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Barasch IB, Grimes JL. The effect of a heat-stable xylanase on digesta viscosity, apparent metabolizable energy and growth performance of broiler chicks fed a wheat-based diet. Poult Sci 2021; 100:101275. [PMID: 34273648 PMCID: PMC8313832 DOI: 10.1016/j.psj.2021.101275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/20/2021] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
Feed costs represent a significant portion of the cost of poultry production. This study, in 3 experiments, was conducted to evaluate the effectiveness of a heat-stable xylanase (XYL) as a dietary supplement and its effect on digesta viscosity, nitrogen-corrected apparent metabolizable energy (AMEn), and live performance in broiler chicks. Experiment 1: the objective was to determine the effects of the amount and type of enzyme supplementation on digesta viscosity, AMEn, and bird performance using 7 diets. The dietary treatments were: no supplementation (C), 5 levels of XYL (1 to 16 ppm), or supplementation with a carbohydrase cocktail (CC). Experiment 2: the objective was to determine the interaction of the dietary XYL and the energy content of the feed. There were 2 levels of XYL (0 and 20 ppm) and 3 dietary energy levels (2,770, 2,920, and 3,070 kcal/kg ME). Experiment 3: the objective was to determine the interaction of the dietary XYL and feed form. The treatments were: 5 levels of XYL (0 to 40 ppm) and 2 feed forms (mash and crumble). Broiler chicks were reared in battery cages to 21 d. Statistical analysis of the data was completed using Proc GLM of SAS (9.2) (SAS Institute, Cary, NC). In experiment 1, increasing XYL (0 to 16 ppm) resulted in a decrease in digesta viscosity and an increase in AMEn. The XYL included as low as 1 ppm resulted in a significant increase in AMEn which reached 5% with 16 ppm XYL. In contrast, increase in BWG (4%) above values with the basal diet was greatest with 1 ppm XYL. In experiment 2, the caloric content of the diet influenced the increase in AMEn with inclusion of XYL, 8% and 6% increases with 2,920 kcal/kg and 3,070 kcal/kg diets, respectively. Without addition of XYL, BWG was significantly lower when fed the diet with the highest energy content. In experiment 3, feed form x XYL influenced the effect of XYL on BWG. The BWG was greater when birds were fed the crumble diet with XYL vs when they were fed the mash feed with XYL. The xylanase proved effective for broilers to 21 d when fed the diets used herein with changes in digesta viscosity, increased dietary AMEn, and improved bird performance represented by either BW gain or FCR.
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Affiliation(s)
- I B Barasch
- Prestage Department of Poultry Science, NC State University, Raleigh, NC 27695-7608
| | - J L Grimes
- Prestage Department of Poultry Science, NC State University, Raleigh, NC 27695-7608.
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Lau MSH, Sheng L, Zhang Y, Minton NP. Development of a Suite of Tools for Genome Editing in Parageobacillus thermoglucosidasius and Their Use to Identify the Potential of a Native Plasmid in the Generation of Stable Engineered Strains. ACS Synth Biol 2021; 10:1739-1749. [PMID: 34197093 DOI: 10.1021/acssynbio.1c00138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The relentless rise in the levels of atmospheric greenhouse gases caused by the exploitation of fossil fuel necessitates the development of more environmentally friendly routes to the manufacture of chemicals and fuels. The exploitation of a fermentative process that uses a thermophilic chassis represents an attractive option. Its use, however, is hindered by a dearth of genetic tools. Here we expand on those available for the engineering of the industrial chassis Parageobacillus thermoglucosidasius through the assembly and testing of a range of promoters, ribosome binding sites, reporter genes, and the implementation of CRISPR/Cas9 genome editing based on two different thermostable Cas9 nucleases. The latter were used to demonstrate that the deletion of the two native plasmids carried by P. thermoglucosidasius, pNCI001 and pNCI002, either singly or in combination, had no discernible effects on the overall phenotypic characteristics of the organism. Through the CRISPR/Cas9-mediated insertion of the gene encoding a novel fluorescent reporter, eCGP123, we showed that pNCI001 exhibited a high degree of segregational stability. As the relatively higher copy number of pNCI001 led to higher levels of eCGP123 expression than when the same gene was integrated into the chromosome, we propose that pNCI001 represents the preferred option for the integration of metabolic operons when stable commercial strains are required.
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Affiliation(s)
- Matthew S. H. Lau
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Lili Sheng
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Ying Zhang
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Nigel P. Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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Noor RS, Sun Y, Qu J, Hussain F, Waqas MM, Shah AN, Noor R. Quantifying the effects of co-composting organic biomass mixtures with inorganic amendments to obtain value-added bio-products. PLoS One 2021; 16:e0253714. [PMID: 34260590 PMCID: PMC8279329 DOI: 10.1371/journal.pone.0253714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022] Open
Abstract
Co-digestion of organic biomass mixed with inorganic amendments could have an impact on composting dynamics. Various studies highlighted fertilizers' role as an additive to lesser the nitrogen loss, while some studies focused on the addition of fertilizers to enhance the efficiency. The changes in carbon, nitrogen components, and humic substances during the organic-inorganic co-compost process were seldom studied. Clarifying these changes might help improve the production process and compost nutrients contents. Thus, this study's purpose is to investigate the effects of inorganic amendments on compost characteristics, compost temperature, biochemical methane production (BMP), and nutritional contents. The inorganic phosphorous (P), sulfur (S), and sulfur solubilizing agent (SSA) were added to Farmyard manure (FYM) mixed with biodegradable waste (BW), including wheat straw, corn stalks, and green lawn waste. The P and S amended treatments were carried out into two sets, with and without SSA. The mixed feedstocks were added in the insulated RBC composting pit (15 x 15 x 10 feet). The compost material's moisture content was maintained 50-65% during the entire composting process for optimum waste digestion i.e., the moisture content (MC) of FYM was 82.7% and for BW ranged 8.8-10.2%, while the C/N ratio was found 10.5 for FYM, 74.5 for wheat straw, 83.5 for corn stalks, and 84.8 for lawn waste. At the condition of compost maturity, the inorganic amendments have no significant effect on composted material's moisture content. The maximum organic matter of 69.7% and C/N ratio of 44.6 was measured in T1. On the 6th day of composting, the temperature reached to thermophilic range (>45 oC) in all the treatments due to aeration of compost increased microbial activities and waste decomposition rate and decreased gradually to mesophilic range (35-45 oC) because the supply of high-energy compounds becomes exhausted. The highest temperature was reached in T4 (58 oC) and lowest in CT (47 oC). The significantly maximum methane of 8.95 m3 and biogas burning was 818 minutes in CT, followed by T1 and T4. The results of this study revealed that P enriched compost is a feasible and sustainable way to overcome P deficiency in the soil as well as in plants and best way to use low-grade P and organic waste material.
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Affiliation(s)
- Rana Shahzad Noor
- Department of Agriculture, Biological, Environment and Energy Engineering, College of Engineering, Northeast Agricultural University, Harbin, China
- Faculty of Agricultural Engineering and Technology, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Yong Sun
- Department of Agriculture, Biological, Environment and Energy Engineering, College of Engineering, Northeast Agricultural University, Harbin, China
| | - Jingbo Qu
- Department of Agriculture, Biological, Environment and Energy Engineering, College of Engineering, Northeast Agricultural University, Harbin, China
| | - Fiaz Hussain
- Faculty of Agricultural Engineering and Technology, PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Mohsin Waqas
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, Pakistan
| | - Rabeea Noor
- Department of Agricultural Engineering, Bahauddin Zakariya University, Multan, Pakistan
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Samarasinghe SN, Wanigatunge RP, Magana-Arachchi DN. Bacterial Diversity in a Sri Lankan Geothermal Spring Assessed by Culture-Dependent and Culture-Independent Approaches. Curr Microbiol 2021; 78:3439-3452. [PMID: 34258683 DOI: 10.1007/s00284-021-02608-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
Hot springs harbour diverse and interesting groups of microorganisms adapted to extreme conditions. However, due to limitations in the culture-dependent approach, most of such thermophiles remain uncultured and unexplored. Hence, this study was conducted to gain a comprehensive understanding of the bacterial diversity of Mahapelessa hot spring, Sri Lanka using both culture-dependent and culture-independent approaches. The in situ temperature of the water sample was 44.5 °C and the pH was 8.14. 16S rRNA Sanger sequencing of DNA extracted from the 18 bacterial isolates revealed the presence of eight genera belonging to two phyla: Proteobacteria (84%) and Firmicutes (16%) and the most abundant genus being Klebsiella. A total of 23 bacterial phyla representing 80 classes, 43 orders, 123 families, 205 genera and 83 species were detected by 16S rRNA V3-V4 region by amplicon metagenome sequencing of DNA extracted from water samples, where the most abundant phylum was the Proteobacteria (57.39%), followed by Firmicutes (23.7%) and Chloroflexi (4.14%). The three phyla Actinobacteria, Planctomycetes and Bacteroidetes were also detected less than 3% in abundance while 4.48% of bacteria could not be fit into any known phylum. The most abundant genera were Burkholderia (14.87%), Desulfotomaculum (7.23%) and Stenotrophomonas (6.1%). Four strictly anaerobic bacteria, Anaerosolibacter carboniphilus (0.71%), Bellilinea caldifistulae (0.04%), Salimesophilobacter vulgaris (0.1%), Anaerobacterium chartisolvens (0.12%); two potential plant growth-promoting bacteria, Azospirillum halopraeferens (0.04%) and Bradyrhizobium liaoningense (0.16%) and one potential alkali tolerant and sulphate-reducing bacterium, Desulfovibrio alkalitolerans (0.45%) were recorded. Pigmentiphaga sp. was isolated from Mahapelessa hot spring and to the best of our knowledge, this is the first record of this genus from a hot spring. This study gives insight into the vast bacterial diversity present in the Mahapelessa hot spring from the culture-independent approach which could not be identified using standard culturing techniques.
