Transcriptional regulation of organohalide pollutant utilisation in bacteria

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.

In situ reductive dehalogenation of groundwater driven by innovative organic carbon source materials: Insights into the organohalide-respiratory electron transport chain

In situ bioremediation using organohalide-respiring bacteria (OHRB) is a prospective method for the removal of persistent halogenated organic pollutants from groundwater, as OHRB can utilize H₂ or organic compounds produced by carbon source materials as electron donors for cell growth through organohalide respiration. However, few previous studies have determined the suitability of different carbon source materials to the metabolic mechanism of reductive dehalogenation from the perspective of electron transfer. The focus of this critical review was to reveal the interactions and relationships between carbon source materials and functional microbes, in terms of the electron transfer mechanism. Furthermore, this review illustrates some innovative strategies that have used the physiological characteristics of OHRB to guide the optimization of carbon source materials, improving the abundance of indigenous dehalogenated bacteria and enhancing electron transfer efficiency. Finally, it is proposed that future research should combine multi-omics analysis with machine learning (ML) to guide the design of effective carbon source materials and optimize current dehalogenation bioremediation strategies to reduce the cost and footprint of practical groundwater bioremediation applications.

Detoxification of fluoroglucocorticoid by Acinetobacter pittii C3 via a novel defluorination pathway with hydrolysis, oxidation and reduction: Performance, genomic characteristics, and mechanism

Biological dehalogenation degradation was an important detoxification method for the ecotoxicity and teratogenic toxicity of fluorocorticosteroids (FGCs). The functional strain Acinetobacter pittii C3 can effectively biodegrade and defluorinate to 1 mg/L Triamcinolone acetonide (TA), a representative FGCs, with 86 % and 79 % removal proportion in 168 h with the biodegradation and detoxification kinetic constant of 0.031/h and 0.016/h. The dehalogenation and degradation ability of strain C3 was related to its dehalogenation genomic characteristics, which manifested in the functional gene expression of dehalogenation, degradation, and toxicity tolerance. Three detoxification mechanisms were positively correlated with defluorination pathways through hydrolysis, oxidation, and reduction, which were regulated by the expression of the haloacid dehalogenase (HAD) gene (mupP, yrfG, and gph), oxygenase gene (dmpA and catA), and reductase gene (nrdAB and TgnAB). Hydrolysis defluorination was the most critical way for TA detoxification metabolism, which could rapidly generate low-toxicity metabolites and reduce toxic bioaccumulation due to hydrolytic dehalogenase-induced defluorination. The mechanism of hydrolytic defluorination was that the active pocket of hydrolytic dehalogenase was matched well with the spatial structure of TA under the adjustment of the hydrogen bond, and thus induced molecular recognition to promote the catalytic hydrolytic degradation of various amino acid residues. This work provided an effective bioremediation method and mechanism for improving defluorination and detoxification performance.

Naturally Occurring Organohalogen Compounds-A Comprehensive Review

The present volume is the third in a trilogy that documents naturally occurring organohalogen compounds, bringing the total number-from fewer than 25 in 1968-to approximately 8000 compounds to date. Nearly all of these natural products contain chlorine or bromine, with a few containing iodine and, fewer still, fluorine. Produced by ubiquitous marine (algae, sponges, corals, bryozoa, nudibranchs, fungi, bacteria) and terrestrial organisms (plants, fungi, bacteria, insects, higher animals) and universal abiotic processes (volcanos, forest fires, geothermal events), organohalogens pervade the global ecosystem. Newly identified extraterrestrial sources are also documented. In addition to chemical structures, biological activity, biohalogenation, biodegradation, natural function, and future outlook are presented.

Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux

Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N₁₁-ATG), compared to those of odcA/orf419 (CAT-N₁₁-ATG) and odcC (CAT-N₁₁-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.

Mechanistic insight into co-metabolic dechlorination of hexachloro-1,3-butadiene in Dehalococcoides

Hexachloro-1,3-butadiene (HCBD) as one of emerging persistent organic pollutants (POPs) poses potential risk to human health and ecosystems. Organohalide-respiring bacteria (OHRB)-mediated reductive dehalogenation represents a promising strategy to remediate HCBD-contaminated sites. Nonetheless, information on the HCBD-dechlorinating OHRB and their dechlorination pathways remain unknown. In this study, both in vivo and in vitro experiments, as well as quantum chemical calculation, were employed to successfully identify and characterize the reductive dechlorination of HCBD by Dehalococcoides. Results showed that some Dehalococcoides extensively dechlorinated HCBD to (E)-1,2,3-tri-CBD via (E)-1,1,2,3,4-penta-CBD and (Z,E)-1,2,3,4-tetra-CBD in a co-metabolic way. Both qPCR and 16S rRNA gene amplicon sequencing analyses suggested that the HCBD-dechlorinating Dehalococcoides coupled their cell growth with dechlorination of perchloroethene (PCE), rather than HCBD. The in vivo and in vitro ATPase assays indicated ≥78.89% decrease in ATPase activity upon HCBD addition, which suggested HCBD inhibition on ATPase-mediated energy harvest and provided rationality on the Dehalococcoides-mediated co-metabolic dechlorination of HCBD. Interestingly, dehalogenation screening of organohalides with the HCBD-dechlorinating enrichment cultures showed that debromination of bromodichloromethane (BDCM) was active in the in vitro RDase assays but non-active in the in vivo experiments. Further in vitro assays of hydrogenase activity suggested that significant inhibition of BDCM on the hydrogenase activity could block electron derivation from H₂ for consequent reduction of organohalides in the in vivo experiments. Therefore, our results provided unprecedented insight into metabolic, co-metabolic and RDase-active-only dehalogenation of varied organohalides by specific OHRB, which could guide future screening of OHRB for remediation of sites contaminated by HCBD and other POPs.

Genome-Wide Transcription Start Sites Mapping in Methylorubrum Grown with Dichloromethane and Methanol

Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation suggests a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as a sole source of carbon and energy for growth, Methylorubrum extorquens DM4 is a longstanding reference strain. Here, the primary 5′-ends of transcripts were obtained using a differential RNA-seq (dRNA-seq) approach to provide the first transcription start site (TSS) genome-wide landscape of a methylotroph using DCM or methanol. In total, 7231 putative TSSs were annotated and classified with respect to their localization to coding sequences (CDSs). TSSs on the opposite strand of CDS (antisense TSS) account for 31% of all identified TSSs. One-third of the detected TSSs were located at a distance to the start codon inferior to 250 nt (average of 84 nt) with 7% of leaderless mRNA. Taken together, the global TSS map for bacterial growth using DCM or methanol will facilitate future studies in which transcriptional regulation is crucial, and efficient DCM removal at polluted sites is limited by regulatory processes.

Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics

Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.