrease (10-fold) of enzymatic activity of recombinant protein. Despite the differences, the highest activity of Amy1 towards soluble starch, amylopectin, and amylase, in contrast with the lowest activity of Amy1w, points to this protein as being of paramount biotechnological importance with many applications ranging from food industry to the production of biofuels.
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de Barros MC, do Nascimento Silva R, Ramada MHS, Galdino AS, de Moraes LMP, Torres FAG, Ulhoa CJ. The influence of N-glycosylation on biochemical properties of Amy1, an α-amylase from the yeast Cryptococcus flavus. Carbohydr Res 2009; 344:1682-6. [DOI: 10.1016/j.carres.2009.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 05/29/2009] [Accepted: 06/01/2009] [Indexed: 11/16/2022]
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Parachin NS, Siqueira S, de Faria FP, Torres FAG, de Moraes LMP. Xylanases from Cryptococcus flavus isolate I-11: Enzymatic profile, isolation and heterologous expression of CfXYN1 in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Lima LHA, Pinheiro CGDA, de Moraes LMP, de Freitas SM, Torres FAG. Xylitol dehydrogenase from Candida tropicalis: molecular cloning of the gene and structural analysis of the protein. Appl Microbiol Biotechnol 2006; 73:631-9. [PMID: 16896602 DOI: 10.1007/s00253-006-0525-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 05/30/2006] [Accepted: 06/01/2006] [Indexed: 11/30/2022]
Abstract
Yeasts can metabolize xylose by the action of two key enzymes: xylose reductase and xylitol dehydrogenase. In this work, we present data concerning the cloning of the XYL2 gene encoding xylitol dehydrogenase from the yeast Candida tropicalis. The gene is present as a single copy in the genome and is controlled at the transcriptional level by the presence of the inducer xylose. XYL2 was functionally tested by heterologous expression in Saccharomyces cerevisiae to develop a yeast strain capable of producing ethanol from xylose. Structural analysis of C. tropicalis xylitol dehydrogenase, Xyl2, suggests that it is a member of the medium-chain dehydrogenase (MDR) family. This is supported by the presence of the amino acid signature [GHE]xx[G]xxxxx[G]xx[V] in its primary sequence and a typical alcohol dehydrogenase Rossmann fold pattern composed by NAD(+) and zinc ion binding domains.
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de Almeida JRM, de Moraes LMP, Torres FAG. Molecular characterization of the 3-phosphoglycerate kinase gene (PGK1) from the methylotrophic yeast Pichia pastoris. Yeast 2005; 22:725-37. [PMID: 16034819 DOI: 10.1002/yea.1243] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We report the cloning of the 3-phosphoglycerate kinase gene (PGK1) from the methylotrophic yeast Pichia pastoris by a PCR approach. The coding sequence of the PGK1 gene comprises 1251 bp with the potential to encode a polypeptide of 416 amino acid residues, which shows high identity to homologous proteins from other yeasts. The promoter region of this gene (P(PGK1)) contains regulatory cis-elements found in other PGK1 genes, such as TATA box, CT-rich block and a heat shock element. In the 3' downstream region we identified a tripartite element 5'-TAG-TAGT-TTT-3', which is supposed to be important for transcription termination. As in other yeasts, the PGK1 gene from P. pastoris is present as a single-copy gene. Northern blot analysis revealed that the gene is transcribed as a 1.5 kb mRNA; when cells are grown on glucose the levels of this mRNA are increased two-fold in comparison to cells grown on glycerol. The transcriptional regulation of this gene by the carbon source was further confirmed when the alpha-amylase gene from Bacillus subtilis was placed under the control of P(PGK1): higher levels of expression were obtained when cells were grown on glucose as compared to glycerol and methanol. Preliminary results related to the strength of P(PGK1) show that it represents a potential alternative to constitutive heterologous expression in P. pastoris.
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Affiliation(s)
- João Ricardo Moreira de Almeida
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF 70910-900, Brazil
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Reis VCB, Torres FAG, Poças-Fonseca MJ, De-Souza MT, Souza DPD, Almeida JRM, Marinho-Silva C, Parachin NS, Dantas ADS, Mello-de-Sousa TM, Moraes LMPD. Cell cycle, DNA replication, repair, and recombination in the dimorphic human pathogenic fungus Paracoccidioides brasiliensis. Genet Mol Res 2005; 4:232-50. [PMID: 16110444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
DNA replication, together with repair mechanisms and cell cycle control, are the most important cellular processes necessary to maintain correct transfer of genetic information to the progeny. These processes are well conserved throughout the Eukarya, and the genes that are involved provide essential information for understanding the life cycle of an organism. We used computational tools for data mining of genes involved in these processes in the pathogenic fungus Paracoccidiodes brasiliensis. Data derived from transcriptome analysis revealed that the cell cycle of this fungus, as well as DNA replication and repair, and the recombination machineries, are highly similar to those of the yeast Saccharomyces cerevisiae. Among orthologs detected in both species, there are genes related to cytoskeleton structure and assembly, chromosome segregation, and cell cycle control genes. We identified at least one representative gene from each step of the initiation of DNA replication. Major players in the process of DNA damage and repair were also identified.
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Affiliation(s)
- Viviane Castelo Branco Reis
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Universidade de Brasília, 70910-900 Brasília, DF, Brazil
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