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Affiliation(s)
- Supun N Samarasinghe
- Molecular Microbiology and Human Diseases Research Group, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - Rasika P Wanigatunge
- Department of Plant and Molecular Biology, University of Kelaniya, Kelaniya, Sri Lanka
| | - Dhammika N Magana-Arachchi
- Molecular Microbiology and Human Diseases Research Group, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka.
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55
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Ishak SNH, Kamarudin NHA, Ali MSM, Leow ATC, Shariff FM, Rahman RNZRA. Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae. PLoS One 2021; 16:e0251751. [PMID: 34061877 PMCID: PMC8168862 DOI: 10.1371/journal.pone.0251751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/02/2021] [Indexed: 12/27/2022] Open
Abstract
5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl-esters.
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Affiliation(s)
- Siti Nor Hasmah Ishak
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2. Appl Environ Microbiol 2021; 87:AEM.01589-20. [PMID: 33741620 DOI: 10.1128/aem.01589-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 03/09/2021] [Indexed: 11/20/2022] Open
Abstract
A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics.IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.
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Chen Q, He Z, Zhuo Y, Li S, Yang W, Hu L, Zhong H. Rubidium chloride modulated the fecal microbiota community in mice. BMC Microbiol 2021; 21:46. [PMID: 33588762 PMCID: PMC7885239 DOI: 10.1186/s12866-021-02095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
Background The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes. Results The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level. Conclusions Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02095-4.
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Affiliation(s)
- Qian Chen
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Yuting Zhuo
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Wenjing Yang
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Liang Hu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Hui Zhong
- School of Life Sciences, Central South University, Changsha, 410013, China.
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Gavande PV, Basak A, Sen S, Lepcha K, Murmu N, Rai V, Mazumdar D, Saha SP, Das V, Ghosh S. Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization. Sci Rep 2021; 11:3032. [PMID: 33542396 PMCID: PMC7862241 DOI: 10.1038/s41598-021-82163-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Rice (Oryza sativa L.) straw, an agricultural waste of high yield, is a sustainable source of fermentable sugars for biofuel and other chemicals. However, it shows recalcitrance to microbial catalysed depolymerization. We herein describe development of thermotolerant microbial consortium (RSV) from vermicompost with ability to degrade rice straw and analysis of its metagenome for bacterial diversity, and lignocellulolytic carbohydrate active enzymes (CAZymes) and their phylogenetic affiliations. RSV secretome exhibited cellulases and hemicellulases with higher activity at 60 °C. It catalysed depolymerization of chemical pretreated rice straw as revealed by scanning electron microscopy and saccharification yield of 460 mg g-1 rice straw. Microbial diversity of RSV was distinct from other compost habitats, with predominance of members of phyla Firmicutes, Proteobacteria and Bacteroidetes; and Pseudoclostridium, Thermoanaerobacterium, Chelatococcus and Algoriphagus being most abundant genera. RSV harboured 1389 CAZyme encoding ORFs of glycoside hydrolase, carbohydrate esterase, glycosyl transferase, carbohydrate binding module and auxiliary activity functions. Microorganisms of Firmicutes showed central role in lignocellulose deconstruction with importance in hemicellulose degradation; whereas representatives of Proteobacteria and Bacteroidetes contributed to cellulose and lignin degradation, respectively. RSV consortium could be a resource for mining thermotolerant cellulolytic bacteria or enzymes and studying their synergism in deconstruction of chemically pretreated rice straw.
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Affiliation(s)
- Parmeshwar V. Gavande
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Arijita Basak
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Subhajit Sen
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Khusboo Lepcha
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Nensina Murmu
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Vijeta Rai
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Deepika Mazumdar
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Shyama Prasad Saha
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Vaskar Das
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
| | - Shilpi Ghosh
- grid.412222.50000 0001 1188 5260Department of Biotechnology, University of North Bengal, Raja Rammohunpur, P.O.-NBU, Siliguri, West Bengal 734013 India
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Enrichment of Hydrogen Oxidizing Bacteria from High Temperature and Salinity Environments. Appl Environ Microbiol 2021; 87:AEM.02439-20. [PMID: 33257312 PMCID: PMC7851685 DOI: 10.1128/aem.02439-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
There is an urgent need for sustainable protein supply routes with low environmental footprint. Recently, the use of hydrogen oxidizing bacteria (HOB) as a platform for high quality microbial protein (MP) production has regained interest. This study aims to investigate the added value of using conditions such as salt and temperature to steer HOB communities to lower diversities, while maintaining a high protein content and a high quality amino acid profile. Pressure drop and hydrogen consumption were measured for 56 days to evaluate autotrophy of a total of six communities in serum flasks. Of the six communities, four were enriched under saline (0.0, 0.25, 0.5 and 1.0 mol NaCl l-1) and two under thermophilic conditions (65°C). Five communities enriched for HOB were subsequently cultivated in continuously stirred reactors under the same conditions to evaluate their potential as microbial protein producers. The protein percentages ranged from 41 to 80%. The highest protein content was obtained for the thermophilic enrichments. Amino acid profiles were comparable to protein sources commonly used for feed purposes. Members of the genus Achromobacter were found to dominate the saline enrichments while members of the genus Hydrogenibacillus were found to dominate the thermophilic enrichments. Here we show that enriching for HOB while steering the community toward low diversity and maintaining a high quality protein content can be successfully achieved, both in saline and thermophilic conditions.IMPORTANCE Alternative feed and food supply chains are required to decrease water and land use. HOB offer a promising substitute for traditional agricultural practice to produce microbial protein (MP) from residual materials and renewable energy. To safeguard product stability, the composition of the HOB community should be controlled. Defining strategies to maintain the stability of the communities is therefore key for optimization purposes. In this study, we use salt and temperature as independent conditions to stabilize the composition of the HOB communities. Based on the results presented, we conclude that HOB communities can be steered to have low diversity using the presented conditions while producing a desirable protein content with a valuable amino acid profile.
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Soy S, Nigam VK, Sharma SR. Enhanced production and biochemical characterization of a thermostable amylase from thermophilic bacterium Geobacillus icigianus BITSNS038. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2021. [DOI: 10.1080/16583655.2021.2002549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Snehi Soy
- Department of Bio-Engineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Vinod Kumar Nigam
- Department of Bio-Engineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
| | - Shubha Rani Sharma
- Department of Bio-Engineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India
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Acquistapace IM, Zi Etek MA, Li AWH, Salmon M, Kühn I, Bedford MR, Brearley CA, Hemmings AM. Snapshots during the catalytic cycle of a histidine acid phytase reveal an induced-fit structural mechanism. J Biol Chem 2020; 295:17724-17737. [PMID: 33454010 PMCID: PMC7762957 DOI: 10.1074/jbc.ra120.015925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/10/2020] [Indexed: 11/16/2022] Open
Abstract
Highly engineered phytases, which sequentially hydrolyze the hexakisphosphate ester of inositol known as phytic acid, are routinely added to the feeds of monogastric animals to improve phosphate bioavailability. New phytases are sought as starting points to further optimize the rate and extent of dephosphorylation of phytate in the animal digestive tract. Multiple inositol polyphosphate phosphatases (MINPPs) are clade 2 histidine phosphatases (HP2P) able to carry out the stepwise hydrolysis of phytate. MINPPs are not restricted by a strong positional specificity making them attractive targets for development as feed enzymes. Here, we describe the characterization of a MINPP from the Gram-positive bacterium Bifidobacterium longum (BlMINPP). BlMINPP has a typical HP2P-fold but, unusually, possesses a large α-domain polypeptide insertion relative to other MINPPs. This insertion, termed the U-loop, spans the active site and contributes to substrate specificity pockets underpopulated in other HP2Ps. Mutagenesis of U-loop residues reveals its contribution to enzyme kinetics and thermostability. Moreover, four crystal structures of the protein along the catalytic cycle capture, for the first time in an HP2P, a large ligand-driven α-domain motion essential to allow substrate access to the active site. This motion recruits residues both downstream of a molecular hinge and on the U-loop to participate in specificity subsites, and mutagenesis identified a mobile lysine residue as a key determinant of positional specificity of the enzyme. Taken together, these data provide important new insights to the factors determining stability, substrate recognition, and the structural mechanism of hydrolysis in this industrially important group of enzymes.
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Affiliation(s)
| | - Monika A Zi Etek
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Arthur W H Li
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Melissa Salmon
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | | | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Andrew M Hemmings
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom; School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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Evolution of Protein Structure and Stability in Global Warming. Int J Mol Sci 2020; 21:ijms21249662. [PMID: 33352933 PMCID: PMC7767258 DOI: 10.3390/ijms21249662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the molecular signatures of protein structures in relation to evolution and survival in global warming. It is based on the premise that the power of evolutionary selection may lead to thermotolerant organisms that will repopulate the planet and continue life in general, but perhaps with different kinds of flora and fauna. Our focus is on molecular mechanisms, whereby known examples of thermoresistance and their physicochemical characteristics were noted. A comparison of interactions of diverse residues in proteins from thermophilic and mesophilic organisms, as well as reverse genetic studies, revealed a set of imprecise molecular signatures that pointed to major roles of hydrophobicity, solvent accessibility, disulfide bonds, hydrogen bonds, ionic and π-electron interactions, and an overall condensed packing of the higher-order structure, especially in the hydrophobic regions. Regardless of mutations, specialized protein chaperones may play a cardinal role. In evolutionary terms, thermoresistance to global warming will likely occur in stepwise mutational changes, conforming to the molecular signatures, such that each "intermediate" fits a temporary niche through punctuated equilibrium, while maintaining protein functionality. Finally, the population response of different species to global warming may vary substantially, and, as such, some may evolve while others will undergo catastrophic mass extinction.
