Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases

Abstract

Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.

A Reconstructed Common Ancestor of the Fatty Acid Photo‐decarboxylase Clade Shows Photo‐decarboxylation Activity and Increased Thermostability

“…Figure 2 visually illustrates how ANC1 and ANC2 are more similar to WT (more black bars) whereas ANC3 has a lower sequence identity (more white bars). Despite the differences, they all share the conserved amino acid positions that characterize FAPs: C432, R451 and A576 (numbering corresponding to CvFAP) [29,30] . A576 is possibly one of the most striking difference between FAPs and other members of the GMC superfamily.…”

“…A576 is possibly one of the most striking difference between FAPs and other members of the GMC superfamily. At this position, most members of the GMC superfamily have a histidine [30] …”

“…At this position, most members of the GMC superfamily have a histidine. [30] ANC1 showed better production yield and stability So far sCvFAP production in E. coli has shown limited yields of soluble protein in cell-free extract and, particularly, low enzyme production after purification. [17] In general, efforts to regulate the solubility of the protein have included the use of weak promoters, low cultivation temperature during protein production, modified growth media, and fusion with solubility enhancing tags.…”

“…Despite the differences, they all share the conserved amino acid positions that characterize FAPs: C432, R451 and A576 (numbering corresponding to CvFAP). [29,30] A576 is possibly one of the most striking difference between FAPs and other members of the GMC superfamily. At this position, most members of the GMC superfamily have a histidine.…”

Prognostic value of fatty acid metabolism-related genes in patients with hepatocellular carcinoma

“…The most highly enriched molecular functions of the 6 screened genes were nicotinamide adenine dinucleotide (NAD) binding, oxidoreductase activity and fatty acid activity ( Figure 6A ). The involvement of these molecular functions in fatty acid metabolism has been previously reported [ 14 , 15 ]. Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the 6 genes might participate in pathways related to fatty acids ( Figure 6B ).…”