Effect of SpyTag/SpyCatcher cyclization on stability and refolding of green fluorescent protein

Biotechnology Letters - To study the effect of SpyTag/SpyCatcher cyclization on stability and refolding of protein, we constructed a cyclized green fluorescent protein (SRGFP) and its derivative to...     

SpyTag/SpyCatcher cyclization and covalent immobilization in enhancing cephalosporin C acylase stability

A SpyRing cyclized cephalosporin C acylase (SRCCA) was obtained by fusing SpyTag and SpyCatcher to the N- and C- termini of cephalosporin C acylase (CCA), respectively. The results suggested that the introduction of the SpyRing (head-to-tail cyclization via SpyTag and SpyCatcher) did not affect the active center of the SRCCA (the specific activities of CCA and SRCCA are 15.71 U/mg and 13.11 U/mg, respectively). Also, the thermostability, organic solvents tolerance, and denaturant tolerance of the free enzyme SRCCA were improved. Since glyoxyl agarose carrier favors the covalent immobilization of enzymes through its surface regions having the highest lysine residues density, SRCCA permitted its multipoint and oriented immobilization because SpyRing is very rich in Lys residues, while CCA is quite poor in Lys residues and immobilization is via less enzyme support-bonds. When the enzyme loading amount was 10 mg/g carrier, the expressed activity of SRCCA was 22 % higher than that of CCA. The stability of the immobilized SRCCA was also significantly improved; the half-life of the immobilized SRCCA at 50 °C was 125 min, which was about 5 times the half-life of the immobilized CCA.     

A Split-Cre system designed to detect simultaneous expression of two genes based on SpyTag/SpyCatcher conjugation and Split-GFP dimerization

The Split-Cre system is a powerful tool for genetic manipulation and can be used to spatiotemporally control gene expression in vivo. However, the low activity of the reconstituted NCre/CCre recombinase in the Split-Cre system limits its application as an indicator of the simultaneous expression of a pair of genes of interest. Here, we describe two approaches for improving the activity of the Split-Cre system after Cre reconstitution based on self-associating split GFP (Split-GFP) and SpyTag/SpyCatcher conjugation. First, we created the Split-GFP-Cre system by constructing fusion proteins of NCre and CCre with the N-terminal and C-terminal subunits of GFP, respectively. Reconstitution of Cre by GFP-mediated dimerization of the two fusion proteins resulted in recombinase activity approaching that of full-length Cre in living cells. Second, to further increase recombinase activity at low levels of Split-Cre expression, the Split-Spy-GCre system was established by incorporating the sequences for SpyTag and SpyCatcher into the components of the Split-GFP-Cre system. As anticipated, covalent conjugation of the SpyTag and SpyCatcher segments improved Split-GFP dimerization to further increase Cre recombinase activity in living cells. The increased efficiency and robustness of this dual-split system (Split-Cre and Split-GFP) minimize the problems of incomplete double gene-specific KO or low labeling efficiency due to poor NCre/CCre recombinase activity. Thus, this Split-Spy-GCre system allows more precise gene manipulation of cell subpopulations, which will provide advanced analysis of genes and cell functions in complex tissue such as the immune system.     

Structural Analysis and Optimization of the Covalent Association between SpyCatcher and a Peptide Tag

Peptide tagging is a key strategy for observing and isolating proteins. However, the interactions of proteins with peptides are nearly all rapidly reversible. Proteins tagged with the peptide SpyTag form an irreversible covalent bond to the SpyCatcher protein via a spontaneous isopeptide linkage, thereby offering a genetically encoded way to create peptide interactions that resist force and harsh conditions. Here, we determined the crystal structure of the reconstituted covalent complex of SpyTag and SpyCatcher at 2.1 Å resolution. The structure showed the expected reformation of the β-sandwich domain seen in the parental streptococcal adhesin, but flanking sequences at both N- and C-termini of SpyCatcher were disordered. In addition, only 10 out of 13 amino acids of the SpyTag peptide were observed to interact with SpyCatcher, pointing to specific contacts important for rapid split protein reconstitution. Based on these structural insights, we expressed a range of SpyCatcher variants and identified a minimized SpyCatcher, 32 residues shorter, that maintained rapid reaction with SpyTag. Together, these results give insight into split protein β-strand complementation and enhance a distinct approach to ultrastable molecular interaction.     