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Zhao J, Wang L, Wei X, Li K, Liu J. Food-Grade Expression and Characterization of a Dextranase from Chaetomium gracile Suitable for Sugarcane Juice Clarification. Chem Biodivers 2020; 18:e2000797. [PMID: 33245200 DOI: 10.1002/cbdv.202000797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/26/2020] [Indexed: 11/09/2022]
Abstract
The microbial production of dextranase using cheap carbon sources is beneficial to solve the economic loss caused by the accumulation of dextran in syrup. A food-grade microbial cell factory was constructed by introducing the dextranase encoding gene DEX from Chaetomium gracile to the chromosome of Bacillus subtilis, and the antibiotic resistance marker gene was subsequently deleted via the Cre/loxP strategy. The dual-promoter system with a sequentially arranged constitutive P43 promoter resulted in an 85 % increase in DEX expression. Under the optimal fermentation conditions of 10 g/L maltose, 15 g/L casein, 1 g/L Na2 HPO4 , 1 g/L FeSO4 and 8 g/L NaCl, DEX activity was increased from 2.625 to 64.34 U/mL. Recombinant DEX was purified 5.98-fold with a recovery ratio of 26.67 % and specific activity of 3935.02 U/mg. Enzyme activity was optimal at 55 °C and pH 5.0 and remained 80.34 % and 71.36 % of the initial activity at 55 °C and pH 4.0 after 60 min, respectively. The enzyme possessed high activity in the presence of Co2+ , while Ag+ showed the strongest inhibition ability. The optimal substrate was 20 g/L dextran T-2000. The findings could facilitate the low-cost, large-scale production of food-grade DEX for use in the sugar industry.
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Affiliation(s)
- Jingyi Zhao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Leyi Wang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Xin Wei
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Kai Li
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.,Sugar Industry Collaborative Innovation Center, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Jidong Liu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.,Sugar Industry Collaborative Innovation Center, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
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Xie J, Xu H, Jiang J, Zhang N, Yang J, Zhao J, Wei M. Characterization of a novel thermostable glucose-tolerant GH1 β-glucosidase from the hyperthermophile Ignisphaera aggregans and its application in the efficient production of baohuoside I from icariin and total epimedium flavonoids. Bioorg Chem 2020; 104:104296. [DOI: 10.1016/j.bioorg.2020.104296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
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Corrêa CL, Midorikawa GEO, Filho EXF, Noronha EF, Alves GSC, Togawa RC, Silva-Junior OB, Costa MMDC, Grynberg P, Miller RNG. Transcriptome Profiling-Based Analysis of Carbohydrate-Active Enzymes in Aspergillus terreus Involved in Plant Biomass Degradation. Front Bioeng Biotechnol 2020; 8:564527. [PMID: 33123513 PMCID: PMC7573219 DOI: 10.3389/fbioe.2020.564527] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
Given the global abundance of plant biomass residues, potential exists in biorefinery-based applications with lignocellulolytic fungi. Frequently isolated from agricultural cellulosic materials, Aspergillus terreus is a fungus efficient in secretion of commercial enzymes such as cellulases, xylanases and phytases. In the context of biomass saccharification, lignocellulolytic enzyme secretion was analyzed in a strain of A. terreus following liquid culture with sugarcane bagasse (SB) (1% w/v) and soybean hulls (SH) (1% w/v) as sole carbon source, in comparison to glucose (G) (1% w/v). Analysis of the fungal secretome revealed a maximum of 1.017 UI.mL–1 xylanases after growth in minimal medium with SB, and 1.019 UI.mL–1 after incubation with SH as carbon source. The fungal transcriptome was characterized on SB and SH, with gene expression examined in comparison to equivalent growth on G as carbon source. Over 8000 genes were identified, including numerous encoding enzymes and transcription factors involved in the degradation of the plant cell wall, with significant expression modulation according to carbon source. Eighty-nine carbohydrate-active enzyme (CAZyme)-encoding genes were identified following growth on SB, of which 77 were differentially expressed. These comprised 78% glycoside hydrolases, 8% carbohydrate esterases, 2.5% polysaccharide lyases, and 11.5% auxiliary activities. Analysis of the glycoside hydrolase family revealed significant up-regulation for genes encoding 25 different GH family proteins, with predominance for families GH3, 5, 7, 10, and 43. For SH, from a total of 91 CAZyme-encoding genes, 83 were also significantly up-regulated in comparison to G. These comprised 80% glycoside hydrolases, 7% carbohydrate esterases, 5% polysaccharide lyases, 7% auxiliary activities (AA), and 1% glycosyltransferases. Similarly, within the glycoside hydrolases, significant up-regulation was observed for genes encoding 26 different GH family proteins, with predominance again for families GH3, 5, 10, 31, and 43. A. terreus is a promising species for production of enzymes involved in the degradation of plant biomass. Given that this fungus is also able to produce thermophilic enzymes, this first global analysis of the transcriptome following cultivation on lignocellulosic carbon sources offers considerable potential for the application of candidate genes in biorefinery applications.
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Affiliation(s)
- Camila L Corrêa
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Glaucia E O Midorikawa
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | | | - Eliane Ferreira Noronha
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Gabriel S C Alves
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Roberto Coiti Togawa
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica - PqEB, Brasília, Brazil
| | | | | | - Priscila Grynberg
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica - PqEB, Brasília, Brazil
| | - Robert N G Miller
- Departamento de Biologia Celular, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
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66
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Wang Y, Wang G, Moitessier N, Mittermaier AK. Enzyme Kinetics by Isothermal Titration Calorimetry: Allostery, Inhibition, and Dynamics. Front Mol Biosci 2020; 7:583826. [PMID: 33195429 PMCID: PMC7604385 DOI: 10.3389/fmolb.2020.583826] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
Isothermal titration calorimetry (ITC) involves accurately measuring the heat that is released or absorbed in real time when one solution is titrated into another. This technique is usually used to measure the thermodynamics of binding reactions. However, there is mounting interest in using it to measure reaction kinetics, particularly enzymatic catalysis. This application of ITC has been steadily growing for the past two decades, and the method is proving to be sensitive, generally applicable, and capable of providing information on enzyme activity that is difficult to obtain using traditional biochemical assays. This review aims to give a broad overview of the use of ITC to measure enzyme kinetics. It describes several different classes of ITC experiment, their strengths and weaknesses, and recent methodological advancements. A summary of applications in the literature is given and several examples where ITC has been used to investigate challenging aspects of enzyme behavior are presented in more detail. These include examples of allostery, where small-molecule binding outside the active site modulates activity. We describe the use of ITC to measure the strength, mode (i.e., competitive, uncompetitive, or mixed), and association and dissociation kinetics of enzyme inhibitors. Further, we provide examples of ITC applied to complex, heterogeneous mixtures, such as insoluble substrates and live cells. These studies exemplify the wide range of problems where ITC can provide answers, and illustrate the versatility of the technique and potential for future development and applications.
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Affiliation(s)
- Yun Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
| | - Guanyu Wang
- Department of Chemistry, McGill University, Montreal, QC, Canada
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A novel high performance in-silico screened metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions. BMC Biotechnol 2020; 20:56. [PMID: 33076889 PMCID: PMC7574624 DOI: 10.1186/s12896-020-00647-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Background Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant. Results The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. At first, the multi-step in-silico screening approach was utilized to find primary candidate enzymes with superior properties. Among the computationally selected candidates, PersiCel4 was found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes’ kinetic parameters, including Vmax, Km, and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85 °C and was able to retain more than 70% of its activity after 150 h of storage at 85 °C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl and several metal ions contains Mg2+, Mn2+, Cu2+, Fe2+ and Ca2+. Our results showed that treatment with MnCl2 could enhance the enzyme’s activity by 78%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 h in the harsh condition (T = 85 °C, pH = 8.5). Conclusion Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.
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68
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Niu C, Wan X. Engineering a Trypsin-Resistant Thermophilic α-Galactosidase to Enhance Pepsin Resistance, Acidic Tolerance, Catalytic Performance, and Potential in the Food and Feed Industry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10560-10573. [PMID: 32829638 DOI: 10.1021/acs.jafc.0c02175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
α-Galactosidase has potential applications, and attempts to improve proteolytic resistance of enzymes have important values. We use a novel strategy for genetic manipulation of a pepsin-sensitive region specific for a pepsin-sensitive but trypsin-resistant high-temperature-active Gal27B from Neosartorya fischeri to screen mutants with enhanced pepsin resistance. All enzymes were produced in Pichia pastoris to identify the roles of loop 4 (Gal27B-A23) and its key residue at position 156 (Gly156Arg/Pro/His) in pepsin resistance. Gal27B-A23 and Gly156Arg/Pro/His elevated pepsin resistance, thermostability, stability at low pH, activity toward raffinose (5.3-6.9-fold) and stachyose (about 1.3-fold), and catalytic efficiencies (up to 4.9-fold). Replacing the pepsin cleavage site Glu155 with Gly improved pepsin resistance but had no effect on pepsin resistance when Arg/Pro/His was at position 156. Thus, pepsin resistance could appear to occur through steric hindrance between the residue at the altered site and neighboring pepsin active site. In the presence of pepsin or trypsin, all mutations increased the ability of Gal27B to hydrolyze galactosaccharides in soybean flour (up to 9.6- and 4.3-fold, respectively) and promoted apparent metabolizable energy and nutrient digestibility in soybean meal for broilers (1.3-1.8-fold). The high activity and tolerance to heat, low pH, and protease benefit food and feed industry in a cost-effective way.
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Affiliation(s)
- Canfang Niu
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangyuan Wan
- Zhongzhi International Institute of Agricultural Biosciences, Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing 100024, China
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Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation. Microorganisms 2020; 8:microorganisms8091357. [PMID: 32899798 PMCID: PMC7564440 DOI: 10.3390/microorganisms8091357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 02/02/2023] Open
Abstract
A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency.
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Enhanced Thermostability and Enzymatic Activity of Cel6A Variants from Thermobifida fusca by Empirical Domain Engineering (Short Title: Domain Engineering of Cel6A). BIOLOGY 2020; 9:biology9080214. [PMID: 32784797 PMCID: PMC7464639 DOI: 10.3390/biology9080214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Cellulases are a set of lignocellulolytic enzymes, capable of producing eco-friendly low-cost renewable bioethanol. However, low stability and hydrolytic activity limit their wide-scale applicability at the industrial scale. In this work, we report the domain engineering of endoglucanase (Cel6A) of Thermobifida fusca to improve their catalytic activity and thermal stability. Later, enzymatic activity and thermostability of the most efficient variant named as Cel6A.CBC was analyzed by molecular dynamics simulations. This variant demonstrated profound activity against soluble and insoluble cellulosic substrates like filter paper, alkali-treated bagasse, regenerated amorphous cellulose (RAC), and bacterial microcrystalline cellulose. The variant Cel6A.CBC showed the highest catalysis of carboxymethyl cellulose (CMC) and other related insoluble substrates at a pH of 6.0 and a temperature of 60 °C. Furthermore, a sound rationale was observed between experimental findings and molecular modeling of Cel6A.CBC which revealed thermostability of Cel6A.CBC at 26.85, 60.85, and 74.85 °C as well as structural flexibility at 126.85 °C. Therefore, a thermostable derivative of Cel6A engineered in the present work has enhanced biological performance and can be a useful construct for the mass production of bioethanol from plant biomass.
