A rapid and efficient method for multiple-site mutagenesis with a modified overlap extension PCR

Overview of various protein engineering strategies to improve the catalytic activity, thermostability, and acid/base stability of β-glucanase

β-Glucan is highly valued in the food and medical industries due to its various physiological functions. However, its aqueous solution tends to have high viscosity, which negatively impacts the brewing and feed industries. By hydrolyzing β-glucosidic bonds, β-glucanase could reduce the adverse effects of β-glucan. For this reason, β-glucanase is widely utilized in the brewing and animal feed production. The limited thermal and acid stability of β-glucanase restricts its applications in industrial settings. Therefore, it is of great importance to enhance the stability of existing β-glucanases through protein engineering. This review summarizes current integrated technical methods for the molecular modification of β-glucanases, including error-prone PCR, site-saturation mutagenesis, DNA recombination, sequence alignment, N- and C-terminal modifications, surface charge optimization, intermolecular force optimization, and rigidity of flexible regions. The aim is to provide a theoretical basis and practical guidance for the further modification of β-glucanases.

Efficient and easible biocatalysts: Strategies for enzyme improvement. A review

Owing to the environmental friendliness and vast advantages that enzymes offer in the biotechnology and industry fields, biocatalysts are a prolific investigation field. However, the low catalytic activity, stability, and specific selectivity of the enzyme limit the range of the reaction enzymes involved in. A comprehensive understanding of the protein structure and dynamics in terms of molecular details enables us to tackle these limitations effectively and enhance the catalytic activity by enzyme engineering or modifying the supports and solvents. Along with different strategies including computational, enzyme engineering based on DNA recombination, enzyme immobilization, additives, chemical modification, and physicochemical modification approaches can be promising for the wide spread of industrial enzyme usage. This is attributed to the successful application of biocatalysts in industrial and synthetic processes requires a system that exhibits stability, activity, and reusability in a continuous flow process, thereby reducing the production cost. The main goal of this review is to display relevant approaches for improving enzyme characteristics to overcome their industrial application.

P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate

WS9326A is a peptide antibiotic containing a highly unusual N-methyl-E-2-3-dehydrotyrosine (NMet-Dht) residue that is incorporated during peptide assembly on a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) has been shown to be essential for the formation of the alkene moiety in NMet-Dht, but the timing and mechanism of the P450Sas-mediated α,β-dehydrogenation of Dht remained unclear. Here, we show that the substrate of P450Sas is the NRPS-associated peptidyl carrier protein (PCP)-bound dipeptide intermediate (Z)-2-pent-1'-enyl-cinnamoyl-Thr-N-Me-Tyr. We demonstrate that P450Sas-mediated incorporation of the double bond follows N-methylation of the Tyr by the N-methyl transferase domain found within the NRPS, and further that P450Sas appears to be specific for substrates containing the (Z)-2-pent-1'-enyl-cinnamoyl group. A crystal structure of P450Sas reveals differences between P450Sas and other P450s involved in the modification of NRPS-associated substrates, including the substitution of the canonical active site alcohol residue with a phenylalanine (F250), which in turn is critical to P450Sas activity and WS9326A biosynthesis. Together, our results suggest that P450Sas catalyses the direct dehydrogenation of the NRPS-bound dipeptide substrate, thus expanding the repertoire of P450 enzymes that can be used to produce biologically active peptides.

A primer to directed evolution: current methodologies and future directions

Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more suitable for specific applications. Since the first in vitro evolution experiments performed by Sol Spiegelman in 1967, a wide range of techniques have been developed to tackle the main two steps of directed evolution: genetic diversification (library generation), and isolation of the variants of interest. This review covers the main modern methodologies, discussing the advantages and drawbacks of each, and hence the considerations for designing directed evolution experiments. Furthermore, the most recent developments are discussed, showing how advances in the handling of ever larger library sizes are enabling new research questions to be tackled.

Enhanced Rishirilide Biosynthesis by a Rare In-Cluster Phosphopantetheinyl Transferase in Streptomyces xanthophaeus

Phosphopantetheinyl transferases (PPTases) play important roles in activating apo-acyl carrier proteins (apo-ACPs) and apo-peptidyl carrier proteins (apo-PCPs) in both primary and secondary metabolism. PPTases catalyze the posttranslational modifications of those carrier proteins by covalent attachment of the 4'-phosphopantetheine group to a conserved serine residue. The protein-protein interactions between a PPTase and a cognate acyl or peptidyl carrier protein have important regulatory functions in microbial biosynthesis, but the molecular mechanism underlying their specific recognition remains elusive. In this study, we identified a new rishirilide biosynthetic gene cluster with a rare in-cluster PPTase from Streptomyces xanthophaeus no2. The function of this Sfp-type PPTase, SxrX, in rishirilide production was confirmed using genetic mutagenesis and biochemical characterization. We applied molecular modeling and site-directed mutagenesis to identify key residues mediating the protein-protein interaction between SxrX and its cognate ACP. In addition, six natural products were isolated from wild-type S. xanthophaeus no2 and the ΔsxrX mutant, including rishirilide A and lupinacidin A, that exhibited antimicrobial and anticancer activities, respectively. SxrX is the first Sfp-type PPTase identified from an aromatic polyketide biosynthetic gene cluster and shown to be responsible for high-level production of rishirilide derivatives. IMPORTANCE Genome mining has been a vital means for natural product drug discovery in the postgenomic era. The rishirilide-type polyketides have attracted attention due to their potent bioactivity, but the poor robustness of production hosts has limited further research and development. This study not only identifies a hyperproducer of rishirilides but also reveals a rare, in-cluster PPTase SxrX that plays an important role in boosting rishirilide biosynthesis. Experimental and computational investigations revealed new insights on the protein-protein interaction between SxrX and its cognate ACP with wide implications for understanding polyketide biosynthesis.

