Characterization of a cold-active esterase from Serratia sp. and improvement of thermostability by directed evolution

Implementation of Spore Display in Paenibacillus polymyxa with Different Hydrolytic Enzymes

Biotechnological processes are essential for producing climate-friendly high-value chemicals or pharmaceutical compounds, which can include steps catalyzed by enzymes. Therefore, establishing new, robust, and cheap enzyme production processes is desirable. One possible way to enhance processes is through the use of the spore display method. Spore display can present heterologous proteins on the surface of bacterial spores, offering numerous advantages in a range of biotechnological applications. This study demonstrates the implementation of the spore display method in Paenibacillus polymyxa, achieved by modifying the spore surface, incorporating an anchoring protein, and attaching green fluorescent protein to it, allowing the visualization of fluorescent spores. Following the initial experiment, a native lipase (Lip3), a heterologous lipase (LipA) from Bacillus subtilis, a native esterase (PnbA) from P. polymyxa, and a lipoyl synthase were expressed during sporulation and displayed on the spore surface. The activity profiles were determined in the temperature range from 4 °C to 70 °C. The PnbA reached its optimum at 4 °C, whereas the LipA from B. subtilis showed 4.4-fold higher activity at 42 °C compared to the control. Furthermore, we explored a possible new technique for the purification of enzymes with the TEV cleavage site between the anchor and the protein of interest. Finally, we showed a not-yet-described side activity of the lipoyl synthase over a wide temperature range.

Antimicrobial resistance and biotechnological potential of plastic-associated bacteria isolated from an urban estuary

Plastics have quickly become one of the major pollutants in aquatic environments worldwide and solving the plastic pollution crisis is considered a central goal of modern society. In this study, 10 different plastic samples, including high- and low-density polyethylene and polypropylene, were collected from a deeply polluted urban estuary in Brazil. By employing different isolation and analysis approaches to investigate plastic-associated bacteria, a predominance of potentially pathogenic bacteria such as Acinetobacter, Aeromonas, and Vibrio was observed throughout all plastic samples. Bacteria typically found in the aquatic environment harboured clinically relevant genes encoding resistance to carbapenems (blaKPC ) and colistin (such as mcr-3 and mcr-4), along with genetic determinants associated with potentially active gene mobilization. Whole genome sequencing and annotation of three plastic-associated Vibrio strains further demonstrated the carriage of mobile genetic elements and antimicrobial resistance and virulence genes. On the other hand, bacteria isolated from the same samples were also able to produce esterases, lipases, and bioemulsifiers, thus highlighting that the plastisphere could also be of special interest from a biotechnological perspective.

Characterization of the Bacterial Communities in Cichorium intybus According to Cultivation and Storage Conditions

Chicory leaves (Cichorium intybus) are widely consumed due to their health benefits. They are mainly consumed raw or without adequate washing, which has led to an increase in food-borne illness. This study investigated the taxonomic composition and diversity of chicory leaves collected at different sampling times and sites. The potential pathogenic genera (Sphingomonas, Pseudomonas, Pantoea, Staphylococcus, Escherichia, and Bacillus) were identified on the chicory leaves. We also evaluated the effects of various storage conditions (enterohemorrhagic E. coli contamination, washing treatment, and temperature) on the chicory leaves' microbiota. These results provide an understanding of the microbiota in chicory and could be used to prevent food-borne illnesses.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Molecular study on recombinant cold-adapted, detergent- and alkali stable esterase (EstRag) from Lysinibacillus sp.: a member of family VI

Cold-adapted esterases have potential industrial applications. To fulfil the global continuous demand for these enzymes, a cold-adapted esterase member of family VI from Lysinibacillus sp. YS11 was cloned on pET-28b (+) vector and expressed in E. coli BL21(DE3) Rosetta cells for the first time. The open reading frame (654 bp: GenBank MT120818.1) encodes a polypeptide (designated EstRag: 217 amino acid residues). EstRag amino acid sequence has conserved esterase signature motifs: pentapeptide (GFSQG) and catalytic triad Ser¹¹⁰-Asp¹⁶³-His¹⁹⁴. EstRag 3D predicted model, built with LOMETS3 program, showed closest structural similarity to PDB 1AUO_A (esterase: Pseudomonas fluorescens); TM-align score program inferences. Purified EstRag to 9.28-fold, using Ni²⁺affinity agarose matrix, showed a single protein band (25 kDa) on SDS-PAGE, Km (0.031 mM) and Kcat/Km (657.7 s⁻¹ mM⁻¹) on p-NP-C2. Temperature and pH optima of EstRag were 35 °C and 8.0, respectively. EstRag was fully stable at 5–30 °C for 120 min and at pH(s) 8.0–10.0 after 24 h. EstRag activity (391.46 ± 0.009%) was impressively enhanced after 30 min preincubation with 5 mM Cu²⁺. EstRag retained full stability after 30 min pre-incubation with 0.1%(v/v) SDS, Triton X-100, and Tween-80. EstRag promising characteristics motivate performing guided evolution and industrial applications prospective studies.