Overexpression and characterization of a thermostable trehalose synthase from Meiothermus ruber

A thermostable trehalose synthase (TreS) gene from Meiothermus ruber CBS-01 was cloned and overexpressed in Escherichia coli. The purified recombinant TreS could utilize maltose to produce trehalose, and showed an optimum pH and temperature of 6.5 and 50°C, respectively. Kinetic analysis showed that the enzyme had a twofold higher catalytic efficiency (k _cat/K _m) for maltose than for trehalose, indicating maltose as the preferred substrate. The TreS also had a weak hydrolytic property with glucose as the byproduct, and glucose was a strong competitive inhibitor of the enzyme. The maximum production of trehalose by the enzyme reached 65% at 20°C. The most importantly the enzyme could maintain very high activity (above 90%) at pH 4.0–8.0 and 60°C 5 h. These results provided that the stable TreS was suitable for the industrial production of trehalose from maltose in a one-step reaction.     

Effects of the N-terminal and C-terminal domains of <Emphasis Type="Italic">Meiothermus ruber</Emphasis> CBS-01 trehalose synthase on thermostability and activity

Numerous trehalose synthases (TreS) from thermophilic microorganisms have extra C-terminal domains. To determine the function of the N- and C-terminal domains of TreS from the thermophilic bacterium Meiothermus ruber CBS-01, the two domains were expressed. From the findings, the N-terminal domain from M. ruber was not active when compared with that from Thermus thermophilus, which had been studied previously. The circular dichroism spectrum showed that the secondary structure of N-terminal domain from M. ruber underwent a greater change than that of C terminus. In addition, the N-terminal domain from T. thermophilus and C terminus from M. ruber were fused. The fusion protein TSTtMr was more efficient and thermostable than the TreS from M. ruber. The N-terminal domain from M. ruber and C terminus from T. thermophilus were fused. The optimum temperature and thermostability of fusion protein TSMrTt were similar to the TreS from M. ruber. It was presumed that aside from the C-terminal domain, the N-terminal domain of TreS from thermophilic bacteria could influence thermostability. For the TreS from M. ruber, the mutant protein R392F led to a complete loss in activity, and R392A showed a sharp decrease in activity.     

Identification and Characterization of a Novel Trehalose Synthase Gene Derived from Saline-Alkali Soil Metagenomes

A novel trehalose synthase (TreS) gene was identified from a metagenomic library of saline-alkali soil by a simple activity-based screening system. Sequence analysis revealed that TreS encodes a protein of 552 amino acids, with a deduced molecular weight of 63.3 kDa. After being overexpressed in Escherichia coli and purified, the enzymatic properties of TreS were investigated. The recombinant TreS displayed its optimal activity at pH 9.0 and 45 °C, and the addition of most common metal ions (1 or 30 mM) had no inhibition effect on the enzymatic activity evidently, except for the divalent metal ions Zn²⁺ and Hg²⁺. Kinetic analysis showed that the recombinant TreS had a 4.1-fold higher catalytic efficientcy (Kcat/K _m) for maltose than for trehalose. The maximum conversion rate of maltose into trehalose by the TreS was reached more than 78% at a relatively high maltose concentration (30%), making it a good candidate in the large-scale production of trehalsoe after further study. In addition, five amino acid residues, His172, Asp201, Glu251, His318 and Asp319, were shown to be conserved in the TreS, which were also important for glycosyl hydrolase family 13 enzyme catalysis.     

