Mini Review: Advances in 2-Haloacid Dehalogenases

Hydrolytic Dehalogenation of Toxic Haloacetic Acids via Carbon Metabolism Regulation during Microbial Denitrification

Microbial denitrification is essential in the nitrogen cycle to enhance the quality of the reclaimed water. In addition to nitrogen removal, it has the potential to control trace pollutants. However, the fates of toxic disinfection byproducts (DBPs) on denitrification remain unelucidated. The current study focused on Paracoccus denitrificans (P. denitrificans) to investigate the response mechanisms of denitrifying microorganisms to HAAs, one of the main categories of DBPs. Upon exposure to 20 μM monoiodoacetic acid (MIAA), the number of extracellular reactive oxygen species in P. denitrificans increased to 2.7 times at 16 h. Concurrently, the specific nitrate reduction rate dropped by 9.3% and the specific growth rate declined by 26.7%, leading to the slowdown of the denitrification process. Nevertheless, P. denitrificans increased the activity of the tricarboxylic acid cycle and electron transport for sustainable denitrification under MIAA stress. Microbial hydrolytic dehalogenation contributed to over 70.0% MIAA removal, and it led to the release of iodine ions. MIAA was detoxified and concerted into low-molecular-weight organic acids, which then participated in carbon metabolism. The removal efficiency of different toxic HAAs was also compared to evaluate the adaptiveness of the DBP control. This research highlighted the interactions between denitrifying microorganisms and DBPs, providing new insights into the ecological safety protection of high-quality reclaimed water.

Survival strategies of Rhinocladiella similis in perchlorate-rich Mars like environments

Studying the survival of terrestrial microorganisms under Martian conditions, particularly in the presence of perchlorates, provides crucial insights for astrobiology. This research investigates the resilience of the extremophile black fungus Rhinocladiella similis to magnesium perchlorate and UV-C radiation. Results show R. similis, known for its tolerance to acidic conditions, exhibits remarkable resistance to UV-C radiation combined with perchlorate, as well as to high concentrations of magnesium perchlorate, surpassing Exophiala sp. strain 15Lv1, a eukaryotic model organism for Mars-like conditions. Growth curve analyses revealed both strains can thrive in perchlorate concentrations mimicking Martian perchlorate-rich environments, with R. similis adapting better to higher concentrations. Morphological and protein production changes were investigated, and mass spectrometry identified perchlorate-induced proteins, advancing molecular understanding of potential microbial life on Mars. These findings advance knowledge of extremophile capabilities, contributing to the search for life beyond Earth and informing the design of future Martian rovers equipped for biosignature detection.

Computational Studies of Enzymes for C-F Bond Degradation and Functionalization

Organofluorine compounds have revolutionized chemical and pharmaceutical industries, serving as essential components in numerous applications and aspects of modern life. However, their bioaccumulation and resistance to degradation have resulted in environmental pollution, posing significant risks to human and animal health. The exceptionally strong C-F bond in these compounds makes their degradation challenging, with current methods often requiring extreme experimental conditions. Therefore, the development of eco-friendly approaches that operate under milder conditions is crucial, with enzyme-mediated C-F bond cleavage strategies emerging as a particularly promising solution. In this review, we present an overview of how computational approaches, including molecular docking, molecular dynamics simulations, quantum mechanics/molecular mechanics calculations, and bioinformatics, have been utilized to investigate the mechanisms underlying enzymatic C-F bond degradation and functionalization. This review highlights how these computational approaches provide critical insights into the atomic-level interactions and energetics underlying enzymatic processes, offering a foundation for the rational design and engineering of enzymes capable of addressing the challenges posed by fluorinated compounds. This review covers several types of enzymes including: fluoroacetate dehalogenases, cysteine dioxygenase, L-2-haloacid dehalogenase, cytochrome P450, fluorinase and tyrosine hydroxylase.

Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface

The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.

Stereoselective Synthesis of Oxetanes Catalyzed by an Engineered Halohydrin Dehalogenase

Although biocatalysis has garnered widespread attention in both industrial and academic realms, the enzymatic synthesis of chiral oxetanes remains an underdeveloped field. Halohydrin dehalogenases (HHDHs) are industrially relevant enzymes that have been engineered to accomplish the reversible transformation of epoxides. In this study, a biocatalytic platform was constructed for the stereoselective kinetic resolution of chiral oxetanes and formation of 1,3-disubstituted alcohols. HheC from Agrobacterium radiobacter AD1 was engineered to identify key variants capable of catalyzing the dehalogenation of γ-haloalcohols (via HheC M1-M3) and ring opening of oxetanes (via HheC M4-M5) to access both (R)- and (S)-configured products with high stereoselectivity and remarkable catalytic activity, yielding up to 49 % with enantioselectivities exceeding 99 % ee and E>200. The current strategy is broadly applicable as demonstrated by expansion of the substrate scope to include up to 18 examples for dehalogenation and 16 examples for ring opening. Additionally, the functionalized products are versatile building blocks for pharmaceutical applications. To shed light on the molecular recognition mechanisms for the relevant variants, molecular dynamic (MD) simulations were performed. The current strategy expands the scope of HHDH-catalyzed chiral oxetane ring construction, offering efficient access to both enantiomers of chiral oxetanes and 1,3-disubstituted alcohols.

Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

BACKGROUND

Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

RESULTS

To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

CONCLUSION

The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

X-ray structure and mechanism of ZgHAD, a l-2-haloacid dehalogenase from the marine Flavobacterium Zobellia galactanivorans

Haloacid dehalogenases are potentially involved in bioremediation of contaminated environments and few have been biochemically characterized from marine organisms. The l-2-haloacid dehalogenase (l-2-HAD) from the marine Bacteroidetes Zobellia galactanivorans Dsij^T (ZgHAD) has been shown to catalyze the dehalogenation of C2 and C3 short-chain l-2-haloalkanoic acids. To better understand its catalytic properties, its enzymatic stability, active site, and 3D structure were analyzed. ZgHAD demonstrates high stability to solvents and a conserved catalytic activity when heated up to 60°C, its melting temperature being at 65°C. The X-ray structure of the recombinant enzyme was solved by molecular replacement. The enzyme folds as a homodimer and its active site is very similar to DehRhb, the other known l-2-HAD from a marine Rhodobacteraceae. Marked differences are present in the putative substrate entrance sites of the two enzymes. The H179 amino acid potentially involved in the activation of a catalytic water molecule was confirmed as catalytic amino acid through the production of two inactive site-directed mutants. The crystal packing of 13 dimers in the asymmetric unit of an active-site mutant, ZgHAD-H179N, reveals domain movements of the monomeric subunits relative to each other. The involvement of a catalytic His/Glu dyad and substrate binding amino acids was further confirmed by computational docking. All together our results give new insights into the catalytic mechanism of the group of marine l-2-HAD.