A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool

Genomic Insights into the Landfill Microbial Community: Denitrifying Activity Supporting One-Carbon Utilization

In spite of the developments in understanding of denitrifying methylotrophy in the recent years, challenges still exist in unravelling the overall biochemistry of nitrate-dependent methane oxidation in novel or poorly characterized/not-yet-cultured bacteria. In the present study, landfill site was mined for novel C1-carbon-metabolizing bacteria which can use nitrate/nitrite as an electron acceptor. A high-throughput rapid plate assay identified three bacterial isolates with eminent ability for nitrate-dependent methane metabolism under anaerobic conditions. Taxonomic identification by whole-genome sequence-based overall genome relatedness indices accurately assigned the isolates AAK_M13, AAK_M29, and AAK_M39 at the species level to Enterobacter cloacae, Bacillus subtilis, and Bacillus halotolerans, respectively. Several genes encoding sub-components involved in alcohol utilization and denitrification pathways, such as adh, fdh, fdo, nar, nir, and nor, were identified in all the genomes. Though no gene clusters encoding MMO/AMO were annotated, sequencing of PCR amplicons revealed similarity with pMMO/AMO gene using translated nucleotide sequence of strains AAK_M29 and AAK_M39, while strain AAK_M13 showed similarity with XRE family transcriptional regulator. This suggests the horizontal gene transfer and/or presence of a truncated version of a housekeeping enzyme encoded by genes exhibiting partial sequence similarity with pMMO genes that mimicked its function at greenhouse gas emission sites. Owing to lack of conclusive evidence for presence of methane metabolism genes in the selected isolates, further experiment was performed to validate their nitrate-dependent methane oxidation capacities. Bacillus subtilis AAK_M29, Bacillus halotolerans AAK_M39, and Enterobacter cloacae AAK_M13 could oxidize 60%, 75%, and 85% of the added methane respectively accompanied by high nitrate reduction (56-62%) thus supporting the correlation between these two activities. The remarkable ability of these isolates for nitrate-dependent methane metabolism has highlighted their role in ecological contribution and biotechnological potential to serve as methane and nitrate sinks in the landfill sites.

A pH-dependent shift of redox cofactor specificity in a benzyl alcohol dehydrogenase of aromatoleum aromaticum EbN1

We characterise a reversible bacterial zinc-containing benzyl alcohol dehydrogenase (BaDH) accepting either NAD+ or NADP+ as a redox cofactor. Remarkably, its redox cofactor specificity is pH-dependent with the phosphorylated cofactors favored at lower and the dephospho-forms at higher pH. BaDH also shows different steady-state kinetic behavior with the two cofactor forms. From a structural model, the pH-dependent shift may affect the charge of a histidine in the 2'-phosphate-binding pocket of the redox cofactor binding site. The enzyme is phylogenetically affiliated to a new subbranch of the Zn-containing alcohol dehydrogenases, which share this conserved residue. BaDH appears to have some specificity for its substrate, but also turns over many substituted benzyl alcohol and benzaldehyde variants, as well as compounds containing a conjugated C=C double bond with the aldehyde carbonyl group. However, compounds with an sp3-hybridised C next to the alcohol/aldehyde group are not or only weakly turned over. The enzyme appears to contain a Zn in its catalytic site and a mixture of Zn and Fe in its structural metal-binding site. Moreover, we demonstrate the use of BaDH in an enzyme cascade reaction with an acid-reducing tungsten enzyme to reduce benzoate to benzyl alcohol. KEY POINTS: •Zn-containing BaDH has activity with either NAD + or NADP+ at different pH optima. •BaDH converts a broad range of substrates. •BaDH is used in a cascade reaction for the reduction of benzoate to benzyl alcohol.

