Helicases from All Domains of Life

Renu Tuteja

• Publisher: Academic Press
• Year: 2018
• Print ISBN: 9780128146859
• eBook ISBN: 9780128146866
• Topic: Biological Sciences
• Subtopic: Cell Biology
• Index: Biological Sciences

Helicases from All Domains of Life is the first book to compile information about helicases from many different organisms in a single volume. Research in the helicase field has been going on for a long time now, but the completion of so many genomes of these ubiquitous enzymes has made it difficult to keep up with new discoveries. As the huge number of identified DNA and RNA helicases, along with the structural and functional differences among them, make it difficult for the interested scholar to grasp a comprehensive view of the field, this book helps fill in the gaps.- Presents updates on the functions and features of helicases across the different kingdoms- Begins with a chapter on the evolutionary history of helicases- Contains specific chapters on selected helicases of great importance from a biological/applicative point-of-view

Chapter 1

Archaeal SF1 and SF2 Helicases

Unwinding in the Extreme

Mirna Hajj^1,3, Samar El-Hamaoui², Manon Batista³, Marie Bouvier³, Ziad Abdel-Razzak², Béatrice Clouet d'Orval³ and Hala Chamieh^1,2, ¹Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Tripoli, Lebanon, ²Department of Life and Earth Sciences, Faculty of Science, Lebanese University, Tripoli, Lebanon, ³Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France

Abstract

Archaea, the third domain of life, are significant microorganism models in understanding fundamental aspects of molecular biology. Since the archaeal informational system shares many eukaryal features, structure–function studies using Archaea as models have largely contributed to our understanding of many eukaryotic cellular processes. Helicases of superfamilies 1 (SF1) and 2 (SF2) have been shown to be of major importance in RNA and DNA metabolism in Eukarya and in Bacteria. In Archaea, the cellular functions of these enzymes remain dispersed and only few members were characterized. In this chapter, we review our knowledge on the archaeal SF1 and SF2 helicases. We focus on phylogenomic studies that revealed archaeal helicase families and give insights into their respective biochemical and structural properties. Finally, we raise the question of the mode of actions of these helicases in archaeal DNA and RNA metabolism.

Keywords

Archaea; SF1; SF2; helicase; DNA metabolism; RNA metabolism; phylogenomics; extremophiles

Acknowledgments

This work is financed by the Lebanese University (UL) and National Center for research in Lebanon (CNRS-L). MH is a recipient of the AZM-UL excellency fellowship.

Introduction

In 1977 Carl Woese and collaborators identified Archaea as a separate domain of life. Since then, Archaea have been considered as valuable study models to understand the diversity of life styles on earth [1]. The first-discovered Archaea were distinguished by their ability to thrive in challenging habitats such as high salinity, pH, temperature, and high pressure. However, novel high-throughput sequencing methods permitted the identification that Archaea constitute a considerable fraction of the Earth’s ecosystems with astonishing diversity and omnipresence. Remarkably, archaeal microorganisms are found to play pivotal roles in geochemical cycles as well as being part of human gut microbiota [2,3].

Original classification based on 16S rRNA showed that the archaeal phylogeny embraces two major phylogenetic groups, named Euryarchaeota and Crenarchaeota [4]. Subsequently, phylogenomic analyses using an increasing number of sequenced archaeal genomes led to the characterization of several phyla, including Euryarchaeota and two main “superphyla,” namely the TACK superphylum (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota) and the DPANN superphylum (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and NanohaloArchaea) [5,6]. Metagenomics analyses allowed the identification of a novel archaeal clade, named Asgard, with an expanded repertoire of eukaryotic signatures. These findings provide novel hypothesis on the origin of Eukarya within the archaeal domain [7].

At first glance, archaeal cells look like bacterial cells, however unusual composition of membrane lipids and cell envelope made irrevocably clear the existence of profound differences between Archaea and Bacteria. Archaeal membranes are composed of ether lipids instead of ester lipids and the cell envelope does not contain peptidoglycan [8]. While Archaea share some bacterial essential functioning systems of energy metabolism, the informational processing system which includes DNA replication, transcription, and translation, are closely related to Eukarya [9–12]. Moreover, the archaeal genome is organized by either eukaryotic-like histone proteins or bacterial-like nucleoid-associated proteins [13]. In this mosaic setting, we are interested in deciphering the panel of helicases existing in Archaea that would drive numerous fundamental metabolic pathways.