Siderophore mediated plant growth promotion at low temperature by mutant of fluorescent pseudomonad⋆

A cold resistant mutant of Pseudomonas fluorescens ATCC 13525 was developed, which could grow equally well at 25 and 10 °C and its effect on plant growth promotion under in vitro and in situ conditions was observed. Siderophore estimation revealed it to be a siderophore-overproducing mutant (17-fold increase) when compared to its wild type counterpart. A gnotobiotic root elongation assay indicated that the mutant (CRPF₉) promoted growth more than its wild type both at 25 and 10 °C, indicating its effectiveness at low temperature. Further, root colonization studies showed that CRPF₉ was an efficient rhizosphere colonizer, inducing a significant increase in root (35%) and shoot length (28%) of mung bean plants in unsterilized soil system. The persistence and stability of the mutant was evident in rhizospheric soil. A sand culture experiment showed that ferric citrate was better than Fe(OH)₃ as an iron source for plant growth, but in the presence of CRPF₉ both salts were comparable. This study demonstrates the potential of chemical mutagenesis for improving the plant growth promoting properties of a P. fluorescens strain and its stimulating impact on plant growth promotion at low temperature both under in vitro and in situ conditions.     

Cold adaptation of a mesophilic subtilisin-like protease by laboratory evolution

Enzymes isolated from organisms native to cold environments generally exhibit higher catalytic efficiency at low temperatures and greater thermosensitivity than their mesophilic counterparts. In an effort to understand the evolutionary process and the molecular basis of cold adaptation, we have used directed evolution to convert a mesophilic subtilisin-like protease from Bacillus sphaericus, SSII, into its psychrophilic counterpart. A single round of random mutagenesis followed by recombination of improved variants yielded a mutant, P3C9, with a catalytic rate constant (k(cat)) at 10 degrees C 6.6 times and a catalytic efficiency (k(cat)/K(M)) 9.6 times that of wild type. Its half-life at 70 degrees C is 3.3 times less than wild type. Although there is a trend toward decreasing stability during the progression from mesophile to psychrophile, there is not a strict correlation between decreasing stability and increasing low temperature activity. A first generation mutant with a >2-fold increase in k(cat) is actually more stable than wild type. This suggests that the ultimate decrease in stability may be due to random drift rather than a physical incompatibility between low temperature activity and high temperature stability. SSII shares 77. 4% identity with the naturally psychrophilic protease subtilisin S41. Although SSII and S41 differ at 85 positions, four amino acid substitutions were sufficient to generate an SSII whose low temperature activity is greater than that of S41. That none of the four are found in S41 indicates that there are multiple routes to cold adaptation.     

<Emphasis Type="Italic">Arabidopsis</Emphasis> <Emphasis Type="Italic">thaliana</Emphasis> expressing a thermostable chimeric Rubisco activase exhibits enhanced growth and higher rates of photosynthesis at moderately high temperatures

Temperature is one of the most important factors controlling growth, development, and reproduction in plants. The rate of photosynthesis declines at moderately high temperatures in plants and particularly in temperate species like Arabidopsis thaliana. This can be attributed to a reduced ability of Rubisco activase to achieve optimum activation of Rubisco, leading to reduced Rubisco activity. In order to overcome this problem, we transformed the Arabidopsis rca mutant with a more thermostable, chimeric activase where a Rubisco recognition domain in the more thermostable tobacco activase was replaced with that from Arabidopsis. Transgenic lines expressing this activase showed higher rates of photosynthesis than the wild type after a short exposure to higher temperatures and they also recovered better, when they were returned to the normal temperature. Moreover, under extended exposure to moderately elevated temperature, the transgenic lines had higher biomass and seed yield when compared with the wild type plants.     

Loop optimization of Trichoderma reesei endoglucanases for balancing the activity–stability trade-off through cross-strategy between machine learning and the B-factor analysis

Trichoderma reesei endoglucanases (EGs) have limited industrial applications due to its low thermostability and activity. Here, we aimed to improve the thermostability of EGs from T. reesei without reducing its activity counteracting the activity–stability trade-off. A cross-strategy combination of machine learning and B-factor analysis was used to predict beneficial amino acid substitution in EG loop optimization. Experimental validation showed single-site mutated EG concomitantly improved enzymatic activity and thermal properties by 17.21%–18.06% and 49.85%–62.90%, respectively, compared with wild-type EGs. Furthermore, the mechanism explained mutant variants had lower root mean square deviation values and a more stable overall structure than the wild type. According to this study, EGs loop optimization is crucial for balancing the activity–stability trade-off, which may provide new insights into how loop region function interacts with enzymatic characteristics. Moreover, the cross-strategy between machine learning and B-factor analysis improved superior enzyme activity–stability performance, which integrated structure-dependent and sequence-dependent information.     