A patent-based consideration of latest platforms in the art of directed evolution: a decade long untold story

Directed (or in vitro) evolution of proteins and metabolic pathways requires tools for creating genetic diversity and identifying protein variants with new or improved functional properties. Besides simplicity, reliability, speed, versatility, universal applicability and economy of the technique, the new science of synthetic biology requires improved means for construction of smart and high-quality mutant libraries to better navigate the sequence diversity. In vitro CRISPR/Cas9-mediated mutagenic (ICM) system and machine-learning (ML)-assisted approaches to directed evolution are now in the field to achieve the goal. This review describes the gene diversification strategies, screening and selection methods, in silico (computer-aided), Cas9-mediated and ML-based approaches to mutagenesis, developed especially in the last decade, and their patent position. The objective behind is to emphasize researchers the need for noting which mutagenesis, screening or selection method is patented and then selecting a suitable restriction-free approach to sequence diversity. Techniques and evolved products subject to patent rights need commercial license if their use is for purposes other than private or experimental research.

Ancestral Sequence Reconstruction and Alternate Amino Acid States Guide Protein Library Design for Directed Evolution

Engineered proteins possess nearly limitless possibilities in medical and industrial applications but finding a precise amino acid sequence for these applications is challenging. A robust approach for discovering protein sequences with a desired functionality uses a library design method in which combinations of mutations are applied to a robust starting point. Determining useful mutations can be tortuous, yet rewarding; in this chapter, we present a novel library design method that uses information provided by ancestral sequence reconstruction (ASR) to create a library likely to have stable proteins with diverse function. ASR computational tools use a multi-sequence alignment of homologous proteins and an evolutionary model to estimate the protein sequences of the numerous common ancestors. For all ancestors, these tools calculate the probability of every amino acid occurring at each position within the sequence alignment. The alternate amino acid states at individual positions corelate to a region of stability in sequence space around the ancestral sequence which can inform site-wise diversification within a combinatorial library. The method presented in this chapter balances the quality of results, the computational resources needed, and ease of use.

Site-wise Diversification of Combinatorial Libraries Using Insights from Structure-guided Stability Calculations

Many auspicious clinical and industrial accomplishments have improved the human condition by means of protein engineering. Despite these achievements, our incomplete understanding of the sequence-structure-function relationship prevents rapid innovation. To tackle this problem, we must develop and integrate new and existing technologies. To date, directed evolution and rational design have dominated as protein engineering principles. Even so, prior to screening for novel or improved functions, a large collection of variants, within a protein library, exist along an ambiguous mutational terrain. Complicating things further, the choice of where to initialize investigation along a vast sequence space becomes even more difficult given that the majority of any sequence lacks function entirely. Unfortunately, even when considering functionally relevant positions, random substitutions can prove to be destabilizing, causing a hindrance to an otherwise function-inducing, stability-reliant folding process. To enhance productivity in the field, we seek to address this issue of destabilization, and subsequent disfunction, at protein-protein and protein-ligand interacting regions. Herein, the process of choosing amenable positions - and amino acids at those positions - allows for a refined, knowledge-based approach to combinatorial library design. Using structural data, we perform computational stability prediction with FoldX's PositionScan and Rosetta's ddG_monomer in tandem, allowing for the refinement of our thermodynamic stability data through the comparison of results. In turn, we provide a process for selecting in silico predicted mutually stabilizing positions and avoiding overly destabilizing ones that guides the site-wise diversification of combinatorial libraries.

The evolving art of creating genetic diversity: From directed evolution to synthetic biology

The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.

Directed Evolution: Methodologies and Applications

Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.

Fine-Tuning Multi-Gene Clusters via Well-Characterized Gene Expression Regulatory Elements: Case Study of the Arginine Synthesis Pathway in C. glutamicum

Promoters and ribosome binding sites (RBSs) are routinely applied in gene expression regulation, but their orthogonality and combinatorial effects have not yet been systematically studied in Corynebacterium glutamicum. Here, 17 core promoters and 29 RBSs in C. glutamicum were characterized, which exhibited 470-fold and 430-fold in transcriptional and translational activity, respectively. By comparing the expression of two reporter genes regulated by multiple RBSs, the RBS efficacy showed significant dependence on the gene context, besides the RBSs' strength, reflecting the poor orthogonality of RBSs. Bicistron-modified RBS (referred as bc-RBS) was adapted to C. glutamicum, which improved RBS reliability. By coupling a series of promoters with RBSs/bc-RBSs, a much broader regulation range that spanned 4 orders of magnitude was observed compared with that of a sole element, and the contribution to gene expression of RBS was more than that of promoter. Finally, promoters and RBSs were applied as built-in elements to fine-tune the gene cluster in the arginine synthesis pathway in C. glutamicum. Compared with the original strain, more arginine (1.61-fold) or citrulline (2.35-fold) was accumulated in a 7 L bioreactor by strains with the gene expression regulation system rationally engineered. We demonstrated that, via combination of well-characterized gene elements, and overall consideration for both transcription and translation, the biosynthesis pathway can be effectively balanced, and the yield of a target metabolite can be further improved.

In Vitro Construction of Large-scale DNA Libraries from Fragments Containing Random Regions using Deoxyinosine-containing Oligonucleotides and Endonuclease V

Efficient and precise construction of DNA libraries is a fundamental starting point for directed evolution of polypeptides. Recently, several in vitro selection methods have been reported that do not rely on cells for protein expression, where peptide libraries in the order of 10¹³ species are used for in vitro affinity selection. To maximize their potential, simple yet versatile construction of DNA libraries from several fragments containing random regions without bacterial transformation is essential. To address this issue, we herein propose a novel DNA construction methodology based on the use of polymerase chain reaction (PCR) primers containing a single deoxyinosine (I) residue near their 5' end. Treatment of the PCR products with endonuclease V generates 3' overhangs with customized lengths and sequences, which can be ligated accurately and efficiently with other fragments having exactly complementary overhangs. As a proof of concept, we constructed an artificial gene library of single-domain antibodies from four DNA fragments.

