Identification and characterization of an ectoine biosynthesis gene cluster from Aestuariispira ectoiniformans sp. nov., isolated from seawater

The tropical marine actinomycete Nocardiopsis dassonvillei NCIM 5124 as novel source of ectoine: Genomic and transcriptomic insights

Since ectoine is a high-value product, overviewing strategies for identifying novel microbial sources becomes relevant. In the current study, by following a genome mining approach, the ectoine biosynthetic cluster in a tropical marine strain of Nocardiopsis dassonvillei (NCIM 5124) was located and compared with related organisms. Transcriptome analysis of Control and Test samples (with 0 and 5% NaCl, respectively) was carried out to understand salt induced stress response at the molecular level. There were 4950 differentially expressed genes with 25 transcripts being significantly upregulated in Test samples. NaCl induced upregulation of the ectoine biosynthesis cluster and some other genes (stress response, chaperone/Clp protease, cytoplasm, ribonucleoprotein and protein biosynthesis). The production of ectoine as a stress response molecule was experimentally validated via LCMS analysis. The investigation sheds light on the responses exhibited by this actinomycete in coping up with salt stress and provides a foundation for understanding salt induced molecular interactions.

Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica

Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.

Biotechnological production of ectoine: current status and prospects

Ectoine is an important natural secondary metabolite in halophilic microorganisms. It protects cells against environmental stressors, such as salinity, freezing, drying, and high temperatures. Ectoine is widely used in medical, cosmetic, and other industries. Due to the commercial market demand of ectoine, halophilic microorganisms are the primary method for producing ectoine, which is produced using the industrial fermentation process "bacterial milking." The method has some limitations, such as the high salt concentration fermentation, which is highly corrosive to the equipment, and this also increases the difficulty of downstream purification and causes high production costs. The ectoine synthesis gene cluster has been successfully heterologously expressed in industrial microorganisms, and the yield of ectoine was significantly increased and the cost was reduced. This review aims to summarize and update microbial production of ectoine using different microorganisms, environments, and metabolic engineering and fermentation strategies and provides important reference for the development and application of ectoine.

Recent advances in production and applications of ectoine, a compatible solute of industrial relevance

Extremophilic bacteria growing in saline ecosystems are potential producers of biotechnologically important products including compatible solutes. Ectoine/hydroxyectoine are two such solutes that protect cells and associated macromolecules from osmotic, heat, cold and UV stress without interfering with cellular functions. Since ectoine is a high value product, overviewing strategies for improving yields become relevant. Screening of natural isolates, use of inexpensive substrates and response surface methodology approaches have been used to improve bioprocess parameters. In addition, genome mining exercises can aid in identifying hitherto unreported microorganisms with a potential to produce ectoine that can be exploited in the future. Application wise, ectoine has various biotechnological (protein protectant, membrane modulator, DNA protectant, cryoprotective agent, wastewater treatment) and biomedical (dermatoprotectant and in overcoming respiratory and hypersensitivity diseases) uses. The review summarizes current updates on the potential of microorganisms in the production of this industrially relevant metabolite and its varied applications.

Ectoine Globally Hypomethylates DNA in Skin Cells and Suppresses Cancer Proliferation

Epigenetic modifications, mainly aberrant DNA methylation, have been shown to silence the expression of genes involved in epigenetic diseases, including cancer suppression genes. Almost all conventional cancer therapeutic agents, such as the DNA hypomethylation drug 5-aza-2-deoxycytidine, have insurmountable side effects. To investigate the role of the well-known DNA protectant (ectoine) in skin cell DNA methylation and cancer cell proliferation, comprehensive methylome sequence analysis, 5-methyl cytosine (5mC) analysis, proliferation and tumorigenicity assays, and DNA epigenetic modifications-related gene analysis were performed. The results showed that extended ectoine treatment globally hypomethylated DNA in skin cells, especially in the CpG island (CGIs) element, and 5mC percentage was significantly reduced. Moreover, ectoine mildly inhibited skin cell proliferation and did not induce tumorigenicity in HaCaT cells injected into athymic nude mice. HaCaT cells treated with ectoine for 24 weeks modulated the mRNA expression levels of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l, Hdac1, Hdac2, Kdm3a, Mettl3, Mettl14, Snrpn, and Mest. Overall, ectoine mildly demethylates DNA in skin cells, modulates the expression of epigenetic modification-related genes, and reduces cell proliferation. This evidence suggests that ectoine is a potential anti-aging agent that prevents DNA hypermethylation and subsequently activates cancer-suppressing genes.