Changes in Thermostability of Photosystem Ⅱ and Leaf Lipid Composition of Rice Mutant with Deficiency of Light-harvesting Chlorophyll a/b Protein Complexes

We studied the difference in thermostability of photosystem Ⅱ （PSII） and leaf lipid composition between a T-DNA insertion mutant rice （Oryza sativa L.） VG28 and its wild type Zhonghuau. Native green gel and SDS-PAGE electrophoreses revealed that the mutant VG28 lacked all light-harvesting chlorophyll a/b protein complexes. Both the mutant and wild type were sensitive to high temperatures, and the maximal efficiency of PSII photochemistry （FJ Fm） and oxygen-evolving activity of PSII in leaves significantly decreased with increasing temperature. However, the PSII activity of the mutant was markedly more sensitive to high temperatures than that of the wild type. Lipid composition analysis showed that the mutant had less phosphatidylglycerol and sulfoquinovosyl diacylglycerol compared with the wild type. Fatty acid analysis revealed that the mutant had an obvious decrease in the content of 16：1t and a marked increase in the content of 18：3 compared with the wild type. The effects of lipid composition and unsaturation of membrane lipids on the thermostability of PSII are discussed.     

Site-directed mutagenesis of an alkaline phytase: influencing specificity, activity and stability in acidic milieu

Site-directed mutagenesis of a thermostable alkaline phytase from Bacillus sp. MD2 was performed with an aim to increase its specific activity and activity and stability in an acidic environment. The mutation sites are distributed on the catalytic surface of the enzyme (P257R, E180N, E229V and S283R) and in the active site (K77R, K179R and E227S). Selection of the residues was based on the idea that acid active phytases are more positively charged around their catalytic surfaces. Thus, a decrease in the content of negatively charged residues or an increase in the positive charges in the catalytic region of an alkaline phytase was assumed to influence the enzyme activity and stability at low pH. Moreover, widening of the substrate-binding pocket is expected to improve the hydrolysis of substrates that are not efficiently hydrolysed by wild type alkaline phytase. Analysis of the phytase variants revealed that E229V and S283R mutants increased the specific activity by about 19% and 13%, respectively. Mutation of the active site residues K77R and K179R led to severe reduction in the specific activity of the enzyme. Analysis of the phytase mutant-phytate complexes revealed increase in hydrogen bonding between the enzyme and the substrate, which might retard the release of the product, resulting in decreased activity. On the other hand, the double mutant (K77R-K179R) phytase showed higher stability at low pH (pH 2.6-3.0). The E227S variant was optimally active at pH 5.5 (in contrast to the wild type enzyme that had an optimum pH of 6) and it exhibited higher stability in acidic condition. This mutant phytase, displayed over 80% of its initial activity after 3 h incubation at pH 2.6 while the wild type phytase retained only about 40% of its original activity. Moreover, the relative activity of this mutant phytase on calcium phytate, sodium pyrophosphate and p-nitro phenyl phosphate was higher than that of the wild type phytase.     

Carbohydrate transporters of the bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS)

The glucose transporter of Escherichia coli couples translocation with phosphorylation of glucose. The IICB(Glc) subunit spans the membrane eight times. Split, circularly permuted and cyclized forms of IICB(Glc) are described. The split variant was 30 times more active when the two proteins were encoded by a dicistronic mRNA than by two genes. The stability and activity of circularly permuted forms was improved when they were expressed as fusion proteins with alkaline phosphatase. Cyclized IICB(Glc) and IIA(Glc) were produced in vivo by RecA intein-mediated trans-splicing. Purified, cyclized IIA(Glc) and IICB(Glc) had 100% and 30% of wild-type glucose phosphotransferase activity, respectively. Cyclized IIA(Glc) displayed increased stability against temperature and GuHCl-induced unfolding.     

