Reconstructing the evolutionary history of F420-dependent dehydrogenases

M Laura Mascotti,Maximiliano Juri Ayub,Quoc-Thai Nguyen,Marco W Fraaije,Hemant Kumar

doi:10.1038/s41598-018-35590-2

Abstract

During the last decade the number of characterized F420-dependent enzymes has significantly increased. Many of these deazaflavoproteins share a TIM-barrel fold and are structurally related to FMN-dependent luciferases and monooxygenases. In this work, we traced the origin and evolutionary history of the F420-dependent enzymes within the luciferase-like superfamily. By a thorough phylogenetic analysis we inferred that the F420-dependent enzymes emerged from a FMN-dependent common ancestor. Furthermore, the data show that during evolution, the family of deazaflavoproteins split into two well-defined groups of enzymes: the F420-dependent dehydrogenases and the F420-dependent reductases. By such event, the dehydrogenases specialized in generating the reduced deazaflavin cofactor, while the reductases employ the reduced F420 for catalysis. Particularly, we focused on investigating the dehydrogenase subfamily and demonstrated that this group diversified into three types of dehydrogenases: the already known F420-dependent glucose-6-phosphate dehydrogenases, the F420-dependent alcohol dehydrogenases, and the sugar-6-phosphate dehydrogenases that were identified in this study. By reconstructing and experimentally characterizing ancestral and extant representatives of F420-dependent dehydrogenases, their biochemical properties were investigated and compared. We propose an evolutionary path for the emergence and diversification of the TIM-barrel fold F420-dependent dehydrogenases subfamily.

Highlights

The naturally existing deazaflavin cofactor F420 is a peculiar cofactor involved in central metabolism of some specific Archaea and Bacteria lineages
Most research has focused on studying Mycobacterium tuberculosis F420-dependent enzymes which are involved in prodrug activation[10,11]
Aflatoxin degrading F420-dependent reductases from Mycobacterium smegmatis were shown to belong to a class called F420-dependent reductases (FDR-A, FDR-B) which are related by sequence similarity to members of the PPOX family[13]

Summary

Introduction

The naturally existing deazaflavin cofactor F420 is a peculiar cofactor involved in central metabolism of some specific Archaea and Bacteria lineages. 5′-phosphate oxidases (PPOX), and deazaflavin-dependent nitroreductases (DDN), most of them belonging to the LLM family[12] All these classes include FAD and FMN-dependent enzymes. The three above-mentioned major deazaflavoprotein families are structurally distinct, there is a common pattern: they include proteins that rely on other flavin cofactors or even non-related ones, such as heme or tetrahydromethanopterin (HMPT). This opens the question on what the evolutionary paths of these different families were and which constraints determined how the cofactor switching events could have occurred. To thoroughly understand the sequence of changes that led to the emergence of the different dehydrogenase functionalities, we reconstructed ancestral sequences and characterized an ancestral F420-dependent dehydrogenase

Objectives

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Results

Conclusion