Structural and functional analysis of an l-serine O-phosphate decarboxylase involved in norcobamide biosynthesis

Structural diversity of natural cobamides (Cbas, B₁₂ vitamers) is limited to the nucleotide loop. The loop is connected to the cobalt-containing corrin ring via an (R)-1-aminopropan-2-ol O-2-phosphate (AP-P) linker moiety. AP-P is produced by the l-threonine O-3-phosphate (l-Thr-P) decarboxylase CobD. Here, the CobD homolog SMUL_1544 of the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans was characterized as a decarboxylase that produces ethanolamine O-phosphate (EA-P) from l-serine O-phosphate (l-Ser-P). EA-P is assumed to serve as precursor of the linker moiety of norcobamides that function as cofactors in the respiratory reductive dehalogenase. SMUL_1544 (SmCobD) is a pyridoxal-5'-phosphate (PLP)-containing enzyme. The structural analysis of the SmCobD apoprotein combined with the characterization of truncated mutant proteins uncovered a role of the SmCobD N-terminus in efficient l-Ser-P conversion.

The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase

Only a few overlapping gene pairs are known in the best-analyzed bacterial model organism Escherichia coli. Automatic annotation programs usually annotate only one out of six reading frames at a locus, allowing only small overlaps between protein-coding sequences. However, both RNAseq and RIBOseq show signals corresponding to non-trivially overlapping reading frames in antisense to annotated genes, which may constitute protein-coding genes. The transcription and translation of the novel 264 nt gene asa, which overlaps in antisense to a putative TEGT (Testis-Enhanced Gene Transfer) transporter gene is detected in pathogenic E. coli, but not in two apathogenic E. coli strains. The gene in E. coli O157:H7 (EHEC) was further analyzed. An overexpression phenotype was identified in two stress conditions, i.e. excess in salt or arginine. For this, EHEC overexpressing asa was grown competitively against EHEC with a translationally arrested asa mutant gene. RT-qPCR revealed conditional expression dependent on growth phase, sodium chloride, and arginine. Two potential promoters were computationally identified and experimentally verified by reporter gene expression and determination of the transcription start site. The protein Asa was verified by Western blot. Close homologues of asa have not been found in protein databases, but bioinformatic analyses showed that it may be membrane associated, having a largely disordered structure.

Efficient strategy for introducing large and multiple changes in plasmid DNA

While the QuikChange site-directed mutagenesis method and its later modifications are extremely useful and simple, they suffer from several drawbacks. Here, we propose a new method, named LFEAP mutagenesis (Ligation of Fragment Ends After PCR) for creating various mutations in plasmid by leveraging three existing concepts: inverse PCR, single primer PCR, and sticky-end assembly. The first inverse PCR on the target plasmid yielded linearized DNA fragments with mutagenic ends, and a second single primer PCR resulted in complementary single-stranded DNA fragments with the addition of overhangs at the 5' end of each strand. The resulting single strands were then annealed to produce double-stranded DNA with free 5' single-stranded DNA tails. These products with compatible sticky ends were efficiently assembled into a circular, mutagenized plasmid. With this strategy, multiple simultaneous changes (up to 15) and mutations in large plasmids (up to 50 kb) were achieved with high efficiency and fidelity. LFEAP mutagenesis is a versatile method that offers significant advantages for introducing large and multiple changes in plasmid DNA.

Identification of a transcriptional activation domain in yeast repressor activator protein 1 (Rap1) using an altered DNA-binding specificity variant

Repressor activator protein 1 (Rap1) performs multiple vital cellular functions in the budding yeast Saccharomyces cerevisiae These include regulation of telomere length, transcriptional repression of both telomere-proximal genes and the silent mating type loci, and transcriptional activation of hundreds of mRNA-encoding genes, including the highly transcribed ribosomal protein- and glycolytic enzyme-encoding genes. Studies of the contributions of Rap1 to telomere length regulation and transcriptional repression have yielded significant mechanistic insights. However, the mechanism of Rap1 transcriptional activation remains poorly understood because Rap1 is encoded by a single copy essential gene and is involved in many disparate and essential cellular functions, preventing easy interpretation of attempts to directly dissect Rap1 structure-function relationships. Moreover, conflicting reports on the ability of Rap1-heterologous DNA-binding domain fusion proteins to serve as chimeric transcriptional activators challenge use of this approach to study Rap1. Described here is the development of an altered DNA-binding specificity variant of Rap1 (Rap1AS). We used Rap1AS to map and characterize a 41-amino acid activation domain (AD) within the Rap1 C terminus. We found that this AD is required for transcription of both chimeric reporter genes and authentic chromosomal Rap1 enhancer-containing target genes. Finally, as predicted for a bona fide AD, mutation of this newly identified AD reduced the efficiency of Rap1 binding to a known transcriptional coactivator TFIID-binding target, Taf5. In summary, we show here that Rap1 contains an AD required for Rap1-dependent gene transcription. The Rap1AS variant will likely also be useful for studies of the functions of Rap1 in other biological pathways.

