A Novel Cold-Adapted Leucine Dehydrogenase from Antarctic Sea-Ice Bacterium Pseudoalteromonas sp. ANT178

Genome-guided development of a bacterial two-strain system for low-temperature soil biocementation

Degradation and erosion of soil is a significant threat to global food security and overall agricultural productivity. This issue is exacerbated by climate change and intensive human activity, meaning that the development of sustainable solutions for those problems is critical. Microbially induced calcite precipitation (MICP) offers a promising approach to stabilise soil particles; however, its applicability at low temperatures remains limited. In our study, we introduce a novel two-strain system combining the type strain for biocementation experiments, Sporosarcina pasteurii DSM 33, and Sporosarcina sp. ANT_H38, a novel, psychrotolerant strain obtained from the Antarctic. The novel strain enabled enhanced biocementation performance when combined with the type strain. Biocementation experiments showed a 3.5-fold increase in soil cohesion, while maintaining a similar internal friction angle compared to the type strain alone (10.7 kPa vs 34.12 kPa; 0.55 kPa for untreated soil). The increased cohesion significantly reduces susceptibility to erosion, offering a practical and sustainable solution. Furthermore, to better understand the mechanisms driving this process, we conducted a comprehensive bioinformatic analysis of the ANT_H38 genome, revealing unique cold-adaptive genes, as well as urease genes, which are evolutionarily distant from other Sporosarcina ureases. Those results provide valuable insights into the strain's functional adaptations, particularly under low-temperature conditions. Overall, our study addresses a critical issue, offering a robust, nature-based solution that enhances soil resilience through MICP. Performed laboratory work confirms the potential of the system for real-world applications, while the comprehensive bioinformatic analysis provides the much needed context and information regarding the possible mechanisms behind the process. KEY POINTS: • Antarctic Sporosarcina sp. ANT_H38 contains unique urease genes • Two-strain ANT_H38/DSM33 system effectively stabilises soil at low temperatures • Two-strain system has potential for stopping soil erosion and desertification.

Semi-rational engineering of leucine dehydrogenase for enhanced L-tert-leucine production

Leucine dehydrogenase (LeuDH) is a promising enzyme for the industrial production of L-tert-leucine (L-Tle), but its catalytic activity toward trimethylpyruvate (TMP) requires enhancement. In this study, we employed a semi-rational design approach involving homology modeling of LeuDH from Exiguobacterium sibiricum (EsiLeuDH) and molecular docking with TMP to predict potential mutation sites. These sites were tested using an alanine scanning strategy to assess their impact on enzymatic activity, followed by site-saturation mutagenesis and iterative saturation mutagenesis. The resulting mutant, EsiLeuDH-M3, exhibited a remarkable 306 % increase in specific enzymatic activity (104.69 U·mg-1), compared to the wild-type EsiLeuDH (WT). Molecular docking indicated that EsiLeuDH-M3 had an increased number of hydrogen bonds, improved stability, and an enlarged substrate-binding pocket. Moreover, molecular dynamics simulations suggested that EsiLeuDH-M3 possessed a more stable conformation but a more flexible pocket, allowing TMP to access the catalytic center more easily. Experiments examining the effects of different substrate concentrations on TMP bioconversion catalyzed by WT and EsiLeuDH-M3 indicated that EsiLeuDH-M3 tolerated higher TMP concentrations than the WT enzyme. Finally, L-Tle was produced using EsiLeuDH-M3 coupled with an NADH regeneration system, achieving a high conversion rate (91 %) of TMP at a substrate concentration of 0.7 M, which is expected to reduce production costs in the industrial application of L-Tle.

Exploring the Antarctic aminopeptidase P from Pseudomonas sp. strain AMS3 through structural analysis and molecular dynamics simulation

Aminopeptidase P (APPro) is a crucial metalloaminopeptidase involved in amino acid cleavage from peptide N-termini, playing essential roles as versatile biocatalysts with applications ranging from pharmaceuticals to industrial processes. Despite acknowledging its potential for catalysis in lower temperatures, detailed molecular basis and biotechnological implications in cold environments are yet to be explored. Therefore, this research aims to investigate the molecular mechanisms underlying the cold-adapted characteristics of APPro from Pseudomonas sp. strain AMS3 (AMS3-APPro) through a detailed analysis of its structure and dynamics. In this study, structure analysis and molecular dynamics (MD) simulation of a predicted model of AMS3-APPro has been performed at different temperatures to assess structural flexibility and thermostability across a temperature range of 0-60 °C over 100 ns. The MD simulation results revealed that the structure were able to remain stable at low temperatures. Increased temperatures present a potential threat to the overall stability of AMS3-APPro by disrupting the intricate hydrogen bond networks crucial for maintaining structural integrity, thereby increasing the likelihood of protein unfolding. While the metal binding site at the catalytic core exhibits resilience at higher temperatures, highlighting its local structural integrity, the overall enzyme structure undergoes fluctuations and potential denaturation. This extensive structural instability surpasses the localized stability observed at the metal binding site. Consequently, these assessments offer in-depth understanding of the cold-adapted characteristics of AMS3-APPro, highlighting its capability to uphold its native conformation and stability in low-temperature environments. In summary, this research provides valuable insights into the cold-adapted features of AMS3-APPro, suggesting its efficient operation in low thermal conditions, particularly relevant for potential biotechnological applications in cold environments.

