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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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2
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Xia Y, Guo W, Han L, Shen W, Chen X, Yang H. Significant Improvement of Both Catalytic Efficiency and Stability of Fructosyltransferase from Aspergillus niger by Structure-Guided Engineering of Key Residues in the Conserved Sequence of the Catalytic Domain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:7202-7210. [PMID: 35649036 DOI: 10.1021/acs.jafc.2c01699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fructosyltransferase is a key enzyme in fructo-oligosaccharide production, while the highly demanding conditions of industrial processes may reduce its stability and activity. This study employs sequence alignment and structural analysis to target three potential residues (Gln38, Ile39, and Cys43) around the active center of FruSG from Aspergillus niger, and mutants with greatly improved activity and stability were obtained through site-directed mutagenesis. The Km values of C43N and Q38Y were, respectively, reduced to 60.8 and 93.1% compared to those of WT. Meanwhile, the kcat of C43N was increased by 21.2-fold compared to that of WT. These imply that both the affinity and catalytic efficiency of C43N were significantly enhanced compared to WT. The Glide docking score of sucrose inside C43N was calculated to be -5.980, which was lower than that of WT (-4.887). What is more, the proposed general acid/base catalyst Glu273 with a lower pKa value of C43N calculated by PROPKA might contribute to an easier catalytic reaction compared to that of WT. The thermal stability and pH stability of the mutant C43N were significantly enhanced compared to those of WT, and more hydrogen bonds formed during molecular dynamics simulations might contribute to the improved stability of C43N.
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Affiliation(s)
- Yuanyuan Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenwen Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Laichuang Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wei Shen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xianzhong Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Haiquan Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Ho PW, Piampongsant S, Gallone B, Del Cortona A, Peeters PJ, Reijbroek F, Verbaet J, Herrera B, Cortebeeck J, Nolmans R, Saels V, Steensels J, Jarosz DF, Verstrepen KJ. Massive QTL analysis identifies pleiotropic genetic determinants for stress resistance, aroma formation, and ethanol, glycerol and isobutanol production in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:211. [PMID: 34727964 PMCID: PMC8564995 DOI: 10.1186/s13068-021-02059-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The brewer's yeast Saccharomyces cerevisiae is exploited in several industrial processes, ranging from food and beverage fermentation to the production of biofuels, pharmaceuticals and complex chemicals. The large genetic and phenotypic diversity within this species offers a formidable natural resource to obtain superior strains, hybrids, and variants. However, most industrially relevant traits in S. cerevisiae strains are controlled by multiple genetic loci. Over the past years, several studies have identified some of these QTLs. However, because these studies only focus on a limited set of traits and often use different techniques and starting strains, a global view of industrially relevant QTLs is still missing. RESULTS Here, we combined the power of 1125 fully sequenced inbred segregants with high-throughput phenotyping methods to identify as many as 678 QTLs across 18 different traits relevant to industrial fermentation processes, including production of ethanol, glycerol, isobutanol, acetic acid, sulfur dioxide, flavor-active esters, as well as resistance to ethanol, acetic acid, sulfite and high osmolarity. We identified and confirmed several variants that are associated with multiple different traits, indicating that many QTLs are pleiotropic. Moreover, we show that both rare and common variants, as well as variants located in coding and non-coding regions all contribute to the phenotypic variation. CONCLUSIONS Our findings represent an important step in our understanding of the genetic underpinnings of industrially relevant yeast traits and open new routes to study complex genetics and genetic interactions as well as to engineer novel, superior industrial yeasts. Moreover, the major role of rare variants suggests that there is a plethora of different combinations of mutations that can be explored in genome editing.