Characterization of a New S8 serine Protease from Marine Sedimentary Photobacterium sp. A5-7 and the Function of Its Protease-Associated Domain

Bacterial extracellular proteases are important for bacterial nutrition and marine sedimentary organic nitrogen degradation. However, only a few proteases from marine sedimentary bacteria have been characterized. Some subtilases have a protease-associated (PA) domain inserted in the catalytic domain. Although structural analysis and deletion mutation suggests that the PA domain in subtilases is involved in substrate binding, direct evidence to support this function is still absent. Here, a protease, P57, secreted by Photobacterium sp. A5-7 isolated from marine sediment was characterized. P57 could hydrolyze casein, gelatin and collagen. It showed the highest activity at 40°C and pH 8.0. P57 is a new subtilase, with 63% sequence identity to the closest characterized protease. Mature P57 contains a catalytic domain and an inserted PA domain. The recombinant PA domain from P57 was shown to have collagen-binding ability, and Phe349 and Tyr432 were revealed to be key residues for collagen binding in the PA domain. This study first shows direct evidence that the PA domain of a subtilase can bind substrate, which provides a better understanding of the function of the PA domain of subtilases and bacterial extracellular proteases from marine sediment.

Facile Construction of Random Gene Mutagenesis Library for Directed Evolution Without the Use of Restriction Enzyme in Escherichia coli

A foolproof protocol was developed for the construction of mutant DNA library for directed protein evolution. First, a library of linear mutant gene was generated by error-prone PCR or molecular shuffling, and a linear vector backbone was prepared by high-fidelity PCR. Second, the amplified insert and vector fragments were assembled by overlap-extension PCR with a pair of 5'-phosphorylated primers. Third, full-length linear plasmids with phosphorylated 5'-ends were self-ligated with T4 ligase, yielding circular plasmids encoding mutant variants suitable for high-efficiency transformation. Self-made competent Escherichia coli BL21(DE3) showed a transformation efficiency of 2.4 × 10(5) cfu/µg of the self-ligated circular plasmid. Using this method, three mutants of mCherry fluorescent protein were found to alter their colors and fluorescent intensities under visible and UV lights, respectively. Also, one mutant of 6-phosphorogluconate dehydrogenase from a thermophilic bacterium Moorella thermoacetica was found to show the 3.5-fold improved catalytic efficiency (kcat /Km ) on NAD(+) as compared to the wild-type. This protocol is DNA-sequence independent, and does not require restriction enzymes, special E. coli host, or labor-intensive optimization. In addition, this protocol can be used for subcloning the relatively long DNA sequences into any position of plasmids.

Controlling the transcription levels of argGH redistributed l-arginine metabolic flux in N-acetylglutamate kinase and ArgR-deregulated Corynebacterium crenatum

Corynebacterium crenatum SYPA5-5, an l-arginine high-producer obtained through multiple mutation-screening steps, had been deregulated by the repression of ArgR that inhibits l-arginine biosynthesis at genetic level. Further study indicated that feedback inhibition of SYPA5-5 N-acetylglutamate kinase (CcNAGK) by l-arginine, as another rate-limiting step, could be deregulated by introducing point mutations. Here, we introduced two of the positive mutations (H268N or R209A) of CcNAGK into the chromosome of SYPA5-5, however, resulting in accumulation of large amounts of the intermediates (l-citrulline and l-ornithine) and decreased production of l-arginine. Genetic and enzymatic levels analysis involved in l-arginine biosynthetic pathway of recombinants SYPA5-5-NAGKH268N (H-7) and SYPA5-5-NAGKR209A (R-8) showed that the transcription levels of argGH decreased accompanied with the reduction of argininosuccinate synthase and argininosuccinase activities, respectively, which led to the metabolic obstacle from l-citrulline to l-arginine. Co-expression of argGH with exogenous plasmid in H-7 and R-8 removed this bottleneck and increased l-arginine productivity remarkably. Compared with SYPA5-5, fermentation period of H-7/pDXW-10-argGH (H-7-GH) reduced to 16 h; meanwhile, the l-arginine productivity improved about 63.6 %. Fed-batch fermentation of H-7-GH in 10 L bioreactor produced 389.9 mM l-arginine with the productivity of 5.42 mM h−1. These results indicated that controlling the transcription of argGH was a key factor for regulating the metabolic flux toward l-arginine biosynthesis after deregulating the repression of ArgR and feedback inhibition of CcNAGK, and therefore functioned as another regulatory mode for l-arginine production. Thus, deregulating all these three regulatory modes was a powerful strategy to construct l-arginine high-producing C. crenatum.

Regulatory function of the C-terminal segment of guanylate cyclase-activating protein 2

Neuronal responses to Ca2+-signals are provided by EF-hand-type neuronal Ca2+-sensor (NCS) proteins, which have similar core domains containing Ca2+-binding and target-recognizing sites. NCS proteins vary in functional specificity, probably depending on the structure and conformation of their non-conserved C-terminal segments. Here, we investigated the role of the C-terminal segment in guanylate cyclase activating protein-2, GCAP2, an NCS protein controlling the Ca2+-dependent regulation of photoreceptor guanylate cyclases. We obtained two chimeric proteins by exchanging C-terminal segments between GCAP2 and its photoreceptor homolog recoverin, a Ca2+-sensor controlling rhodopsin kinase (RK) activity. The exchange affected neither the structural integrity of GCAP2 and recoverin nor the Ca2+-sensitivity of GCAP2. Intrinsic fluorescence, circular dichroism, biochemical studies and hydrophobic dye probing revealed Ca2+-dependent conformational transition of the C-terminal segment of GCAP2 occurring in the molecular environment of both proteins. In Ca2+-GCAP2, the C-terminal segment was constrained and its replacement provided the protein with approximately two-fold inhibitory activity towards RK, suggesting that the segment contributes to specific target recognition by interfering with RK-binding. Upon Ca2+-release, it became less constrained and more available for phosphorylation by cyclic nucleotide-dependent protein kinase. The transition from the Ca2+-bound to the apo-state exposed hydrophobic sites in GCAP2, and was associated with its activating function without affecting its dimerization. The released C-terminal segment participated further in photoreceptor membrane binding making it sensitive to phosphorylation. Thus, the C-terminal segment in GCAP2 confers target selectivity, facilitates membrane binding and provides sensitivity of the membrane localization of the protein to phosphorylation by signaling kinases.

