Prebiotic properties of Bacillus coagulans MA-13: production of galactoside hydrolyzing enzymes and characterization of the transglycosylation properties of a GH42 β-galactosidase

Background: The spore-forming lactic acid bacterium Bacillus coagulans MA-13 has been isolated from canned beans manufacturing and successfully employed for the sustainable production of lactic acid from lignocellulosic biomass. Among lactic acid bacteria, B. coagulans strains are generally recognized as safe (GRAS) for human consumption. Low-cost microbial production of industrially valuable products such as lactic acid and various enzymes devoted to the hydrolysis of oligosaccharides and lactose, is of great importance to the food industry. Specifically, α- and β-galactosidases are attractive for their ability to hydrolyze not-digestible galactosides present in the food matrix as well as in the human gastrointestinal tract. Results: In this work we have explored the potential of B. coagulans MA-13 as a source of metabolites and enzymes to improve the digestibility and the nutritional value of food. A combination of mass spectrometry analysis with conventional biochemical approaches has been employed to unveil the intra- and extra- cellular glycosyl hydrolase (GH) repertoire of B. coagulans MA-13 under diverse growth conditions. The highest enzymatic activity was detected on β-1,4 and α-1,6-glycosidic linkages and the enzymes responsible for these activities were unambiguously identified as β-galactosidase (GH42) and α-galactosidase (GH36), respectively. Whilst the former has been found only in the cytosol, the latter is localized also extracellularly. The export of this enzyme may occur through a not yet identified secretion mechanism, since a typical signal peptide is missing in the α-galactosidase sequence. A full biochemical characterization of the recombinant β-galactosidase has been carried out and the ability of this enzyme to perform homo- and hetero-condensation reactions to produce galacto-oligosaccharides, has been demonstrated. Conclusions: Probiotics which are safe for human use and are capable of producing high levels of both α-galactosidase and β-galactosidase are of great importance to the food industry. In this work we have proven the ability of B. coagulans MA-13 to over-produce these two enzymes thus paving the way for its potential use in treatment of gastrointestinal diseases. [Figure not available: see fulltext.

Draft genome sequence of bacillus coagulans ma-13, a thermophilic lactic acid producer from lignocellulose

Bacillus coagulans MA-13 is an efficient lactic acid producer which withstands high concentrations of the growth inhibitors formed during the pretreatment of lignocellulosic feedstock. This draft genome sequence is expected to pave the way toward the understanding of mechanisms responsible for the robustness of MA-13 during simultaneous saccharification and fermentation

Probing the role of an invariant active site His in family GH1 β-glycosidases

The reaction mechanism of glycoside hydrolases belonging to family 1 (GH1) of carbohydrate-active enzymes classification, hydrolysing β-O-glycosidic bonds, is well characterised. This family includes several thousands of enzymes with more than 20 different EC numbers depending on the sugar glycone recognised as substrate. Most GH1 β-glycosidases bind their substrates with similar specificity through invariant amino acid residues. Despite extensive studies, the clear identification of the roles played by each of these residues in the recognition of different glycones is not always possible. We demonstrated here that a histidine residue, completely conserved in the active site of the enzymes of this family, interacts with the C2-OH of the substrate in addition to the C3-OH as previously shown by 3 D-structure determination

(Hyper)thermophilic biocatalysts for second generation biorefineries

In bioeconomy, the development of next generation biorefineries, utilizing energy crops and waste materials, are considered one of the most promising actions toward the sustainable production of fuel and the building blocks for chemicals and polymers with a global market in 2016 of $466.6 billion and a compounded average growth rate of 8.9% between 2016-2021. This complex process is far from being optimized and the application of novel carbohydrate active enzymes justify great expectations. Here we briefly summarise how, for to the advances in (meta)genomics, glycoside hydrolases from (hyper)thermophilic organisms, thanks to their intrinsic stability, can significantly improve lignocellulosic degradation in second generation biorefineries. © 2016, TeknoScienze. All rights reserved

A novel Streptomyces strain isolated by functional bioprospecting for laccases

In discovering novel laccase enzymes with interesting catalytic and stability properties, there is still scope for improvement in exploring new sites in Algeria. The bio-prospecting approach allowed the isolation of a novel strain, Streptomyces sp. HBD30 from the Agrioun River, northern Algeria. Following a functional approach, two laccases (LacI and LacII) were purified and characterised, showing appealing properties as thermostable enzymes, and oxidised typical phenolic and non-phenolic substrates with a higher affinity towards syringaldazine, followed by 2,6-dimethoxyphenol and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid). Further analyses revealed that the Streptomyces sp. HDB30 genome contained an array of genes coding for carbohydrate active enzymes (CAZome) and lignin-degrading enzymes to degrade lignocellulose. In addition to enlarging the repertoire of thermostable laccases, this study uncovered the metabolic potential of a new Streptomyces strain, which is useful for a wide range of applications

Extremophilic Archaea in Astrobiology

Extremophiles are organisms capable of adapt themselves, survive and thrive in hostile habitats that were previously thought to be adverse for life or lethal. Extreme conditions drive the evolution of their inhabitants, highlighting the role of extremophiles as models for the study of the origin and evolution of life on Earth. Indeed, the investigation of both the microbial communities populating these environments and their biocatalysts, as well as of gene expression control by translational recoding in Archaea provide key insights into the boundaries of life, allowing us to speculate mightily about possible extraterrestrial life form. In this framework, we report here recent advances of our research groups in the astrobiology investigation

Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia

Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life

Programmed Deviations of Ribosomes From Standard Decoding in Archaea

Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed –1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed

Xyloglucan oligosaccharides hydrolysis by exo‐acting glycoside hydrolases from hyperthermophilic microorganism saccharolobus solfataricus

In the field of biocatalysis and the development of a bio‐based economy, hemicellulases have attracted great interest for various applications in industrial processes. However, the study of the catalytic activity of the lignocellulose‐degrading enzymes needs to be improved to achieve the efficient hydrolysis of plant biomasses. In this framework, hemicellulases from hyperthermophilic archaea show interesting features as biocatalysts and provide many advantages in industrial applications thanks to their stability in the harsh conditions encountered during the pretreatment process. However, the hemicellulases from archaea are less studied compared to their bacterial counterpart, and the activity of most of them has been barely tested on natural substrates. Here, we investigated the hydrolysis of xyloglucan oligosaccharides from two different plants by using, both synergistically and individually, three glycoside hydrolases from Saccharolobus solfataricus: a GH1 β‐gluco‐/β‐galactosidase, a α‐fucosidase belonging to GH29, and a α‐xylosidase from GH31. The results showed that the three enzymes were able to release monosaccharides from xyloglucan oligosaccharides after incubation at 65 °C. The concerted actions of β‐gluco‐/β‐galactosidase and the α‐xylosidase on both xyloglucan oligosaccharides have been observed, while the α‐fucosidase was capable of releasing all α‐linked fucose units from xyloglucan from apple pomace, representing the first GH29 enzyme belonging to subfamily A that is active on xyloglucan