A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius

Kun Wang,Hassan Ramadan Maklad,Bettina Siebers,Christopher Bräsen,Karin Valegård,Ann-Christin Lindås,Xiaoxiao Zhou,Frank Schult,David Sybers,Eveline Peeters,Charlotte Lewyllie,Liesbeth Lemmens

doi:10.1038/s41467-019-09479-1

Abstract

Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes. By contrast, although certain archaea appear to metabolize fatty acids, the regulation of the underlying pathways in these organisms remains unclear. Here, we show that a TetR-family transcriptional regulator (FadRSa) is involved in regulation of fatty acid metabolism in the crenarchaeon Sulfolobus acidocaldarius. Functional and structural analyses show that FadRSa binds to DNA at semi-palindromic recognition sites in two distinct stoichiometric binding modes depending on the operator sequence. Genome-wide transcriptomic and chromatin immunoprecipitation analyses demonstrate that the protein binds to only four genomic sites, acting as a repressor of a 30-kb gene cluster comprising 23 open reading frames encoding lipases and β-oxidation enzymes. Fatty acyl-CoA molecules cause dissociation of FadRSa binding by inducing conformational changes in the protein. Our results indicate that, despite its similarity in overall structure to bacterial TetR-family FadR regulators, FadRSa displays a different acyl-CoA binding mode and a distinct regulatory mechanism.

Highlights

Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes
S. acidocaldarius harbors a 30-kb gene cluster consisting of genes encoding enzymes involved in lipid and fatty acid metabolism and a putative regulator (Saci_1107, Fig. 1a)
Gene synteny is not strictly conserved, the extent of some of these gene clusters, especially in other Sulfolobus species, suggests the potential existence of similar FadR-mediated acyl-CoA responsive repression. This hypothesis is supported by the prediction of putative FadR binding sites in the neighborhood of fadR promoters and at distant locations, either in intergenic regions or in open reading frame (ORF), for the gene clusters in other Sulfolobus species (Fig. 8b). It is well-established that archaea harbor typical bacterial-like transcription regulators[34,35], which are proposed to result from shared ancestry as well as from extensive horizontal gene transfers, especially from bacteria to archaea[36]

Summary

Introduction

Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes. Given the absence of genes encoding acyl-carrier protein (ACP) or ACP synthase[13], it has been postulated that a β-oxidation pathway might operate in the reverse direction in conjunction with acetyl-CoA C-acetyltransferase enzymes[10]. These are abundantly encoded in archaeal genomes, sometimes in the direct neighborhood of β-oxidation genes[10,14]. Gram-positive bacteria such as Bacillus subtilis use an identically named transcription factor FadR that belongs to the TetR family for the acyl-CoA dependent regulation of β-oxidation degradation[21] and a DeoR family member FapR that regulates biosynthesis of saturated fatty acids and phospholipids[22]. The mechanism of action of the bacterial acyl-CoA responsive TetR-like regulator has been unraveled by analysis of apo, ligand-bound, and DNAbound crystal structures[23,24,25,26]

Methods

Results

Conclusion