Engineering protein translocation and unfolded protein response enhanced human PH-20 secretion in Pichia pastoris

Hyaluronidases catalyze the degradation of hyaluronan (HA), which is finding rising applications in medicine, cosmetic, and food industries. Recombinant expression of hyaluronidases in microbial hosts has been given special attention as a sustainable way to substitute animal tissue-derived hyaluronidases. In this study, we focused on optimizing the secretion of hyaluronidase from Homo sapiens in Pichia pastoris by secretion pathway engineering. The recombinant hyaluronidase was first expressed under the control of a constitutive promoter PGCW14. Then, two endoplasmic reticulum-related secretory pathways were engineered to improve the secretion capability of the recombinant strain. Signal peptide optimization suggested redirecting the protein into co-translational translocation using the ost1-proα signal sequence improved the secretion level by 20%. Enhancing the co-translational translocation by overexpressing signal recognition particle components further enhanced the secretory capability by 48%. Then, activating the unfolded protein response by overexpressing a transcriptional factor ScHac1p led to a secreted hyaluronidase activity of 4.06 U/mL, which was 2.1-fold higher than the original strain. Finally, fed-batch fermentation elevated the production to 19.82 U/mL. The combined engineering strategy described here could be applied to enhance the secretion capability of other proteins in yeast hosts. KEY POINTS: • Improving protein secretion by enhancing co-translational translocation in P. pastoris was reported for the first time. • Overexpressing Hac1p homologous from different origins improved the rhPH-20 secretion. • A 4.9-fold increase in rhPH-20 secretion was achieved after fermentation optimization and fed-batch fermentation.

Semiautomated design and soluble expression of a chimeric antigen TbpAB01 from Glaesserella parasuis

Pathogenic bacterial membrane proteins (MPs) are a class of vaccine and antibiotic development targets with widespread clinical application. However, the inherent hydrophobicity of MPs poses a challenge to fold correctly in living cells. Herein, we present a comprehensive method to improve the soluble form of MP antigen by rationally designing multi-epitope chimeric antigen (ChA) and screening two classes of protein-assisting folding element. The study uses a homologous protein antigen as a functional scaffold to generate a ChA possessing four epitopes from transferrin-binding protein A of Glaesserella parasuis. Our engineered strain, which co-expresses P17 tagged-ChA and endogenous chaperones groEL-ES, yields a 0.346 g/L highly soluble ChA with the property of HPS-positive serum reaction. Moreover, the protein titer of ChA reaches 4.27 g/L with >90% soluble proportion in 5-L bioreactor, which is the highest titer reported so far. The results highlight a timely approach to design and improve the soluble expression of MP antigen in industrially viable applications.

Efficient production and characterization of a newly identified trehalase for inhibiting the formation of bacterial biofilms

Trehalase has attracted widespread attention in medicine, agriculture, food, and ethanol industry due to its ability to specifically degrade trehalose. Efficient expression of trehalase remains a challenge. In this study, a putative trehalase-encoding gene (Tre-zm) from Zunongwangia mangrovi was explored using gene-mining strategy and heterologously expressed in E. coli. Trehalase activity reached 3374 U·mL-1 after fermentation optimization. The scale-up fermentation in a 15 L fermenter was achieved with a trehalase production of 15,068 U·mL-1. The recombinant trehalase TreZM was purified and characterized. It displayed optimal activity at 35 °C and pH 8.5, with Mn2+, Sn2+, Na+, and Fe2+ promoting the activity. Notably, TreZM showed significant inhibition effect on biofilm forming of Staphylococcus epidermidis. The combination of TreZM with a low concentration of antibiotics could inhibit 70 % biofilm formation of Staphylococcus epidermidis and 28 % of Pseudomonas aeruginosa. Hence, this study provides a promising candidate for industrial production of trehalase and highlights its potential application to control harmful biofilms.

High-Level Extracellular Expression of Hyaluronate Lyase HylP in Bacillus subtilis for Hyaluronan Degradation

Hyaluronate lyase (HA lyase) has potential in the industrial processing of hyaluronan. In this study, HylP, an HA lyase from Streptococcus pyogenes phage (SPB) was successfully expressed in Bacillus subtilis. To improve the extracellular enzyme activity of HylP in B. subtilis, signal peptide engineering systematic optimization was carried out, and cultured it from shake flasks and fermenters, followed by purification, characterization, and analysis of degradation products. The results showed that the replacement of the signal peptide increased the extracellular enzyme activity of HylP from 1.0 × 104 U/mL to 1.86 × 104 U/mL in the shake flask assay, and using a 20 L fermenter in a batch fermentation process, the extracellular enzyme activity achieved the level of 1.07 × 105 U/mL. HylP exhibited significant thermal and pH stability in the temperature range of 40 °C and pH range of 4-8, respectively. The enzyme showed optimum activity at 40 °C and pH 6, with significant activity in the presence of Na+, Mg2+, and Co2+ ions. Degradation analysis showed that HylP efficiently degraded hyaluronan as an endonuclease, releasing unsaturated disaccharides. These comprehensive findings underscore the substantial industrial potential of HylP for hyaluronan processing applications, offering valuable insights into enzyme characterization and optimization of expression for potential industrial utilization.

Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies

Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.

Geometric Remodeling of Nitrilase Active Pocket Based on ALF-Scanning Strategy To Enhance Aromatic Nitrile Substrate Preference and Catalytic Efficiency