A computational strategy for altering an enzyme in its cofactor preference to NAD(H) and/or NADP(H)

Coenzyme engineering, especially for altered coenzyme specificity, has been a research hotspot for more than a decade. In the present study, a novel computational strategy that enhances the hydrogen-bond interaction between an enzyme and a coenzyme was developed and utilized to alter the coenzyme preference. This novel computational strategy only required the structure of the target enzyme. No other homologous enzymes were needed to achieve alteration in the coenzyme preference of a certain enzyme. Using our novel strategy, Gox2181 was reconstructed from exhibiting complete NADPH preference to exhibiting dual cofactor specificity for NADH and NADPH. Structure-guided Gox2181 mutants were designed in silico and molecular dynamics simulations were performed to evaluate the strength of hydrogen-bond interactions between the enzyme and the coenzyme NADPH. Three Gox2181 mutants displaying high structure stability and structural compatibility to NADH/NADPH were chosen for experimental confirmation. Among the three Gox2181 mutants, Gox2181-Q20R&D43S showed the highest enzymatic activity by utilizing NADPH as its coenzyme, which was even better than the wild-type enzyme. In addition, isothermal titration calorimetry analysis further verified that Gox2181-Q20R&D43S was able to interact with NADPH but the wild-type enzyme could not. This novel computational strategy represents an insightful approach for altering the cofactor preference of target enzymes.

Altered microRNA expression in bovine skeletal muscle with age

Age-dependent decline in skeletal muscle function leads to several inherited and acquired muscular disorders in elderly individuals. The levels of microRNAs (miRNAs) could be altered during muscle maintenance and repair. We therefore performed a comprehensive investigation for miRNAs from five different periods of bovine skeletal muscle development using next-generation small RNA sequencing. In total, 511 miRNAs, including one putatively novel miRNA, were identified. Thirty-six miRNAs were differentially expressed between prenatal and postnatal stages of muscle development including several myomiRs (miR-1, miR-206 and let-7 families). Compared with miRNA expression between different muscle tissues, 14 miRNAs were up-regulated and 22 miRNAs were down-regulated in the muscle of postnatal stage. In addition, a novel miRNA was predicted and submitted to the miRBase database as bta-mir-10020. A dual luciferase reporter assay was used to demonstrate that bta-mir-10020 directly targeted the 3'-UTR of the bovine ANGPT1 gene. The overexpression of bta-mir-10020 significantly decreased the DsRed fluorescence in the wild-type expression cassette compared to the mutant type. Using three computational approaches - miranda, pita and rnahybrid - these differentially expressed miRNAs were also predicted to target 3609 bovine genes. Disease and biological function analyses and the KEGG pathway analysis revealed that these targets were statistically enriched in functionality for muscle growth and disease. Our miRNA expression analysis findings from different states of muscle development and aging significantly expand the repertoire of bovine miRNAs now shown to be expressed in muscle and could contribute to further studies on growth and developmental disorders in this tissue type.

Identification of borrelidin binding site on threonyl-tRNA synthetase

Borrelidin exhibits a wide spectrum of biological activities and has been considered as a non-competitive inhibitor of threonyl-tRNA synthetase (ThrRS). However, the detailed mechanisms of borrelidin against ThrRS, especially borrelidin binding site on ThrRS, are still unclear, which limits the development of novel borrelidin derivatives and rational design of structure-based ThrRS inhibitors. In this study, the binding site of borrelidin on Escherichia coli ThrRS was predicted by molecular docking. To validate our speculations, the ThrRS mutants of E. coli (P424K, E458Δ, and G459Δ) were constructed and their sensitivity to borrelidin was compared to that of the wild-type ThrRS by enzyme kinetics and stopped-flow fluorescence analysis. The docking results showed that borrelidin binds the pocket outside but adjacent to the active site of ThrRS, consisting of residue Y313, R363, R375, P424, E458, G459, and K465. Site-directed mutagenesis results showed that sensitivities of P424K, E458Δ, and G459Δ ThrRSs to borrelidin were reduced markedly. All the results showed that residue Y313, P424, E458, and G459 play vital roles in the binding of borrelidin to ThrRS. It indicated that borrelidin may induce the cleft closure, which blocks the release of Thr-AMP and PPi, to inhibit activity of ThrRS rather than inhibit the binding of ATP and threonine. This study provides new insight into inhibitory mechanisms of borrelidin against ThrRS.

Kinetic regulation of a corrinoid-reducing metallo-ATPase by its substrates

Corrinoid cofactors play a crucial role as methyl group carriers in the C1 metabolism of anaerobes, e.g. in the cleavage of phenyl methyl ethers by O-demethylases. For the methylation, the protein-bound corrinoid has to be in the super-reduced [Co(I) ]-state, which is highly sensitive to autoxidation. The reduction of inadvertently oxidized corrinoids ([Co(II) ]-state) is catalysed in an ATP-dependent reaction by RACE proteins, the reductive activators of corrinoid-dependent enzymes. In this study, a reductive activator of O-demethylase corrinoid proteins was characterized with respect to its ATPase and corrinoid reduction activity. The reduction of the corrinoid cofactor was dependent on the presence of potassium or ammonium ions. In the absence of the corrinoid protein, a basal slow ATP hydrolysis was observed which was obviously not coupled to corrinoid reduction. ATP hydrolysis was significantly stimulated by the corrinoid protein in the [Co(II) ]-state of the corrinoid cofactor. The stoichiometry of ATP hydrolysed per mol corrinoid reduced was near 1:1. Site-directed mutagenesis was applied to study the impact of a highly conserved region possibly involved in nucleotide binding of RACE proteins, indicating that an aspartate and a glycine residue may play an essential role for the function of the enzyme.