Random mutants of a Pleurotus ostreatus laccase as new biocatalysts for industrial effluents bioremediation

Aims: To select better performing laccase variants among the 2300 randomly mutated variants of Pleurotus ostreatus POXA1b laccase to develop improved laccase‐based biocatalysts. Methods and Results: Screening of collections of 2300 randomly mutated variants of POXA1b was performed by assaying activity towards the phenolic substrate 2,6‐dimethoxyphenol. Two new variants endowed with higher enzyme activity than the wild‐type laccase were characterized, and their ability to decolourize industrial dyes with complex trisazo‐, polyazo‐ and stilbene‐type structures, in the absence of mediators, was demonstrated. One of the mutants (2L4A) was also proved to be highly stable at both acidic and alkaline pH values (displaying a half‐life of around 1 month at the pH levels of both 5 and 10). Conclusions: In comparison with the wild‐type laccase, the new selected 2L4A mutant shows a significant increase in stability at acidic pH, whilst storing its high stability at alkaline pH. This variant also represents a more versatile enzyme with respect to both the variety of xenobiotics degraded and the operative conditions. Significance and Impact of the Study: This work represents the first example of improvement of a basidiomycete laccase for industrial effluents bioremediation by directed evolution.     

The Enzymatic Production of Adipic Acid

Mutants of Brevibacterium sp. R312 were isolated for the production of adipic acid from 1,4-dicyanobutane (adiponitrile). One mutant (Ad), with a modified cell wall showed activity against adipamide three times greater than the wild type. Another mutant (ACV2) derived from the Ad strain had 30 times more activity on 5-cyanovaleric acid, and 7 times more on adipamide than the wild type.

The nitrile hydratase from the mutant strain ACV2 was purified and compared to that from the wild type R312. The nitrile hydratase of the mutant strain is different from that of the wild type by its pHi, optimum activity pH, and its rates of hydrolysis of 5-cyanovaleramide and 5-cyanovaleric acid which were 30 and 15 folds greater.

The presence of a new amidase named “adipamidase” acting on amide intermediates in the hydrolysis of dinitriles to organic acids was demonstrated in this mutant ACV2.     

Role of the C-terminal tail on the quaternary structure of aldehyde dehydrogenases

To assess the importance of the C-terminal tail in the structure of aldehyde dehydrogenases (ALDH), mutants of tetrameric ALDH1 were generated by adding a tail of 5 amino acids (ALDH1-5aa) or the tail from the class 3 enzyme. A mutant of dimeric ALDH3 was made, where 17 amino acids from the C-terminus were deleted to generate ALDH3ΔTail. The expression and solubility of the ALDH1 mutants was slightly lower than the wild type. Expression of ALDH3ΔTail mutant was similar to wild type, but the solubility was only about 30%. The activity of ALDH1-5aa mutant was 30%, while ALDH1-H3Tail mutant was 60% active, compared to the wild type. The activity of the class 3 mutant was similar to the activity of the parent ALDH3 enzyme. Analysis of stability against temperature demonstrated that ALDH1-5aa was more stable than ALDH1 wild type, while the ALDH1-H3Tail mutant was considerably less stable than ALDH1, showing a stability similar to ALDH3. However, native gel and size exclusion analysis, showed no changes in the oligomerization state of these mutants. ALDH3ΔTail mutant was more stable than wild type; the stability against temperature was similar to ALDH1. The ALDH3ΔTail mutant showed an elution similar to that of ALDH1 from the size exclusion column, indicating that it was possibly a tetramer. These results show that the tail in ALDH3, is involved in the determination of the quaternary structure of ALDH3, but has no effect on the ALDH1 enzyme; the absence of the C-terminal tail is not the only factor participating in holding the dimers together. Thus, the interaction between single residues, or interactions with the N-terminal region might be more important for maintaining stable tetramers.     