Nitrilase can catalyze nitrile compounds to generate corresponding carboxylic acids. Nitrilases as promiscuous enzymes can catalyze a variety of nitrile substrates, such as aliphatic nitriles, aromatic nitriles, etc. However, researchers tend to prefer enzymes with high substrate specificity and high catalytic efficiency. In this study, we developed an active pocket remodeling (ALF-scanning) based on modulating the geometry of the nitrilase active pocket to alter substrate preference and improve catalytic efficiency. Using this strategy, combined with site-directed saturation mutagenesis, we successfully obtained 4 mutants with strong aromatic nitrile preference and high catalytic activity, W170G, V198L, M197F, and F202M, respectively. To explore the synergistic relationship of these 4 mutations, we constructed 6 double-combination mutants and 4 triple-combination mutants. By combining mutations, we obtained the synergistically enhanced mutant V198L/W170G, which has a significant preference for aromatic nitrile substrates. Compared with the wild type, its specific activities for 4 aromatic nitrile substrates are increased to 11.10-, 12.10-, 26.25-, and 2.55-fold, respectively. By mechanistic dissection, we found that V198L/W170G introduced a stronger substrate-residue π-alkyl interaction in the active pocket and obtained a larger substrate cavity (225.66 Å3 to 307.58 Å3), making aromatic nitrile substrates more accessible to be catalyzed by the active center. Finally, we conducted experiments to rationally design the substrate preference of 3 other nitrilases based on the substrate preference mechanism and also obtained the corresponding aromatic nitrile substrate preference mutants of these three nitrilases and these mutants with greatly improved catalytic efficiency. Notably, the substrate range of SmNit is widened. IMPORTANCE In this study, the active pocket was largely remodeled based on the ALF-scanning strategy we developed. It is believed that ALF-scanning not only could be employed for substrate preference modification but might also play a role in protein engineering of other enzymatic properties, such as substrate region selectivity and substrate spectrum. In addition, the mechanism of aromatic nitrile substrate adaptation we found is widely applicable to other nitrilases in nature. To a large extent, it could provide a theoretical basis for the rational design of other industrial enzymes.

Technology and functional insights into the nicotinamide mononucleotide for human health

Nicotinamide mononucleotide (NMN), a naturally occurring biologically active nucleotide, mainly functions via mediating the biosynthesis of NAD⁺. In recent years, its excellent pharmacological activities including anti-aging, treating neurodegenerative diseases, and protecting the heart have attracted increasing attention from scholars and entrepreneurs for production of a wide range of formulations, including functional food ingredients, health care products, active pharmaceuticals, and pharmaceutical intermediates. Presently, the synthesis methods of NMN mainly include two categories: chemical synthesis and biosynthesis. With the development of biocatalyst engineering and synthetic biology strategies, bio-preparation has proven to be efficient, economical, and sustainable methods. This review summarizes the chemical synthesis and biosynthetic pathways of NMN and provides an in-depth investigation on the mining and modification of enzyme resources during NMN biosynthesis, as well as the screening of hosts and optimization of chassis cells via metabolic engineering, which provide effective strategies for efficient production of NMN. In addition, an overview of the significant physiological functions and activities of NMN is elaborated. Finally, future research on technical approaches to further enhance NMN synthesis and strengthen clinical studies of NMN are prospected, which would lay the foundation for further promoting the application of NMN in nutrition, healthy food, and medicine in the future. KEY POINTS: • NMN supplementation effectively increases the level of NAD⁺. • The chemical and biological synthesis of NMN are comprehensively reviewed. • The impact of NMN on the treatment of various diseases is summarized.

Efficient secretory expression of phospholipase D for the high-yield production of phosphatidylserine and phospholipid derivates from soybean lecithin

Phospholipase D (PLD) is an essential biocatalyst for the biological production of phosphatidylserine and phospholipid modification. However, the efficient heterologous expression of PLD is limited by its cell toxicity. In this study, a PLD was secretory expressed efficiently in Bacillus subtilis with an activity around 100 U/mL. A secretory expression system containing the signal peptide SP_EstA and the dual-promoter P_HpaII-SrfA was established, and the extracellular PLD activity further reached 119.22 U/mL through scale-up fermentation, 191.30-fold higher than that of the control. Under optimum reaction conditions, a 61.61% conversion ratio and 21.07 g/L of phosphatidylserine production were achieved. Finally, the synthesis system of PL derivates was established, which could efficiently synthesis novel PL derivates. The results highlight that the secretory expression system constructed in this study provides a promising PLD producing strain in industrial application, and laid the foundation for the biosynthesis of phosphatidylserine and other PL derivates. As far as we know, this work reports the highest level of extracellular PLD expression to date and the enzymatic production of several PL derivates for the first time.

Characterization of Cinnamomum kanehirae Extract-Stimulated Triterpenoids Synthesis in Submerged Fermentation of Antrodia camphorata via Untargeted Metabolomics

The underlying mechanisms of Cinnamomum kanehirae-stimulated growth and metabolism of Antrodia camphorata remain unknown. Herein, we first observed that the methanol extract of C. kanehirae trunk (MECK) (2 g/L) showed a potent stimulatory effect on A. camphorata triterpenoids production (115.6 mg/L). Second, MECK treatment considerably increased the category and abundance of many secondary metabolites in the mycelia. We identified 93 terpenoids (8 newly formed and 49 upregulated) in the MECK-treated mycelia, wherein 21 terpenoids were the same as those in the fruiting bodies. Third, 42 out of the 93 terpenoids were annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, mainly involving monoterpenoids and diterpenoids syntheses. Finally, 27 monoterpenes and 16 sesquiterpenes were detected in the MECK, and the two terpenoids with the highest abundance (linalool and α-pinene) were selected for verification and found to considerably increase the terpenoids production of A. camphorata and demonstrate the regulation of mRNA expression levels of nine key genes in the mevalonate pathway via RT-qPCR. This study is beneficial for elucidating the terpenoids synthesis mechanism in A. camphorata.

High-level expression and characterization of a highly active hyaluronate lyase HylC with significant potential in hyaluronan oligosaccharide preparation

Hyaluronate lyases (HA lyases) have been proved to distribute widely among microorganisms, with large potential in hyaluronan processing. Here, a highly active HA lyase HylC from Citrobacter freundii strain Cf1 is reported. HylC was expressed in Escherichia coli BL21(DE3) under the regulation of T7 promoter, and purified to electrophoretic homogeneity for enzymatic characterization, which suggested its suitable thermo- and pH stability under 45 °C and pH rang of 4-8, and high halotolerancy in 1.5 M NaCl. The enzyme exhibited the optimal activity under 37 °C and pH 5.5, and was activated by Ca²⁺, K⁺, Zn²⁺, Ni²⁺ and Li⁺. Analysis of degradation product proved it cleave HA in endolytic manner, releasing unsaturated disaccharides as final product. Then, through optimization of promoter and construction of dual promoter, expression level of HylC improved from 1.10 × 10⁴ U/mL to 2.64 × 10⁴ U/mL on shake-flask level. Finally, through batch fermentation, a highest activity of 2.65×10⁵ U/mL was achieved in a 5-L fermenter. Taken together, this work demonstrates the potential of HylC and its recombinant strain in industrial applications. To our knowledge, the HA lyase production reported in this study was the highest level in literatures to date.

