Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex

Rational engineering of Halomonas salifodinae to enhance hydroxyectoine production under lower-salt conditions

Hydroxyectoine is an important compatible solute that holds potential for development into a high-value chemical with broad applications. However, the traditional high-salt fermentation for hydroxyectoine production presents challenges in treating the high-salt wastewater. Here, we report the rational engineering of Halomonas salifodinae to improve the bioproduction of hydroxyectoine under lower-salt conditions. The comparative transcriptomic analysis suggested that the increased expression of ectD gene encoding ectoine hydroxylase (EctD) and the decreased expressions of genes responsible for tricarboxylic acid (TCA) cycle contributed to the increased hydroxyectoine production in H. salifodinae IM328 grown under high-salt conditions. By blocking the degradation pathway of ectoine and hydroxyectoine, enhancing the expression of ectD, and increasing the supply of 2-oxoglutarate, the engineered H. salifodinae strain HS328-YNP15 (ΔdoeA::PUP119-ectD p-gdh) produced 8.3-fold higher hydroxyectoine production than the wild-type strain and finally achieved a hydroxyectoine titer of 4.9 g/L in fed-batch fermentation without any detailed process optimization. This study shows the potential to integrate hydroxyectoine production into open unsterile fermentation process that operates under low-salinity and high-alkalinity conditions, paving the way for next-generation industrial biotechnology. KEY POINTS: • Hydroxyectoine production in H. salifodinae correlates with the salinity of medium • Transcriptomic analysis reveals the limiting factors for hydroxyectoine production • The engineered strain produced 8.3-fold more hydroxyectoine than the wild type.

Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase

Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.

Highly efficient production of ectoine via an optimized combination of precursor metabolic modules in Escherichia coli BL21

Ectoine is an osmotic pressure protectant observed in various microorganisms and is widely used in cosmetics and pharmaceuticals. The market value of ectoine has increased considerably with social progress, resulting in high demand for ectoine production technology. Herein, a microbial cell factory in Escherichia coli that produces ectoine at high titers is described as developing efficient and environmentally friendly bio-based ectoine production technology. The ectoine biosynthetic pathway of Halomonas hydrothermalis was introduced into E. coli BL21 (DE3). Subsequent overexpression of precursor metabolic modules, including aspartate branching, pyruvate-oxoacetate, and glutamate biosynthesis pathways, resulted in the final strain, E. coli BCT08, which produced ectoine at a titer of 36.58 g/L during 30 h of fermentation. Sugar feeding speed optimization improved the ectoine titer to 131.8 g/L after 96 h of cultivation. This represents a remarkable achievement in ectoine production from glucose under low-salt conditions and has vast potential for industrial applications.

Ectoines production from biogas in pilot bubble column bioreactors and their subsequent extraction via bio-milking

Despite the potential of biogas from waste/wastewater treatment as a renewable energy source, the presence of pollutants and the rapid decrease in the levelized cost of solar and wind power constrain the use of biogas for energy generation. Biogas conversion into ectoine, one of the most valuable bioproducts (1000 €/kg), constitutes a new strategy to promote a competitive biogas market. The potential for a stand-alone 20 L bubble column bioreactor operating at 6% NaCl and two 10 L interconnected bioreactors (at 0 and 6% NaCl, respectively) for ectoine production from biogas was comparatively assessed. The stand-alone reactor supported the best process performance due to its highest robustness and efficiency for ectoine accumulation (20-52 mgectoine/gVSS) and CH4 degradation (up to 84%). The increase in N availability and internal gas recirculation did not enhance ectoine synthesis. However, a 2-fold increase in the internal gas recirculation resulted in an approximately 1.3-fold increase in CH4 removal efficiency. Finally, the recovery of ectoine through bacterial bio-milking resulted in efficiencies of >70% without any negative impact of methanotrophic cell recycling to the bioreactors on CH4 biodegradation or ectoine synthesis.

Properties and biotechnological applications of microbial deacetylase

Deacetylases, a class of enzymes that can catalyze the hydrolysis of acetylated substrates to remove the acetyl group, used in producing various products with high qualities, are one of the most influential industrial enzymes. These enzymes are highly specific, non-toxic, sustainable, and eco-friendly biocatalysts. Deacetylases and deacetylated compounds have been widely applicated in pharmaceuticals, medicine, food, and the environment. This review synthetically summarizes deacetylases' sources, characterizations, classifications, and applications. Moreover, the typical structural characteristics of deacetylases from different microbial sources are summarized. We also reviewed the deacetylase-catalyzed reactions for producing various deacetylated compounds, such as chitosan-oligosaccharide (COS), mycothiol, 7-aminocephalosporanic acid (7-ACA), glucosamines, amino acids, and polyamines. It is aimed to expound on the advantages and challenges of deacetylases in industrial applications. Moreover, it also serves perspectives on obtaining promising and innovative biocatalysts for enzymatic deacetylation. KEYPOINTS: • The fundamental properties of microbial deacetylases of various microorganisms are presented. • The biochemical characterizations, structures, and catalyzation mechanisms of microbial deacetylases are summarized. • The applications of microbial deacetylases in food, pharmaceutical, medicine, and the environment were discussed.

