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Zhang, Min

Publications and source records attributed to Zhang, Min.

14 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Streamlining heterologous expression of top carbonic anhydrases in Escherichia coli : bioinformatic and experimental approaches

Carbonic anhydrase (CA) enzymes facilitate the reversible hydration of CO 2 to bicarbonate ions and protons. Identifying efficient and robust CAs and expressing them in model host cells, such as Escherichia coli, enables more efficient engineering of these enzymes for industrial CO 2 capture. However, expression of CAs in E. coli is challenging due to the possible formation of insoluble protein aggregates, or inclusion bodies. This makes the production of soluble and active CA protein a prerequisite for downstream applications. In this study, we streamlined the process of CA expression by selecting seven top CA candidates and used two bioinformatic tools to predict their solubility for expression in E. coli. The prediction results place these enzymes in two categories: low and high solubility. Our expression of high solubility score CAs (namely CA5-SspCA, CA6-SazCAtrunc, CA7-PabCA and CA8-PhoCA) led to significantly higher protein yields (5 to 75 mg purified protein per liter) in flask cultures, indicating a strong correlation between the solubility prediction score and protein expression yields. Furthermore, phylogenetic tree analysis demonstrated CA class-specific clustering patterns for protein solubility and production yields. Unexpectedly, we also found that the unique N-terminal, 11-amino acid segment found after the signal sequence (not present in its homologs), was essential for CA6-SazCA activity. Overall, this work demonstrated that protein solubility prediction, phylogenetic tree analysis, and experimental validation are potent tools for identifying top CA candidates and then producing soluble, active forms of these enzymes in E. coli. The comprehensive approaches we report here should be extendable to the expression of other heterogeneous proteins in E. coli.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Shear band velocity and activation volume during shear deformation by acoustic emission in a Zr-based bulk metallic glass

Here, an analysis is presented for the shear band velocity of plastic deformation and activation volume of the shear transformation zone (STZ) in a Zr 60 Cu 30 Al 10 bulk metallic glass (BMG). Compared to the values calculated by the stick-slip model, the values of shear band velocity calculated after optimization by the acoustic emission technique are much larger than those reported previously. Plastic flow in BMGs is found to be described by a power-law correlation between the maximum velocity of the shear band and the strain rates. Combining the free volume theory and the STZ theory, the relationship between the volume change in the STZ and the shear band velocity is derived as $Ω=A$(27–ln$v/l$). The value of A, which is a material dependent constant, is 5.43 × 10 –3 for the current BMG at room temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO 2 and H 2

The decarbonization of the chemical industry and a shift toward circular economies because of high global CO 2 emissions make CO 2 an attractive feedstock for manufacturing chemicals. Moreover, H 2 is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water (scH 2 O) gasification enable sustainable production of molecular hydrogen (H 2 ). We review the recent advances in engineering Ralstonia eutropha, the representative species of "Knallgas" bacteria, for utilizing CO 2 and H 2 to autotrophically produce 2,3-butanediol (2,3-BDO). This assessment is focused on state-of-the-art approaches for splitting H 2 to supply energy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO 2 fixation. Major challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO 2 and H 2 -utilizing microorganisms, exemplified by Zymomonas mobilis.

42 ENGINEERING↗
DOE OSTI2022

Evaluating the Feasibility of Higher Titers and Yields for 2,3-Butanediol Production to Achieve the Biofuel Industry Economic Goal of Under $3.50 GGE

To achieve the economic goal of producing biofuels that can compete with petroleum-based products, we increased titers of 2,3-butanediol (BDO) production. BDO has many advantages over ethanol; including lower toxicity, higher heat of capacity, and is a precursor to various valuable applications. To produce BDO for fuel upgrading, we have genetically modified Zymomonas mobilis (YC-1). Several materials and feed strategies were evaluated to determine the best titer and economic feasibility. Titers from DMR corn stover in a batch process were in the range of 70-80 g/L. The fully hydrolyzed material was easy to work with but suffered from dilution issues. We pushed the concentration of solids to above 25% w/w and were met with numerous challenges. This included an initial sugar concentration above 150 g/L, the high solid concentration altered the oxygen mass transfer rate and affected which products were produced, and the fermentation conditions were not optimal for the enzyme. Despite these challenges, our current results yielded 100 g/L of upgradeable products (70 g/L BDO and 30 g/L acetoin) and 83% fermentation process yield. However, the poor enzymatic hydrolysis yield of 64%, unconverted xylose, and the high acetoin levels warrant further exploration for optimization. Using unhydrolyzed solids as the feed material, we achieved titers in the range of 75-95 g/L BDO. The raw solids feed, though operationally more challenging to work with, proved to be promising as the rate of hydrolysis promoted co-utilization of the sugars. We reached 150 g/L BDO using concentrated DDR liquors under boules and continuous feeding strategies. The clarified liquors showed high titers, high productivity, high yield, and high sugar utilization with little drawback operationally. The target goal of under $3.50 GGE was achieved in several feeding strategies. Scale-up feasibility has also been demonstrated at the 100L scale using both whole slurry and liquor hydrolysates.