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Affiliation(s)
- Ping-Wei Ho
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Supinya Piampongsant
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Brigida Gallone
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Andrea Del Cortona
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Pieter-Jan Peeters
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Frank Reijbroek
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jules Verbaet
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Beatriz Herrera
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jeroen Cortebeeck
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Robbe Nolmans
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Veerle Saels
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Jan Steensels
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Kevin J. Verstrepen
- VIB–KU Leuven Center for Microbiology, Leuven, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium
- Leuven Institute for Beer Research, Leuven, Belgium
- Labo VIB-CMPG, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Heverlee Belgium
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Sucrose Hydrolysis in a Continuous Packed-Bed Reactor with Auto-immobilise Aspergillus niger Biocatalyst Obtained by Solid-State Fermentation. Appl Biochem Biotechnol 2021; 194:1327-1339. [PMID: 34699041 DOI: 10.1007/s12010-021-03737-z] [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: 06/28/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Invertase from Aspergillus niger C28B25 was produced by solid-state fermentation (SSF). Fermented solids were used directly as a biocatalyst for batch and continuous hydrolysis of sucrose in a packed-bed reactor under different operational conditions with various temperatures, sucrose concentrations, and feed flow rates. The SSF allowed obtaining a biocatalyst with an invertase activity of 82.2 U/g db. The biocatalyst maintained its activity in the range of 40 to 70 °C for at least 70 h of continuous operation. In a 20-mL packed bed reactor, the highest hydrolysis rate (12.3 g/g db h) was obtained at 40 °C with 2 M sucrose. Continuous hydrolysis in 20-mL and 200-mL reactors at 60 °C led to sucrose hydrolysis above 60% (8.5 residence times) and above 55% (4.5 residence times), respectively. The auto-immobilised biocatalyst produced by SSF without recovery, purification, and immobilisation stages offers an economical alternative for developing accessible biocatalysts that can be applied in batch or continuous sucrose hydrolysis processes. This study shows the potential of biocatalyst production by SSF for other enzymatic systems.
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Zhang Y, Wu G, Zhang Y, Wang X, Jin Q, Zhang H. Advances in exogenous docosahexaenoic acid-containing phospholipids: Sources, positional isomerism, biological activities, and advantages. Compr Rev Food Sci Food Saf 2020; 19:1420-1448. [PMID: 33337094 DOI: 10.1111/1541-4337.12543] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/05/2020] [Accepted: 01/13/2020] [Indexed: 12/16/2022]
Abstract
In recent years, docosahexaenoic acid-containing phospholipids (DHA-PLs) have attracted much attention because of theirs unique health benefits. Compared with other forms of docosahexaenoic acid (DHA), DHA-PLs possess superior biological effects (e.g., anticancer, lipid metabolism regulation, visual development, and brain and nervous system biochemical reactions), more intricate metabolism mechanisms, and a stronger attraction to consumer. The production of DHA-PLs is hampered by several challenges associated with the limited content of DHA-PLs in natural sources, incomplete utilization of by-products, few microorganisms for DHA-PLs production, high cost, and complex process of artificial preparation of DHA-PLs. In this article, the sources, biological activities, and commercial applications of DHA-PLs were summarized, with intensive discussions on advantages of DHA-PLs over DHA, isomerism of DHA in phospholipids (PLs), and brain health. The excellent biological characteristics of DHA-PLs are primarily concerned with DHA and PLs. The metabolic fate of different DHA-PLs varies from the position of DHA in PLs to polar groups in DHA-PLs. Overall, well understanding of DHA-PLs about their sources and characteristics is critical to accelerate the production of DHA-PLs, economically enhance the value of DHA-PLs, and improve the applicability of DHA-PLs and the acceptance of consumers.
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Affiliation(s)
- Yao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Gangcheng Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
| | - Yanjie Zhang
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Xingguo Wang
- School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Qingzhe Jin
- School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China.,Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, China
| | - Hui Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, China
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B da Silva F, M de Oliveira V, Sanches MN, Contessoto VG, Leite VBP. Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. J Chem Inf Model 2019; 60:982-988. [PMID: 31794216 DOI: 10.1021/acs.jcim.9b00911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Rational design of proteins via mutagenesis is crucial for several biotechnological applications. A significant challenge of the computational strategies used to predict optimized mutations is to understand the influence of each amino acid during the folding process. In the present work, chymotrypsin inhibitor 2 (CI2) and several of its designed mutants have been simulated using a non-native hydrophobic and electrostatic potential as a structure-based Cα model. Through these simulations, we could identify the most critical folding stage to accelerate CI2 and also the charged residues responsible for providing its thermostability. The replacement of ionizable residues for hydrophobic ones tended to promote the formation of the CI2 secondary structure in the early transition state, which speeds up folding. However, this same replacement destabilized the native structure, and there was a decrease in the protein thermostability. Such a simple method proved to be capable of providing valuable information about thermodynamics and kinetics of CI2 and its mutations, thus being a fast alternative to the study of rational protein design.
