A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

All sequence data from this study were deposited at the European Bioinformatics Institute under the accession numbers ERS1670018 to ERS1670023. Further, all assigned genes, taxonomy, function, sequences of contigs, genes and proteins can be found in Table S3.In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (2136% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.This study was supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. The research of A.J.M. Stams is supported by an ERC grant (project 323009) and the gravitation grant “Microbes for Health and Environment” (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science. F. Hugenholtz was supported by the same gravitation grant (project 024.002.002). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023).info:eu-repo/semantics/publishedVersio

Anaerobic radical enzymes for biotechnology

Enzymes that proceed through radical intermediates have a rich chemistry that includes functionalisation of otherwise unreactive carbon atoms, carbon-skeleton rearrangements, aromatic reductions, and unusual eliminations. Especially under anaerobic conditions, organisms have developed a wide range of approaches for managing these transformations that can be exploited to generate new biological routes towards both bulk and specialty chemicals. These routes are often either much more direct or allow access to molecules that are inaccessible through standard (bio)chemical approaches. This review gives an overview of some of the key enzymes in this area: benzoyl-CoA reductases (that effect the enzymatic Birch reduction), ketyl radical dehydratases, coenzyme B12-dependant enzymes, glycyl radical enzymes, and radical SAM (AdoMet radical) enzymes. These enzymes are discussed alongside biotechnological applications, highlighting the wide range of actual and potential uses. With the increased diversity in biotechnological approaches to obtaining these enzymes and information about them, even more of these amazing enzymes can be expected to find application in industrial processes

2-Oxoglutarate:NADP(+) Oxidoreductase in Azoarcus evansii: Properties and Function in Electron Transfer Reactions in Aromatic Ring Reduction

The conversion of [(14)C]benzoyl-coenzyme A (CoA) to nonaromatic products in the denitrifying β-proteobacterium Azoarcus evansii grown anaerobically on benzoate was investigated. With cell extracts and 2-oxoglutarate as the electron donor, benzoyl-CoA reduction occurred at a rate of 10 to 15 nmol min(−1) mg(−1). 2-Oxoglutarate could be replaced by dithionite (200% rate) and by NADPH (∼10% rate); in contrast NADH did not serve as an electron donor. Anaerobic growth on aromatic compounds induced 2-oxoglutarate:acceptor oxidoreductase (KGOR), which specifically reduced NADP(+), and NADPH:acceptor oxidoreductase. KGOR was purified by a 76-fold enrichment. The enzyme had a molecular mass of 290 ± 20 kDa and was composed of three subunits of 63 (γ), 62 (α), and 37 (β) kDa in a 1:1:1 ratio, suggesting an (αβγ)(2) composition. The native enzyme contained Fe (24 mol/mol of enzyme), S (23 mol/mol), flavin adenine dinucleotide (FAD; 1.4 mol/mol), and thiamine diphosphate (0.95 mol/mol). KGOR from A. evansii was highly specific for 2-oxoglutarate as the electron donor and accepted both NADP(+) and oxidized viologens as electron acceptors; in contrast NAD(+) was not reduced. These results suggest that benzoyl-CoA reduction is coupled to the complete oxidation of the intermediate acetyl-CoA in the tricarboxylic acid cycle. Electrons generated by KGOR can be transferred to both oxidized ferredoxin and NADP(+), depending on the cellular needs. N-terminal amino acid sequence analysis revealed that the open reading frames for the three subunits of KGOR are similar to three adjacently located open reading frames in Bradyrhizobium japonicum. We suggest that these genes code for a very similar three-subunit KGOR, which may play a role in nitrogen fixation. The α-subunit is supposed to harbor one FAD molecule, two [4Fe-4S] clusters, and the NADPH binding site; the β-subunit is supposed to harbor one thiamine diphosphate molecule and one further [4Fe-4S] cluster; and the γ-subunit is supposed to harbor the CoA binding site. This is the first study of an NADP(+)-specific KGOR. A similar NADP(+)-specific pyruvate oxidoreductase, which contains all domains in one large subunit, has been reported for the mitochondrion of the protist Euglena gracilis and the apicomplexan Cryptosporidium parvum

Identification of amino acids within the MHC molecule important for the interaction with the adenovirus protein E3/19K.

The E3/19K protein of human adenovirus type 2 binds to class I MHC Ags thereby interfering with their cell surface expression and Ag presentation function. Currently, it is unclear exactly which structure of MHC molecules is recognized by the E3/19K protein. We have previously demonstrated that the murine H-2Kd Ag is able to associate with E3/19K, whereas the allelic H-2Kk molecule is not. By using exon shuffling between Kd and Kk molecules, the alpha 1 and alpha 2 domains of MHC class I molecules were identified as essential structures for binding the viral protein. In this report, we have examined the contribution of individual amino acids within the alpha 2 domain of MHC for binding E3/19K. First, we show that within this domain the alpha-helical part is most important for the interaction with E3/19K. By using site-directed mutagenesis, Kd-specific amino acids were introduced into the alpha-helix of the alpha 2 domain of Kk. By using the expression of mutagenized proteins in E3/19K+ cells, we have identified Tyr 156 and Leu 180 as being essential for the association with the E3/19K protein. In addition, Kd residue Glu 163 seems to contribute to the complex formation. Furthermore, analysis of a panel of Kd/Dd recombinants indicates that a similar region in the Dd molecule, namely, the C-terminal half of the alpha 2 domain, affects binding to E3/19K. Combining these results with Ab binding data, we present two alternative models of how the adenovirus protein may bind to the alpha 1 and alpha 2 domains