Bioactivity profiling of the extremolyte ectoine as a promising protectant and its heterologous production

Ectoine is a compatible solutes that is diffusely dispersed in bacteria and archaea. It plays a significant role as protectant against various external pressures, such as high temperature, high osmolarity, dryness and radiation, in cells. Ectoine can be utilized in cosmetics due to its properties of moisturizing and antiultraviolet. It can also be used in the pharmaceutical industry for treating various diseases. Therefore, strong protection of ectoine creates a high commercial value. Its current market value is approximately US$1000 kg-1. However, traditional ectoine production in high-salinity media causes high costs of equipment loss and wastewater treatment. There is a growing attention to reduce the salinity of the fermentation broth without sacrificing the production of ectoine. Thus, heterologous production of ectoine in nonhalophilic microorganisms may represent the new generation of the industrial production of ectoine. In this review, we summarized and discussed the biological activities of ectoine on cell and human health protection and its heterologous production.

The Retrospective on Atypical Brucella Species Leads to Novel Definitions

The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.

The MocR/GabR Ectoine and Hydroxyectoine Catabolism Regulator EnuR: Inducer and DNA Binding

The compatible solutes ectoine and 5-hydroxyectoine are widely synthesized by bacteria as osmostress protectants. These nitrogen-rich tetrahydropyrimidines can also be exploited as nutrients by microorganisms. Many ectoine/5-hydroxyectoine catabolic gene clusters are associated with a regulatory gene (enuR: ectoine nutrient utilization regulator) encoding a repressor protein belonging to the MocR/GabR sub-family of GntR-type transcription factors. Focusing on EnuR from the marine bacterium Ruegeria pomeroyi, we show that the dimerization of EnuR is mediated by its aminotransferase domain. This domain can fold independently from its amino-terminal DNA reading head and can incorporate pyridoxal-5′-phosphate (PLP) as cofactor. The covalent attachment of PLP to residue Lys302 of EnuR was proven by mass-spectrometry. PLP interacts with system-specific, ectoine and 5-hydroxyectoine-derived inducers: alpha-acetyldiaminobutyric acid (alpha-ADABA), and hydroxy-alpha-acetyldiaminobutyric acid (hydroxy-alpha-ADABA), respectively. These inducers are generated in cells actively growing with ectoines as sole carbon and nitrogen sources, by the EutD hydrolase and targeted metabolic analysis allowed their detection. EnuR binds these effector molecules with affinities in the low micro-molar range. Studies addressing the evolutionary conservation of EnuR, modelling of the EnuR structure, and docking experiments with the inducers provide an initial view into the cofactor and effector binding cavity. In this cavity, the two high-affinity inducers for EnuR, alpha-ADABA and hydroxy-alpha-ADABA, are positioned such that their respective primary nitrogen group can chemically interact with PLP. Purified EnuR bound with micro-molar affinity to a 48 base pair DNA fragment containing the sigma-70 type substrate-inducible promoter for the ectoine/5-hydroxyectoine importer and catabolic gene cluster. Consistent with the function of EnuR as a repressor, the core elements of the promoter overlap with two predicted EnuR operators. Our data lend themselves to a straightforward regulatory model for the initial encounter of EnuR-possessing ectoine/5-hydroxyectoine consumers with environmental ectoines and for the situation when the external supply of these compounds has been exhausted by catabolism.

Mixed-acidic cation-exchange material for the separation of underivatized amino acids

Mixed-acidic cation-exchange (MCX) columns with both strongly (SCX) and weakly (WCX) acidic functional groups were developed for the separation of standard amino acids. The resins were prepared by carboxylation of highly crosslinked monodisperse poly(styrene-divinylbenzene) copolymer particles with performic acid and subsequent sulfonation with sulfuric acid. The degree of functionalization was varied independently for each processing step and controlled by measuring pH dependent retention of the obtained resins. A series of mixed-acidic resins with different SCX/WCX-ratios was chromatographically characterized by variation of formic acid and acetonitrile concentration in the aqueous eluent. The overall cation-exchange capacity was varied from 33 to 68 µmol/mL. The comparison with two commercial columns (Metrohm Metrosep C6, WCX and Hamilton PRP X-200, SCX) revealed the additive character of the different functional group properties within MCX columns and a unique selectivity which can be adjusted by both eluent composition and SCX/WCX-ratio of the resin. The retention window between neutral and basic amino acids was altered by varying the amount of sulfonic acid groups attached to the polymer. Orthogonality plots demonstrated constant selectivity for neutral amino acids. Correlating the retention data with log P data demonstrated the influence of non-ionic hydrophobic and π-π-interactions for the separation of amino acids on PS/DVB-based cation-exchangers. An isocratic IC-ESI-MS method was developed to separate and quantitate 20 underivatized standard amino acids within 30 min. Limits of detection were between 4 and 64 nmol L^-1 and a high linearity of calibration curves was obtained for all analytes. The method was validated by comparing a certified reference standard with external calibration data.