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Affiliation(s)
- Fernando B da Silva
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials , LNBio/CNPEM , Campinas , São Paulo 13083-970 , Brazil
| | - Murilo N Sanches
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Vinícius G Contessoto
- Brazilian Biorenewables National Laboratory - LNBR , Brazilian Center for Research in Energy and Materials - CNPEM , Campinas , São Paulo 13083-100 , Brazil.,Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences , São Paulo State University (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
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7
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Low-resolution structure, oligomerization and its role on the enzymatic activity of a sucrose-6-phosphate hydrolase from Bacillus licheniformis. Amino Acids 2019; 51:599-610. [DOI: 10.1007/s00726-018-02690-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/17/2018] [Indexed: 11/25/2022]
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Ortiz CLD, Matel HD, Nellas RB. In Silico insights on enhancing thermostability and activity of a plant Fructosyltransferase from Pachysandra terminalis via introduction of disulfide bridges. J Mol Graph Model 2019; 89:250-260. [PMID: 30933883 DOI: 10.1016/j.jmgm.2019.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 12/18/2022]
Abstract
Drawbacks of industrially-used fructosyltransferases (FTs) such as low optimum temperature and low fructooligosaccharides (FOS) yield necessitates the search for engineered FTs that are highly thermostable and active. With the availability of the first plant FT crystal structure from Pachysandra terminalis (PDB ID: 3UGH), computer-aided protein engineering of plant FT is now feasible. To obtain insights on the effect of specific mutations i.e. disulfide bridge introduction, wild-type and mutant FTs were subjected to a 15 μs Martini Coarse-grained Molecular Dynamics (CGMD) simulations at 303 K and 334 K. We report here the five mutants, M31C-Q49C, L144C-S193C, P34C-W300C, S219C-L226C and V470C-S498C with enhanced thermostabilities and/or activities relative to the wild type. Interestingly, M31C-Q49C, which is located within the catalytic-carrying blade of the catalytic domain, has an activity enhancement at both temperatures. At 334 K, three mutations, L144C-S193C, P34C-W300C and V470C-S498C, achieved thermostability relative to the wild type. Intriguingly, both activity and stability enhancement exhibited only at 334 K can be achieved provided that the mutation is located either on the catalytic-carrying residue blade of the catalytic domain or on the non-catalytic domain. Our results suggest that V470C-S498C and L144C-S193C are promising mutants and that domain-specific approach may be exploited to customize enzyme properties.
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Affiliation(s)
| | - Hosea D Matel
- Research Center, Cavite State University, Don Severino De Las Alas Campus, Indang, Cavite, Philippines; Department of Physical Sciences, College of Arts and Sciences, Cavite State University, Don Severino De Las Alas Campus, Indang, Cavite, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Diliman, Quezon City, Philippines.
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Jakobson CM, She R, Jarosz DF. Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae. Nat Commun 2019; 10:1222. [PMID: 30874558 PMCID: PMC6420628 DOI: 10.1038/s41467-019-09166-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 02/21/2019] [Indexed: 02/06/2023] Open
Abstract
Quantitative genetics aims to map genotype to phenotype, often with the goal of understanding how organisms evolved. However, it remains unclear whether the genetic variants identified are exemplary of evolution. Here we analyzed progeny of two wild Saccharomyces cerevisiae isolates to identify 195 loci underlying complex metabolic traits, resolving 107 to single polymorphisms with diverse molecular mechanisms. More than 20% of causal variants exhibited patterns of emergence inconsistent with neutrality. Moreover, contrary to drift-centric expectation, variation in diverse wild yeast isolates broadly exhibited this property: over 30% of shared natural variants exhibited phylogenetic signatures suggesting that they are not neutral. This pattern is likely attributable to both homoplasy and balancing selection on ancestral polymorphism. Variants that emerged repeatedly were more likely to have done so in isolates from the same ecological niche. Our results underscore the power of super-resolution mapping of ecologically relevant traits in understanding adaptation and evolution.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Richard She
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel F Jarosz
- Department of Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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