scholarly journals Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 950
Author(s):  
Mirna Hajj ◽  
Petra Langendijk-Genevaux ◽  
Manon Batista ◽  
Yves Quentin ◽  
Sébastien Laurent ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Dna Recombination ◽  
Rna Helicase ◽  
Dna Helicases ◽  
Taxonomic Distribution ◽  
Dna And Rna ◽  
Repair Mechanisms ◽  
Cellular Integrity ◽  
Protein Nucleic Acid ◽  
Phylogenomic Analyses

Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.

scholarly journals Phylogenetic Diversity of Lhr Proteins and Miochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase

2021 ◽  
Author(s):  
Mirna Hajj ◽  
Petra Langendijk-Genevaux ◽  
Manon Batista ◽  
Yves Quentin ◽  
Sébastien Laurent ◽  
...  
Keyword(s):  
Phylogenetic Diversity ◽  
Dna Recombination ◽  
Rna Helicase ◽  
Dna Helicase ◽  
Taxonomic Distribution ◽  
Dna And Rna ◽  
Repair Mechanisms ◽  
Cellular Integrity ◽  
Protein Nucleic Acid ◽  
Phylogenomic Analyses

Helicases are proteins that use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of the DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. Helicases are classified into 6 superfamilies (SF1-6). The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be a DNA helicase that acts in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In parallel, a protein annotated as an Lhr2 protein was also found in the network of proteins involved in RNA metabolism in Thermococcales. To this respect, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in archaeal cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase acting on DNA:RNA and RNA:RNA duplexes and proposed that aLhr2 helicases are involved in processes dependent of DNA and RNA transactions.

Alkylation damage in DNA and RNA—repair mechanisms and medical significance

DNA Repair ◽  
2004 ◽  
Vol 3 (11) ◽  
pp. 1389-1407 ◽  
Author(s):  
Finn Drabløs ◽  
Emadoldin Feyzi ◽  
Per Arne Aas ◽  
Cathrine B. Vaagbø ◽  
Bodil Kavli ◽  
...  
Keyword(s):  
Rna Repair ◽  
Alkylation Damage ◽  
Dna And Rna ◽  
Repair Mechanisms

Human RecQ helicases in transcription-associated stress management: bridging the gap between DNA and RNA metabolism

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Tulika Das ◽  
Surasree Pal ◽  
Agneyo Ganguly
Keyword(s):  
Genome Integrity ◽  
Complex Structures ◽  
Huge Number ◽  
Dna Helicases ◽  
Dna Structures ◽  
Recq Helicases ◽  
Dna And Rna ◽  
Cellular Dna ◽  
Almost All ◽  
Transcription And Replication

Abstract RecQ helicases are a highly conserved class of DNA helicases that play crucial role in almost all DNA metabolic processes including replication, repair and recombination. They are able to unwind a wide variety of complex intermediate DNA structures that may result from cellular DNA transactions and hence assist in maintaining genome integrity. Interestingly, a huge number of recent reports suggest that many of the RecQ family helicases are directly or indirectly involved in regulating transcription and gene expression. On one hand, they can remove complex structures like R-loops, G-quadruplexes or RNA:DNA hybrids formed at the intersection of transcription and replication. On the other hand, emerging evidence suggests that they can also regulate transcription by directly interacting with RNA polymerase or recruiting other protein factors that may regulate transcription. This review summarizes the up to date knowledge on the involvement of three human RecQ family proteins BLM, WRN and RECQL5 in transcription regulation and management of transcription associated stress.

Structure, function and evolution of the XPD family of iron–sulfur-containing 5′→3′ DNA helicases

2009 ◽  
Vol 37 (3) ◽  
pp. 547-551 ◽  
Author(s):  
Malcolm F. White
Keyword(s):  
Xeroderma Pigmentosum ◽  
Dna Recombination ◽  
Complementation Group ◽  
Iron Sulfur Cluster ◽  
Dna Helicases ◽  
Sulfur Cluster ◽  
Binding Domains ◽  
Iron Sulfur ◽  
Domains Of Life ◽  
Xpd Helicase

The XPD (xeroderma pigmentosum complementation group D) helicase family comprises a number of superfamily 2 DNA helicases with members found in all three domains of life. The founding member, the XPD helicase, is conserved in archaea and eukaryotes, whereas the closest homologue in bacteria is the DinG (damage-inducible G) helicase. Three XPD paralogues, FancJ (Fanconi's anaemia complementation group J), RTEL (regular of telomere length) and Chl1, have evolved in eukaryotes and function in a variety of DNA recombination and repair pathways. All family members are believed to be 5′→3′ DNA helicases with a structure that includes an essential iron–sulfur-cluster-binding domain. Recent structural, mutational and biophysical studies have provided a molecular framework for the mechanism of the XPD helicase and help to explain the phenotypes of a considerable number of mutations in the XPD gene that can cause three different genetic conditions: xeroderma pigmentosum, trichothiodystrophy and Cockayne's syndrome. Crystal structures of XPD from three archaeal organisms reveal a four-domain structure with two canonical motor domains and two unique domains, termed the Arch and iron–sulfur-cluster-binding domains. The latter two domains probably collaborate to separate duplex DNA during helicase action. The role of the iron–sulfur cluster and the evolution of the XPD helicase family are discussed.