Genetic variation reveals the enhanced microbial hyaluronan biosynthesis via atmospheric and room temperature plasma

This study reveals the genetic and biochemical changes underlying the enhanced hyaluronan (HA) biosynthesis in Streptococcus zooepidemicus. After multiple rounds of atmospheric and room temperature plasma (ARTP) mutagenesis combined with novel bovine serum albumin/cetyltrimethylammonium bromide coupled high-throughput screening assay, the HA yield of the mutant was increased by 42.9% and reached 0.813 g L^-1 with a molecular weight of 0.54 × 10⁶ Da within 18 h by shaking flask culture. HA production was increased to 4.56 g L^-1 by batch culture in 5-L fermenter. Transcriptome sequencing exhibits that distinct mutants have similar genetic changes. Regulation in direction of metabolic flow into the HA biosynthesis, by enhancing genes responsible for the biosynthesis of HA including hasB, glmU and glmM, weaking downstream gene (nagA and nagB) of UDP-GlcNAc and significantly down-regulating transcription of wall-synthesizing genes, resulting in the accumulation of precursors (UDP-GlcA and UDP-GlcNAc) increased by 39.74% and 119.22%, respectively. These associated regulatory genes may provide control point for engineering of the efficient HA-producing cell factory.

Development of a Growth-Dependent System to Regulate Cell Growth and Keratinase Production in B. subtilis

Keratinases specifically degrade insoluble keratin waste, thus contributing to environmental protection and sustainable biomass development. However, their industrial application is hindered by inefficient enzyme production and poor biomass generation. In this study, the heterologous expression of keratinase was found to have cytotoxicity and might block host cell growth due to its proteolytic property. To address this problem, an autoregulatory expression system based on quorum sensing was developed to synergistically regulate cell growth and keratinase production in Bacillus subtilis. The growth-dependent promoter P_aprE was chosen and shown to be effective in delaying keratinase production while promoting host cell proliferation. Copy number screening and core region mutations further balanced the two states. Carbon supplement optimization indicated that addition of 2% glucose facilitated biomass accumulation during the early stage of fermentation. Cell density increased to 15.6 (OD_600 nm) from 8 with keratinase activity raised to 4200 U·mL^-1 from 1162 U·mL^-1. Keratinase was then utilized in the bioconversion of feather waste to prepare soluble keratins, polypeptides, and amino acids. This study provides a powerful system for efficient production of keratinase and paves the way for keratin waste recycling.

Protein engineering of NADH pyrophosphatase for efficient biocatalytic production of reduced nicotinamide mononucleotide

Introduction: NADH pyrophosphatase, a hydrolase catalyzing the phosphate bond of NADH to reduced nicotinamide mononucleotide, has potential applications in the food, cosmetic and pharmaceutical industry. Methods: Here, we investigated the effects of vector screening, promoter and RBS strategies on NADH pyrophosphatase expression and protein engineering on its enzymatic activity and thermal stability. Results: In this study, we describe a NADH pyrophosphatase derived from Escherichia coli (EcNudc). Strategies focusing on expression regulation including screening vectors, optimizing promoters and ribosome binding sites were utilized to enhance the productivity of EcNudc (1.8 U/mL). Moreover, protein engineering was adopted to further improve the catalytic properties of EcNudc, achieving 3.3-fold higher activity and 3.6-fold greater thermostability at 50°C. Furthermore, fermentation for the combined mutant R148A-H149E (EcNudc-M) production in a 7 L fermenter was implemented and the enzyme activity of EcNudc-M reached 33.0 U/mL. Finally, the EcNudc-M was applied in the catalysis of NADH with the highest NMNH yield of 16.65 g/L. Discussion: In conclusion, we constructed a commercially available genetically engineered strain with high activity and thermal stability of NADH pyrophosphatase, laying a broad foundation for the biocatalytic industrial production of NMNH and expand its application range.

High-efficiency secretory expression and characterization of the recombinant type III human-like collagen in Pichia pastoris

Collagen, the highest content protein in the body, has irreplaceable biological functions, and it is widespread concerned in food, beauty, and medicine with great market demand. The gene encoding the recombinant type III human-like collagen α1 chain fragment was integrated into P. pastoris genome after partial amino acids were substituted. Combined with promoter engineering and high-density fermentation technology, soluble secretory expression with the highest yield of 1.05 g L-1 was achieved using two-stage feeding method, and the purity could reach 96% after affinity purification. The determination of N/C-terminal protein sequence were consistent with the theoretical expectation and showed the characteristics of Gly-X-Y repeated short peptide sequence. In amino acid analysis, glycine shared 27.02% and proline 23.92%, which were in accordance with the characteristics of collagen. Ultraviolet spectrum combined with Fourier transform infrared spectroscopy as well as mass spectrometry demonstrated that the target product conformed to the characteristics of collagen spectrums and existed as homologous dimer and trimer in the broth. This work provided a sustainable and economically viable source of the recombinant type III human-like collagen.

A keratin/chitosan sponge with excellent hemostatic performance for uncontrolled bleeding

Uncontrolled bleeding leads to a higher fatality rate in the situation of surgery, traffic accidents and warfare. Traditional hemostatic materials such as bandages are not ideal for uncontrolled or incompressible bleeding. Therefore, it is of great significance to develop a new medical biomaterial with excellent rapid hemostatic effect. Keratin is a natural, biocompatible and biodegradable protein which contains amino acid sequences that induce cell adhesion. As a potential biomedical material, keratin has been developed and paid attention in tissue engineering fields such as promoting wound healing and nerve repair. Herein, a keratin/chitosan (K/C) sponge was prepared to achieve rapid hemostasis. The characterizations of K/C sponge were investigated, including SEM, TGA, liquid absorption and porosity, showing that the high porosity up to 90.12 ± 2.17 % resulted in an excellent blood absorption. The cytotoxicity test and implantation experiment proved that the K/C sponge was biocompatible and biodegradable. Moreover, the prepared K/C sponge showed better hemostatic performance than chitosan sponge (CS) and the commercially available gelatin sponge in both rat tail amputation and liver trauma bleeding models. Further experiments showed that K/C sponge plays a hemostatic role through the endogenous coagulation pathway, thus shortening the activated partial thromboplastin time (APTT) effectively. Therefore, this study provided a K/C sponge which can be served as a promising biomedical hemostatic material.