Machine learning methods for predicting the key metabolic parameters of Halomonas elongata DSM 2581 T

Ectoine is generally produced by the fermentation process of Halomonas elongata DSM 2581 ^T, which is one of the primary industrial ectoine production techniques. To effectively monitor and control the fermentation process, the important parameters require accurate real-time measurement. However, for ectoine fermentation, three critical parameters (cell optical density, glucose, and product concentration) cannot be measured conveniently in real-time due to time variation, strong coupling, and other constraints. As a result, our work effectively created a series of hybrid models to predict the values of these three parameters incorporating both fermentation kinetics and machine learning approaches. Compared with the traditional machine learning models, our models solve the problem of insufficient data which is common in fermentation. In addition, a simple kinetic modeling is only applicable to specific physical conditions, so different physical conditions require refitting the function, which is tedious to operate. However, our models also overcome this limitation. In this work, we compared different hybrid models based on 5 feature engineering methods, 11 machine-learning approaches, and 2 kinetic models. The best models for predicting three key parameters, respectively, are as follows: CORR-Ensemble (R²: 0.983 ± 0.0, RMSE: 0.086 ± 0.0, MAE: 0.07 ± 0.0), SBE-Ensemble (R²: 0.972 ± 0.0, RMSE: 0.127 ± 0.0, MAE: 0.078 ± 0.0), and SBE-Ensemble (R²:0.98 ± 0.0, RMSE: 0.023 ± 0.001, MAE: 0.018 ± 0.001). To verify the universality and stability of constructed models, we have done an experimental verification, and its results showed that our proposed models have excellent performance. KEY POINTS: • Using the kinetic models for producing simulated data • Through different feature engineering methods for dimension reduction • Creating a series of hybrid models to predict the values of three parameters in the fermentation process of Halomonas elongata DSM 2581 ^T.

Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative β-agarase

Marine microbes, particularly Bacteroidetes, are a rich source of enzymes that can degrade diverse marine polysaccharides. Aquimarina sp. ERC-38, which belongs to the Bacteroidetes phylum, was isolated from seawater in South Korea. It showed agar-degrading activity and required an additional carbon source for growth on marine broth 2216. Here, the genome of the strain was sequenced to understand its agar degradation mechanism, and 3615 protein-coding sequences were predicted, which were assigned putative functions according to their annotated functional feature categories. In silico genome analysis revealed that the ERC-38 strain has several carrageenan-degrading enzymes but could not degrade carrageenan because it lacked genes encoding κ-carrageenanase and S1_19A type sulfatase. Moreover, the strain possesses multiple genes predicted to encode enzymes involved in agarose degradation, which are located in a polysaccharide utilization locus. Among the enzymes, Aq1840, which is closest to ZgAgaC within the glycoside hydrolase 16 family, was characterized using a recombinant enzyme expressed in Escherichia coli BL21 (DE3) cells. An enzyme assay revealed that recombinant Aq1840 mainly converts agarose to NA4. Moreover, recombinant Aq1840 could weakly hydrolyze A5 into A3 and NA2. These results showed that Aq1840 is involved in at least the initial agar degradation step prior to the metabolic pathway that uses agarose as a carbon source for growth of the strain. Thus, this enzyme can be applied to development and manufacturing industry for prebiotic and antioxidant food additive. Furthermore, our genome sequence analysis revealed that the strain is a potential resource for research on marine polysaccharide degradation mechanisms and carbon cycling.

Production and Recovery of Ectoine: A Review of Current State and Future Prospects

Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is a revolutionizing substance with vast applications in the cosmetic and food industries. Ectoine is often sourced from halobacteria. The increasing market demand for ectoine has urged the development of cost-effective and sustainable large-scale production of ectoine from microbial sources. This review describes the existing and potential microbial sources of ectoine and its derivatives, as well as microbial production and fermentation approaches for ectoine recovery. In addition, conventional methods and emerging technologies for enhanced production and recovery of ectoine from microbial fermentation with a focus on the aqueous biphasic system (ABS) are discussed. The ABS is a practically feasible approach for the integration of fermentation, cell disruption, bioconversion, and clarification of various biomolecules in a single-step operation. Nonetheless, the implementation of the ABS on an industrial-scale basis for the enhanced production and recovery of ectoine is yet to be exploited. Therefore, the feasibility of the ABS to integrate the production and direct recovery of ectoine from microbial sources is also highlighted in this review.

Phenotypic and genomic characterization provide new insights into adaptation to environmental stressors and biotechnological relevance of mangrove Alcaligenes faecalis D334

Alcaligenes faecalis D334 was determined in this study as a salt-tolerant bacterium isolated from mangrove sediment. In response to 6% (w/v) NaCl, strain D334 produced the highest ectoines of 14.14 wt%. To understand adaptive features to mangrove environment, strain D334 was sequenced using Pacific BioScience platform, resulting in a circular chromosome of 4.23 Mb. Of note, D334 genome harbored 81 salt-responsive genes, among which two membrane-associated genes ompc and eric were absent in 3 selected A. faecalis genomes. Apart from that, a complete pathway for ectoine and 5-hydroxyectoine synthesis was predicted. To resist 40 mM H₂O₂, 46 genetic determinants contributing to oxidative stress response were employed. Moreover, two operons involved in polyhydroxyalkanoate (PHA) production were identified in the D334 genome, resulting in maximum PHA content of 5.03 ± 0.04 wt% and PHA concentration of 0.13 ± 0.001 g/L. A large flagellar biosynthesis operon contributing to swimming motility was found to be conserved in D334 and 8 other A. faecalis genomes. These findings shed light for the first time on the high versatility of A. faecalis D334 genome to adapt to mangrove lifestyle and the possibility to develop D334 as an industrial platform for PHA and 5-hydroxyectoine production.