Site-saturation mutagenesis by overlap extension PCR

Site-saturation mutagenesis is a proven strategy for generating high-quality variant gene libraries of a defined size. Variation is introduced via incorporation of degenerate base combinations at specific codon locations, giving rise to a precise series of amino acid substitutions in the encoded protein. Here we describe a simple and efficient overlap PCR protocol for the introduction of degenerate bases at either single or multiple codon locations. The resulting libraries can then be directly screened for improved protein function as either an independent directed evolution study or an adjunct to random mutagenesis strategies (such as error-prone PCR) that are, in isolation, unlikely to access the full repertoire of possible amino acid substitutions at any given position.

Simultaneous splicing of multiple DNA fragments in one PCR reaction

Background

Rapid and simultaneous splicing of multiple DNA fragments is frequently required in many recombinant DNA projects. However, former overlap extension PCRs, the most common methods for splicing DNA fragments, are not really simultaneous fusing of multiple DNA fragments.

Results

We performed an optimized method which allowed simultaneous splicing of multiple DNA fragments in one PCR reaction. Shorter outermost primers were prior mixed with other PCR components at the same time. A sequential thermo cycling program was adopted for overlap extension reaction and amplification of spliced DNA. Annealing temperature was relatively higher in the overlap extension reaction stage than in the fused DNA amplification. Finally we successfully harvested target PCR products deriving from fusion of two to seven DNA fragments after 5–10 cycles for overlap extension reaction and then 30 cycles for fused DNA amplification.

Conclusions

Our method provides more rapid, economical and handy approach to accurately splice multiple DNA fragments. We believe that our simultaneous splicing overlap extension PCR can be used to fuse more than seven DNA fragments as long as the DNA polymerase can match.

Amino acid mutations in the caldesmon COOH-terminal functional domain increase force generation in bladder smooth muscle

Caldesmon (CaD), a component of smooth muscle thin filaments, binds actin, tropomyosin, calmodulin, and myosin and inhibits actin-activated ATP hydrolysis by smooth muscle myosin. Internal deletions of the chicken CaD functional domain that spans from amino acids (aa) 718 to 731, which corresponds to aa 512-530 including the adjacent aa sequence in mouse CaD, lead to diminished CaD-induced inhibition of actin-activated ATP hydrolysis by myosin. Transgenic mice with mutations of five aa residues (Lys(523) to Gln, Val(524) to Leu, Ser(526) to Thr, Pro(527) to Cys, and Lys(529) to Ser), which encompass the ATPase inhibitory determinants located in exon 12, were generated by homologous recombination. Homozygous (-/-) animals did not develop, but heterozygous (+/-) mice carrying the expected mutations in the CaD ATPase inhibitory domain (CaD mutant) matured and reproduced normally. The peak force produced in response to KCl and electrical field stimulation by the detrusor smooth muscle from the CaD mutant was high compared with that of the wild type. CaD mutant mice revealed nonvoiding contractions during bladder filling on awake cystometry, suggesting that the CaD ATPase inhibitory domain suppresses force generation during the filling phase and this suppression is partially released by mutations in 50% of CaD in heterozygous. Our data show for the first time a functional phenotype, at the intact smooth muscle tissue and in vivo organ levels, following mutation of a functional domain at the COOH-terminal region of CaD.

Computational design of short-chain dehydrogenase Gox2181 for altered coenzyme specificity

Short-chain dehydrogenase Gox2181 from Gluconobacter oxydans catalyzes the reduction of 2,3-pentanedione by using NADH as the physiological electron donor. To realize its synthetic biological application for coenzyme recycling use, computational design and site-directed mutagenesis have been used to engineer Gox2181 to utilize not only NADH but also NADPH as the electron donor. Single and double mutations at residues Q20 and D43 were made in a recombinant expression system that corresponded to Gox2181-D43Q and Gox2181-Q20R&D43Q, respectively. The design of mutant Q20R not only resolved the hydrogen bond interaction and electrostatic interaction between R and 2'-phosphate of NADPH, but also could enhance the binding with 2'-phophated of NADPH by combining with D43Q. Molecular dynamics simulation has been carried out to testify the hydrogen bond interactions between mutation sites and 2'-phosphate of NADPH. Steady-state turnover measurement results indicated that Gox2181-D43Q could use both NADH and NADPH as its coenzyme, and so could Gox2181-Q20R&D43Q. Meanwhile, compared to the wild-type enzyme, Gox2181-D43Q exhibited dramatically reduced enzymatic activity while Gox2181-Q20R&D43Q successfully retained the majority of enzymatic activity.

Expression and purification of SenX3 from the Mycobacterium tuberculosis strain H37Rv in Escherichia coli

Infection with the bacterium Mycobacterium tuberculosis (MTB) causes tuberculosis, a pulmonary infection that may be fatal if left untreated. Misuse or mismanagement of tuberculosis drugs may lead to drug-resistant pathogen forms that are difficult to treat and contribute to a global health problem. The MTB SenX3/RegX3 signal transduction system allows bacteria to externally sense the environment and mediate an appropriate internal response; SenX3 is also associated with MTB virulence, suggesting that this protein may provide a potential therapeutic target. To investigate the role of SenX3 and MTB drug resistance, SenX3 was cloned, expressed and purified in Escherichia coli. SenX3 was cloned from the genome of the MTB strain H37Rv by polymerase chain reaction and an internal NcoI restriction site was destroyed by site-directed mutagenesis to allow cloning into the pET-28b prokaryotic expression vector. SenX3 expression from the resulting pET‑28b-mSenX3 plasmid was induced with isopropyl β-D-thiogalactoside and the protein was purified using Ni-NTA agarose affinity chromatography. A pure protein of the expected size was identified. The examination of purified SenX3 protein is considered to enable the in‑depth investigation of SenX3-mediated drug resistance.