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Ishak SNH, Kamarudin NHA, Ali MSM, Leow ATC, Rahman RNZRA. Ion-Pair Interaction and Hydrogen Bonds as Main Features of Protein Thermostability in Mutated T1 Recombinant Lipase Originating from Geobacillus zalihae. Molecules 2020; 25:E3430. [PMID: 32731607 PMCID: PMC7435748 DOI: 10.3390/molecules25153430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 01/19/2023] Open
Abstract
A comparative structure analysis between space- and an Earth-grown T1 recombinant lipase from Geobacillus zalihae had shown changes in the formation of hydrogen bonds and ion-pair interactions. Using the space-grown T1 lipase validated structure having incorporated said interactions, the recombinant T1 lipase was re-engineered to determine the changes brought by these interactions to the structure and stability of lipase. To understand the effects of mutation on T1 recombinant lipase, five mutants were developed from the structure of space-grown T1 lipase and biochemically characterized. The results demonstrate an increase in melting temperature up to 77.4 °C and 76.0 °C in E226D and D43E, respectively. Moreover, the mutated lipases D43E and E226D had additional hydrogen bonds and ion-pair interactions in their structures due to the improvement of stability, as observed in a longer half-life and an increased melting temperature. The biophysical study revealed differences in β-Sheet percentage between less stable (T118N) and other mutants. As a conclusion, the comparative analysis of the tertiary structure and specific residues associated with ion-pair interactions and hydrogen bonds could be significant in revealing the thermostability of an enzyme with industrial importance.
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Affiliation(s)
- Siti Nor Hasmah Ishak
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd. Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Improving the fermentable sugar yields of wheat straw by high-temperature pre-hydrolysis with thermophilic enzymes of Malbranchea cinnamomea. Microb Cell Fact 2020; 19:149. [PMID: 32711527 PMCID: PMC7382850 DOI: 10.1186/s12934-020-01408-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 07/20/2020] [Indexed: 12/23/2022] Open
Abstract
Background Enzymatic hydrolysis is a key step in the conversion of lignocellulosic polysaccharides to fermentable sugars for the production of biofuels and high-value chemicals. However, current enzyme preparations from mesophilic fungi are deficient in their thermostability and biomass-hydrolyzing efficiency at high temperatures. Thermophilic fungi represent promising sources of thermostable and highly active enzymes for improving the biomass-to-sugar conversion process. Here we present a comprehensive study on the lignocellulosic biomass-degrading ability and enzyme system of thermophilic fungus Malbranchea cinnamomea N12 and the application of its enzymes in the synergistic hydrolysis of lignocellulosic biomass. Results Malbranchea cinnamomea N12 was capable of utilizing untreated wheat straw to produce high levels of xylanases and efficiently degrading lignocellulose under thermophilic conditions. Temporal analysis of the wheat straw-induced secretome revealed that M. cinnamomea N12 successively degraded the lignocellulosic polysaccharides through sequential secretion of enzymes targeting xylan and cellulose. Xylanase-enriched cocktail from M. cinnamomea N12 was more active on native and alkali‑pretreated wheat straw than the commercial xylanases from Trichoderma reesei over temperatures ranging from 40 to 75 °C. Integration of M. cinnamomea N12 enzymes with the commercial cellulase preparation increased the glucose and xylose yields of alkali‑pretreated wheat straw by 32 and 166%, respectively, with pronounced effects at elevated temperature. Conclusions This study demonstrated the remarkable xylanase-producing ability and strategy of sequential lignocellulose breakdown of M. cinnamomea N12. A new process for the hydrolysis of lignocellulosic biomass was proposed, comprising thermophilic enzymolysis by enzymes of M. cinnamomea N12 followed with mesophilic enzymolysis by commercial cellulases. Developing M. cinnamomea N12 as platforms for thermophilic enzyme mixture production will provide new perspectives for improved conversion yields for current biomass saccharification schemes.
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Koendjbiharie JG, Post WB, Palmer MM, van Kranenburg R. Effects of CO 2 limitation on the metabolism of Pseudoclostridium thermosuccinogenes. BMC Microbiol 2020; 20:149. [PMID: 32513108 PMCID: PMC7282089 DOI: 10.1186/s12866-020-01835-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/28/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bio-based succinic acid holds promise as a sustainable platform chemical. Its production through microbial fermentation concurs with the fixation of CO2, through the carboxylation of phosphoenolpyruvate. Here, we studied the effect of the available CO2 on the metabolism of Pseudoclostridium thermosuccinogenes, the only known succinate producing thermophile. Batch cultivations in bioreactors sparged with 1 and 20% CO2 were conducted that allowed us to carefully study the effect of CO2 limitation. RESULTS Formate yield was greatly reduced at low CO2 concentrations, signifying a switch from pyruvate formate lyase (PFL) to pyruvate:ferredoxin oxidoreductase (PFOR) for acetyl-CoA formation. The corresponding increase in endogenous CO2 production (by PFOR) enabled succinic acid production to be largely maintained as its yield was reduced by only 26%, thus also maintaining the concomitant NADH re-oxidation, essential for regenerating NAD+ for glycolysis. Acetate yield was slightly reduced as well, while that of lactate was slightly increased. CO2 limitation also prompted the formation of significant amounts of ethanol, which is only marginally produced during CO2 excess. Altogether, the changes in fermentation product yields result in increased ferredoxin and NAD+ reduction, and increased NADPH oxidation during CO2 limitation, which must be linked to reshuffled (trans) hydrogenation mechanisms of those cofactors, in order to keep them balanced. RNA sequencing, to investigate transcriptional effects of CO2 limitation, yielded only ambiguous results regarding the known (trans) hydrogenation mechanisms. CONCLUSIONS The results hinted at a decreased NAD+/NADH ratio, which could ultimately be responsible for the stress observed during CO2 limitation. Clear overexpression of an alcohol dehydrogenase (adhE) was observed, which may explain the increased ethanol production, while no changes were seen for PFL and PFOR expression that could explain the anticipated switch based on the fermentation results.
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Affiliation(s)
| | | | - Martí Munar Palmer
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Richard van Kranenburg
- Corbion, Gorinchem, Netherlands. .,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.
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74
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Han C, Yang R, Sun Y, Liu M, Zhou L, Li D. Identification and Characterization of a Novel Hyperthermostable Bifunctional Cellobiohydrolase- Xylanase Enzyme for Synergistic Effect With Commercial Cellulase on Pretreated Wheat Straw Degradation. Front Bioeng Biotechnol 2020; 8:296. [PMID: 32328483 PMCID: PMC7160368 DOI: 10.3389/fbioe.2020.00296] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/20/2020] [Indexed: 12/19/2022] Open
Abstract
The novel cellobiohydrolase gene ctcel7 was identified from Chaetomium thermophilum, and its recombinant protein CtCel7, a member of glycoside hydrolase family 7, was heterologously expressed in Pichia pastoris and biochemically characterized. Compared with commercial hydrolases, purified CtCel7 exhibited superior bifunctional cellobiohydrolase and xylanase activities against microcrystalline cellulose and xylan, respectively, under optimal conditions of 60°C and pH 4.0. Moreover, CtCel7 displayed remarkable thermostability with over 90% residual activity after heat (60°C) treatment for 180 min. CtCel7 was insensitive to most detected cations and reagents and preferentially cleaved the β-1,4-glycosidic bond to generate oligosaccharides through the continuous saccharification of lignocellulosic substrates, which are crucial for various practical applications. Notably, the hydrolysis effect of a commercial cellulase cocktail on pretreated wheat straw was substantively improved by its combination with CtCel7. Taken together, these excellent properties distinguish CtCel7 as a robust candidate for the biotechnological production of biofuels and biobased chemicals.
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Affiliation(s)
- Chao Han
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Ruirui Yang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Yanxu Sun
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Mengyu Liu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Lifan Zhou
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Duochuan Li
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
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75
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Puglia MK, Malhotra M, Kumar CV. Engineering functional inorganic nanobiomaterials: controlling interactions between 2D-nanosheets and enzymes. Dalton Trans 2020; 49:3917-3933. [PMID: 31799574 DOI: 10.1039/c9dt03893k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A better understanding of the enzyme-nanosheet interface is imperative for the design of functional, robust inorganic nanobiomaterials and biodevices, now more than ever, for use in a broad spectrum of applications. This feature article discusses recent advances in controlling the enzyme-nanosheet interface with regards to α-zirconium(iv) phosphate (α-ZrP), graphene oxide (GO), graphene, and MoS2 nanosheets. Specific focus will be placed on understanding the mechanisms with which these materials interact with enzymes and elaborate on particular ways to engineer and control these interactions. Our main discoveries include: (1) upon adsorption to the nanosheet surface, a decrease in the entropy of the enzyme's denatured state enhances stability; (2) proteins are used to create biophilic landing pads for increased enzyme stability on many different types of nanosheets; (3) proteins and enzymes are used as exfoliants by shear force to produce biofunctionalized nanosheet suspensions; and (4) bionfunctionalized nanosheets exhibit no acute toxicity. Recognizing proper methods to engineer the interface between enzymes and 2D-nanosheets, therefore, is an important step towards making green, sustainable, and environmentally conscious inorganic bionanomaterials for sensing, catalysis and drug delivery applications, as well as towards the successful manipulation of enzymes for advanced applications.
