Characterization and engineering of two new GH9 and GH48 cellulases from a Bacillus pumilus isolated from Lake Bogoria

Role of carbohydrate binding modules, CBM3A and CBM3B in stability and catalysis by a β-1,4 endoglucanase, AtGH9C-CBM3A-CBM3B from Acetivibrio thermocellus ATCC 27405

A recombinant β-1,4 endoglucanase, AtGH9C-CBM3A-CBM3B from Acetivibrio thermocellus ATCC27405 was explored for biochemical properties and the role of its associated CBMs in catalysis. The gene expressing full-length multi-modular β-1,4-endoglucanase (AtGH9C-CBM3A-CBM3B) and its truncated derivatives (AtGH9C-CBM3A, AtGH9C, CBM3A and CBM3B) were independently cloned and expressed in Escherichia coli BL21(DE3) cells and purified. AtGH9C-CBM3A-CBM3B showed maximal activity at 55 °C and pH 7.5. AtGH9C-CBM3A-CBM3B exhibited highest activity against carboxy methyl cellulose (58.8 U/mg) followed by lichenan (44.5 U/mg), β-glucan (36.2 U/mg) and hydroxy ethyl cellulose (17.9 U/mg). Catalytic module, AtGH9C showed insignificant activity against the substrates, signifying the essential requirement of CBMs in catalysis. AtGH9C-CBM3A-CBM3B displayed stability in pH range, 6.0-9.0 and thermostability up to 60 °C for 90 min with unfolding transition midpoint (T_m) of 65 °C. The generation of cellotetraose and other higher oligosaccharides by AtGH9C-CBM3A-CBM3B confirmed it as an endo-β-1,4-glucanase. AtGH9C activity was partially recovered by the addition of equimolar concentration of CBM3A, CBM3B or CBM3A + CBM3B by 47 %, 13 % or 50 %, respectively. Moreover, the associated CBMs imparted thermostability to the catalytic module, AtGH9C. These results showed that the physical association of AtGH9C with its associated CBMs and the cross-talk between CBMs are necessary for AtGH9C-CBM3A-CBM3B in effective cellulose catalysis.

Protein dynamics: The future is bright and complicated!

Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions occurring on micro to milliseconds. An outstanding challenge in contemporary biophysics and structural biology is a quantitative understanding of the linkages among protein structure, dynamics, and function. These linkages are becoming increasingly explorable due to conceptual and methodological advances. In this Perspective article, we will point toward future directions of the field of protein dynamics with an emphasis on enzymes. Research questions in the field are becoming increasingly complex such as the mechanistic understanding of high-order interaction networks in allosteric signal propagation through a protein matrix, or the connection between local and collective motions. In analogy to the solution to the "protein folding problem," we argue that the way forward to understanding these and other important questions lies in the successful integration of experiment and computation, while utilizing the present rapid expansion of sequence and structure space. Looking forward, the future is bright, and we are in a period where we are on the doorstep to, at least in part, comprehend the importance of dynamics for biological function.

Insight into CAZymes of Alicyclobacillus mali FL18: Characterization of a New Multifunctional GH9 Enzyme

In the bio-based era, cellulolytic and hemicellulolytic enzymes are biocatalysts used in many industrial processes, playing a key role in the conversion of recalcitrant lignocellulosic waste biomasses. In this context, many thermophilic microorganisms are considered as convenient sources of carbohydrate-active enzymes (CAZymes). In this work, a functional genomic annotation of Alicyclobacillus mali FL18, a recently discovered thermo-acidophilic microorganism, showed a wide reservoir of putative CAZymes. Among them, a novel enzyme belonging to the family 9 of glycosyl hydrolases (GHs), named AmCel9, was identified; in-depth in silico analyses highlighted that AmCel9 shares general features with other GH9 members. The synthetic gene was expressed in Escherichia coli and the recombinant protein was purified and characterized. The monomeric enzyme has an optimal catalytic activity at pH 6.0 and has comparable activity at temperatures ranging from 40 °C to 70 °C. It also has a broad substrate specificity, a typical behavior of multifunctional cellulases; the best activity is displayed on β-1,4 linked glucans. Very interestingly, AmCel9 also hydrolyses filter paper and microcrystalline cellulose. This work gives new insights into the properties of a new thermophilic multifunctional GH9 enzyme, that looks a promising biocatalyst for the deconstruction of lignocellulose.