Sustainable Biosynthesis of Esterase Enzymes of Desired Characteristics of Catalysis for Pharmaceutical and Food Industry Employing Specific Strains of Microorganisms

Reactions catalysed by sustainably produced enzymes can contribute to the bioeconomy supporting several industries. Low-value compounds can be transformed into added-value products or high-resolution chemicals could be prepared in reactions catalysed by biocatalyst esterase enzymes. These enzymes can be synthesised by purposely isolated or genetically modified strains of microorganisms. Enzymes belonging to the hydrolase family catalyse the formation and hydrolysis of ester bonds to produce the desired esterified molecule. The synthesis of homo-chiral compounds can be accomplished either by chemical or biocatalytic processes, the latter being preferred with the use of microbial esterases. For varied applications, esterases with high stability and retained activity at lower and higher temperatures have been produced with strains isolated from extreme environments. For sustainable production of enzymes, higher productivity has been achieved by employing fast-growing Escherichia coli after incorporating plasmids of required characteristics from specific isolates. This is a review of the isolated and engineered strains used in the biosynthesis of esterase of the desired property, with the objective of a sustainable supply of enzymes, to produce products of industrial importance contributing to the economy.

Formation of recombinant bifunctional fusion protein: A newer approach to combine the activities of two enzymes in a single protein

The tissue of insects, pests, and fungi has a chitin layer followed by protein in the cell membrane. The complete biodegradation of chitin and protein-present in the waste requires the action of two enzymes, namely chitinase, and protease. Combining chitinase and protease in a single protein/enzyme will serve as a bifunctional enzyme that can efficiently degrade the chitin and protein-rich biomass. The present study was aimed to fuse these two enzymes to produce a single protein and study the kinetics of the recombinant fusion protein. A chitinase and alkaline protease genes were isolated, cloned, and expressed successfully as a fusion product in heterologous host Escherichia coli. The two native genes were successfully fused in E.coli by using flexible glycine–serine (G₄S)₂ linker (GGGGS, GS linker). The recombinant fusion protein in E.coli showed hydrolyzed chitin and protein on chitin and bovine serum albumin agar plates confirming the successful cloning and expression of chitinase and protease enzymes in a single fusion protein. The common pUC18-T7 mini vector with the ompA signal sequence helps the extracellular expression of fusion protein efficiently. The native gel electrophoresis revealed a molecular mass of purified protein as 92.0 kDa. The fusion protein’s maximal chitinase and protease activity occurred at pH 5.0 and 8.0 and 30 ⁰C, respectively resembling the individual enzymes’. In the kinetic studies of the fusion protein, it was observed that the presence of metal ions such as Cu²⁺, Na²⁺, and Ca²⁺; significantly enhanced the enzyme activities while organic solvents oxidants and chemicals have drastically affected the activities of both the enzymes in the fusion protein. No such fusion protein has been produced in a heterologous host yet. The reports on fusion protein with biomass-degrading capacity are also scarce. This is probably the first report of a bifunctional chitinase/protease expressed in E. coli.

Challenges and Recent Advances in Enzyme-Mediated Wastewater Remediation-A Review

Different classes of artificial pollutants, collectively called emerging pollutants, are detected in various water bodies, including lakes, rivers, and seas. Multiple studies have shown the devastating effects these emerging pollutants can have on human and aquatic life. The main reason for these emerging pollutants in the aquatic environment is their incomplete removal in the existing wastewater treatment plants (WWTPs). Several additional treatments that could potentially supplement existing WWTPs to eliminate these pollutants include a range of physicochemical and biological methods. The use of enzymes, specifically, oxidoreductases, are increasingly being studied for their ability to degrade different classes of organic compounds. These enzymes have been immobilized on different supports to promote their adoption as a cost-effective and recyclable remediation approach. Unfortunately, some of these techniques have shown a negative effect on the enzyme, including denaturation and loss of catalytic activity. This review focuses on the major challenges facing researchers working on the immobilization of peroxidases and the recent progress that has been made in this area. It focuses on four major areas: (1) stability of enzymes upon immobilization, enzyme engineering, and evolution; (2) recyclability and reusability, including immobilization on membranes and solid supports; (3) cost associated with enzyme-based remediation; and (4) scaling-up and bioreactors.