BIOMASS FUELS↗
DOE OSTI2021

Disruption of the Snf1 Gene Enhances Cell Growth and Reduces the Metabolic Burden in Cellulase-Expressing and Lipid-Accumulating Yarrowia lipolytica

Yarrowia lipolytica is known to be capable of metabolizing glucose and accumulating lipids intracellularly; however, it lacks the cellulolytic enzymes needed to break down cellulosic biomass directly. To develop Y. lipolytica as a consolidated bioprocessing (CBP) microorganism, we previously expressed the heterologous CBH I, CBH II, and EG II cellulase enzymes both individually and collectively in this microorganism. We concluded that the coexpression of these cellulases resulted in a metabolic drain on the host cells leading to reduced cell growth and lipid accumulation. The current study aims to build a new cellulase coexpressing platform to overcome these hinderances by (1) knocking out the sucrose non-fermenting 1 ( Snf1 ) gene that represses the energetically expensive lipid and protein biosynthesis processes, and (2) knocking in the cellulase cassette fused with the recyclable selection marker URA3 gene in the background of a lipid-accumulating Y. lipolytica strain overexpressing ATP citrate lyase ( ACL ) and diacylglycerol acyltransferase 1 ( DGA1 ) genes. We have achieved a homologous recombination insertion rate of 58% for integrating the cellulases- URA3 construct at the disrupted Snf1 site in the genome of host cells. Importantly, we observed that the disruption of the Snf1 gene promoted cell growth and lipid accumulation and lowered the cellular saturated fatty acid level and the saturated to unsaturated fatty acid ratio significantly in the transformant YL163t that coexpresses cellulases. The result suggests a lower endoplasmic reticulum stress in YL163t, in comparison with its parent strain Po1g ACL-DGA1. Furthermore, transformant YL163t increased in vitro cellulolytic activity by 30%, whereas the “total in vivo newly formed FAME (fatty acid methyl esters)” increased by 16% in comparison with a random integrative cellulase-expressing Y. lipolytica mutant in the same YNB-Avicel medium. The Snf1 disruption platform demonstrated in this study provides a potent tool for the further development of Y. lipolytica as a robust host for the expression of cellulases and other commercially important proteins.

09 BIOMASS FUELS↗
DOE OSTI2021

Chimeric cellobiohydrolase I expression, activity, and biochemical properties in three oleaginous yeast

Consolidated bioprocessing using oleaginous yeast is a promising modality for the economic conversion of plant biomass to fuels and chemicals. However, yeast are not known to produce effective biomass degrading enzymes naturally and this trait is essential for efficient consolidated bioprocessing. We expressed a chimeric cellobiohydrolase I gene in three different oleaginous, industrially relevant yeast: Yarrowia lipolytica, Lipomyces starkeyi, and Saccharomyces cerevisiae to study the biochemical and catalytic properties and biomass deconstruction potential of these recombinant enzymes. Our results showed differences in glycosylation, surface charge, thermal and proteolytic stability, and efficacy of biomass digestion. L. starkeyi was shown to be an inferior active cellulase producer compared to both the Y. lipolytica and S. cerevisiae enzymes, whereas the cellulase expressed in S. cerevisiae displayed the lowest activity against dilute-acid-pretreated corn stover. Comparatively, the chimeric cellobiohydrolase I enzyme expressed in Y. lipolytica was found to have a lower extent of glycosylation, better protease stability, and higher activity against dilute-acid-pretreated corn stover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression

Abstract Background Zymomonas mobilis has recently been shown to be capable of producing the valuable platform biochemical, 2,3-butanediol (2,3-BDO). Despite this capability, the production of high titers of 2,3-BDO is restricted by several physiological parameters. One such bottleneck involves the conversion of acetoin to 2,3-BDO, a step catalyzed by 2,3-butanediol dehydrogenase (Bdh). Several Bdh enzymes have been successfully expressed in Z. mobilis, although a highly active enzyme is yet to be identified for expression in this host. Here, we report the application of a phylogenetic approach to identify and characterize a superior Bdh, followed by validation of its structural attributes using a mutagenesis approach. Results Of the 11 distinct bdh genes that were expressed in Z. mobilis, crude extracts expressing Serratia marcescens Bdh ( Sm Bdh) were found to have the highest activity (8.89 µmol/min/mg), when compared to other Bdh enzymes (0.34–2.87 µmol/min/mg). The Sm Bdh crystal structure was determined through crystallization with cofactor (NAD + ) and substrate (acetoin) molecules bound in the active site. Active Sm Bdh was shown to be a tetramer with the active site populated by a Gln247 residue contributed by the diagonally opposite subunit. Sm Bdh showed a more extensive supporting hydrogen-bond network in comparison to the other well-studied Bdh enzymes, which enables improved substrate positioning and substrate specificity. This protein also contains a short α6 helix, which provides more efficient entry and exit of molecules from the active site, thereby contributing to enhanced substrate turnover. Extending the α6 helix to mimic the lower activity Enterobacter cloacae ( Ec Bdh) enzyme resulted in reduction of Sm Bdh function to nearly 3% of the total activity. In great contrast, reduction of the corresponding α6 helix of the Ec Bdh to mimic the Sm Bdh structure resulted in ~ 70% increase in its activity. Conclusions This study has demonstrated that Sm Bdh is superior to other Bdhs for expression in Z. mobilis for 2,3-BDO production. Sm Bdh possesses unique structural features that confer biochemical advantage to this protein. While coordinated active site formation is a unique structural characteristic of this tetrameric complex, the smaller α6 helix and extended hydrogen network contribute towards improved activity and substrate promiscuity of the enzyme.

09 BIOMASS FUELS↗