Reductive metabolism of the important atmospheric gas isoprene by homoacetogens

Kronen, Miriam; Lee, Matthew; Jones, Zackary L.; Manefield, Michael

doi:10.1038/s41396-018-0338-z

Cited by 18 publications

(63 citation statements)

References 78 publications

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“…There is evidence of the enrichment of particular taxa when soils are subjected to atmospherically relevant concentrations of isoprene [39,87], and the cultivation of such bacteria might allow potentially different catabolic pathways to be discovered, and thus broaden the base from which primers/probes can be refined or new ones designed. In addition, there is a culture of a homoacetogen that can use isoprene as an electron acceptor [63], and there may well be more anaerobes that can metabolise isoprene that have evaded cultivation. Undoubtedly, such anaerobes would have catabolic pathways that are different from aerobes and potentially distinct from, e.g., alkene-oxidising anaerobes.…”

Section: Discussionmentioning

confidence: 99%

“…Details about the isoprene-degrading strains belonging to these genera are provided in [62]. Finally, to our knowledge, no anaerobic bacteria, archaea, or fungi have been reported to use isoprene as a sole carbon and energy source, although Kronen et al [63] have recently shown that strict anaerobes can use isoprene as an electron acceptor to support homoacetogenesis, and thus anaerobic degradation of isoprene also warrants further attention.…”

Section: Diversity Of Isoprene-degrading Bacteriamentioning

confidence: 99%

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Molecular Ecology of Isoprene-Degrading Bacteria

2020

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Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth’s climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle.

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Section: Discussionmentioning

confidence: 99%

Section: Diversity Of Isoprene-degrading Bacteriamentioning

confidence: 99%

Molecular Ecology of Isoprene-Degrading Bacteria

2020

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“…Finally, the potential lyase substrate 2-hydroxy-2-methylbut-3-enoyl-CoA could be formed which is likely cleaved to methyl vinyl ketone and formyl-CoA. Another substrate for the lyase may be formed by isoprene reduction to isoamylene (Kronen et al, 2019). The latter alkene could be processed analogous to isobutene and isoprene oxidation to 2-hydroxy-2-methylbutyryl-CoA, which is readily used as substrate by the lyase from strain DSM 45062.…”

Section: Discussionmentioning

confidence: 99%

“…Besides, several other putative alcohol and aldehyde dehydrogenases are substantially induced on acetone, 2-HIBA or both substrates and might play a role in acetone degradation as well, for example, the Adh1related WP_018331648.1 ( Table 1). Among these enzymes are also alcohol dehydrogenases (WP_018332348.1 mainly induced on acetone at an abundance of about 4% and WP_018334013.1 on both substrates at values between 0.4 and 0.8%) that are predicted to use 4-nitroso-N,N-dimethylaniline as artificial and mycofactocin as endogenous cofactor, as has recently been elucidated for a related dehydrogenase involved in ethanol oxidation (Krishnamoorthy et al, 2019). Remarkably, among the most abundant proteins is also a putative catalase/peroxidase (WP_033414714.1 with an abundance between 1.6 and 4.2%) which is indicative of high stress by reactive oxygen species, possibly produced in the course of uncoupled MimABCD activity.…”

