(S)-3-Hydroxybutyryl-CoA Dehydrogenase From the Autotrophic 3-Hydroxypropionate/4-Hydroxybutyrate Cycle in Nitrosopumilus maritimus

Abstract

Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant organisms that exert primary control of oceanic and soil nitrification and are responsible for a large part of dark ocean primary production. They assimilate inorganic carbon via an energetically efficient version of the 3-hydroxypropionate/4-hydroxybutyrate cycle. In this cycle, acetyl-CoA is carboxylated to succinyl-CoA, which is then converted to two acetyl-CoA molecules with 4-hydroxybutyrate as the key intermediate. This conversion includes the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Here, we heterologously produced the protein Nmar_1028 catalyzing this reaction in thaumarchaeon Nitrosopumilus maritimus, characterized it biochemically and performed its phylogenetic analysis. This NAD-dependent dehydrogenase is highly active with its substrate, (S)-3-hydroxybutyryl-CoA, and its low Km value suggests that the protein is adapted to the functioning in the 3-hydroxypropionate/4-hydroxybutyrate cycle. Nmar_1028 is homologous to the dehydrogenase domain of crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase that is present in many Archaea. Apparently, the loss of the dehydratase domain of the fusion protein in the course of evolution was accompanied by lateral gene transfer of 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase from Bacteria. Although (S)-3-hydroxybutyryl-CoA dehydrogenase studied here is neither unique nor characteristic for the HP/HB cycle, Nmar_1028 appears to be the only (S)-3-hydroxybutyryl-CoA dehydrogenase in N. maritimus and is thus essential for the functioning of the 3-hydroxypropionate/4-hydroxybutyrate cycle and for the biology of this important marine archaeon.

Carbon fixation pathways across the bacterial and archaeal tree of life

“…The HP/HB cycle was first discovered in the thermoacidophilic, iron-oxidizing archaeon Metallosphaera sedula ( 65 ) and has been more recently described in detail for the ammonium-oxidizing archaeaon Nitrosopumilus maritimus ( 66 , 67 ). So far, this cycle has only been reported for the Archaea .…”

Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil’s Hole, Bermuda

“…This change is further corroborated by the decreasing molar contribution of alanine and glycine, two amino acids that are more resistant to degradation, when compared to the control during the same time frame ( Figure 4A ). The labile DOM might come from new production by chemolithoautotrophy during the incubations, as Nitrosopumilus strains have been shown to fix carbon ( Könneke et al, 2014 ; Liu et al, 2021 ), and produce DOM consisting of labile amino acids such as alanine, leucine, and serine ( Bayer et al, 2019 ). In this study, Thaumarcheaota cell abundances increased from days 6 to 21 in the S/D treatment ( Figure 5D ).…”

Perspectives for Using CO2 as a Feedstock for Biomanufacturing of Fuels and Chemicals

“…From an application standpoint, there have been attempts to harness these pathways for biotechnological purposes. (S)-3-hydroxybutyryl-CoA dehydrogenase, which is one of the important enzymes of the HP/HB cycle, has been characterized, and different enzymes from Nitrosopumilus maritimus and Metallosphaera sedula were compared to explore the enzymatic differences in these processes within the DC/HB and HP/HB cycles, which helps protect marine habitats [50]. However, attempts to fully recreate and utilize these pathways in common microbial hosts like E. coli have faced challenges [5].…”