Efficient multi-site-directed mutagenesis directly from genomic template

In this article, the traditional multi-site-directed mutagenesis method based on overlap extension PCR was improved specifically for complicated templates, such as genomic sequence or complementary DNA. This method was effectively applied for multi-site-directed mutagenesis directly from mouse genomic DNA, as well as for combination, deletion or insertion of DNA fragments.

Gene synthesis method based on overlap extension PCR and DNAWorks program

Gene synthesis by chemical methods provides a powerful tool for modifying genes and exploring their structure, expression, and function in the post-genomic era. However, a bottleneck in recent gene synthesis technologies is the high cost of oligonucleotide synthesis and post-synthesis sequencing. Here, we describe a simple, rapid, and low-cost gene synthesis method based on overlap extension PCR (OE-PCR) and the DNAWorks program. This method enables DNA sequences with sizes ranging from 200 bp to 3 kb to be synthesized with few errors, and these errors can be easily corrected by site-directed mutagenesis. Thus, it is amenable to automation for the multiplexed synthesis of different genes and has a potential for high-throughput gene synthesis.

Parallel assembly for multiple site-directed mutagenesis of plasmids

A parallel assembly method for multiple site-directed mutagenesis of plasmids was developed here based on Golden Gate cloning. It takes advantage of type IIs restriction enzymes and T4 DNA ligase to assemble multiple DNA fragments into a plasmid by a defined order. This method can accommodate multiple plasmid mutagenesis at any desired position with all three sequence modification types (substitution, deletion, and insertion) simultaneously. Furthermore, it can be used to create otherwise difficult-to-make mutants-larger deletions and insertions and mutagenesis on larger plasmids. The processes of mutagenesis can be completed quickly by a single restriction-ligation reaction.

Rapid gene splicing and multi-sited mutagenesis by one-step overlap extension polymerase chain reaction

Gene splicing and site-directed mutagenesis (SDM) are important to introduce desired sequences in target DNA. However, introducing mutations at multiple sites requires multiple steps of DNA manipulation, which is time-consuming and labor-intensive. Here, we present a rapid efficient gene splicing and multi-sited mutagenesis method that introduces mutations at two distant sites via sequential connection of DNA fragments by one-step overlap extension polymerase chain reaction (OE-PCR). This bottom-up approach for DNA engineering can be broadly used to study protein structure-function, to optimize codon use for protein expression, and to assemble genes of interest.

Combinatorial reshaping of the Candida antarctica lipase A substrate pocket for enantioselectivity using an extremely condensed library

A highly combinatorial structure-based protein engineering method for obtaining enantioselectivity is reported that results in a thorough modification of the substrate binding pocket of Candida antarctica lipase A (CALA). Nine amino acid residues surrounding the entire pocket were simultaneously mutated, contributing to a reshaping of the substrate pocket to give increased enantioselectivity and activity for a sterically demanding substrate. This approach seems to be powerful for developing enantioselectivity when a complete reshaping of the active site is required. Screening toward ibuprofen ester 1, a substrate for which previously used methods had failed, gave variants with a significantly increased enantioselectivity and activity. Wild-type CALA has a moderate activity with an E value of only 3.4 toward this substrate. The best variant had an E value of 100 and it also displayed a high activity. The variation at each mutated position was highly reduced, comprising only the wild type and an alternative residue, preferably a smaller one with similar properties. These minimal binary variations allow for an extremely condensed protein library. With this highly combinatorial method synergistic effects are accounted for and the protein fitness landscape is explored efficiently.

Phosphorylation of a PDZ domain extension modulates binding affinity and interdomain interactions in postsynaptic density-95 (PSD-95) protein, a membrane-associated guanylate kinase (MAGUK)

Postsynaptic density-95 is a multidomain scaffolding protein that recruits glutamate receptors to postsynaptic sites and facilitates signal processing and connection to the cytoskeleton. It is the leading member of the membrane-associated guanylate kinase family of proteins, which are defined by the PSD-95/Discs large/ZO-1 (PDZ)-Src homology 3 (SH3)-guanylate kinase domain sequence. We used NMR to show that phosphorylation of conserved tyrosine 397, which occurs in vivo and is located in an atypical helical extension (α3), initiates a rapid equilibrium of docked and undocked conformations. Undocking reduced ligand binding affinity allosterically and weakened the interaction of PDZ3 with SH3 even though these domains are separated by a ~25-residue linker. Additional phosphorylation at two linker sites further disrupted the interaction, implicating α3 and the linker in tuning interdomain communication. These experiments revealed a novel mode of regulation by a detachable PDZ element and offer a first glimpse at the dynamic interaction of PDZ and SH3-guanylate kinase domains in membrane-associated guanylate kinases.