Insights into the source, mechanism and biotechnological applications of hyaluronidases

It has long been found that hyaluronidases exist in a variety of organisms, playing their roles in various biological processes including infection, envenomation and metabolic regulation through degrading hyaluronan. However, exploiting them as a bioresource for specific applications had not been extensively studied until the latest decades. In recent years, new application scenarios have been developed, which extended the field of application, and emphasized the research value of hyaluronidase. This critical review comprehensively summarizes existing studies on hyaluronidase from different source, particularly in their structures, action patterns, and biological functions in human and mammals. Furthermore, we give in-depth insight into the resource mining and protein engineering process of hyaluronidase, as well as strategies for their high-level production, indicating that mixed strategies should be adopted to obtain well-performing hyaluronidase with efficiency. In addition, advances in application of hyaluronidase were summarized and discussed. Finally, prospects for future researches are proposed, highlighting the importance of further investigation into the characteristics of hyaluronidases, and the necessity of investigating their products for the development of their application value.

A combination of bioinformatics analysis and rational design strategies to enhance keratinase thermostability for efficient biodegradation of feathers

Keratinase has shown great significance and application potentials in the biodegradation and recycle of keratin waste due to its unique and efficient hydrolysis ability. However, the inherent instability of the enzyme limits its practical utilization. Herein, we obtained a thermostability-enhanced keratinase based on a combination of bioinformatics analysis and rational design strategies for the efficient biodegradation of feathers. A systematical in silico analysis combined with filtering of virtual libraries derived a smart library for experimental validation. Synergistic mutations around the highly flexible loop, the calcium binding site and the non-consensus amino acids generated a dominant mutant which increased the optimal temperature of keratinase from 40 °C to 60 °C, and the half-life at 60 °C was increased from 17.3 min to 66.1 min. The mutant could achieve more than 66% biodegradation of 50 g/L feathers to high-valued keratin product with a major molecular weight of 36 kDa. Collectively, this work provided a promising keratinase variant with enhanced thermostability for efficient conversion of keratin wastes to valuable products. It also generated a general strategy to facilitate enzyme thermostability design which is more targeted and predictable.

Directed evolution driving the generation of an efficient keratinase variant to facilitate the feather degradation

Keratinases can specifically degrade keratins, which widely exist in hair, horns, claws and human skin. There is a great interest in developing keratinase to manage keratin waste generated by the poultry industry and reusing keratin products in agriculture, medical treatment and feed industries. Degradation of keratin waste by keratinase is more environmentally friendly and more sustainable compared with chemical and physical methods. However, the wild-type keratinase-producing strains usually cannot meet the requirements of industrial production, and some are pathogenic, limiting their development and utilization. The main purpose of this study is to improve the catalytic performance of keratinase via directed evolution technology for the degradation of feathers. We first constructed a mutant library through error-prone PCR and screened variants with enhanced enzyme activity. The keratinase activity was further improved through fermentation conditions optimization and fed-batch strategies in a 7-L bioreactor. As a result, nine mutants with enhanced activity were identified and the highest enzyme activity was improved from 1150 to 8448 U/mL finally. The mutant achieved efficient biodegradation of feathers, increasing the degradation rate from 49 to 88%. Moreover, a large number of amino acids and soluble peptides were obtained as degradation products, which were excellent protein resources to feed. Therefore, the study provided a keratinase mutant with application potential in the management of feather waste and preparation of protein feed additive.

Heterologous expression, fermentation strategies and molecular modification of collagen for versatile applications

Collagen is a kind of high macromolecular protein with unique tissue distribution and distinctive functions in the body. At present, most collagen products are extracted from the tissues and organs of mammals or marine fish. However, this method exhibits several disadvantages, including low efficiency and serious waste generation, which makes it difficult to meet the current market demand. With the rapid development of synthetic biology and the deepening of high-density fermentation technology, the collagen preparation by biosynthesis strategy emerges as the times require. Co-expression with the proline hydroxylase gene can solve the problem of non-hydroxylated collagen, but the yield may be affected. Therefore, improving the expression through molecular modification and dynamic regulation of synthesis is an entry point for future research. Due to the defects in certain properties of the natural collagen, modification of properties would be benefit for meeting the requirements of practical application. In this paper, in-depth investigations on recombinant expression, fermentation, and modification studies of collagen are conducted. Also, it summarizes the research progress of collagen in food, medicine, and beauty industry in recent years. Furthermore, the future development trend and application prospect of collagen are discussed, which would provide guidance for its preparation and application.

Phospholipids (PLs) know-how: exploring and exploiting phospholipase D for its industrial dissemination

Owing to their numerous nutritional and bioactive functions, phospholipids (PLs), which are major components of biological membranes in all living organisms, have been widely applied as nutraceuticals, food supplements, and cosmetic ingredients. To date, PLs are extracted solely from soybean or egg yolk, despite the diverse market demands and high cost, owing to a tedious and inefficient manufacturing process. A microbial-based manufacturing process, specifically phospholipase D (PLD)-based biocatalysis and biotransformation process for PLs, has the potential to address several challenges associated with the soybean- or egg yolk-based supply chain. However, poor enzyme properties and inefficient microbial expression systems for PLD limit their wide industrial dissemination. Therefore, sourcing new enzyme variants with improved properties and developing advanced PLD expression systems are important. In the present review, we systematically summarize recent achievements and trends in the discovery, their structural properties, catalytic mechanisms, expression strategies for enhancing PLD production, and its multiple applications in the context of PLs. This review is expected to assist researchers to understand current advances in this field and provide insights for further molecular engineering efforts toward PLD-mediated bioprocessing.