Manganese Stress Adaptation Mechanisms of Bacillus safensis Strain ST7 From Mine Soil

The mechanism of bacterial adaption to manganese-polluted environments was explored using 50 manganese-tolerant strains of bacteria isolated from soil of the largest manganese mine in China. Efficiency of manganese removal by the isolated strains was investigated using atomic absorption spectrophotometry. Bacillus safensis strain ST7 was the most effective manganese-oxidizing bacteria among the tested isolates, achieving up to 82% removal at a Mn(II) concentration of 2,200 mg/L. Bacteria-mediated manganese oxide precipitates and high motility were observed, and the growth of strain ST7 was inhibited while its biofilm formation was promoted by the presence of Mn(II). In addition, strain ST7 could grow in the presence of high concentrations of Al(III), Cr(VI), and Fe(III). Genome-wide analysis of the gene expression profile of strain ST7 using the RNA-seq method revealed that 2,580 genes were differently expressed under Mn(II) exposure, and there were more downregulated genes (n = 2,021) than upregulated genes (n = 559) induced by Mn stress. KAAS analysis indicated that these differently expressed genes were mainly enriched in material metabolisms, cellular processes, organism systems, and genetic and environmental information processing pathways. A total of twenty-six genes from the transcriptome of strain ST7 were involved in lignocellulosic degradation. Furthermore, after 15 genes were knocked out by homologous recombination technology, it was observed that the transporters, multicopper oxidase, and proteins involved in sporulation and flagellogenesis contributed to the removal of Mn(II) in strain ST7. In summary, B. safensis ST7 adapted to Mn exposure by changing its metabolism, upregulating cation transporters, inhibiting sporulation and flagellogenesis, and activating an alternative stress-related sigB pathway. This bacterial strain could potentially be used to restore soil polluted by multiple heavy metals and is a candidate to support the consolidated bioprocessing community.

Fungal cellulases: protein engineering and post-translational modifications

Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.

Effects of fertilizer practice on fungal and actinobacterial cellulolytic community with different humified particle-size fractions in double-cropping field

Cellulose plays an important role in maintaining or improving soil carbon (C) cycling and soil fertility of paddy field. There had close relationship between functional cellulose genes (cbhI and GH48) with characterize of soil organic matter chemical components (fulvic acid and humic acid) and soil physical fractions. However, there is still limited information about how functional cellulose degradation response to long-term fertilizer management and their relative importance for C sequestration under the double-cropping rice paddy field in southern of China. Therefore, the objective of this study were investigated the effects of 34-years long-term fertilizer regime on community abundance of cbhI and GH48 genes in five soil particle-size fractions (> 2000 μm, 2000–200 μm, 200–50 μm, 50–2 μm and 2–0.1 μm) by using polarization magic angle spinning ¹³C nuclear magnetic resonance spectroscopy. The field experiment was included four different fertilizer treatments: chemical fertilizer alone (MF), rice straw and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). The results showed that distribution of soil humus and cellulolytic microbial community abundance was significant increased under long-term application of crop residue and organic manure condition. And the FA, HA and HM C contents in > 2000 μm and 2000–50 μm fractions with MF, RF and OM treatments were significant higher than that of CK treatment. Meanwhile, the alkyl C and Oalkyl C groups of FA and HA in > 2000 μm fraction with MF, RF, OM and CK treatments were higher than that of the other fractions. There had higher AL% and lower ARO% of FA and HA in different particle-size fractions with MF, RF, OM and CK treatments. The results indicated that abundance of cbhI and GH48 genes in different particle-size fractions with RF and OM treatments were significant increased, compared with CK treatment. There had significant positive correlation between soil humus C components (FA and HA) with abundance of cbhI and GH48 genes, and the o-alkyl C and AL% of FA were positively correlated with abundance of cbhI and GH48 genes. As a result, the community abundance of cbhI and GH48 genes were significant increased under combined application of crop residue and organic manure with chemical fertilizer condition.