Mini Review: Advances in 2-Haloacid Dehalogenases

Wang, Yayue; Qiao, Xin; Zhou, Qingfeng; Xu, Jingliang; Pei, Dongli

doi:10.3389/fmicb.2021.758886

Cited by 3 publications

(5 citation statements)

References 147 publications

(162 reference statements)

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“…2 ). The putative hydrolytic dehalogenases encoded by the assembled MAGs are known to convert a wide range of halocarbons, including halogenated alkanes, cycloalkanes, alkenes, ethers, alcohols, ketones, cyclic dienes, alkanoic acids, and acetates [ 67 , 68 ]. Genes encoding these BRENDA-EC42 functions were particularly abundant in MAGs corresponding with Microtrichales , UBA9160, UBA10353, Pseudomonadales , Caulobacterales , and Rhizobiales (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Hydrolytic dehalogenases, a prominent gene group among the annotated BRENDA-EC42 functions, play a crucial role in economical and environmentally friendly industrial processes and biotechnological applications [ 68 , 95 – 97 ]. While extensively studied in soil bacteria commonly exposed to manufactured organohalogens (e.g., herbicides and pesticides) [ 98 ], recent marine genomics and metagenomics investigations have revealed microbial hydrolytic dehalogenases with unique functional and structural properties [ 91 , 92 , 99 ].…”

Section: Discussionmentioning

confidence: 99%

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Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

Lavecchia,

Fosso,

Engelen

et al. 2024

Microbiome

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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.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

Lavecchia,

Fosso,

Engelen

et al. 2024

Microbiome

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“…In all enzymes, a conserved aspartate residue (D14 in ZgHAD) is the main catalytic amino acid, performing the first step of the reaction. The activation of the water molecule is done by a His/Glu dyad for both ZgHAD and DehRhb, whereas various other amino acid dyads, such as Asp/Asn, Asp/Lys, or Lys/Tyr, have been proposed to be responsible of this step in other l ‐2‐HAD enzymes (Hisano et al, 1996 ; Nakamura et al, 2009 ; Novak et al, 2013 ; Schmidberger et al, 2007 ; Wang et al, 2021 ). A similar His/Glu dyad is well‐known to operate in an equivalent manner in haloalkane dehalogenases that are widespread in the marine environment (Janssen, 2004 ).…”

Section: Discussionmentioning

confidence: 99%

“…d ‐2‐HADs (EC 3.8.1.9) and dl ‐2‐HADs (EC 3.8.1.10 and EC 3.8.1.11) are part of Group I and l ‐2‐HADs (E.C. 3.8.1.2) belong to Group II (Ang et al, 2018 ; Wang et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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“…catalyst activity alcohol dehydrogenases (ADH) 171 and ketoreductases (KRED) 172 asymmetric reduction of carbonyl compounds α-ketoacid carboligases 173 or aldolases 174 decarboxylative or regular aldol reactions hydroxynitrile lyases (HNL) 175 addition of cyanide to aldehydes forming cyanohydrins (Michael) hydratases 176 addition of water to unactivated or α,β-unsaturated compounds epoxide hydrolases 177 enantioselective hydrolysis of epoxides affording vicinal diols oxidases 178 oxidative functionalization of C−H bonds haloacid dehalogenases, 179 haloalkane dehalogenases 180 or halohydrin dehalogenases 181 hydrolysis of 2-haloalkanoic acids, halogenated aliphatics, or vicinal haloalcohols lipases 182 or esterases 183 (dynamic) kinetic resolution of racemic mixtures CYP153A35 oxidase to enhance its ω-hydroxylation activity toward palmitic acid. 192 Luciferase can be used to further oxidize aldehydes (produced via ADH catalysis from the target alcohols) to quantify alcohol production by the emergence of a blue-green luminescence (λ em,max = 490 nm).…”

Section: Table 1 List Of Enzyme Classes For the Enantioselective Synt...mentioning

confidence: 99%

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

et al. 2023

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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.

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Mini Review: Advances in 2-Haloacid Dehalogenases

Cited by 3 publications

References 147 publications

Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

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

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

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