Improving the Intensity of Integrated Expression for Microbial Production

Chromosomal integration of exogenous genes is preferred for industrially related fermentation, as plasmid-mediated fermentation leads to extra metabolic burden and genetic instability. Moreover, with the development and advancement of genome engineering and gene editing technologies, inserting genes into chromosomes has become more convenient; integration expression is extensively utilized in microorganisms for industrial bioproduction and expected to become the trend of recombinant protein expression. However, in actual research and application, it is important to enhance the expression of heterologous genes at the host genome level. Herein, we summarized the basic principles and characteristics of genomic integration; furthermore, we highlighted strategies to improve the expression of chromosomal integration of genes and pathways in host strains from three aspects, including chassis cell optimization, regulation of expression elements in gene expression cassettes, optimization of gene dose level and integration sites on chromosomes. Moreover, we reviewed and summarized the relevant studies on the application of integrated expression in the exploration of gene function and the various types of industrial microorganism production. Consequently, this review would serve as a reference for the better application of integrated expression.

Controlled expression of lysis gene E by a mutant of the promoter pL of the thermo-inducible λcI857-pL system

AIMS

To identify a lambda promoter pL mutant that could extend the thermal stability of the thermo-inducible λcI857-pR/pL system and to evaluate the effects of the modified system for the controlled expression of lysis gene E during the production of bacterial ghosts (BGs).

METHODS AND RESULTS

The promoter pL mutant was identified by random mutagenesis and site-directed mutagenesis. The results showed that a T → 35C mutation in the pL promoter was responsible for the phenotype alteration. Under the same induction conditions, the lysis rates of the modified lytic system on Escherichia coli and Salmonella enteritidis were significantly lower than that of the control, while the lysis rates of Escherichia coli with the thermo-inducible lytic system were significantly higher than that of S. enteritidis with the corresponding plasmid (P < 0·05).

CONCLUSIONS

Increasing the heat stability of the thermo-inducible lytic systems decreased lysis efficiency during the production of BGs. There exist differences in the lysis efficiency of thermo-inducible lytic systems between different bacterial strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings enrich current knowledge about modifications to thermo-inducible systems and provide a reference for the application of these modified systems for the production of BGs and controlled gene expression in bacteria.

The tale of a versatile enzyme: Molecular insights into keratinase for its industrial dissemination

Keratinases are unique among proteolytic enzymes for their ability to degrade recalcitrant insoluble proteins, and they are of critical importance in keratin waste management. Over the past few decades, researchers have focused on discovering keratinase producers, as well as producing and characterizing keratinases. The application potential of keratinases has been investigated in the feed, fertilizer, leathering, detergent, cosmetic, and medical industries. However, the commercial availability of keratinases is still limited due to poor productivity and properties, such as thermostability, storage stability and resistance to organic reagents. Advances in molecular biotechnology have provided powerful tools for enhancing the production and functional properties of keratinase. This critical review systematically summarizes the application potential of keratinase, and in particular certain newly discovered catalytic capabilities. Furthermore, we provide comprehensive insight into mechanistic and molecular aspects of keratinases including analysis of gene sequences and protein structures. In addition, development and current advances in protein engineering of keratinases are summarized and discussed, revealing that the engineering of protein domains such as signal peptides and pro-peptides has become an important strategy to increase production of keratinases. Finally, prospects for further development are also proposed, indicating that advanced protein engineering technologies will lead to improved and additional commercial keratinases for various industrial applications.

iTRAQ-based quantitative proteomic analysis of Colletotrichum lini reveals ethanol induced mechanism for enhancing dihydroxylation efficiency of DHEA

Colletotrichum lini is used as an industrial stain for the dihydroxylation of steroid compound dehydroepiandrosterone (DHEA) to biosynthesize 3β,7α,15α-trihydroxy-5-androstene-17-one (7α,15α-diOH-DHEA), a key intermediate of the most popular oral contraceptive "Yasmin". This work aimed to enhance 7α,15α-diOH-DHEA production in C. lini CGMCC 6051 through ethanol induction. With 0.6% (v/v) ethanol induction and 10 g/L DHEA concentration, the 7α,15α-diOH-DHEA molar yield reached 58.8%, which was increased by 67.5% than that of the control. iTRAQ-based quantitative proteomic analysis was applied to explore the probable molecular mechanism of C. lini response to ethanol induction. A total of 50 differential expressed proteins was affected by ethanol induction, and could be related to multiple metabolic pathways. Most of differently expressed proteins were functionally mapped into pathways of transport, steroids metabolism, or redox reaction. Other proteins for energy, transcription and translation, and carbohydrate metabolism might have important roles in the cellular response to ethanol induction. In addition, the levels of cytochrome P450 and NAD(P)H-cytochrome P450 reductase were remarkably higher under ethanol induction, and their functions on DHEA dihydroxylation were first proposed in C. lini. Our results provide critical clues in revealing the dihydroxylation mechanism and are important for efficient microbiological hydroxylation of steroidal compounds in the future. BIOLOGICAL SIGNIFICANCE: iTRAQ strategy was first used to compare the proteomes of ethanol induction during the dihydroxylation reaction by Colletotrichum lini CGMCC 6051. The changes in protein provided a comprehensive overview of DHEA dihydroxylation in C. lini, including the proteins for steroids metabolism, redox reaction, transport, transcription and translation, energy and carbohydrate metabolism. Cytochrome P450, NADPH-cytochrome P450 reductase, and NADH-cytochrome b5 reductase were highlighted due to their outstanding contribution to DHEA dihydroxylation. The results help us understand the molecular mechanism underlying ethanol induction in C. lini and would guide strain engineering to further improve dihydroxylation efficiency.

Enzymatic Extraction of Bioactive and Self-Assembling Wool Keratin for Biomedical Applications

Keratin is widely recognized as a high-quality renewable protein resource for biomedical applications. Despite their extensive existence, keratin resources such as feathers, wool, and hair exhibit high stability and mechanical properties because of their high disulfide bond content. Consequently, keratin extraction is challenging and its application is greatly hindered. In this work, a biological extraction strategy is proposed for the preparation of bioactive keratin and the fabrication of self-assembled keratin hydrogels (KHs). Based on moderate and controlled hydrolysis by keratinase, keratin with a high molecular weight of approximately 45 and 28 kDa that retain its intrinsic bioactivities is obtained. The keratin products show excellent ability to promote cell growth and migration and are conferred with significant antioxidant ability because of their intrinsically high cysteine content. In addition, without the presence of any cross-linking agent, the extracted keratin can self-assemble into injectable hydrogels. The KHs exhibit a porous network structure and 3D culture ability, showing potential in promoting wound healing. This enzyme-driven keratin extraction strategy opens up a new approach for the preparation of keratin that can self-assemble into injectable hydrogels for biomedical engineering.