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

An ectoine-producing bacterium, designated SWCN16^T, was isolated from seawater and could be grown in a medium containing up to 12 % NaCl. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SWCN16^T belonged to the genus Aestuariispira, class Alphaproteobacteria, and shared the highest 16S rRNA gene sequence similarity of 96.8% with Aestuariispira insulae CECT 8488^T. The phenotypic, chemotaxonomic, and genotypic characteristics findings of this study suggested that strain SWCN16^T represented a novel species of the genus Aestuariispira. We propose the name Aestuariispira ectoiniformans sp. nov. for this species. Whole-genome sequencing analysis of the isolate revealed a putative ectABC gene cluster for ectoine biosynthesis. These genes were found to be functional using ectoine synthesis testing and S16-ectBAC cells, which were pET21a-ectBAC-transformed E. coli BL21 cells. We found that S16-ectBAC synthesized about 1.67 g/L extracellular ectoine and about 0.59 g/L intracellular ectoine via bioconversion at optimum conditions.

The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient

Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.

Microbial production of ectoine and hydroxyectoine as high-value chemicals

Ectoine and hydroxyectoine as typical representatives of compatible solutes are not only essential for extremophiles to survive in extreme environments, but also widely used in cosmetic and medical industries. Ectoine was traditionally produced by Halomonas elongata through a "bacterial milking" process, of which the marked feature is using a high-salt medium to stimulate ectoine biosynthesis and then excreting ectoine into a low-salt medium by osmotic shock. The optimal hydroxyectoine production was achieved by optimizing the fermentation process of Halomonas salina. However, high-salinity broth exacerbates the corrosion to fermenters, and more importantly, brings a big challenge to the subsequent wastewater treatment. Therefore, increasing attention has been paid to reducing the salinity of the fermentation broth but without a sacrifice of ectoine/hydroxyectoine production. With the fast development of functional genomics and synthetic biology, quite a lot of progress on the bioproduction of ectoine/hydroxyectoine has been achieved in recent years. The importation and expression of an ectoine producing pathway in a non-halophilic chassis has so far achieved the highest titer of ectoine (~ 65 g/L), while rational flux-tuning of halophilic chassis represents a promising strategy for the next-generation of ectoine industrial production. However, efficient conversion of ectoine to hydroxyectoine, which could benefit from a clearer understanding of the ectoine hydroxylase, is still a challenge to date.

Enhancing ectoine production by recombinant Escherichia coli through step-wise fermentation optimization strategy based on kinetic analysis

In this study, the recombinant ectoine-producing Escherichia coli ET01 was constructed by introducing the ectABC operon from Halomonas venusta ZH. To further improve ectoine production, the regulation of the fermentation process was systematically investigated. First, the effects of the initial glucose concentrations and glucose feeding mode on ectoine production were analyzed. Using a combination of pH-feedback feeding and glucose-controlled feeding, the ectoine titer reached 25.5 g/L, representing an 8.8-fold increase over standard batch culture. Then, the effects of dissolved oxygen (DO) levels (50, 40, 30, or 20%) on ectoine production were studied, and a DO control strategy was developed based on the fermentation kinetics. When the final optimized two-stage fermentation strategy was used, the ectoine titer reached 47.8 g/L, which was the highest level of ectoine produced by E. coli fermentation. The fermentation regulation strategy developed in this study might be useful for scaling up the commercial production of ectoine.

Stressed out: Bacterial response to high salinity using compatible solute biosynthesis and uptake systems, lessons from Vibrionaceae

Bacteria have evolved mechanisms that allow them to adapt to changes in osmolarity and some species have adapted to live optimally in high salinity environments such as in the marine ecosystem. Most bacteria that live in high salinity do so by the biosynthesis and/or uptake of compatible solutes, small organic molecules that maintain the turgor pressure of the cell. Osmotic stress response mechanisms and their regulation among marine heterotrophic bacteria are poorly understood. In this review, we discuss what is known about compatible solute metabolism and transport and new insights gained from studying marine bacteria belonging to the family Vibrionaceae.