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Affiliation(s)
- Megan K Puglia
- University of Connecticut, Department of Chemistry, Storrs, CT 06269, USA.
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76
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Huang P, Chu SKS, Frizzo HN, Connolly MP, Caster RW, Siegel JB. Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset. ACS OMEGA 2020; 5:6487-6493. [PMID: 32258884 PMCID: PMC7114132 DOI: 10.1021/acsomega.9b04105] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/06/2020] [Indexed: 05/04/2023]
Abstract
Engineering proteins to enhance thermal stability is a widely utilized approach for creating industrially relevant biocatalysts. The development of new experimental datasets and computational tools to guide these engineering efforts remains an active area of research. Thus, to complement the previously reported measures of T 50 and kinetic constants, we are reporting an expansion of our previously published dataset of mutants for β-glucosidase to include both measures of T M and ΔΔG. For a set of 51 mutants, we found that T 50 and T M are moderately correlated, with a Pearson correlation coefficient and Spearman's rank coefficient of 0.58 and 0.47, respectively, indicating that the two methods capture different physical features. The performance of predicted stability using nine computational tools was also evaluated on the dataset of 51 mutants, none of which are found to be strong predictors of the observed changes in T 50, T M, or ΔΔG. Furthermore, the ability of the nine algorithms to predict the production of isolatable soluble protein was examined, which revealed that Rosetta ΔΔG, FoldX, DeepDDG, PoPMuSiC, and SDM were capable of predicting if a mutant could be produced and isolated as a soluble protein. These results further highlight the need for new algorithms for predicting modest, yet important, changes in thermal stability as well as a new utility for current algorithms for prescreening designs for the production of mutants that maintain fold and soluble production properties.
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Affiliation(s)
- Peishan Huang
- Biophysics
Graduate Group, University of California, Davis 95616, California, United States
| | - Simon K. S. Chu
- Biophysics
Graduate Group, University of California, Davis 95616, California, United States
| | - Henrique N. Frizzo
- Genome
Center, University of California, Davis 95616, California, United States
| | - Morgan P. Connolly
- Microbiology
Graduate Group, University of California, Davis 95616, California, United States
| | - Ryan W. Caster
- Genome
Center, University of California, Davis 95616, California, United States
| | - Justin B. Siegel
- Genome
Center, University of California, Davis 95616, California, United States
- Department
of Biochemistry & Molecular Medicine, University of California, Davis 95616, California, United States
- Department
of Chemistry, University of California, Davis 95616, California, United States
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77
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Cann I, Pereira GV, Abdel-Hamid AM, Kim H, Wefers D, Kayang BB, Kanai T, Sato T, Bernardi RC, Atomi H, Mackie RI. Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products. Appl Environ Microbiol 2020; 86:e02296-19. [PMID: 31980431 PMCID: PMC7082577 DOI: 10.1128/aem.02296-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.
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Affiliation(s)
- Isaac Cann
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Gabriel V Pereira
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel Wefers
- Karlsruhe Institute of Technology, Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
| | - Boniface B Kayang
- Department of Animal Science, School of Agriculture, University of Ghana, Legon, Ghana
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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78
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Kahn A, Moraïs S, Chung D, Sarai NS, Hengge NN, Kahn A, Himmel ME, Bayer EA, Bomble YJ. Glycosylation of hyperthermostable designer cellulosome components yields enhanced stability and cellulose hydrolysis. FEBS J 2020; 287:4370-4388. [DOI: 10.1111/febs.15251] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/06/2020] [Accepted: 02/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Amaranta Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
- Faculty of Natural Sciences Ben‐Gurion University of the Negev Beer‐Sheva Israel
| | - Daehwan Chung
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Nicholas S. Sarai
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Neal N. Hengge
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Audrey Kahn
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Michael E. Himmel
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Edward A. Bayer
- Department of Biomolecular Sciences The Weizmann Institute of Science Rehovot Israel
| | - Yannick J. Bomble
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
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79
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Elucidating the preference of dimeric over monomeric form for thermal stability of Thermus thermophilus isopropylmalate dehydrogenase: A molecular dynamics perspective. J Mol Graph Model 2020; 96:107530. [PMID: 31986322 DOI: 10.1016/j.jmgm.2020.107530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/23/2022]
Abstract
An oligomer usually refers to a macromolecular complex formed by non-covalent interactions of monomers. Several thermophilic proteins are oligomers. The significance of oligomerization of individual proteins for stability at higher temperature is of prime importance for understanding evolution and increasing industrial productivity. The functional form of Thermus thermophilius isopropylmalate dehydrogenase (IPMDH), a widely studied protein to understand the factors affecting the thermal stability of a protein is a dimer, a simplest oligomer. To decipher the relationship between the effects of oligomerization on thermal stability of a protein, we have applied all-atom molecular mechanics approach by analyzing how temperature effects dynamics of a subunit in the presence and absence of another subunit in dimeric (SS) and monomeric forms (SA), respectively, before its denaturation begins. Comparing the difference in overall dynamic structural aspects at two different temperatures, 300 K and 337 K. Analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and Cα-Cα distance with an increase in temperature from 300 K to 337 K for a total of 0.2 μs reveals higher thermal stability of the dimer as compared to monomer. In contrast to dimeric form, the monomer is relatively stable at 300 K but cannot withstand the structural stability at 337 K leading to loosening of intramolecular interactions with maximum fluctuation at B23-B24 within a subunit. Energetic and structural properties indicate that B24-B24' is the major contributor to maintaining subunit-subunit interaction at 337 K. Correlation between the favorable interaction energy (IE) with the minimal perturbance in Cα atoms of domain 2 in a subunit in the presence of another subunit enhances the rigidity of the domain with subunit-subunit interaction. Overall, the study indicates that the dimeric over monomeric form enhances the protein's thermal stability and not all major subunit interacting regions contribute equally in maintaining the former.
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80
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Zhu M, Zhang L, Yang F, Cha Y, Li S, Zhuo M, Huang S, Li J. A Recombinant β-Mannanase from Thermoanaerobacterium aotearoense SCUT27: Biochemical Characterization and Its Thermostability Improvement. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:818-825. [PMID: 31845578 DOI: 10.1021/acs.jafc.9b06246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
β-Mannanase was expressed in Thermoanaerobacterium aotearoense SCUT27 induced by locust bean gum (LBG). The open reading frame encoding a GH26 β-mannanase was identified and encoded a preprotein of 515 amino acids with a putative signal peptide. The enzyme without a signal sequence (Man25) was overexpressed in Escherichia coli with a specific activity of 1286.2 U/mg. Moreover, a facile method for β-mannanase activity screening was established based on agar plates. The optimum temperature for the purified Man25 using LBG as a substrate was 55 °C. The catalytic activity and thermostability of Man25 displayed a strong dependence on calcium ions. Through saturation mutagenesis at the putative Ca2+ binding sites in Man25, the best mutant ManM3-3 (D143A) presented improvements in thermostability with 3.6-fold extended half-life at 55 °C compared with that of the wild-type. The results suggest that mutagenesis at metal binding sites could be an efficient approach to increase enzyme thermostability.
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Affiliation(s)
- Muzi Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology , Guangdong Academy of Sciences , Guangzhou 510070 , China
| | | | - Fang Yang
- Integrative Microbiology Research Centre , South China Agricultural University , Guangzhou 510642 , China
| | | | | | | | | | - Jianjun Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology , Guangdong Academy of Sciences , Guangzhou 510070 , China
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81
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Deshwal A, Chitra H, Maity M, Pal SK, Maiti S. Sucrose-mediated heat-stiffening microemulsion-based gel for enzyme entrapment and catalysis. Chem Commun (Camb) 2020; 56:10698-10701. [DOI: 10.1039/d0cc04294c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Formation of a thermo-stiffening microemulsion-based-gel showing the nanoconfinement effect of carbohydrates as an efficient batch bioreactor for entrapped enzymes has been reported.
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Affiliation(s)
- Akshi Deshwal
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Knowledge City
- India
| | - Himanshu Chitra
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Knowledge City
- India
| | - Madhusudan Maity
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Knowledge City
- India
| | - Santanu Kumar Pal
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Knowledge City
- India
| | - Subhabrata Maiti
- Department of Chemical Sciences
- Indian Institute of Science Education and Research (IISER) Mohali
- Knowledge City
- India
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82
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Abstract
Thermophilic microbes are an attractive bioproduction platform due to their inherently lower contamination risk and their ability to perform thermostable enzymatic processes which may be required for biomass processing and other industrial applications. The engineering of microbes for industrial scale processes requires a suite of genetic engineering tools to optimize existing biological systems as well as to design and incorporate new metabolic pathways within strains. Yet, such tools are often lacking and/or inadequate for novel microbes, especially thermophiles. This chapter focuses on genetic tool development and engineering strategies, in addition to challenges, for thermophilic microbes. We provide detailed instructions and techniques for tool development for an anaerobic thermophile, Caldanaerobacter subterraneus subsp. tengcongensis, including culturing, plasmid construction, transformation, and selection. This establishes a foundation for advanced genetic tool development necessary for the metabolic engineering of this microbe and potentially other thermophilic organisms.