Improving the biocatalytic performance of co-immobilized cells harboring nitrilase via addition of silica and calcium carbonate

To improve nicotinic acid (NA) yield and meet industrial application requirements of sodium alginate-polyvinyl alcohol (SA-PVA) immobilized cells of Pseudomonas putida mut-D3 harboring nitrilase, inorganic materials were added to the SA-PVA immobilized cells to improve mechanical strength and mass transfer performance. The concentrations of inorganic materials were optimized to be 2.0% silica and 0.6% CaCO₃. The optimal pH and temperature for SA-PVA immobilized cells and composite immobilized cells were both 8.0 and 45 °C, respectively. The half-lives of composite immobilized cells were 271.48, 150.92, 92.92 and 33.12 h, which were 1.40-, 1.35-, 1.22- and 1.63-fold compared to SA-PVA immobilized cells, respectively. The storage stability of the composite immobilized cells was slightly increased. The composite immobilized cells could convert 14 batches of 3-cyanopyridine with feeding concentration of 250 mM and accumulate 418 g ·L^-1 nicotinic acid, while the SA-PVA immobilized cells accumulated 346 g L^-1 nicotinic acid.

Recombinant expression and molecular engineering of the keratinase from Brevibacillus parabrevis for dehairing performance

Keratinase is capable of distinctive degradation of keratin, which provides an eco-friendly approach for keratin waste management towards sustainable development. In this study, the recombinant keratinase (KERBP) from Brevibacillus parabrevis was successfully expressed in Escherichia coli. The purified KERBP had the specific activity of 6005.3 U/mg. It showed remarkable tolerance to various surfactants and also no collagenolytic activity. However, the moderate thermal stability limited its further application. Thus, protein engineering was further adopted to improve its stability. The variants of T218S, S236C and N181D were constructed by site-directed mutagenesis and combinatorial mutagenesis. Compared with the wild type, the t_1/2 at 60 °C for the variants T218S, S236C and N181D were 3.05-, 1.18- and 1-fold increase, respectively. Moreover, the double variants N181D-T218S and N181D-S236C significantly improved thermostability with 5.1 and 2.9 °C increase of T₅₀, and prolonging t_1/2 at 60 °C with 4.09 and 1.54-fold, respectively. And the catalytic efficiency of the T218S and N181D-T218S variants was also significantly improved. Furthermore, the keratinase displayed favorable ability to dehair wool from skin within 7 h, which showed potential in leather dehairing. Our work contributes to a further insight into the thermostability of keratinase and offers a promising alternative for industrial leather application.

Fabrication and characterization of high molecular keratin based nanofibrous membranes for wound healing

Keratin is widely used in the biomaterial application, but the keratin prepared by the physical or chemical approach has relatively low molecular weight and mechanical properties. Here we report the preparation of high molecular keratin (HMK) with molecular weight of 120 kDa via multi-enzyme cascade pathway and its application in wound healing. Briefly, we prepared the soluble keratin from wool by keratinase and improved the molecular weight of keratin by transglutaminase (TGase). The HMK was coelectrospun with poly(3-hydroxybutyric acid-co-3-hydroxyvaleric acid) (PHBV) and the prepared nanofibrous mats demonstrated improved mechanical properties. Ag nanoparticles (AgNPs) were synthesized on the nanofibers via in situ bioreduction, using the above-mentioned keratinase as the reducing agent. It is demonstrated that the PHBV/HMK/AgNPs nanofibrous mats possess favorable antibacterial properties and good biocompatibility. Moreover, in vivo wound healing assessment, the PHBV/HMK/AgNPs membrane displayed better wound healing ability than the control group. These results indicate that PHBV/HMK/AgNPs mats exhibit significant potential in tissue engineering.

Efficient keratinase expression via promoter engineering strategies for degradation of feather wastes

Keratinases are promising alternatives over ordinary proteases in several industrial applications due to their unique properties compared with their counterparts in the protease categories. However, their large-scale industrial application is limited by the low expression and poor fermentation efficiency of keratinase. Here, we demonstrate that the expression level of keratinase can be improved by constructing a more efficient enzyme expression system hereby enables the highest production titer as regarding recombinant keratinase production to date. Specially, ten promoters were evaluated and the aprE promoter exhibits a significant promotion of keratinase (kerBv) titer from 165 U/mL to 2605 U/mL in Bacillus subtilis. The batch fermentation mode resulted in a maximum keratinase activity of 7176 U/mL at 36 h in a 5-L fermenter. Furthermore, the extracellular keratinase activity attained up to 16,860 U/mL via fed-batch fermentation within 30 h. The combination of keratinase with l-cysteine brings about 66.4 % degree of degradation of feather. Our work provides a new insight into the development of efficient keratinase fermentation processes with B. subtilis cell factory.

Two-Stage Semi-Continuous 2-Keto-Gluconic Acid (2KGA) Production by Pseudomonas plecoglossicida JUIM01 From Rice Starch Hydrolyzate

A two-stage semi-continuous strategy for producing 2-keto-gluconic acid (2KGA) by Pseudomonas plecoglossicida JUIM01 from rice starch hydrolyzate (RSH) has been developed. The initial glucose concentration (140 g/L) was selected for first-stage fermentation due to its highest 2KGA productivity of 7.58 g/(L⋅h), cell weight of 3.91 g/L, and residual glucose concentration of 25.00 g/L. Followed by removing 70.0% (v/v) of the first-stage broth and feeding 400.0 g/L of glucose to the second-stage fermentor, a total of 50680.0 g glucose was consumed, and 50005.20 g 2KGA was obtained with a yield of 0.9867 g/g by P. plecoglossicida JUIM01 after a 3-cycle two-stage semi-continuous fermentation. Our results indicated that the developed two-stage semi-continuous fermentation could be industrially applied due to its high 2KGA concentration, 2KGA yield and operation efficiency.