Identification and Biochemical Characterization of a Novel Hormone-Sensitive Lipase Family Esterase Est19 from the Antarctic Bacterium Pseudomonas sp. E2-15

Esterases represent an important class of enzymes with a wide variety of industrial applications. A novel hormone-sensitive lipase (HSL) family esterase, Est19, from the Antarctic bacterium Pseudomonas sp. E2-15 is identified, cloned, and expressed. The enzyme possesses a GESAG motif containing an active serine (S) located within a highly conserved catalytic triad of Ser155, Asp253, and His282 residues. The catalytic efficiency (kcat/Km) of Est19 for the pNPC6 substrate is 148.68 s-1mM-1 at 40 °C. Replacing Glu154 juxtaposed to the critical catalytic serine with Asp (E154→D substitution) reduced the activity and catalytic efficiency of the enzyme two-fold, with little change in the substrate affinity. The wild-type enzyme retained near complete activity over a temperature range of 10-60 °C, while ~50% of its activity was retained at 0 °C. A phylogenetic analysis suggested that Est19 and its homologs may represent a new subfamily of HSL. The thermal stability and stereo-specificity suggest that the Est19 esterase may be useful for cold and chiral catalyses.

Genetic dissection of maize seedling traits in an IBM Syn10 DH population under the combined stress of lead and cadmium

The heavy metals lead and cadmium have become important pollutants in the environment, which exert negative effects on plant morphology, growth and photosynthesis. It is particularly significant to uncover the genetic loci and the causal genes for lead and cadmium tolerance in plants. This study used an IBM Syn10 DH population to identify the quantitative trait loci (QTL) controlling maize seedling tolerance to lead and cadmium by linkage mapping. The broad-sense heritability of these seedling traits ranged from 65.8-97.3% and 32.0-98.8% under control (CK) and treatment (T) conditions, respectively. A total of 53 and 64 QTL were detected under CK and T conditions, respectively. Moreover, 42 QTL were identified using lead and cadmium tolerance coefficient (LCTC). Among these QTL, five and two major QTL that explained > 10% of phenotypic variation were identified under T condition and using LCTC, respectively. Furthermore, eight QTL were simultaneously identified by T and LCTC, explaining 5.23% to 9.21% of the phenotypic variations. Within these major and common QTL responsible for the combined heavy metal tolerance, four candidate genes (Zm00001d048759, Zm00001d004689, Zm00001d004843, Zm00001d033527) were previously reported to correlate with heavy metal transport and tolerance. These findings will contribute to functional gene identification and molecular marker-assisted breeding for improving heavy metal tolerance in maize.

A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity

Halotolerant lipolytic enzymes have gained growing interest, due to potential applications under harsh conditions, such as hypersalinity and presence of organic solvents. In this study, a lipolytic gene, est56, encoding 287 amino acids was identified by functional screening of a compost metagenome. Subsequently, the gene was heterologously expressed, and the recombinant protein (Est56) was purified and characterized. Est56 is a mesophilic (T_opt 50 °C) and moderate alkaliphilic (pH_opt 8) enzyme, showing high thermostability at 30 and 40 °C. Strikingly, Est56 is halotolerant as it exhibited high activity and stability in the presence of up to 4 M NaCl or KCl. Est56 also displayed enhanced stability against high temperatures (50 and 60 °C) and urea (2, 4, and 6 M) in the presence of NaCl. In addition, the recently reported halotolerant lipolytic enzymes were summarized. Phylogenetic analysis grouped these enzymes into 13 lipolytic protein families. The majority (45%) including Est56 belonged to family IV. To explore the haloadaptation of halotolerant enzymes, the amino acid composition between halotolerant and halophilic enzymes was statistically compared. The most distinctive feature of halophilic from non-halophilic enzymes are the higher content of acidic residues (Asp and Glu), and a lower content of lysine, aliphatic hydrophobic (Leu, Met and Ile) and polar (Asn) residues. The amino acid composition and 3-D structure analysis suggested that the high content of acidic residues (Asp and Glu, 12.2%) and low content of lysine residues (0.7%), as well as the excess of surface-exposed acidic residues might be responsible for the haloadaptation of Est56.