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83
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Bilal M, Iqbal HMN. State-of-the-art strategies and applied perspectives of enzyme biocatalysis in food sector - current status and future trends. Crit Rev Food Sci Nutr 2020; 60:2052-2066. [PMID: 31210055 DOI: 10.1080/10408398.2019.1627284] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the recent progress in biotechnology, a wide variety of novel enzymes with unique physicochemical properties and diverse applications has been introduced, and new application list continues to extend in the future. Enzymes obtained from microorganisms, including bacteria, fungi, yeast are widely applied in numerous food formulations for intensifying their texture and taste. Owing to several desirable characteristics such as easy, cost-efficient and stable production, microbial-derived enzymes are preferred source in contrast to animals or plants. Enzymatic processes have a considerable impact in controlling the characteristics such as (1) physiochemical properties, (2) rheological functionalities, (3) facile process as compared to the chemical-based processing, (4) no or minimal consumption of harsh chemicals, (5) overall cost-effective ratio, (6) sensory and flavor qualities, and (7) intensifying the stability, shelf life and overall quality of the product, etc. in the food industry. Also, enzyme-catalyzed processing has also been designed for new food applications such as extraction of bioactive compounds, nutrient-rich and texture improved foods production, and eliminating food safety hazards. Herein, we reviewed recent applications of food-processing enzymes and highlighted promising technologies to diversify their application range in food industries. Immobilization technology enabled biocatalysts to be used cost-effectively due to reusability with negligible or no activity loss. Integrated progress in novel enzyme discovery, and recombinant DNA technology, as well as protein engineering and bioprocess engineering strategies, are believed to rapidly propagate biocatalysis at industrial-scale food processing or green and sustainable chemical manufacturing.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Hafiz M N Iqbal
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, N.L., Mexico
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84
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Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles. Microorganisms 2019; 8:microorganisms8010059. [PMID: 31905784 PMCID: PMC7023208 DOI: 10.3390/microorganisms8010059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/25/2022] Open
Abstract
SecA is an evolutionarily conserved protein that plays an indispensable role in the secretion of proteins across the bacterial cell membrane. Comparative analyses of SecA homologs have identified two large conserved signature inserts (CSIs) that are unique characteristics of thermophilic bacteria. A 50 aa conserved insert in SecA is exclusively present in the SecA homologs from the orders Thermotogales and Aquificales, while a 76 aa insert in SecA is specific for the order Thermales and Hydrogenibacillus schlegelii. Phylogenetic analyses on SecA sequences show that the shared presence of these CSIs in unrelated groups of thermophiles is not due to lateral gene transfers, but instead these large CSIs have likely originated independently in these lineages due to their advantageous function. Both of these CSIs are located in SecA protein in a surface exposed region within the ATPase domain. To gain insights into the functional significance of the 50 aa CSI in SecA, molecular dynamics (MD) simulations were performed at two different temperatures using ADP-bound SecA from Thermotoga maritima. These analyses have identified a conserved network of water molecules near the 50 aa insert in which the Glu185 residue from the CSI is found to play a key role towards stabilizing these interactions. The results provide evidence for the possible role of the 50 aa CSI in stabilizing the binding interaction of ADP/ATP, which is required for SecA function. Additionally, the surface-exposed CSIs in SecA, due to their potential to make novel protein-protein interactions, could also contribute to the thermostability of SecA from thermophilic bacteria.
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85
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Zhang S, Luo J, Xie J, Wang Z, Xiao W, Zhao L. Cooperated biotransformation of ginsenoside extracts into ginsenoside 20(
S
)‐Rg3 by three thermostable glycosidases. J Appl Microbiol 2019; 128:721-734. [DOI: 10.1111/jam.14513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/29/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022]
Affiliation(s)
- S. Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing China
- College of Chemical Engineering Nanjing Forestry University Nanjing China
| | - J. Luo
- Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing China
- College of Chemical Engineering Nanjing Forestry University Nanjing China
| | - J. Xie
- Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing China
- College of Chemical Engineering Nanjing Forestry University Nanjing China
| | - Z. Wang
- Jiangsu Kanion Pharmaceutical Co. Ltd Lianyungang China
| | - W. Xiao
- Jiangsu Kanion Pharmaceutical Co. Ltd Lianyungang China
| | - L. Zhao
- Co‐Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry University Nanjing China
- College of Chemical Engineering Nanjing Forestry University Nanjing China
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86
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Peng M, Maier M, Esch J, Schug A, Rabe KS. Direct coupling analysis improves the identification of beneficial amino acid mutations for the functional thermostabilization of a delicate decarboxylase. Biol Chem 2019; 400:1519-1527. [PMID: 31472057 DOI: 10.1515/hsz-2019-0156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022]
Abstract
The optimization of enzyme properties for specific reaction conditions enables their tailored use in biotechnology. Predictions using established computer-based methods, however, remain challenging, especially regarding physical parameters such as thermostability without concurrent loss of activity. Employing established computational methods such as energy calculations using FoldX can lead to the identification of beneficial single amino acid substitutions for the thermostabilization of enzymes. However, these methods require a three-dimensional (3D)-structure of the enzyme. In contrast, coevolutionary analysis is a computational method, which is solely based on sequence data. To enable a comparison, we employed coevolutionary analysis together with structure-based approaches to identify mutations, which stabilize an enzyme while retaining its activity. As an example, we used the delicate dimeric, thiamine pyrophosphate dependent enzyme ketoisovalerate decarboxylase (Kivd) and experimentally determined its stability represented by a T50 value indicating the temperature where 50% of enzymatic activity remained after incubation for 10 min. Coevolutionary analysis suggested 12 beneficial mutations, which were not identified by previously established methods, out of which four mutations led to a functional Kivd with an increased T50 value of up to 3.9°C.
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Affiliation(s)
- Martin Peng
- Institute for Biological Interfaces I, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Manfred Maier
- Institute for Biological Interfaces I, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Jan Esch
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Alexander Schug
- Institute for Advanced Simulation, Jülich Supercomputing Center, D-52428 Jülich, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces I, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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Mirzaee Z, Jafarian V, Shirdel SA, Khalifeh K. Structural and functional consequences of replacement of His403 with Arg near the catalytic site of Anoxybacillus flavithermus cyclomaltodextrinase. Enzyme Microb Technol 2019; 131:109421. [PMID: 31615670 DOI: 10.1016/j.enzmictec.2019.109421] [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: 04/25/2019] [Revised: 08/24/2019] [Accepted: 09/03/2019] [Indexed: 11/26/2022]
Abstract
The hydrolytic activity of a thermophilic cyclomaltodextrinase (CMD) from Anoxybacillus flavithermus ZNU-NGA and a representative single mutant were investigated against soluble substrates including α-, β- and γ-cyclomaltodestrines (CDs). Based on the occurrence of arginine (Arg) at position 403 in some homologue proteins, His403 in Wild-type (WT) CMD was replaced with Arg (H403R variant) with site-directed mutagenesis procedures. According to bioinformatics data, Arg403 in mutant protein is located near Glu357 as one of the catalytic residues in a manner that they are able to create a medium-range attractive electrostatistic interaction. Structural studies by Far UV-CD showed that this mutation is accompanied by conversion of a small fraction of α-helix to β-form structure. Fluorescence data reveals that, the hydrophobic regions at the surface of protein, as the binding sites for ANS (8-Anilinonaphthalene-1-sulfonic acid) increase in mutant protein, demonstrating relative inflation of H403R variant compared with WT protein. However, the polarity of microenvironment around chromophores did not change upon mutation. Activity measurement in different ranges of pH and temperatures showed that the optimum values of pH and temperature in mutant enzyme is the same as WT enzyme, however; the activity at optimum points increased in H403R variant. It was also revealed that the H403R variant had slightly improved catalytic efficiency for γ-CD. The same value of activation parameters for both protein variants indicates that mutation does not alter the mechanism of catalysis during enzyme-substrate formation.
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Affiliation(s)
- Ziba Mirzaee
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
| | - Vahab Jafarian
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
| | - Seyedeh Akram Shirdel
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
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dos Santos Gomes AC, Falkoski D, Battaglia E, Peng M, Nicolau de Almeida M, Coconi Linares N, Meijnen JP, Visser J, de Vries RP. Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:220. [PMID: 31534479 PMCID: PMC6745793 DOI: 10.1186/s13068-019-1556-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Myceliophthora thermophila is a thermophilic ascomycete fungus that is used as a producer of enzyme cocktails used in plant biomass saccharification. Further development of this species as an industrial enzyme factory requires a detailed understanding of its regulatory systems driving the production of plant biomass-degrading enzymes. In this study, we analyzed the function of MtXlr1, an ortholog of the (hemi-)cellulolytic regulator XlnR first identified in another industrially relevant fungus, Aspergillus niger. RESULTS The Mtxlr1 gene was deleted and the resulting strain was compared to the wild type using growth profiling and transcriptomics. The deletion strain was unable to grow on xylan and d-xylose, but showed only a small growth reduction on l-arabinose, and grew similar to the wild type on Avicel and cellulose. These results were supported by the transcriptome analyses which revealed reduction of genes encoding xylan-degrading enzymes, enzymes of the pentose catabolic pathway and putative pentose transporters. In contrast, no or minimal effects were observed for the expression of cellulolytic genes. CONCLUSIONS Myceliophthora thermophila MtXlr1 controls the expression of xylanolytic genes and genes involved in pentose transport and catabolism, but has no significant effects on the production of cellulases. It therefore resembles more the role of its ortholog in Neurospora crassa, rather than the broader role described for this regulator in A. niger and Trichoderma reesei. By revealing the range of genes controlled by MtXlr1, our results provide the basic knowledge for targeted strain improvement by overproducing or constitutively activating this regulator, to further improve the biotechnological value of M. thermophila.
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Affiliation(s)
- Ana Carolina dos Santos Gomes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Daniel Falkoski
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Novozymes Latin America, Professor Francisco Ribeiro Street 683, Araucária, PR 83707-660 Brazil
| | - Evy Battaglia
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maira Nicolau de Almeida
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- DuPont Industrial Biosciences, Archimedesweg 30, 2333 CN Leiden, The Netherlands
- Present Address: Federal University of São João del Rei, Praça Dom Helvécio, 74, São João del Rei, Minas Gerais Brazil
| | - Nancy Coconi Linares
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jean-Paul Meijnen
- DuPont Industrial Biosciences, Archimedesweg 30, 2333 CN Leiden, The Netherlands
- Present Address: Dutch DNA Biotech BV, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jaap Visser
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Torktaz I, Hemmat J, Karkhane AA, Rigi G, Rostami A, Khezri J, Behroozi R. Molecular Engineering of the Geobacillus stearothermophilus α-Amylase and Cel5E from Chlostridium thermocellim; In Silico Approach. IRANIAN JOURNAL OF BIOTECHNOLOGY 2019; 16:e1284. [PMID: 31457020 PMCID: PMC6697822 DOI: 10.15171/ijb.1284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 11/23/2022]
Abstract
Background Considering natural thermal stability, Geobacillus stearothermophilus amylase and Cel5E from Clostridium thermocellum are good candidates for industrial applications. To be compatible with the industrial applications, this enzyme should be stable in the high temperatures, so any improvement in their thermal stability is valuable. Objectives Using in silico approach and identifying point mutations in the structure amylase of G. stearothermophilus and Cel5E from C. termocellum we tried to increase thermal stability of the enzymes along with their catalytic activity to reach a new industrial amylase with higher thermostability and an improved function. Materials and Methods In this study we predicted the 3D structure of the enzymes, then simulated the molecular docking study using MolDock, PLANTS, and Lamarkian genetic algorithm as scoring functions for the docking and in silico engineering of the protein aiming to increase the thermal stability and catalytic activity. Results A series of thermal stability increasing point mutations were exerted around the active site of the enzyme, then by docking procedure, the binding affinity was measured and finally a list of mutations which theoretically improved the increased thermal stability as well as catalytic activity were proposed. Conclusions Based on the in silico results obtained the modified enzymes seems to be suitable candidates for considering in both laboratory and industrial scales.
