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

Li Liu,Daniel M Schubert,Martin Könneke,Ivan A Berg

doi:10.3389/fmicb.2021.712030

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.

Highlights

Biological inorganic carbon fixation, the oldest and quantitatively most important biosynthetic process in Nature, proceeds via at least seven natural pathways (Berg, 2011; Fuchs, 2011; Sánchez-Andrea et al, 2020)
(S)-3-Hydroxybutyryl-CoA Dehydrogenase From Nitrosopumilus maritimus is responsible for a large part of dark ocean inorganic carbon fixation (Meador et al, 2020)
A recent phylogenomic analysis suggested that ammonia-oxidizing Thaumarchaeota (AOA) originated from the terrestrial nonammonia-oxidizing ancestors and expanded to the shallow and deep ocean upon their oxygenation (Ren et al, 2019), while ammonia-oxidizing bacteria are much younger (Ward et al, 2021)

Summary

Introduction

Biological inorganic carbon fixation, the oldest and quantitatively most important biosynthetic process in Nature, proceeds via at least seven natural pathways (Berg, 2011; Fuchs, 2011; Sánchez-Andrea et al, 2020) Two of these pathways, the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) and the dicarboxylate/4-hydroxybutyrate (DC/HB) cycles were found only in Archaea (S)-3-Hydroxybutyryl-CoA Dehydrogenase From Nitrosopumilus maritimus (Berg et al, 2010a). The carboxylases in the DC/HB cycle are ferredoxin-dependent pyruvate synthase and phosphoenolpyruvate carboxylase (Huber et al, 2008; Ramos-Vera et al, 2009), while a promiscuous acetyl-CoA/propionyl-CoA carboxylase catalyzes both acetylCoA and propionyl-CoA carboxylations in the HP/HB cycle (Chuakrut et al, 2003; Hügler et al, 2003) In the latter case, a number of specific enzymes are responsible for the conversion of malonyl-CoA, the product of the acetyl-CoA carboxylase reaction, to propionyl-CoA, which is carboxylated and isomerized to succinyl-CoA (Figure 1). Crotonyl-CoA conversion to two acetyl-CoA molecules proceeds through the reactions known from β-oxidation: hydration of crotonyl-CoA to (S)-3-hydroxybutyryl-CoA, its oxidation to acetoacetyl-CoA and cleavage to two acetyl-CoA molecules (Figure 1)

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Results

Conclusion