Construction of a reference plasmid molecule containing eight targets for the detection of genetically modified crops

A standard plasmid containing eight targets was developed for quantitative detection of genetically modified (GM) soybeans and cotton. These eight targets were joined in tandem to form the pTLE8 plasmid with a length of 3,680 bp. This plasmid contains part of the endogenous soybean Lec1 gene, the Cauliflower mosaic virus (CaMV) 35S promoter, the Agrobacterium tumefaciens nopaline synthase (NOS) terminator, the PAT gene of the soybean line A2704-12, the event-specific 5'-junction region of Roundup-Ready Soya (RRS, 35SG), the Cry1A(c) gene from Bacillus thuringiensis (Bt), the endogenous cotton Sad1 gene, and a part of RRS EPSPS gene. The PCR efficiencies with pTLE8 as a calibrator ranged from 99.4% to 100.2% for the standard curves of the RRS EPSPS gene and the taxon-specific Lec1 gene (R(2)≥0.996). The limits of detection and quantification were nine and 15 copies, respectively. The standard deviation (SD) and relative standard deviation (RSD) values of repeatability were from 0.09 to 0.52 and from 0.28% to 2.11%, and those for reproducibility were from 0.12 to 1.15 and 0.42% to 3.85%, respectively. The average conversion factor (Cf) for the CRMs RRS quantification was 0.91. The RSD of the mean values for known samples ranged from 3.09% to 18.53%, and the biases were from 0.5% to 40%. These results show that our method using the pTLE8 plasmid as a reference material (RM) is reliable and feasible in the identification of GM soybeans, thus paving the way for the establishment of identification management systems for various products containing GMO components.

Asymmetric overlap extension PCR method for site-directed mutagenesis

Overlap extension PCR (OE-PCR) has been widely used in site-directed mutagenesis. The original OE-PCR included two rounds of PCRs and required tedious steps to purify the first-round PCR product. By combining asymmetric PCR and overlap extension, a novel asymmetric overlap extension PCR (AOE-PCR) method has been developed. This method consists of two separate asymmetric PCRs of around 30 cycles and a single cycle of annealing and extension after directly mixing the first-round PCR products. AOE-PCR eliminates intermediate purification steps and amplification of wild-type template and requires fewer PCR cycles, and is, therefore, a much simpler and faster and more efficient site-directed mutagenesis method than the original OE-PCR approach.

Phosphorylation of α-synuclein upregulates tyrosine hydroxylase activity in MN9D cells

Hyperphosphorylated α-synuclein is considered an important event in the pathogenesis of Parkinson's disease but its function remains elusive. In this study we provide evidence that tyrosine hydroxylase (TH) expression was unaffected by overexpression of wild-type and phospho-mimic mutant α-synuclein (S129D) in dopaminergic MN9D cells. However, α-synuclein overexpression evidently inhibited TH phosphorylation at Ser40 and dopamine synthesis, while α-synuclein (S129D) mutant enhanced TH phosphorylation and dopamine synthesis. This phospho-mimic mutant prevented wild-type α-synuclein cytotoxicity to MN9D cells, which might be due to aggregation of mutant α-synuclein in the cytoplasm and nuclei. These results demonstrated that phosphorylation at Ser129 was involved in the regulation of TH activity, as well as in eliminating the neurotoxicity of wild-type α-synuclein overexpression in MN9D cells.

GAS3, a developmentally regulated gene, encodes a highly mannosylated and inactive protein of the Gas family of Saccharomyces cerevisiae

The multigene GAS family of Saccharomyces cerevisiae is constituted by five genes encoding GPI-anchored proteins required for cell wall or spore wall assembly. GAS1 and GAS5 are expressed in vegetative growth and repressed during sporulation, whereas GAS2 and GAS4 exhibit the opposite expression pattern. This study focuses on GAS3, a still poorly characterized member of the family. To date, attempts to reveal the glucan elongase activity typical of Gas proteins have been unsuccessful, suggesting that Gas3p is the only inactive member of the family. Here, we compared the mRNA levels of GAS1, GAS3 and GAS5 and demonstrate that GAS3 is the weakest-expressed paralogue in vegetative growth. Moreover, GAS3 mRNA increased during sporulation, showing a bimodal profile typical of the early-middle meiotic genes. GAS3 product was identified as a low-abundance, polydisperse mannoprotein. Loss of Gas3p did not affect growth and sporulation. The overexpression of GAS3, driven by the GAS1 promoter, slightly reduced growth rate in a wild-type strain and led to hyperaccumulation of Gas3p in the membranes and in the cell wall. To determine whether GAS3 could replace GAS1 function in vivo, GAS3 was also overexpressed in a gas1Delta mutant. Increased amounts of Gas3p were not only unable to complement the defects of the gas1Delta cells but exacerbated them. A mutated Gas3p-E283Q, where one of the catalytic glutamate residues essential for GH72 enzyme activity was replaced by glutamine, was also noxious to gas1Delta cells, indicating that the increased expression of Gas3p, rather than a potential activity, is deleterious for gas1Delta cells.

Processing DNA molecules as text

Polymerase Chain Reaction (PCR) is the DNA-equivalent of Gutenberg’s movable type printing, both allowing large-scale replication of a piece of text. De novo DNA synthesis is the DNA-equivalent of mechanical typesetting, both ease the setting of text for replication. What is the DNA-equivalent of the word processor? Biology labs engage daily in DNA processing—the creation of variations and combinations of existing DNA—using a plethora of manual labor-intensive methods such as site-directed mutagenesis, error-prone PCR, assembly PCR, overlap extension PCR, cleavage and ligation, homologous recombination, and others. So far no universal method for DNA processing has been proposed and, consequently, no engineering discipline that could eliminate this manual labor has emerged. Here we present a novel operation on DNA molecules, called Y, which joins two DNA fragments into one, and show that it provides a foundation for DNA processing as it can implement all basic text processing operations on DNA molecules including insert, delete, replace, cut and paste and copy and paste. In addition, complicated DNA processing tasks such as the creation of libraries of DNA variants, chimeras and extensions can be accomplished with DNA processing plans consisting of multiple Y operations, which can be executed automatically under computer control. The resulting DNA processing system, which incorporates our earlier work on recursive DNA composition and error correction, is the first demonstration of a unified approach to DNA synthesis, editing, and library construction.