A functional and structural study of three bacterial nucleic acid-interacting proteins. The story of a Ferric Uptake Regulator, an Oligoribonuclease and an ATP-dependent DNA ligase

Abstract

Nucleic acid-interacting proteins are essential players in cellular processes of all living organisms. In the present study, we explore three psychrophilic-derived proteins involved in gene regulation, RNA degradation and DNA ligation in bacterial cells, with one common feature; they perform their activity by interacting with nucleic acids.

The Ferric uptake regulator (Fur) is a global transcription factor that controls expression of a wide variety of genes in an iron-dependent fashion. As a key player in bacterial infections, Fur is an interesting target in the fight against pathogenic bacteria. This study provides new insight into the mechanisms behind Fur regulation in the fish pathogen Aliivibrio salmonicida. The identification of Fur-DNA interaction partners in A. salmonicida provides potential for future development of antibacterial drugs.

The Oligoribonuclease (Orn) degrades small oligoribonucleotides to monoribonucleotides in the final step of the mRNA decay, an action essential for the viability of many bacteria. This work reveals the molecular mechanisms in mRNA degradation in metagenomic Orn (MG Orn), isolated from marine Arctic environments, presents the three-dimensional structure of the protein and highlights the importance of dimer formation for function. In light of the bioprospecting aspect of our research, MG Orn shows potential as a target in the search for novel cold adapted enzymes in biotechnological applications. Ligases are enzymes that join DNA fragments, important for many processes in the cell. Motivated by the potential advantages of DNA ligases operating at low temperatures in biotechnological applications, three minimal Lig E-type ATP-dependent ligases originating from psychrophilic bacteria are characterized in terms of temperature optima and thermal stability; ATP-dependent DNA ligase type Lig Es from A. salmonicida, Psychromonas sp. Strain SP041 and Pseudoalteromonas arctica. Lig E from A. salmonicida shows typical cold adapted behavior and likely cold adapted determinants are revealed.

The results presented in this work add knowledge to the nature of the nucleic-acid interacting mechanisms of three proteins originating from psychrophilic bacteria, elucidates features behind cold adaptation and identifies potential use in biotechnological applications and antibacterial drug development.