Helicases are molecular motors that couple the use of energy to countless biological processes. By catalyzing the separation of double stranded nucleic acids into a single stranded one and the dissociation of nucleic-acid associated proteins, helicases participate in all aspects of DNA and RNA metabolism, and help in chromatin remodeling [14–17]. Helicases are grouped into six superfamilies (SF1–6) based on amino acid sequence similarity, oligomeric state (monomeric or hexameric), activity (substrate as single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), or RNA, translocating activity), and polarity (5′→3′, 3′→5′) [16] (Fig. 1.1). The two largest acknowledged superfamilies, SF1 and SF2, which group nonhexameric helicases, perform diverse cellular functions in DNA replication, repair, recombination, RNA metabolism, and protein translation. SFs3–6 form hexameric toroid structures (Fig. 1.1) [18–20]. SF3 helicases comprise viral helicases. SF4 and SF5 function as replicative and transcription termination factors, respectively. SF6 include the minichromosome maintenance helicases and the RuvB helicase [20,21].

Figure 1.1 (A) Domain organization of SF superfamilies and (B) occurrence of SF1 and SF2 helicases in Archaea.
Helicases are classified into six superfamilies which include the hexameric helicases SF3 to SF6 and the non hexameric helicases SF1 and SF2. SF1 and SF2 helicases share a conserved helicase core composed of two RecA-like domain folds (HD1 in yellow and HD2 in red). SF1 helicases present multiple insertions within the helicase core. SF1 and SF2 helicases are divergent in their N- and C-terminus which are attributed to the diversity of helicase functions in vivo (represented by gray boxes). Crystal structure of SF2 DEAD-box helicase from Methanococcus janaschii, Pdb: 1HV8. Crystal structure of hexameric helicase E1 from papillomavirus, Pdb: 5A9K.

The SF1 and SF2 helicases are characterized by a conserved helicase core formed by two RecA domains which consist of nine characteristic sequence motifs named Q, I, Ia, Ib, and II to VI. These motifs slightly differ between SF1 and SF2 and among those Walker A (motif I) and Walker B (motif II) bind NTPs (Fig. 1.1) [22,23]. The specificity of action of SF1 and SF2 helicases has been mostly attributed to their accessory domains present at their N- and C-terminus in addition to their conserved helicase core. SF1 and SF2 were also classified based on their translocation polarity. Two groups emerged: the SF1/2A and SF1/2B with 3′–5′ or 5′–3′ translocation polarity, respectively [16]. Another classification was further refined based on the sequence conservation of bacterial and eukaryal-like helicases and on structural and mechanistic features allowing the identification of twelve distinct families (Fig. 1.1) [24]. The SF1 includes UvrD-like/Rep, Pif-1-like, and Upf1-like families, whereas the SF2 accounts for the Rec-G like, RecQ-like, XPD/Rad3/DinG, Ski-2 like, type 1 restriction enzyme helicase subunit (T1R), Swi2/Snf, XPF/Hef/ERCC4/RIG-I nuclease helicase, DEAD-box, and the DEAH/RHA families [18,25,26].

To overcome the gap of knowledge on archaeal helicase families, a comprehensive in silico analysis allowed retrieving the first exhaustive list of SF1 and SF2 helicases in Archaea. Each family was named based on knowledge of the function of their bacterial and eukaryot...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• List of Contributors
• Preface
• Acknowledgments
• Chapter 1. Archaeal SF1 and SF2 Helicases: Unwinding in the Extreme
• Chapter 2. Structure and Function of Helicases in Archaea the Third Domain of Life
• Chapter 3. Role of Plant Helicases in Imparting Salinity Stress Tolerance to Plants
• Chapter 4. Evolution of RNA Helicases in Plants: Molecular and Functional Insights
• Chapter 5. Genome Wide In Silico Identification of Helicases From Leishmania donovani
• Chapter 6. Genome Wide In Silico Characterization of Ded1 Family of Helicases from Plasmodium Falciparum
• Chapter 7. Overview of Posttranslational Modifications of Biochemically Characterized Plasmodium falciparum Helicases
• Chapter 8. Role of Human Xeroderma Pigmentosum Group D (XPD) Helicase in Various Cellular Pathways
• Chapter 9. Diverse Roles of DEAD/DEAH-Box Helicases in Innate Immunity and Diseases
• Chapter 10. Role of Zinc-Binding Domains of RecQ Helicases
• Chapter 11. Helicase Dysfunctions in Human Diseases
• Chapter 12. A General Model of DNA Unwinding by Monomeric Helicases
• Chapter 13. Assaying the Activity of Helicases: An Overview
• Chapter 14. An Overview of AAA+ Superfamily Proteins Associated Helicases
• Index