[Effects of tranexamic acid on the blood conservation and the long-term prognosis in pediatric patients undergoing repair for tetralogy of fallot]

Objective: To evaluate the perioperative tranexamic acid (TXA) on blood conservation in pediatric patients undergoing complete repair for tetralogy of fallot (TOF) and its impact on short-term or long-term adverse event and mortality. Methods: The study was a retrospective cohort study. From January 2009 to December 2010, 386 consecutive patients aged from 31 days to 8 years old, ASA physical status Ⅱ or Ⅲ, receiving primary complete repair for TOF in Fuwai Hospital were enrolled in the study. They were divided into two groups: the control group (n=161) and the TXA group (n=225), according to whether TXA was used during the operation. Patients and their families were followed up by telephone in the 8th-year after surgery. The amount of perioperative blood loss, allogeneic transfusion, short-term or long-term adverse event and mortality were recorded and analyzed. Results: The patients in the TXA group were associated with significant decreased 12 h and total postoperative blood loss compared with the control group [(7.8±0.3) ml/kg vs (8.8±0.3) ml/kg, t=2.412, P<0.05; and (14.0±0.6) ml/kg vs (17.0±0.7) ml/kg, t=3.141, P<0.05]. There were no significant differences in both the volume and incidence of red blood cell, plasma, and platelet transfusion, postoperatively (P>0.05). There were no significant differences in the incidence of reoperation for bleeding and prolonged mechanical ventilation, ICU stay, postoperative hospital length of stay, the short-term and long-term incidence of seizure, stroke, renal failure, deep venous thrombosis, pulmonary embolism and death between the two groups(P>0.05). Conclusion: TXA can decrease postoperative blood loss, but has little impact on the allogeneic blood transfusion, as well as the short-term or long-term adverse event and mortality in pediatric patients undergoing complete repair for TOF.

Phospholipase D engineering for improving the biocatalytic synthesis of phosphatidylserine

Phosphatidylserine is widely used in food, health, chemical and pharmaceutical industries. The phospholipase D-mediated green synthesis of phosphatidylserine has attracted substantial attention in recent years. In this study, the phospholipase D was heterologously expressed in Bacillus subtilis, Pichia pastoris, and Corynebacterium glutamicum, respectively. The highest activity of phospholipase D was observed in C. glutamicum, which was 0.25 U/mL higher than these in B. subtilis (0.14 U/mL) and P. pastoris (0.22 U/mL). System engineering of three potential factors, including (1) signal peptides, (2) ribosome binding site, and (3) promoters, was attempted to improve the expression level of phospholipase D in C. glutamicum. The maximum phospholipase D activity reached 1.9 U/mL, which was 7.6-fold higher than that of the initial level. The enzyme displayed favorable transphosphatidylation activity and it could efficiently catalyze the substrates L-serine and soybean lecithin for synthesis of phosphatidylserine after optimizing the conversion reactions in detail. Under the optimum conditions (trichloromethane/enzyme solution 4:2, 8 mg/mL soybean lecithin, 40 mg/mL L-serine, and 15 mM CaCl₂, with shaking under 40 °C for 10 h), the reaction process showed 48.6% of conversion rate and 1.94 g/L of accumulated phosphatidylserine concentration. The results highlight the use of heterologous expression, system engineering, and process optimization strategies to adapt a promising phospholipase D for efficient phosphatidylserine production in synthetic application.

Combining Pro-peptide Engineering and Multisite Saturation Mutagenesis To Improve the Catalytic Potential of Keratinase

Keratinases are becoming biotechnologically important since they have shown potential in hydrolysis of recalcitrant keratins with highly rigid and strongly cross-linked structures. However, the large-scale application of keratinases has been limited by the inefficient expression level and low enzyme activity. In this work, we employed pro-peptide engineering and saturation mutagenesis to construct excellent keratinase variants with improved activities. It turned out that amino acid substitutions at the pro-peptide cleavage site (P1) could accelerate the release of active mature enzymes, resulting in a 3-fold activity increase. Eighteen sites of the pro-peptide area were targeted for codon mutagenesis, and a multisite saturation mutagenesis library of the six potential sites was generated, achieving a significant improvement of keratinase activity from 179 to 1114 units/mL. Also, the mutants exhibited alterant catalytic properties. Finally, fermentation for keratinase production in a 15 L fermenter was carried out, and the enzyme activity reached up to over 3000 units/mL. Our results demonstrated that pro-peptide engineering played a crucial role in high expression and engineering of proteases. This study provides a universal route toward improvement of industrial enzymes that were first synthesized as precursors in the form of pre-pro-protein.

A Membrane-Bound Gluconate Dehydrogenase from 2-Keto-D-Gluconic Acid Industrial Producing Strain Pseudomonas plecoglossicida JUIM01: Purification, Characterization, and Gene Identification

The membrane-bound gluconate dehydrogenase (mGADH) is a critical enzyme for 2-keto-D-gluconic acid (2KGA) production in Pseudomonas plecoglossicida JUIM01. The purified native flavin adenine dinucleotide-dependent mGADH (FAD-mGADH) was consisted of a gamma subunit, a flavoprotein subunit, and a cytochrome c subunit with molecular mass of ~ 27, 65, and 47 kDa, respectively. The specific activity of FAD-mGADH was determined as 90.71 U/mg at optimum pH and temperature of 6.0 and 35 °C. The K_m and V_max values of calcium D-gluconate were 0.631 mM and 0.734 mM/min. The metal ions Mg²⁺ and Mn²⁺ showed slight positive effects on FAD-mGADH activity. On the other hand, a 3868-bp-length gad gene cluster was amplified and expressed in Escherichia coli BL21(DE3). The recombinant protein showed the same molecular weight and enzyme activity as the native FAD-mGADH, which confirmed it as a FAD-mGADH encoding gene. The flavoprotein subunit and the cytochrome c subunit containing a putative FAD-binding motif and three possible heme-binding motifs concluded from alignment results of mGADHs. This study characterized the native and recombinant FAD-mGADH and would provide the basis for further genetic modification of Pseudomonas plecoglossicida JUIM01 with the intention of 2KGA productivity improvement.