Section: Proteome Of Acetone-and 2-hiba-grown Cellsmentioning

confidence: 94%

Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction

et al. 2020

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The tertiary branched short-chain 2-hydroxyisobutyric acid (2-HIBA) has been associated with several metabolic diseases and lysine 2-hydroxyisobutyrylation seems to be a common eukaryotic as well as prokaryotic post-translational modification in proteins. In contrast, the underlying 2-HIBA metabolism has thus far only been detected in a few microorganisms, such as the betaproteobacterium Aquincola tertiaricarbonis L108 and the Bacillus group bacterium Kyrpidia tusciae DSM 2912. In these strains, 2-HIBA can be specifically activated to the corresponding CoA thioester by the 2-HIBA-CoA ligase (HCL) and is then isomerized to 3-hydroxybutyryl-CoA in a reversible and B 12-dependent mutase reaction. Here, we demonstrate that the actinobacterial strain Actinomycetospora chiangmaiensis DSM 45062 degrades 2-HIBA and also its precursor 2-methylpropane-1,2-diol via acetone and formic acid by employing a thiamine pyrophosphate-dependent lyase. The corresponding gene is located directly upstream of hcl, which has previously been found only in operonic association with the 2-hydroxyisobutyryl-CoA mutase genes in other bacteria. Heterologous expression of the lyase gene from DSM 45062 in E. coli established a 2-hydroxyisobutyryl-CoA lyase activity in the latter. In line with this, analysis of the DSM 45062 proteome reveals a strong induction of the lyase-HCL gene cluster on 2-HIBA. Acetone is likely degraded via hydroxylation to acetol catalyzed by a MimABCD-related binuclear iron monooxygenase and formic acid appears to be oxidized to CO 2 by selenium-dependent dehydrogenases. The presence of the lyase-HCL gene cluster in isoprene-degrading Rhodococcus strains and Pseudonocardia associated with tropical leafcutter ant species points to a role in degradation of biogenic short-chain ketones and highly branched organic compounds.

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“…The genus appears to have varied metabolic capabilities, including low-temperature growth [32], debromination of polybrominated diphenyl ethers (PBDEs) [33], hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation [34,35], electrode-mediated acetogenesis [36], enhanced iron corrosion [37], and isoprene degradation [38]. To provide a more robust genome dataset, we sequenced and manually curated the genomes of four Acetobacterium strains, including A. malicum and three psychrophilic strains (A.…”

Section: Introductionmentioning

confidence: 99%

The defining genomic and predicted metabolic features of the Acetobacterium genus

Ross

Marshall

Gulliver

et al. 2020

Preprint

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Acetogens are anaerobic bacteria capable of fixing CO 2 or CO to produce acetyl-CoA and ultimately acetate using the Wood-Ljungdahl pathway (WLP). This autotrophic metabolism plays a major role in the global carbon cycle. Acetobacterium woodii, which is a member of the Eubacteriaceae family and type strain of the Acetobacterium genus, has been critical for understanding the biochemistry and energy conservation in acetogens. Other members of the Acetobacterium genus have been isolated from a variety of environments or have had genomes recovered from metagenome data, but no systematic investigation has been done into the unique and varying metabolisms of the genus. Using the 4 sequenced isolates and 5 metagenome-assembled genomes available, we sequenced the genomes of an additional 4 isolates (A. fimetarium, A. malicum, A. paludosum, and A. tundrae) and conducted a comparative genome analysis of 13 different Acetobacterium genomes to obtain better phylogenomic resolution and understand the metabolic diversity of the Acetobacterium genus. Our findings suggest that outside of the reductive acetyl-CoA (Wood-Ljungdahl) pathway, the Acetobacterium genus is more phylogenetically and metabolically diverse than expected, with metabolism of fructose, lactate, and H 2 :CO 2 constant across the genus, and ethanol, methanol, caffeate, and 2,3-butanediol varying across the genus. While the gene arrangement and predicted proteins of the methyl (Cluster II) and carbonyl (Cluster III) branches of the Wood Ljungdahl pathway are highly conserved across all sequenced Acetobacterium genomes, Cluster 1, encoding the formate dehydrogenase, is not. Furthermore, the accessory WLP components, including the Rnf cluster and electron bifurcating hydrogenase, were also well conserved, though all but four strains encode for two Rnf clusters. Additionally, comparative genomics revealed clade-specific potential functional capabilities, such as amino acid transport and metabolism in the psychrophilic group, and biofilm formation in the A. wieringae clade, which may afford these groups an advantage in low-temperature growth or attachment to solid surfaces, respectively. Overall, the data presented herein provides a framework for examining the ecology and evolution of the Acetobacterium genus and highlights the potential of these species as a source of fuels and chemicals from CO 2 -feedstocks.

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Reductive metabolism of the important atmospheric gas isoprene by homoacetogens

Cited by 18 publications

References 78 publications

Molecular Ecology of Isoprene-Degrading Bacteria

Molecular Ecology of Isoprene-Degrading Bacteria

Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction

The defining genomic and predicted metabolic features of the Acetobacterium genus

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