Cold-adapted enzymes: mechanisms, engineering and biotechnological application

Most cold-adapted enzymes display high catalytic activity at low temperatures (20-25 °C) and can still maintain more than 40-50% of their maximum activity at lower temperatures (0-10 °C) but are inactivated after a moderate increase in temperature. The activity of some cold-adapted enzymes increases significantly in the presence of high salt concentrations and metal ions. Interestingly, we also observed that some cold-adapted enzymes have a wide range of optimum temperatures, exhibiting not only maximum activity under low-temperature conditions but also the ability to maintain high enzyme activity under high-temperature conditions, which is a novel feature of cold-adapted enzymes. This unique property of cold-adapted enzymes is generally attractive for biotechnological and industrial applications because these enzymes can reduce energy consumption and the chance of microbial contamination, thereby lowering the production costs and maintaining the flavor, taste and quality of foods. How high catalytic activity is maintained at low temperatures remains unknown. The relationship between the structure of cold-adapted enzymes and their activity, flexibility and stability is complex, and thus far, a unified explanation has not been provided. Herein, we systematically review the sources, catalytic characteristics and cold adaptation of enzymes from four enzymes categories systematically and discuss how these properties may be exploited in biotechnology. A thorough understanding of the properties, catalytic mechanisms, and engineering of cold-adapted enzymes is critical for future biotechnological applications in the detergent industry and food and beverage industries.

Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules

Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.

Advances in cold-adapted enzymes derived from microorganisms

Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.

Novel Salt-Tolerant Leucine Dehydrogenase from Marine Pseudoalteromonas rubra DSM 6842

This study reported the cloning, expression, and characterization of a new salt-tolerant leucine dehydrogenase (PrLeuDH) from Pseudoalteromonas rubra DSM 6842. A codon-optimized 1038 bp gene encoding PrLeuDH was successfully expressed on pET-22b( +) in E. coli BL21(DE3). The purified recombinant PrLeuDH showed a single band of about 38.7 kDa on SDS-PAGE. It exhibited the maximum activity at 40 °C and pH 10.5, while kept high activities in the range of 25-45 °C and pH 9.5-12. The K_m value and turnover number k_cat for leucine of PrLeuDH were 2.23 ± 0.12 mM and 35.39 ± 0.05 s^-1, respectively, resulting in a catalytic efficiency k_cat/K_m of 15.87 s^-1/mM. Importantly, PrLeuDH remained 92.1 ± 2.67% active in the presence of 4.0 M NaCl. The study provides the first in-depth understanding of LeuDH from marine Pseudoalteromonas rubra, meanwhile the unique properties of high activity at low temperature and high salt tolerance make it a promising biocatalyst for the synthesis of non-protein amino acids and α-ketoacids under special conditions in pharmaceutical industry.

Industrial applications of cold-adapted enzymes: challenges, innovations and future perspective

Extreme cold environments are potential reservoirs of microorganisms producing unique and novel enzymes in response to environmental stress conditions. Such cold-adapted enzymes prove to be valuable tools in industrial biotechnology to meet the increasing demand for efficient biocatalysts. The inherent properties like high catalytic activity at low temperature, high specific activity and low activation energy make the cold-adapted enzymes well suited for application in various industries. The interest in this group of enzymes is expanding as they are the preferred alternatives to harsh chemical synthesis owing to their biodegradable and non-toxic nature. Irrespective of the multitude of applications, the use of cold-adapted enzymes at the industrial level is still limited. The current review presents the unique adaptive features and the role of cold-adapted enzymes in major industries like food, detergents, molecular biology and bioremediation. The review highlights the significance of omics technology i.e., metagenomics, metatranscriptomics and metaproteomics in enzyme bioprospection from extreme environments. It further points out the challenges in using cold-adapted enzymes at the industrial level and the innovations associated with novel enzyme prospection strategies. Documentations on cold-adapted enzymes and their applications are abundant; however, reports on the role of omics tools in exploring cold-adapted enzymes are still scarce. So, the review covers the aspect concerning the novel techniques for enzyme discovery from nature.

Enzymes from Marine Polar Regions and Their Biotechnological Applications

The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.