A systematic analysis of affinity tags in the haloarchaeal expression system, Haloferax volcanii for protein purification

Extremophilic proteins are valuable in various fields, but their expression can be challenging in traditional hosts like Escherichia coli due to misfolding and aggregation. Haloferax volcanii (H. volcanii), a halophilic expression system, offers a solution. This study examined cleavable and non-cleavable purification tags at both the N- and C-termini when fused with the superfolder green fluorescent protein (sfGFP) in H. volcanii. Our findings reveal that an N-terminal 8xHis-tag or Strep-tag®II significantly enhances protein production, purity, and yield in H. volcanii. Further experiments with mCherry and halophilic alcohol dehydrogenase (ADH) showed improved expression and purification yields when the 8xHis-tag or Strep-tag®II was positioned at the C-terminus for mCherry and at the N-terminus for ADH. Co-positioning 8xHis-tag and Twin-Strep-tag® at the N-terminus of sfGFP, mCherry, and ADH yielded significantly enhanced results. These findings highlight the importance of thoughtful purification tag design and selection in H. volcanii, providing valuable insights for improving protein production and purification with the potential to advance biotechnological applications.

Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System

Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.

Bioengineering of air-filled protein nanoparticles by genetic and chemical functionalization

BACKGROUND

Various bacteria and archaea, including halophilic archaeon Halobacterium sp. NRC-1 produce gas vesicle nanoparticles (GVNPs), a unique class of stable, air-filled intracellular proteinaceous nanostructures. GVNPs are an attractive tool for biotechnological applications due to their readily production, purification, and unique physical properties. GVNPs are spindle- or cylinder-shaped, typically with a length of 100 nm to 1.5 μm and a width of 30-250 nm. Multiple monomeric subunits of GvpA and GvpC proteins form the GVNP shell, and several additional proteins are required as minor structural or assembly proteins. The haloarchaeal genetic system has been successfully used to produce and bioengineer GVNPs by fusing several foreign proteins with GvpC and has shown various applications, such as biocatalysis, diagnostics, bioimaging, drug delivery, and vaccine development.

RESULTS

We demonstrated that native GvpC can be removed in a low salt buffer during the GVNP purification, leaving the GvpA-based GVNP's shell intact and stable under physiological conditions. Here, we report a genetic engineering and chemical modification approach for functionalizing the major GVNP protein, GvpA. This novel approach is based on combinatorial cysteine mutagenesis within GvpA and genetic expansion of the N-terminal and C-terminal regions. Consequently, we generated GvpA single, double, and triple cysteine variant libraries and investigated the impact of mutations on the structure and physical shape of the GVNPs formed. We used a thiol-maleimide chemistry strategy to introduce the biotechnological relevant activity by maleimide-activated streptavidin-biotin and maleimide-activated SpyTag003-SpyCatcher003 mediated functionalization of GVNPs.

CONCLUSION

The merger of these genetic and chemical functionalization approaches significantly extends these novel protein nanomaterials' bioengineering and functionalization potential to assemble catalytically active proteins, biomaterials, and vaccines onto one nanoparticle in a modular fashion.

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.

Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil

Municipal landfills are known for methane production and a source of nitrate pollution leading to various environmental issues. Therefore, this niche was selected for the isolation of one-carbon (C1) utilizing bacteria with denitrifying capacities using anaerobic enrichment on nitrate mineral salt medium supplemented with methanol as carbon source. Eight axenic cultures were isolated of which, isolate AAK/M5 demonstrated the highest methanol removal (73.28%) in terms of soluble chemical oxygen demand and methane removal (41.27%) at the expense of total nitrate removal of 100% and 33% respectively. The whole genome characterization with phylogenomic approach suggested that the strain AAK/M5 could be assigned to Pseudomonas aeruginosa with close neighbours as type strains DVT779, AES1M, W60856, and LES400. The circular genome annotation showed the presence of complete set of genes essential for methanol utilization and complete denitrification process. The study demonstrates the potential of P. aeruginosa strain AAK/M5 in catalysing methane oxidation thus serving as a methane sink vis-à-vis utilization of nitrate. Considering the existence of such bacteria at landfill site, the study highlights the need to develop strategies for their enrichment and designing of efficient catabolic activity for such environments.

Industrial Biotechnology Based on Enzymes From Extreme Environments

Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.

Novel Enzymes From the Red Sea Brine Pools: Current State and Potential

The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.

Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods

Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.

Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase

Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.

Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest

Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.