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Affiliation(s)
- Ibrahim Torktaz
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.,Biotechnology Department. Iranian Research Organization for Science and Technology (IROST) Tehran-Iran
| | - Jafar Hemmat
- Biotechnology Department. Iranian Research Organization for Science and Technology (IROST) Tehran-Iran
| | | | - Garshasb Rigi
- Department of Genetics, Faculty of Basic Science, University of Shahrekord, Shahrekord, Iran
| | - Amin Rostami
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jafar Khezri
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Reza Behroozi
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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90
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Bashir Z, Sheng L, Anil A, Lali A, Minton NP, Zhang Y. Engineering Geobacillus thermoglucosidasius for direct utilisation of holocellulose from wheat straw. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:199. [PMID: 31452680 PMCID: PMC6701081 DOI: 10.1186/s13068-019-1540-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/06/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND A consolidated bioprocessing (CBP), where lignocellulose is converted into the desired product(s) in a single fermentative step without the addition of expensive degradative enzymes, represents the ideal solution of renewable routes to chemicals and fuels. Members of the genus Geobacillus are able to grow at elevated temperatures and are able to utilise a wide range of oligosaccharides derived from lignocellulose. This makes them ideally suited to the development of CBP. RESULTS In this study, we engineered Geobacillus thermoglucosidasius NCIMB 11955 to utilise lignocellulosic biomass, in the form of nitric acid/ammonia treated wheat straw to which expensive hydrolytic enzymes had not been added. Two different strains, BZ9 and BZ10, were generated by integrating the cglT (β-1,4-glucosidase) gene from Thermoanaerobacter brockii into the genome, and localising genes encoding different cellulolytic enzymes on autonomous plasmids. The plasmid of strain BZ10 carried a synthetic cellulosomal operon comprising the celA (Endoglucanase A) gene from Clostridium thermocellum and cel6B (Exoglucanase) from Thermobifida fusca; whereas, strain BZ9 contained a plasmid encoding the celA (multidomain cellulase) gene from Caldicellulosiruptor bescii. All of the genes were successfully expressed, and their encoded products secreted in a functionally active form, as evidenced by their detection in culture supernatants by Western blotting and enzymatic assay. In the case of the C. bescii CelA enzyme, this is one of the first times that the heterologous production of this multi-functional enzyme has been achieved in a heterologous host. Both strains (BZ9 and BZ10) exhibited improved growth on pre-treated wheat straw, achieving a higher final OD600 and producing greater numbers of viable cells. To demonstrate that cellulosic ethanol can be produced directly from lignocellulosic biomass by a single organism, we established our consortium of hydrolytic enzymes in a previously engineered ethanologenic G. thermoglucosidasius strain, LS242. We observed approximately twofold and 1.6-fold increase in ethanol production in the recombinant G. thermoglucosidasius equivalent to BZ9 and BZ10, respectively, compared to G. thermoglucosidasius LS242 strain at 24 h of growth. CONCLUSION We engineered G. thermoglucosidasius to utilise a real-world lignocellulosic biomass substrate and demonstrated that cellulosic ethanol can be produced directly from lignocellulosic biomass in one step. Direct conversion of biomass into desired products represents a new paradigm for CBP, offering the potential for carbon neutral, cost-effective production of sustainable chemicals and fuels.
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Affiliation(s)
- Zeenat Bashir
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Lili Sheng
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Annamma Anil
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parikh Marg, Mumbai, 400019 India
| | - Arvind Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathalal Parikh Marg, Mumbai, 400019 India
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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Abstract
Dextran aldehyde (dexOx), resulting from the periodate oxidative cleavage of 1,2-diol moiety inside dextran, is a polymer that is very useful in many areas, including as a macromolecular carrier for drug delivery and other biomedical applications. In particular, it has been widely used for chemical engineering of enzymes, with the aim of designing better biocatalysts that possess improved catalytic properties, making them more stable and/or active for different catalytic reactions. This polymer possesses a very flexible hydrophilic structure, which becomes inert after chemical reduction; therefore, dexOx comes to be highly versatile in a biocatalyst design. This paper presents an overview of the multiple applications of dexOx in applied biocatalysis, e.g., to modulate the adsorption of biomolecules on carrier surfaces in affinity chromatography and biosensors design, to serve as a spacer arm between a ligand and the support in biomacromolecule immobilization procedures or to generate artificial microenvironments around the enzyme molecules or to stabilize multimeric enzymes by intersubunit crosslinking, among many other applications.
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92
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Li G, Rabe KS, Nielsen J, Engqvist MKM. Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima. ACS Synth Biol 2019; 8:1411-1420. [PMID: 31117361 DOI: 10.1021/acssynbio.9b00099] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Enzymes that catalyze chemical reactions at high temperatures are used for industrial biocatalysis, applications in molecular biology, and as highly evolvable starting points for protein engineering. The optimal growth temperature (OGT) of organisms is commonly used to estimate the stability of enzymes encoded in their genomes, but the number of experimentally determined OGT values are limited, particularly for thermophilic organisms. Here, we report on the development of a machine learning model that can accurately predict OGT for bacteria, archaea, and microbial eukaryotes directly from their proteome-wide 2-mer amino acid composition. The trained model is made freely available for reuse. In a subsequent step we use OGT data in combination with amino acid composition of individual enzymes to develop a second machine learning model-for prediction of enzyme catalytic temperature optima ( Topt). The resulting model generates enzyme Topt estimates that are far superior to using OGT alone. Finally, we predict Topt for 6.5 million enzymes, covering 4447 enzyme classes, and make the resulting data set available to researchers. This work enables simple and rapid identification of enzymes that are potentially functional at extreme temperatures.
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Affiliation(s)
- Gang Li
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG 1) , Karlsruhe Institute of Technology (KIT) , Group for Molecular Evolution, 76131 Karlsruhe , Germany
| | - Jens Nielsen
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
- Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , DK-2800 Kgs. Lyngby , Denmark
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
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93
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Ahan RE, Saltepe B, Apaydin O, Seker UOS. Cellular Biocatalysts Using Synthetic Genetic Circuits for Prolonged and Durable Enzymatic Activity. Chembiochem 2019; 20:1799-1809. [DOI: 10.1002/cbic.201800767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/08/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Recep Erdem Ahan
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
| | - Behide Saltepe
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
| | - Onur Apaydin
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
| | - Urartu Ozgur Safak Seker
- UNAM-Institute of Materials Science and NanotechnologyNational Nanotechnology Research Center Bilkent University 06800 Ankara Turkey
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94
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Patel AK, Singhania RR, Sim SJ, Pandey A. Thermostable cellulases: Current status and perspectives. BIORESOURCE TECHNOLOGY 2019; 279:385-392. [PMID: 30685132 DOI: 10.1016/j.biortech.2019.01.049] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 05/18/2023]
Abstract
It is envisaged that the utilization of lignocellulosic biomass for ethanol production for transport sector, would make cellulases the most demanded industrial enzyme. The greatest potential of cellulolytic enzymes lies in ethanol production from biomass by enzymatic hydrolysis of cellulose but low thermostability and low titer of cellulase production resulting into high cost of the enzyme which is the major set-back. A number of research groups are working on cellulase to improve its thermostability so as to be able to perform hydrolysis at elevated temperatures which would eventually increase the efficiency of cellulose hydrolysis. The technologies developed from lignocellulosic biomass via cellulose hydrolysis promise environmental and economical sustainability in the long run along with non-dependence on nonrenewable energy source. This review deals with the important sources of thermostable cellulases, mechanism, its regulation, strategies to enhance the thermostability further with respect to its importance for biofuel applications.
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Affiliation(s)
- Anil K Patel
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | | | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, Indian Institute of Toxicological Research, Lucknow 226 001, India
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95
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Azman NF, Megat Mohd Noor MJ, Md Akhir FN, Ang MY, Hashim H, Othman N, Zakaria Z, Hara H. Depolymerization of lignocellulose of oil palm empty fruit bunch by thermophilic microorganisms from tropical climate. BIORESOURCE TECHNOLOGY 2019; 279:174-180. [PMID: 30721818 DOI: 10.1016/j.biortech.2019.01.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
Previous studies on screening of lignin-degrading bacteria mainly focused on the ligninolytic ability of the isolated bacteria for the utilization of lignin monomers. In this study, we focused on the depolymerization of alkali lignin to prove the ability of the isolated thermophilic bacterial strains to utilize and depolymerize more than a monomer of alkali lignin within 7 days of incubation. Indigenous thermophilic bacterial isolates from the palm oil plantation were used to evaluate the depolymerization and utilization of alkali lignin. The confirmation of the bacterium-mediated depolymerization of oil palm empty fruit bunch was achieved through the removal of silica bodies, as observed with scanning electron microscopy. Stenotrophomonas sp. S2 and Bacillus subtilis S11Y were able to reduce approximately 50% and 20% of alkali lignin at 7 days of incubation without the requirement for additional carbon sources.