Multiple Functions of Nuclear DNA Helicase II (RNA Helicase A) in Nucleic Acid Metabolism

2004 ◽  
Vol 36 (3) ◽  
pp. 177-183 ◽  
Author(s):  
Suisheng Zhang ◽  
Frank Grosse
Keyword(s):  
Nuclear Dna ◽  
Rna Helicase ◽  
Dna Helicase ◽  
Nucleic Acid Metabolism ◽  
Rna Helicase A ◽  
Dna Helicase Ii ◽  
Dna And Rna ◽  
Sequence Homologies ◽  
Drosophila Protein ◽  
Purification Methods

Abstract Nuclear DNA helicase II (NDH II), or RNA helicase A (RHA), was initially discovered in mammals by conventional protein purification methods. Molecular cloning identified apparent sequence homologies between NDH II and a Drosophila protein named maleless (MLE), the latter being essential for the Drosophila X-chromosome dosage compensation. Increasing amounts of evidence suggest that NDH II is involved in multiple aspects of cellular and viral DNA and RNA metabolism. Moreover the functions of NDH II may have potential clinical implications related to viral infection, autoimmune diseases, or even tumorigenesis.

scholarly journals Srs2 and Sgs1 DNA Helicases Associate with Mre11 in Different Subcomplexes following Checkpoint Activation and CDK1-Mediated Srs2 Phosphorylation

2005 ◽  
Vol 25 (13) ◽  
pp. 5738-5751 ◽  
Author(s):  
Irene Chiolo ◽  
Walter Carotenuto ◽  
Giulio Maffioletti ◽  
John H. J. Petrini ◽  
Marco Foiani ◽  
...  
Keyword(s):  
Dna Damage ◽  
Cellular Response ◽  
Genome Instability ◽  
Dna Recombination ◽  
Dna Helicase ◽  
Checkpoint Activation ◽  
Dna Helicases ◽  
Checkpoint Response ◽  
Checkpoint Kinases ◽  
Genes Encoding

ABSTRACT Mutations in the genes encoding the BLM and WRN RecQ DNA helicases and the MRE11-RAD50-NBS1 complex lead to genome instability and cancer predisposition syndromes. The Saccharomyces cerevisiae Sgs1 RecQ helicase and the Mre11 protein, together with the Srs2 DNA helicase, prevent chromosome rearrangements and are implicated in the DNA damage checkpoint response and in DNA recombination. By searching for Srs2 physical interactors, we have identified Sgs1 and Mre11. We show that Srs2, Sgs1, and Mre11 form a large complex, likely together with yet unidentified proteins. This complex reorganizes into Srs2-Mre11 and Sgs1-Mre11 subcomplexes following DNA damage-induced activation of the Mec1 and Tel1 checkpoint kinases. The defects in subcomplex formation observed in mec1 and tel1 cells can be recapitulated in srs2-7AV mutants that are hypersensitive to intra-S DNA damage and are altered in the DNA damage-induced and Cdk1-dependent phosphorylation of Srs2. Altogether our observations indicate that Mec1- and Tel1-dependent checkpoint pathways modulate the functional interactions between Srs2, Sgs1, and Mre11 and that the Srs2 DNA helicase represents an important target of the Cdk1-mediated cellular response induced by DNA damage.

Exploring Structural, Functional, and Kinetic Aspects of Nucleic Acid–Protein Complexes with Pressure: Nucleosomes and RNA Polymerase

1996 ◽  
Author(s):  
Mauro Villas-Boas ◽  
Ana Sepulveda De Rezende
Keyword(s):  
High Pressure ◽  
Nucleic Acid ◽  
Rna Polymerase ◽  
Molecular Complexes ◽  
Protein Assemblies ◽  
Structural Hierarchy ◽  
Dna And Rna ◽  
Protein Nucleic Acid ◽  
Multiple Conformations

High pressure has provided us with new insights into two complex DNA-protein systems: nucleosomes and RNA polymerase. In spite of their complexity, we can derive new and useful information about them by coupling high pressure with a variety of other physical techniques and functional assays. These studies have shown clearly that multiple conformations of these large–molecular weight DNA-protein assemblies are present simultaneously in solution, although both molecular assemblies are generally considered to be single structures in most in vitro experiments. Considering the variety of different cellular situations encountered by nucleosomes and RNA polymerases, it is perhaps to be expected that evolution would select structures with flexible and multifarious conformations that possesses sufficient stability, rather than static, rigid, singular, and highly stable structures. The molecular organization in the nucleus of a biological cell is extensive and involves intricate protein-protein and protein–nucleic acid interactions that are changing continually during the cell cycle. These dynamic activities in the nucleus are tightly coordinated with many extranuclear events throughout the cell. Highly organized molecular complexes involving multisubunit proteins (and higher order protein assemblies) interacting with the nucleic acid components are the rule rather than the exception in the nucleus (Alberts et al., 1983; Darnell et al., 1990; Lewin, 1994). For instance, chromosomes are organized in a structural hierarchy culminating in the metaphase state in which they are packed tightly together with proteins in a highly specific and economical manner that still largely eludes our understanding; the DNA of a eukaryotic cell is replicated with the help of a complex assembly of proteins; and information coded within the DNA sequence is transcribed with the assistance of multisubunit DNA-binding proteins, some acting as enzymes and others serving mainly as organizational and structural assistants to the catalytic process. Many important features of protein-nucleic acid (DNA and RNA) interactions have been elucidated in the last decade (Pabo & Sauer, 1992; Steitz, 1990), and exciting results have been obtained for singleprotein molecules and dimers binding to DNA. Although we are a long way from understanding these interactions completely, enough aspects are known so that structural predictions are sometimes possible simply from the amino acid sequence.

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