Expanding the current knowledge and biotechnological applications of the oxygen‐independent ortho

56 p.-7 fig.-1 tab.+8 p.( 4 fig. supl.-1 tab. supl.)ortho ‐Phthalate derives from industrially produced phthalate esters, which are massively used as plasticizers and constitute major emerging environmental pollutants. The pht pathway for the anaerobic bacterial biodegradation of o ‐phthalate involves its activation to phthaloyl‐CoA followed by decarboxylation to benzoyl‐CoA. Here, we have explored further the pht peripheral pathway in denitrifying bacteria and shown that it requires also an active transport system for o ‐phthalate uptake that belongs to the poorly characterized class of TAXI‐TRAP transporters. The construction of a fully functional pht cassette combining both catabolic and transport genes allowed to expand the o ‐phthalate degradation ecological trait to heterologous hosts. Unexpectedly, the pht cassette also allowed the aerobic conversion of o ‐phthalate to benzoyl‐CoA when coupled to a functional box central pathway. Hence, the pht pathway may constitute an evolutionary acquisition for o ‐phthalate degradation by bacteria that thrive either in anoxic environments or in environments that face oxygen limitations and that rely on benzoyl‐CoA, rather than on catecholic central intermediates, for the aerobic catabolism of aromatic compounds. Finally, the recombinant pht cassette was used both to screen for functional aerobic box pathways in bacteria and to engineer recombinant biocatalysts for o ‐phthalate bioconversion into sustainable bioplastics, e.g., polyhydroxybutyrate, in plastic recycling industrial processes.Support was provided by grants BIO2016-79736-R and PCIN-2014-113 from the Ministry of Economy and Competitiveness of Spain; by a grant from the Fundación Ramón Areces XVII CN; by Grant CSIC 2016 2 0E 093; and by European Union H2020 Grant 760994.Peer reviewe

Genes and enzymes involved in the biodegradation of the quaternary carbon compound pivalate in the denitrifying Thauera humireducens strain PIV ‐1

A utilisé MicroScope PlatformInternational audienceQuaternary carbon‐containing compounds exist in natural and fossil oil‐derived products and are used in chemical and pharmaceutical applications up to industrial scale. Due to the inaccessibility of the quaternary carbon atom for a direct oxidative or reductive attack, they are considered as persistent in the environment. Here, we investigated the unknown degradation of the quaternary carbon‐containing model compound pivalate (2,2‐dimethyl‐propionate) in the denitrifying bacterium Thauera humireducens strain PIV‐1 (formerly T hauera pivalivorans ). We provide multiple evidence for a pathway comprising the activation to pivalyl‐CoA and the carbon skeleton rearrangement to isovaleryl‐CoA. Subsequent reactions proceed similar to the catabolic leucine degradation pathway such as the carboxylation to 3‐methylglutaconyl‐CoA and the cleavage of 3‐methyl‐3‐hydroxyglutaryl‐CoA to acetyl‐CoA and acetoacetate. The completed genome of Thauera humireducens strain PIV‐1 together with proteomic data was used to identify pivalate‐upregulated gene clusters including genes putatively encoding pivalate CoA ligase and adenosylcobalamin‐dependent pivalyl‐CoA mutase. A pivalate‐induced gene encoding a putative carboxylic acid CoA ligase was heterologously expressed, and its highly enriched product exhibited pivalate CoA ligase activity. The results provide the first experimental insights into the biodegradation pathway of a quaternary carbon‐containing model compound that serves as a blueprint for the degradation of related quaternary carbon‐containing compounds

Enzymes involved in phthalate degradation in sulphate-reducing bacteria

The complete degradation of the xenobiotic and environmentally harmful phthalate esters is initiated by hydrolysis to alcohols and o-phthalate (phthalate) by esterases. While further catabolism of phthalate has been studied in aerobic and denitrifying microorganisms, the degradation in obligately anaerobic bacteria has remained obscure. Here, we demonstrate a previously overseen growth of the δ-proteobacterium Desulfosarcina cetonica with phthalate/sulphate as only carbon and energy sources. Differential proteome and CoA ester pool analyses together with in vitro enzyme assays identified the genes, enzymes and metabolites involved in phthalate uptake and degradation in D. cetonica. Phthalate is initially activated to the short-lived phthaloyl-CoA by an ATP-dependent phthalate CoA ligase (PCL) followed by decarboxylation to the central intermediate benzoyl-CoA by an UbiD-like phthaloyl-CoA decarboxylase (PCD) containing a prenylated flavin cofactor. Genome/metagenome analyses predicted phthalate degradation capacity also in the sulphate-reducing Desulfobacula toluolica, strain NaphS2, and other δ-proteobacteria. Our results suggest that phthalate degradation proceeds in all anaerobic bacteria via the labile phthaloyl-CoA that is captured and decarboxylated by highly abundant PCDs. In contrast, two alternative strategies have been established for the formation of phthaloyl-CoA, the possibly most unstable CoA ester in biology.publishe