Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO2 Fixation in Metallosphaera sedula

Liu, Li; Huber, Harald; Berg, Ivan A.

doi:10.3389/fmicb.2020.00354

Cited by 7 publications

(17 citation statements)

References 57 publications

(70 reference statements)

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“…Uncharacterized crotonyl-CoA hydratase homolog Msed_0566 was also present in all autotrophic Crenarchaeota , while four other homologs were present only in some strains. Based on this fact, it was proposed that Msed_0566 may be a designated crotonyl-CoA hydratase in the crenarchaeal HP/HB cycle ( 17 ).…”

Section: Resultsmentioning

confidence: 99%

“… a The protein was purified from M. sedula cell extracts and characterized as 3-hydroxypropionyl-CoA hydratase; data from reference 15 . b Data from reference 18 c Data from reference 17 . d Bifunctional crotonyl-CoA hydratase/3-hydroxybutyryl-CoA dehydrogenase Msed_0399 is a fusion protein consisting of an enoyl-CoA hydratase domain and a dehydrogenase domain.…”

Section: Resultsmentioning

confidence: 99%

“…Although it was active with the tested enoyl-CoAs, the activity was low ( Table 2 ). Previous attempts to characterize the heterologously produced Msed_0566 were unsuccessful ( 17 ), probably due to the low expression level of the protein and its poor activity with crotonyl-CoA. Bad catalytic efficiency ( k cat / K m ) with the tested substrates suggests that the protein is specific to unknown substrate(s) and is not involved in the HP/HB cycle.…”

Section: Resultsmentioning

confidence: 99%

“…Nevertheless, this protein is not universally conserved in autotrophic Sulfolobales and thus does not appear to be the sought-after crotonyl-CoA hydratase. Therefore, we decided to reevaluate the function of the 3-hydroxypropionyl-CoA dehydratase Msed_2001 (which is present in all autotrophic Sulfolobales ; reference 17 ) and to characterize this protein with different substrates.…”

Section: Resultsmentioning

confidence: 99%

“…Indeed, the homologous fusion protein consisting of an enoyl-CoA hydratase and a dehydrogenase domain is responsible for the corresponding conversion in the dicarboxylate/4-hydroxybutyrate cycle in anaerobic Crenarchaeota like Ignicoccus hospitalis ( Desulfurococcales ) or Pyrobaculum neutrophilum ( Thermoproteales ) ( 25 , 26 ), and it was logical to propose the same for M. sedula . However, we have recently shown that the ( S )-3-hydroxybutyryl-CoA dehydrogenase reaction is catalyzed in M. sedula by a distinct enzyme ( 17 ). Here we confirm that Msed_0399 is not the main protein responsible for the crotonyl-CoA hydratase reaction.…”

Section: Discussionmentioning

confidence: 99%

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Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota

Liu

Brown

Könneke

et al. 2021

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The autotrophic 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle functions in thermoacidophilic, (micro)aerobic, hydrogen-oxidizing Crenarchaeota of the order Sulfolobales as well as in mesophilic, aerobic, ammonia-oxidizing Thaumarchaeota. Notably, the HP/HB cycle evolved independently in these two archaeal lineages, and crenarchaeal and thaumarchaeal versions differ regarding their enzyme properties and phylogeny. These differences result in altered energetic efficiencies between the variants. Compared to the crenarchaeal HP/HB cycle, the thaumarchaeal variant saves two ATP equivalents per turn, rendering it the most energy-efficient aerobic pathway for carbon fixation. Characteristically, the HP/HB cycle includes two enoyl coenzyme A (CoA) hydratase reactions: the 3-hydroxypropionyl-CoA dehydratase reaction and the crotonyl-CoA hydratase reaction. In this study, we show that both reactions are catalyzed in the aforementioned archaeal groups by a promiscuous 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase (Msed_2001 in crenarchaeon Metallosphaera sedula and Nmar_1308 in thaumarchaeon Nitrosopumilus maritimus). Although these two enzymes are homologous, they are closely related to bacterial enoyl-CoA hydratases and were retrieved independently from the same enzyme pool by the ancestors of Crenarchaeota and Thaumarchaeota, despite the existence of multiple alternatives. This striking similarity in the emergence of enzymes involved in inorganic carbon fixation from two independently evolved pathways highlights that convergent evolution of autotrophy could be much more widespread than anticipated. IMPORTANCE Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaeota of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. Bioinformatic prediction of the autotrophic potential of microorganisms or microbial communities requires identification of enzymes involved in autotrophy. However, many microorganisms possess several isoenzymes that may potentially catalyze the reactions of the cycle. Here, we studied the enzymes catalyzing 3-hydroxypropionyl-CoA dehydration and crotonyl-CoA hydration in Nitrosopumilus maritimus (Thaumarchaeota) as well as in Metallosphaera sedula (Crenarchaeota). We showed that both reactions were catalyzed by homologous promiscuous enzymes, which evolved independently from each other from their bacterial homologs. Furthermore, the HP/HB cycle is of applied value, and knowledge of its enzymes is necessary to transfer them to a heterologous host for synthesis of various value-added products.

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Section: Resultsmentioning

confidence: 99%