[A 3.0 T MRI study on the alterations of the volume and morphology of fifteen subcortical nucleus in patients with early post-stroke depression]

Objective: To investigate the alterations of the volumes and 3D shapes of fifteen subcortical nucleus in patients with post-stroke depression (PSD) and to explore the pathogenesis regularity and mechanism of early PSD. Methods: From 2015 to 2017, a total of 28 patients with PSD and 18 stroke patients without depression (PSND), 13 patients with depression (De) and 11 cases of healthy volunteers (NC) were enrolled to perform 3.0 T high resolution MRI.Computer automatic segmentation and vertex analysis were used to segment and measure the volume of bilateral nucleus accumbens, caudate nucleus, putamen, globus pallidus, thalamus, hippocampus, mygdale and brainstem. Results: The volume of bilateral nucleus accumbens and bilateral thalamus, left pallidum were different among groups with statistical difference (P<0.05). The nucleus volume of the PSD group was (415±128) mm(3) (L-Nac)/(303±90) mm(3) (R-Nac), (7 590±867) mm(3) (L-Th)/(7 459±905) mm(3) (R-Th), (1 675±328) mm(3) (L-Pa), which was smaller than that of PSND group (433±100) mm(3) /(307±88) mm(3), (7 999±961) mm(3) /(7 753± 955) mm(3), (1 790±286) mm(3) and other groups.The nuclei with significantly statistical differences between inter-group were found in following: between PSD group and NC group, right accumbens and bilateral thalamus (P<0.01); between PSD group and De group, right accumbens and right thalamus (P<0.001), left accumbens, left pallidum and left thalamus (P<0.01); between PSND group and NC group, right accumbens (P<0.05); between PSND group and De group, right accumbens (P<0.001), left accumbens and right thalamus (P<0.05). Significant differences in morphology changes of nuclei (P<0.05) by F test mainly located on the top and tail of right accumbens, the anterior and middle body of right caudate nucleus, the most part of bilateral thalamus, the ventromedial body of bilateral hippocampus, the anterior and body of left caudate nucleus, especially in left thalamus. Conclusion: PSD has abnormal volume and morphological structure of subcortical nuclei, which supports the role of subcortical structures changes in the pathophysiology and pathogenesis of early PSD.

Efficient biocatalytic synthesis of nicotinic acid by recombinant nitrilase via high density culture

The constitutively expression system for P. putida nitrilase was firstly constructed to improve the nicotinic acid production and reduce the production costs. High density culture strategy was employed to enhance the biomass and nitrilase production of recombinant strain. The total nitrilase activity reached up to 654 U·mL^-1 without the induction. 541 g·L^-1 nicotinic acid was accumulated via fed batch mode of substrate feeding through 290 min of conversion.

Significantly enhanced substrate tolerance of Pseudomonas putida nitrilase via atmospheric and room temperature plasma and cell immobilization

The objective of the study was to enhance the substrate tolerance of Pseudomonas putida nitrilase via atmospheric and room temperature plasma (ARTP) and cell immobilization. The mutant library was constructed by ARTP and rapidly screened by an OPA-TCA microscale reaction. A mutant strain of mut-D3 was obtained and its optimum substrate concentration was improved to 150mM from 100mM. It could accumulate 189g/L nicotinic acid (NA) from 3-cyanopyridine (3-CP), which was increased by 42% compared with that of wild type (WT). Additionally, composite immobilization of mut-D3 was performed and SA-PVA immobilized cells could catalyze 250mM 3-CP each batch with finally accumulating 346g/L NA, while free cells accumulated 175g/L NA. These results indicated that the free or immobilized catalysts of mut-D3 could serve as a good choice for NA production. This is the first report on mutation breeding of nitrilase-producing microorganisms by ARTP.

Mining of a phospholipase D and its application in enzymatic preparation of phosphatidylserine

Phosphatidylserine (PS) is useful as the additive in industries for memory improvement, mood enhancement and drug delivery. Conventionally, PS was extracted from soybeans, vegetable oils, egg yolk, and biomass; however, their low availability and high extraction cost were limiting factors. Phospholipase D (PLD) is a promising tool for enzymatic synthesis of PS due to its transphosphatidylation activity. In this contribution, a new and uncharacterized PLD was first obtained from GenBank database via genome mining strategy. The open reading frame consisted of 1614 bp and potentially encoded a protein of 538-amino-acid with a theoretical molecular mass of 60 kDa. The gene was successfully cloned and expressed in Escherichia coli. Its enzymatic properties were experimentally characterized. The temperature and pH optima of PLD were determined to be 60°C and 7.5, respectively. Its hydrolytic activity was improved by addition of Ca²⁺ at 5 mM as compared with the control. The enzyme displayed suitable transphosphatidylation activity and PS could be synthesized with L-serine and soybean lecithin as substrates under the catalysis of PLD. This PLD enzyme might be a potential candidate for industrial applications in PS production. To the best of our knowledge, this is the first report on genome mining of PLDs from GenBank database.

Engineering of a fungal nitrilase for improving catalytic activity and reducing by-product formation in the absence of structural information

Semi-rational engineering approach was employed to improve the catalytic activity and reduce the by-product formation of fungal nitrilase.

Production and characterization of surfactant-stable fungal keratinase from Gibberella intermedia CA3-1 with application potential in detergent industry

Surfactant-stable keratinases with good properties are promising candidates for extensive applications in detergent industries. A novel fungal keratinase-producing strain,

Biochemical Characterization of An Arginine-Specific Alkaline Trypsin from Bacillus licheniformis

In the present study, we isolated a trypsin-producing strain DMN6 from the leather waste and identified it as Bacillus licheniformis through a two-step screening strategy. The trypsin activity was increased up to 140 from 20 U/mL through culture optimization. The enzyme was purified to electrophoretic homogeneity with a molecular mass of 44 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the specific activity of purified enzyme is 350 U/mg with Nα-Benzoyl-l-arginine ethylester as the substrate. The optimum temperature and pH for the trypsin are 65 °C and pH 9.0, respectively. Also, the enzyme can be significantly activated by Ba²⁺. This enzyme is relatively stable in alkaline environment and displays excellent activity at low temperatures. It could retain over 95% of enzyme activity after 180 min of incubation at 45 °C. The distinguished activity under low temperature and prominent stability enhance its catalytic potential. In the current work, the open reading frame was obtained with a length of 1371 nucleotides that encoded a protein of 456 amino acids. These data would warrant the B. licheniformis trypsin as a promising candidate for catalytic application in collagen preparation and leather bating through further protein engineering.