[ad_1]
Atashgahi, S., Häggblom, M. M. & Smidt, H. Organohalide respiration in pristine environments: implications for the natural halogen cycle. Environ. Microbiol. 20, 934–948 (2018).
Jugder, B.-E. et al. Organohalide respiring bacteria and reductive dehalogenases: key tools in organohalide bioremediation. Front. Microbiol. 7, 249 (2016).
Wang, S. et al. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol. Adv. 36, 1194–1206 (2018).
Holliger, C., Wohlfarth, G. & Diekert, G. Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22, 383–398 (1998).
Kunze, C., Diekert, G. & Schubert, T. Subtle changes in the active site architecture untangled overlapping substrate ranges and mechanistic differences of two reductive dehalogenases. FEBS J. 284, 3520–3535 (2017).
Fincker, M. & Spormann, A. M. Biochemistry of catabolic reductive dehalogenation. Annu. Rev. Biochem. 86, 357–386 (2017).
Greenhalgh, E. D., Kunze, C., Schubert, T., Diekert, G. & Brunold, T. C. A spectroscopically validated computational investigation of viable reaction intermediates in the catalytic cycle of the reductive dehalogenase PceA. Biochemistry 60, 2022–2032 (2021).
Gruber, K., Puffer, B. & Kräutler, B. Vitamin B12-derivatives – enzyme cofactors and ligands of proteins and nucleic acids. Chem. Soc. Rev. 40, 4346–4363 (2011).
Molenda, O. et al. Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification. Environ. Sci.: Process. Impacts 22, 663–678 (2020).
Regeard, C., Maillard, J., Dufraigne, C., Deschavanne, P. & Holliger, C. Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195. Appl. Environ. Microbiol. 71, 2955–2961 (2005).
McMurdie, P. J. et al. Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLOS Genet. 5, e1000714 (2009).
Maillard, J., Regeard, C. & Holliger, C. Isolation and characterization of Tn-Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1. Environ. Microbiol. 7, 107–117 (2005).
Duret, A., Holliger, C. & Maillard, J. The physiological opportunism of Desulfitobacterium hafniense strain TCE1 towards organohalide respiration with tetrachloroethene. Appl. Environ. Microbiol. 78, 6121–6127 (2012).
Schubert, T., Adrian, L., Sawers, R. G. & Diekert, G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol. Ecol. 94, fiy035 (2018).
Buttet, G. F., Willemin, M. S., Hamelin, R., Rupakula, A. & Maillard, J. The membrane-bound C subunit of reductive dehalogenases: Topology analysis and reconstitution of the FMN-binding domain of PceC. Front. Microbiol. 9, 755 (2018).
Maillard, J., Genevaux, P. & Holliger, C. Redundancy and specificity of multiple trigger factor chaperones in. Desulfitobacteria. Microbiol. 157, 2410–2421 (2011).
Maillard, J. & Willemin, M. S. Regulation of organohalide respiration. Adv. Microb. Physiol. 74, 191–238 (2019).
Cimmino, L., Schmid, A. W., Holliger, C. & Maillard, J. Stoichiometry of the gene products from the tetrachloroethene reductive dehalogenase operon pceABCT. Front. Microbiol 13, 838026 (2022).
Maillard, J. & Holliger, C. Organohalide-Respiring Bacteria: The Genus Dehalobacter Ch. 8 (Springer-Verlag, Berlin, 2016).
Bommer, M. et al. Structural basis for organohalide respiration. Science 346, 455–458 (2014).
Payne, K. A. P. et al. Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature 517, 513–516 (2015).
Johannissen, L. O., Leys, D. & Hay, S. A common mechanism for coenzyme cobalamin-dependent reductive dehalogenases. Phys. Chem. Chem. Phys. 19, 6090–6094 (2017).
Türkowsky, D. et al. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol. Ecol. 94, fiy013 (2018).
Kublik, A. et al. Identification of a multi-protein reductive dehalogenase complex in Dehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement. Environ. Microbiol. 18, 3044–3056 (2016).
Seidel, K., Kühnert, J. & Adrian, L. The Complexome of Dehalococcoides mccartyi reveals its organohalide respiration-complex is modular. Front. Microbiol. 9, 1130 (2018).
Duarte, A. G. et al. Redox loops in anaerobic respiration – The role of the widespread NrfD protein family and associated dimeric redox module. Biochimica et. Biophysica Acta (BBA) – Bioenerg. 1862, 148416 (2021).
Goris, T. et al. Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates. Sci. Rep. 5, 13794 (2015).
Kruse, T. et al. Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. J. Bacteriol. 197, 893–904 (2015).
Willemin, M. S., Hamelin, R., Armand, F., Holliger, C. & Maillard, J. Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms. Front. Microbiol. 14, 1058127 (2023).
Neumann, A., Wohlfarth, G. & Diekert, G. Tetrachloroethene dehalogenase from dehalospirillum multivorans: cloning, sequencing of the encoding genes, and expression of the pceA Gene in Escherichia coli. J. Bacteriol. 180, 4140–4145 (1998).