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Affiliation(s)
- Nadia Farhana Azman
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Megat Johari Megat Mohd Noor
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Fazrena Nadia Md Akhir
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - May Yen Ang
- Analytical and Scientific Instrument Division, Shimadzu Malaysia Sdn. Bhd. Nouvelle Industrial Park 2, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - Hazni Hashim
- Analytical and Scientific Instrument Division, Shimadzu Malaysia Sdn. Bhd. Nouvelle Industrial Park 2, Taman Sains Selangor 1, Kota Damansara, 47810 Petaling Jaya, Selangor, Malaysia
| | - Nor'Azizi Othman
- Department of Mechanical Precision Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Zuriati Zakaria
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia
| | - Hirofumi Hara
- Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia, Jalan Sultan Yahya Petra, 54100 Kuala Lumpur, Malaysia.
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Lusk BG. Thermophiles; or, the Modern Prometheus: The Importance of Extreme Microorganisms for Understanding and Applying Extracellular Electron Transfer. Front Microbiol 2019; 10:818. [PMID: 31080440 PMCID: PMC6497744 DOI: 10.3389/fmicb.2019.00818] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/01/2019] [Indexed: 11/30/2022] Open
Abstract
Approximately four billion years ago, the first microorganisms to thrive on earth were anaerobic chemoautotrophic thermophiles, a specific group of extremophiles that survive and operate at temperatures ∼50 - 125°C and do not use molecular oxygen (O2) for respiration. Instead, these microorganisms performed respiration via dissimilatory metal reduction by transferring their electrons extracellularly to insoluble electron acceptors. Genetic evidence suggests that Gram-positive thermophilic bacteria capable of extracellular electron transfer (EET) are positioned close to the root of the Bacteria kingdom on the tree of life. On the contrary, EET in Gram-negative mesophilic bacteria is a relatively new phenomenon that is evolutionarily distinct from Gram-positive bacteria. This suggests that EET evolved separately in Gram-positive thermophiles and Gram-negative mesophiles, and that EET in these bacterial types is a result of a convergent evolutionary process leading to homoplasy. Thus, the study of dissimilatory metal reducing thermophiles provides a glimpse into some of Earth's earliest forms of respiration. This will provide new insights for understanding biogeochemistry and the development of early Earth in addition to providing unique avenues for exploration and discovery in astrobiology. Lastly, the physiological composition of Gram-positive thermophiles, coupled with the kinetic and thermodynamic consequences of surviving at elevated temperatures, makes them ideal candidates for developing new mathematical models and designing innovative next-generation biotechnologies. KEY CONCEPTS Anaerobe: organism that does not require oxygen for growth. Chemoautotroph: organism that obtains energy by oxidizing inorganic electron donors. Convergent Evolution: process in which organisms which are not closely related independently evolve similar traits due to adapting to similar ecological niches and/or environments. Dissimilatory Metal Reduction: reduction of a metal or metalloid that uses electrons from oxidized organic or inorganic electron donors. Exoelectrogen: microorganism that performs dissimilatory metal reduction via extracellular electron transfer. Extremophiles: organisms that thrive in physical or geochemical conditions that are considered detrimental to most life on Earth. Homoplasy: a character shared by a set of species that is not shared by a common ancestor Non-synonymous Substitutions (K a ): a substitution of a nucleotide that changes a codon sequence resulting in a change in the amino acid sequence of a protein. Synonymous Substitutions (K s ): a substitution of a nucleotide that may change a codon sequence, but results in no change in the amino acid sequence of a protein. Thermophiles: a specific group of extremophiles that survive and operate at temperatures ∼50-125°C.
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Taniguchi H, Imura M, Okano K, Honda K. Developing a single strain for in vitro salvage synthesis of NAD + at high temperatures and its potential for bioconversion. Microb Cell Fact 2019; 18:75. [PMID: 31023312 PMCID: PMC6482498 DOI: 10.1186/s12934-019-1125-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/22/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Thermostable enzymes have several advantages over their mesophilic counterparts for industrial applications. However, trade-offs such as thermal instability of enzyme substrates or co-factors exist. Nicotinamide adenine dinucleotide (NAD+) is an important co-factor in many enzyme-catalyzed oxidation-reduction reactions. This compound spontaneously decomposes at elevated temperatures and basic pH, a property that limits catalysis of NAD+/NADH-dependent bioconversions using thermostable enzymes to short timeframes. To address this issue, an "in vitro metabolic pathway" for salvage synthesis of NAD+ using six thermophilic enzymes was constructed to resynthesize NAD+ from its thermal decomposition products at high temperatures. RESULTS An integrated strain, E. coli DH5α (pBR-CI857, pGETS118-NAD+), that codes for six thermophilic enzymes in a single operon was constructed. Gene-expression levels of these enzymes in the strain were modulated by their sequential order in the operon. An enzyme solution containing these enzymes was prepared by the heat purification from the cell lysate of the integrated strain, and used as an enzyme cocktail for salvage synthesis of NAD+. The salvage activity for synthesis of NAD+ from its thermal decomposition products was found to be 0.137 ± 0.006 µmol min-1 g-1 wet cells. More than 50% of this initial activity remained after 24 h at 60 °C. The enzyme cocktail could maintain a NAD+ concentration of 1 mM for 12 h at 60 °C. Furthermore, this enzyme cocktail supported continuous NAD+/NADH-dependent redox reactions using only NAD+/NADH derived from host cells, without the need for addition of external NAD+. CONCLUSIONS The integrated strain allows preparation of an enzyme cocktail that can solve the problem of NAD+ instability at high temperatures. The strain simplifies preparation of the enzyme cocktail, and thus expands the applicability of the in vitro metabolic engineering method using thermostable enzymes. Further optimization of gene expressions in the integrated strain can be achieved by using various types of ribosome binding sites as well as promoters.
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Affiliation(s)
- Hironori Taniguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - Makoto Imura
- KOHJIN Life Sciences Co., Ltd., Higashihama 1-6, Saiki, Oita, 876-858, Japan
| | - Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan.
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Fortune B, Mhlongo S, van Zyl LJ, Huddy R, Smart M, Trindade M. Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome. BMC Biotechnol 2019; 19:22. [PMID: 30999885 PMCID: PMC6472066 DOI: 10.1186/s12896-019-0510-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails. RESULTS Three fosmids, pFos-H4, E3 and D3 were selected from the cloned metagenome of high temperature compost, expressed in Escherichia coli and subsequently purified to homogeneity from cell lysate. All the AFases were clustered within the GH51 AFase family and shared a homo-hexameric structure. Both AFase-E3 and H4 showed optimal activity at 60 °C while AFase-D3 had unique properties as it showed optimal activity at 25 °C as well as the ability to maintain substantial activity at temperatures as high as 90 °C. However, AFase-E3 was the most thermostable amongst the three AFases showing full activity even at 70 °C. The maximum activity was observed at a pH profile between pH 4.0-6.0 for all three AFases with optimal activity for AFase H4, D3 and E3 at pH 5.0, 4.5 and 4.0, respectively. All the AFases showed KM range between 0.31 mM and 0.43 mM, Kcat range between 131 s- 1 and 219 s- 1 and the specific activity for AFase-H4, AFases-E3 and was 143, 228 and 175 U/mg, respectively. AFases-E3 and D3 displayed activities against pNP-β-L-arabinopyranoside and pNP-β-L-mannopyranoside respectively, and both hydrolysed pNP-β-D-glucopyranoside. CONCLUSION All three AFases displayed different biochemical characteristics despite all showing conserved overall structural similarity with typical domains of AFases belonging to GH51 family. The hydrolysis of cellobiose by a GH51 family AFase is demonstrated for the first time in this study.
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Affiliation(s)
- Brent Fortune
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Sizwe Mhlongo
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Robert Huddy
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Mariette Smart
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.
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Huijbers MME, Wu JW, Westphal AH, Berkel WJH. Dimerization of Proline Dehydrogenase from
Thermus thermophilus
Is Crucial for Its Thermostability. Biotechnol J 2019; 14:e1800540. [DOI: 10.1002/biot.201800540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Mieke M. E. Huijbers
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
| | - Jenny W. Wu
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
| | - Adrie H. Westphal
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
| | - Willem J. H. Berkel
- Laboratory of BiochemistryWageningen University & ResearchStippeneng 4, 6708 WE Wageningen The Netherlands
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Yaşar Yildiz S, Nikerel E, Toksoy Öner E. Genome-Scale Metabolic Model of a Microbial Cell Factory ( Brevibacillus thermoruber 423) with Multi-Industry Potentials for Exopolysaccharide Production. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:237-246. [PMID: 30932743 DOI: 10.1089/omi.2019.0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Brevibacillus thermoruber 423 is a thermophilic bacterium capable of producing high levels of exopolysaccharide (EPS) that has broad applications in nutrition, feed, cosmetics, pharmaceutical, and chemical industries, not to mention in health and bionanotechnology sectors. EPS is a natural, nontoxic, and biodegradable polymer of sugar residues and plays pivotal roles in cell-to-cell interactions, adhesion, biofilm formation, and protection of cell against environmental extremes. This bacterium is a thermophilic EPS producer while exceeding other thermophilic producers by virtue of high level of polymer synthesis. Recently, B. thermoruber 423 was noted for relevance to multiple industry sectors because of its capacity to use xylose, and produce EPS, isoprenoids, ethanol/butanol, lipases, proteases, cellulase, and glucoamylase enzymes as well as its resistance to arsenic. A key step in understanding EPS production with a systems-based approach is the knowledge of microbial genome sequence. To speed biotechnology and industrial applications, this study reports on a genome-scale metabolic model (GSMM) of B. thermoruber 423, constructed using the recently available high-quality genome sequence that we have subsequently validated using physiological data on batch growth and EPS production on seven different carbon sources. The model developed contains 1454 reactions (of which 1127 are assigned an enzyme commission number) and 1410 metabolites from 925 genes. This GSMM offers the promise to enable and accelerate further systems biology and industrial scale studies, not to mention the ability to calculate metabolic flux distribution in large networks and multiomic data integration.
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Affiliation(s)
- Songül Yaşar Yildiz
- 1 Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
| | - Emrah Nikerel
- 2 Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
| | - Ebru Toksoy Öner
- 3 Department of Bioengineering, IBSB, Marmara University, Istanbul, Turkey
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