Structural Basis for the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus aureus

Staphylococcus aureus is a prevalent bacterial pathogen in both community and hospital settings, and its treatment is made particularly difficult by resilience within biofilms. Within this niche, serine hydrolase enzymes play a key role in generating and maintaining the biofilm matrix. Activity-based profiling has previously identified a family of serine hydrolases, designated fluorophosphonate-binding hydrolases (Fph's), some of which contribute to the virulence of S. aureus in vivo. These 10 Fph proteins have limited annotation and have few, if any, characterized bacterial or mammalian homologues. This suggests unique hydrolase functions even within bacterial species. Here we report structures of one of the most abundant Fph family members, FphF. Our structures capture FphF alone, covalently bound to a substrate analogue and bound to small molecule inhibitors that occupy the hydrophobic substrate-binding pocket. In line with these findings, we show that FphF has promiscuous esterase activity toward hydrophobic lipid substrates. We present docking studies that characterize interactions of inhibitors and substrates within the active site environment, which can be extended to other Fph family members. Comparison of FphF to other esterases and the wider Fph protein family suggest that FphF forms a new esterase subfamily. Our data suggest that other Fph enzymes, including the virulence factor FphB, are likely to have more restricted substrate profiles than FphF. This work demonstrates a clear molecular rationale for the specificity of fluorophosphonate probes that target FphF and provides a structural template for the design of enhanced probes and inhibitors of the Fph family of serine hydrolases.

Revisiting the scope and applications of food enzymes from extremophiles

Microorganisms from extreme environments tend to undergo various adaptations due to environmental conditions such as extreme pH, temperature, salinity, heavy metals, and solvents. Thus, they produce enzymes with unique properties and high specificity, making them useful industrially, particularly in the food industries. Despite these enzymes' remarkable properties, only a few instances can be reported for actual exploitation in the food industry. This review's objectives are to highlight the properties of these enzymes and their prospects in the food industry. First, an introduction to extremophilic organisms is presented, followed by the categories and application of food enzymes from extremophiles. Then, the unique structural features of extremozymes are shown. This review also covers the prospective applications of extremozymes in the food industry in a broader sense, including degradation of toxins, deconstruction of polymers into monomers, and catalysis of multistep processes. Finally, the challenges in bioprocessing of extremozymes and applications in food are presented. PRACTICAL APPLICATIONS: Enzymes are important players in food processing and preservation. Extremozymes, by their nature, are ideal for a broad range of food processing applications, particularly those that require process conditions of extreme pH, temperature, and salinity. As the global food industry grows, so too will grow the need to research and develop food products that are diverse, safe, healthy, and nutritious. There is also the need to produce food in a sustainable way that generates less waste or maximizes waste valorization. We anticipate that extremozymes can meet some of the research and development needs of the food industry.

Exploring Metagenomic Enzymes: A Novel Esterase Useful for Short-Chain Ester Synthesis

Enzyme-mediated esterification reactions can be a promising alternative to produce esters of commercial interest, replacing conventional chemical processes. The aim of this work was to verify the potential of an esterase for ester synthesis. For that, recombinant lipolytic enzyme EST5 was purified and presented higher activity at pH 7.5, 45 °C, with a Tm of 47 °C. Also, the enzyme remained at least 50% active at low temperatures and exhibited broad substrate specificity toward p-nitrophenol esters with highest activity for p-nitrophenyl valerate with a Kcat/Km of 1533 s−1 mM−1. This esterase exerted great properties that make it useful for industrial applications, since EST5 remained stable in the presence of up to 10% methanol and 20% dimethyl sulfoxide. Also, preliminary studies in esterification reactions for the synthesis of methyl butyrate led to a specific activity of 127.04 U·mg−1. The enzyme showed higher esterification activity compared to other literature results, including commercial enzymes such as LIP4 and CL of Candida rugosa assayed with butyric acid and propanol which showed esterification activity of 86.5 and 15.83 U·mg−1, respectively. In conclusion, EST5 has potential for synthesis of flavor esters, providing a concept for its application in biotechnological processes.