D-泛解酸内酯水解酶的定向进化

易错PCR结合DNA改组方法向D-泛解酸内酯水解酶基因中引入突变,并构建突变体库。利用酶的催化特点和产物特性建立了基于平板初筛和高效液相复筛的两步法D-泛解酸内酯水解酶活性筛选系统。用该筛选系统以酶活力和pH稳定性为指标对突变体库进行筛选,最终获得一株酶活力高且在低pH条件下稳定性好的突变体Mut E-861。该突变体的酶活力是野生型酶的5.5倍。对突变体和野生型酶在pH 6.0和pH 5.0条件下的残余酶活进行对比,在这两种pH条件下,突变体酶的酶活残留分别为75%和50%,而野生型酶只能保持原来的40%和20%。通过软件对突变体Mut E-861酶基因和野生型酶基因进行分析对比,发现突变体Mut E-861酶基因发生了三处点突变,其中突变使两处氨基酸取代,另一处为沉默突变,未引起氨基酸的变化。     

Role of the C-terminal tail on the quaternary structure of aldehyde dehydrogenases

To assess the importance of the C-terminal tail in the structure of aldehyde dehydrogenases (ALDH), mutants of tetrameric ALDH1 were generated by adding a tail of 5 amino acids (ALDH1-5aa) or the tail from the class 3 enzyme. A mutant of dimeric ALDH3 was made, where 17 amino acids from the C-terminus were deleted to generate ALDH3DeltaTail. The expression and solubility of the ALDH1 mutants was slightly lower than the wild type. Expression of ALDH3DeltaTail mutant was similar to wild type, but the solubility was only about 30%. The activity of ALDH1-5aa mutant was 30%, while ALDH1-H3Tail mutant was 60% active, compared to the wild type. The activity of the class 3 mutant was similar to the activity of the parent ALDH3 enzyme. Analysis of stability against temperature demonstrated that ALDH1-5aa was more stable than ALDH1 wild type, while the ALDH1-H3Tail mutant was considerably less stable than ALDH1, showing a stability similar to ALDH3. However, native gel and size exclusion analysis, showed no changes in the oligomerization state of these mutants. ALDH3DeltaTail mutant was more stable than wild type; the stability against temperature was similar to ALDH1. The ALDH3DeltaTail mutant showed an elution similar to that of ALDH1 from the size exclusion column, indicating that it was possibly a tetramer. These results show that the tail in ALDH3, is involved in the determination of the quaternary structure of ALDH3, but has no effect on the ALDH1 enzyme; the absence of the C-terminal tail is not the only factor participating in holding the dimers together. Thus, the interaction between single residues, or interactions with the N-terminal region might be more important for maintaining stable tetramers.     

Cloning, Expression and Characterization of a Trehalose Synthase Gene From Rhodococcus opacus

Trehalose is a unique disaccharide capable of protecting proteins against environmental stress. A novel trehalose synthase (TreS) gene from Rhodococcus opacus was cloned and expressed in Escherichia coli Top10 and BL21 (DE3) pLysS, respectively. The recombinant TreS showed a molecular mass of 79 kDa. Thin layer chromatography (TLC) result suggested that this enzyme had the ability to catalyze the mutual conversion of maltose and trehalose. Moreover, high-performance liquid chromatography (HPLC) result suggested that glucose appeared as a byproduct with a conversion rate of 12 %. The purified recombinant enzyme had an optimum temperature of 25 °C and pH optimum around 7.0. Kinetic analysis revealed that the K _m for trehalose was around 98 mM, which was a little higher than that of maltose. The preferred substrate of TreS was maltose according to the analysis of k _cat/K _m. Both 1 and 10 mM of Hg²⁺, Cu²⁺ and Al³⁺ could inhibit the TreS activity, while only 1 mM of Ca²⁺ and Mn²⁺ could increase its activity. Five amino acid residues, Asp²⁴⁴, Glu²⁸⁶, Asp³⁵⁴, His¹⁴⁷ and His³⁵³, were shown to be conserved in R. opacus TreS, which were also important for α-amylase family enzyme catalysis.