Maillard, J. et al. Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl. Environ. Microbiol. 69, 4628–4638 (2003).
Miller, E., Wohlfarth, G. & Diekert, G. Studies on tetrachloroethene respiration in Dehalospirillum multivorans. Arch. Microbiol. 166, 379–387 (1997).
van de Pas, B. A. et al. Purification and molecular characterization of ortho-chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans. J. Biol. Chem. 274, 20287–20292 (1999).
Miller, E., Wohlfarth, G. & Diekert, G. Comparative studies on tetrachloroethene reductive dechlorination mediated by Desulfitobacterium sp. strain PCE-S. Arch. Microbiol. 168, 513–519 (1997).
Löffler, F. E., Sanford, R. A. & Tiedje, J. M. Initial characterization of a reductive dehalogenase from Desulfitobacterium chlororespirans Co23. Appl. Environ. Microbiol. 62, 3809–Co3813 (1996).
Schumacher, W. & Holliger, C. The proton/electron ration of the menaquinone-dependent electron transport from dihydrogen to tetrachloroethene in ‘Dehalobacter restrictus’. J. Bacteriol. 178, 2328–2333 (1996).
Gerritse, J. et al. Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1. Appl. Environ. Microbiol. 65, 5212–5221 (1999).
Schumacher, W., Holliger, C., Zehnder, A. J. B. & Hagen, W. R. Redox chemistry of cobalamin and iron-sulfur cofactors in the tetrachloroethene reductase of Dehalobacter restrictus. FEBS Lett. 409, 421–425 (1997).
Kunze, C. et al. Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nat. Commun. 8, 15858 (2017).
Jurcik, A. et al. CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. Bioinformatics 34, 3586–3588 (2018).
Rodrigues, M. L., Scott, K. A., Sansom, M. S. P., Pereira, I. A. C. & Archer, M. Quinol oxidation by c-type cytochromes: structural characterization of the menaquinol binding site of NrfHA. J. Mol. Biol. 381, 341–350 (2008).
Louie, T. M. & Mohn, W. W. Evidence for a chemiosmotic model of dehalorespiration in Desulfomonile tiedjei DCB-1. J. Bacteriol. 181, 40–46 (1999).
Neumann, A. et al. Tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans: substrate specificity of the native enzyme and its corrinoid cofactor. Arch. Microbiol. 177, 420–426 (2002).
Suyama, A., Yamashita, M., Yoshino, S. & Furukawa, K. Molecular characterization of the PceA reductive dehalogenase of Desulfitobacterium sp. strain Y51. J. Bacteriol. 184, 3419–3425 (2002).
Yan, J. et al. Respiratory vinyl chloride reductive dechlorination to ethene in TceA-expressing Dehalococcoides mccartyi. Environ. Sci. Technol. 55, 4831–4841 (2021).
Morson, N., Molenda, O., Picott, K. J., Richardson, R. E. & Edwards, E. A. Long-term survival of Dehalococcoides mccartyi strains in mixed cultures under electron acceptor and ammonium limitation. FEMS Microbes 3, 1–10 (2022).
Phillips, E. et al. Investigation of active site amino acid influence on carbon and chlorine isotope fractionation during reductive dechlorination. FEMS Microbiol. Ecol. 98, fiac072 (2022).
Kokkonen, P., Bednar, D., Pinto, G., Prokop, Z. & Damborsky, J. Engineering enzyme access tunnels. Biotechnol. Adv. 37, 107386 (2019).
Page, C. C., Moser, C. C., Chen, X. & Dutton, P. L. Natural engineering principles of electron tunnelling in biological oxidation–reduction. Nature 402, 47–52 (1999).
Simon, J., van Spanning, R. J. M. & Richardson, D. J. The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. Biochimica et. Biophysica Acta (BBA) – Bioenerg. 1777, 1480–1490 (2008).
Schipp, C. J., Marco-Urrea, E., Kublik, A., Seifert, J. & Adrian, L. Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. Philos. Trans. R. Soc. B 368, 20120321 (2013).
Atashgahi, S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol. Ecol. 95, fiz048 (2019).
Comensoli, L. et al. Use of bacteria to stabilize archaeological iron. Appl. Environ. Microbiol. 83, e03478–16 (2017).
Holliger, C., Schraa, G., Stams, A. J. & Zehnder, A. J. A highly purified enrichment culture couples the reductive dechlorination of tetrachloroethene to growth. Appl. Environ. Microbiol. 59, 2991–2997 (1993).
Wittig, I. & Schägger, H. Features and applications of blue-native and clear-native electrophoresis. Proteomics 8, 3974–3990 (2008).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Cryst. D. 66, 486–501 (2010).
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D. 74, 531–544 (2018).
Goddard, T. D. et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).
Di Tommaso, P. et al. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 39, W13–W17 (2011).
Crooks, G. E., Hon, G., Chandonia, J.-M. & Brenner, S. E. WebLogo: A sequence logo generator. Genome Res. 14, 1188–1190 (2004).
[ad_2]
Source link