"Recombinant cold -adapted halotolerant, organic solvent-stable esterase (estHIJ) from Bacillus halodurans

Esterases and lipases enduring harsh conditions, including low temperature and extreme tolerance to organic solvents, have attracted great attention in recent times. In the current study, a full open reading frame of 747 bp that encodes a novel, cold-adapted esterase (estHIJ) of 248 amino acids from Bacillus halodurans strain NAH-Egypt was heterologously cloned and expressed in E. coli BL21 (DE3) Rosetta. Amino acid sequence analysis revealed that estHIJ belongs to family XIII of lipolytic enzymes, with a characteristic pentapeptide motif (G-L-S-L-G). The recombinant estHIJ was purified using Ni-affinity chromatography to homogeneity with purification fold, yield, specific activity, and molecular weight (MW) of 3.5, 47.5%, 19.8 U/mg and 29 kDa, respectively. The enzyme showed preferential substrate specificity towards pNP-acetate (C2), with catalytic efficiency of 46,825 min-1 mM-1 estHIJ displayed optimal activity at 30 °C and pH (7.0-8.0). estHIJ demonstrated robust stability in the presence of 50% (v/v) non-polar solvents and 4 M NaCl after 15 h and 6 h of incubation, respectively. The promising features of the recombinant estHIJ underpin its potential in several fields, e.g., the synthesis of pharmaceutical compounds and the food industry.

Cold survival strategies for bacteria, recent advancement and potential industrial applications

Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.

A novel cold-adapted esterase from Enterobacter cloacae: Characterization and improvement of its activity and thermostability via the site of Tyr193Cys

Background

In industries lipolytic reactions occur in insensitive conditions such as high temperature thus novel stout esterases with unique properties are attracts to the industrial application. Protein engineering is the tool to obtain desirable characters of enzymes. A novel esterase gene was isolated from South China Sea and subjected to a random mutagenesis and site directed mutagenesis for higher activity and thermo-stability compared to wild type.

Results

A novel esterase showed the highest hydrolytic activity against p-nitrophenyl acetate (pNPA, C2) and the optimal activity at 40 °C and pH 8.5. It was a cold-adapted enzyme and retained approximately 40% of its maximum activity at 0 °C. A mutant, with higher activity and thermo-stability was obtained by random mutagenesis. Kinetic analysis indicated that the mutant Val29Ala/Tyr193Cys shown 43.5% decrease in K_m, 2.6-fold increase in K_cat, and 4.7-fold increase in K_cat/K_m relative to the wild type. Single mutants V29A and Y193C were constructed and their kinetic parameters were measured. The results showed that the values of K_m, K_cat, and K_cat/K_m of V29A were similar to those of the wild type while Y193C showed 52.7% decrease in K_m, 2.7-fold increase in K_cat, and 5.6-fold increase in K_cat/K_m compared with the wild type. The 3-D structure and docking analysis revealed that the replacement of Tyr by Cys could enlarge the binding pocket. Moreover Y193C also showed a better thermo-stability for the reason its higher hydrophobicity and retained 67% relative activity after incubation for 3 h at 50 °C.

Conclusions

The superior quality of modified esterase suggested it has great potential application in extreme conditions and the mutational work recommended that important information for the study of esterase structure and function.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0885-z) contains supplementary material, which is available to authorized users.

Characterization of a novel alkaline esterase from Altererythrobacter epoxidivorans CGMCC 1.7731T

A novel esterase gene (e25) was identified from Altererythrobacter epoxidivorans CGMCC 1.7731^T by genome sequence screening. The e25 gene is 948 nucleotides in length and encodes a 315 amino acid protein (E25) with a predicted molecular mass of 33,683 Da. A phylogenetic tree revealed that E25 belongs to the hormone-sensitive lipase (HSL) family of lipolytic enzymes. An activity assay of E25 showed that it exhibited the highest catalytic efficiency when using p-nitrophenyl caproate (C6) as a substrate. The optimum pH and temperature were determined to be approximately pH 9 and 45°C, and the K_m and V_max values were 0.12 mM and 1,772 µmol/min/mg, respectively. After an incubation at 40°C for 80 min, E25 retained 75% of its basal activity. The enzyme exhibited good tolerance to metal cations, such as Ba²⁺, Ca²⁺, and Cu²⁺ (10 mM), but its activity was strongly inhibited by Co²⁺, Ni²⁺, Mn²⁺, and Zn²⁺. The E25 enzyme was stimulated by glycerol and retained over 60% of its basal activity in the presence of 1% Tween-80 and Triton X-100. Overall, the activity of E25 under alkaline conditions and its organic solvent and detergent tolerance indicate that E25 could be useful as a novel industrial catalyst in biotechnological applications.

Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

Background

Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, and sulphur containing amino acids. In addition, it has C4 photosynthetic carbon assimilation mechanism, which helps to utilize water and nitrogen efficiently under hot and arid conditions without severely affecting yield. Therefore, development and utilization of genomic resources for genetic improvement of this crop is immensely useful.

Results

Experimental results from whole genome sequencing and assembling process of ML-365 finger millet cultivar yielded 1196 Mb covering approximately 82% of total estimated genome size. Genome analysis showed the presence of 85,243 genes and one half of the genome is repetitive in nature. The finger millet genome was found to have higher colinearity with foxtail millet and rice as compared to other Poaceae species. Mining of simple sequence repeats (SSRs) yielded abundance of SSRs within the finger millet genome. Functional annotation and mining of transcription factors revealed finger millet genome harbors large number of drought tolerance related genes. Transcriptome analysis of low moisture stress and non-stress samples revealed the identification of several drought-induced candidate genes, which could be used in drought tolerance breeding.

Conclusions

This genome sequencing effort will strengthen plant breeders for allele discovery, genetic mapping, and identification of candidate genes for agronomically important traits. Availability of genomic resources of finger millet will enhance the novel breeding possibilities to address potential challenges of finger millet improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3850-z) contains supplementary material, which is available to authorized users.

Enhancing the thermostability of α-L-rhamnosidase from Aspergillus terreus and the enzymatic conversion of rutin to isoquercitrin by adding sorbitol

Background

Thermally stable α-L-rhamnosidase with cleaving terminal α-L-rhamnose activity has great potential in industrial application. Therefore, it is necessary to find a proper method to improve the thermal stability of α-L-rhamnosidase.

Results

In this study, addition of sorbitol has been found to increase the thermostability of α-L-rhamnosidase from Aspergillus terreus at temperatures ranging from 65 °C to 80 °C. Half-life and activation free energy with addition of 2.0 M sorbitol at 70 °C were increased by 17.2-fold, 8.2 kJ/mol, respectively. The analyses of the results of fluorescence spectroscopy and CD have indicated that sorbitol helped to protect the tertiary and secondary structure of α-L-rhamnosidase. Moreover, the isoquercitrin yield increased from 60.01 to 96.43% with the addition of 1.5 M of sorbitol at 70 °C.

Conclusion

Our findings provide an effective approach for enhancing the thermostability of α-L-rhamnosidase from Aspergillus terreus, which makes it a good candidate for industrial processes of isoquercitrin preparation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-017-0342-9) contains supplementary material, which is available to authorized users.

Characterization and Applications of Marine Microbial Enzymes in Biotechnology and Probiotics for Animal Health

Marine microorganisms have been recognized as potential sources of novel enzymes because they are relatively more stable than the corresponding enzymes derived from plants and animals. Enzymes from marine microorganisms also differ from homologous enzymes in terrestrial microorganisms based on salinity, pressure, temperature, and lighting conditions. Marine microbial enzymes can be used in diverse industrial applications. This chapter will focus on the biotechnological applications of marine enzymes and also their use as a tool of marine probiotics to improve host digestion (food digestion, food absorption, and mucus utilization) and cleave molecular signals involved in quorum sensing in pathogens to control disease in aquaculture.

Mutational analysis and stability characterization of a novel esterase of lipolytic enzyme family VI from Shewanella sp

Esterases are widely used in different industries. Here, a novel esterase, Esth, with low identity with previously reported esterases, was identified and characterized. The results showed that Esth was a cold-adapted esterase and retained 50% of its maximum activity at 0°C. Besides, Esth showed great activity and stability in high concentrations of NaCl. When treated with some organic solvents, detergents and metal ions, Esth showed high activity as well. The kcat/Km value of Esth was 29.5s^-1mM^-1, suggesting that it has higher catalytic efficiency than all the previously reported esterases from the same family, lipolytic enzyme family VI. The structural modeling showed that changing Ala129 into Gly would form a new hydrogen bond between ser125 and Gly129 and make theα-helix longer, which might influence on the thermostability of enzymes (Kumar, 2000). To confirm this, the mutant Esth_A129G was obtained by site-directed mutagenesis. The result indicated that Esth_A129G retained over 70% of the activity versus 12% for Esth after incubation at 55°C for 120min, showed a nearly six fold increase when compared with wild type. Overall, Esth shows a potential application prospect in extreme conditions and the mutation research can provide some structural information about thermostable enzymes.

Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes

Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.

Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts

In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts.