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Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity
Natalya Yutin, Eugene V Koonin
Biology Direct , 2009, DOI: 10.1186/1745-6150-4-51
Abstract: Phylogenetic analysis of the ATP-dependent and NAD-dependent DNA ligases encoded by the NCLDV reveals an unexpectedly complex evolutionary history. The NAD-dependent ligases are encoded only by a minority of NCLDV (including mimiviruses, some iridoviruses and entomopoxviruses) but phylogenetic analysis clearly indicated that all viral NAD-dependent ligases are monophyletic. Combined with the topology of the NCLDV tree derived by consensus of trees for universally conserved genes suggests that this enzyme was represented in the ancestral NCLDV. Phylogenetic analysis of ATP-dependent ligases that are encoded by chordopoxviruses, most of the phycodnaviruses and Marseillevirus failed to demonstrate monophyly and instead revealed an unexpectedly complex evolutionary trajectory. The ligases of the majority of phycodnaviruses and Marseillevirus seem to have evolved from bacteriophage or bacterial homologs; the ligase of one phycodnavirus, Emiliana huxlei virus, belongs to the eukaryotic DNA ligase I branch; and ligases of chordopoxviruses unequivocally cluster with eukaryotic DNA ligase III.Examination of phyletic patterns and phylogenetic analysis of DNA ligases of the NCLDV suggest that the common ancestor of the extant NCLDV encoded an NAD-dependent ligase that most likely was acquired from a bacteriophage at the early stages of evolution of eukaryotes. By contrast, ATP-dependent ligases from different prokaryotic and eukaryotic sources displaced the ancestral NAD-dependent ligase at different stages of subsequent evolution. These findings emphasize complex routes of viral evolution that become apparent through detailed phylogenomic analysis but not necessarily in reconstructions based on phyletic patterns of genes.This article was reviewed by: Patrick Forterre, George V. Shpakovski, and Igor B. Zhulin.Viruses are ubiquitous parasites of all cellular life forms. In recent years, extensive genome sequencing and comparative analysis of both viral and host genomes yielded
Characterisation of ATP-Dependent Mur Ligases Involved in the Biogenesis of Cell Wall Peptidoglycan in Mycobacterium tuberculosis  [PDF]
Tulika Munshi, Antima Gupta, Dimitrios Evangelopoulos, Juan David Guzman, Simon Gibbons, Nicholas H. Keep, Sanjib Bhakta
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060143
Abstract: ATP-dependent Mur ligases (Mur synthetases) play essential roles in the biosynthesis of cell wall peptidoglycan (PG) as they catalyze the ligation of key amino acid residues to the stem peptide at the expense of ATP hydrolysis, thus representing potential targets for antibacterial drug discovery. In this study we characterized the division/cell wall (dcw) operon and identified a promoter driving the co-transcription of mur synthetases along with key cell division genes such as ftsQ and ftsW. Furthermore, we have extended our previous investigations of MurE to MurC, MurD and MurF synthetases from Mycobacterium tuberculosis. Functional analyses of the pure recombinant enzymes revealed that the presence of divalent cations is an absolute requirement for their activities. We also observed that higher concentrations of ATP and UDP-sugar substrates were inhibitory for the activities of all Mur synthetases suggesting stringent control of the cytoplasmic steps of the peptidoglycan biosynthetic pathway. In line with the previous findings on the regulation of mycobacterial MurD and corynebacterial MurC synthetases via phosphorylation, we found that all of the Mur synthetases interacted with the Ser/Thr protein kinases, PknA and PknB. In addition, we critically analyzed the interaction network of all of the Mur synthetases with proteins involved in cell division and cell wall PG biosynthesis to re-evaluate the importance of these key enzymes as novel therapeutic targets in anti-tubercular drug discovery.
Biochemical characterisation of LigN, an NAD+-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations
Laetitia Poidevin, Stuart A MacNeill
BMC Molecular Biology , 2006, DOI: 10.1186/1471-2199-7-44
Abstract: To characterise the enzymatic properties of the LigN protein, wild-type and three mutant forms of the LigN protein were separately expressed in recombinant form in E.coli and purified to apparent homogeneity by immobilised metal ion affinity chromatography (IMAC). Non-isotopic DNA ligase activity assays using λ DNA restriction fragments with 12 bp cos cohesive ends were used to show that LigN activity was dependent on addition of divalent cations and salt. No activity was detected in the absence of KCl, whereas maximum activity could be detected at 3.2 M KCl, close to the intracellular KCl concentration of Hfx.volcanii cells.LigN is unique amongst characterised DNA ligase enzymes in displaying maximal DNA strand joining activity at high (> 3 M) salt levels. As such the LigN enzyme has potential both as a novel tool for biotechnology and as a model enzyme for studying the adaptation of proteins to high intracellular salt levels.DNA ligases play key roles in all forms of cellular life [1]. Two families of DNA ligase, differing in their cofactor specificity, are characteristic of the two major branches of evolution, the eubacteria and the eukarya/archaea. NAD+-dependent DNA ligases (EC 6.5.1.2) are encoded predominantly by eubacteria [2] but also by certain eukaryotic viruses, such as the entomopoxviruses [3] and mimiviruses [4], and by some bacteriophage [5,6]. In contrast, ATP-dependent DNA ligases (EC 6.5.1.1) are characteristic of eukaryotic and archaeal cells but are also found encoded by certain eukaryotic viruses, bacteriophage and eubacteria [7]. The mechanism of DNA ligation is similar for both types of enzyme [1]. In the first step, attack on the α-phosphorus of either NAD+ or ATP by the enzyme results in formation of an enzyme-adenylate intermediate (AMP is covalently linked to a lysine residue) and release of either NMP or pyrophosphate. In the second step, the AMP moiety is transferred to the 5' end of the nicked DNA strand to form a DNA-adenylate complex.
Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence  [PDF]
Joke J. F. A. van Vugt, Martijn de Jager, Magdalena Murawska, Alexander Brehm, John van Noort, Colin Logie
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006345
Abstract: Background Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. Methodology/Principal Findings We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. Conclusions/Significance Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.
ATP-dependent chromatin remodeling in the DNA-damage response
Hannes Lans, Jurgen A Marteijn, Wim Vermeulen
Epigenetics & Chromatin , 2012, DOI: 10.1186/1756-8935-5-4
Abstract: All living organisms depend on faithful preservation and transmission of genetic information to the next generation. Genetic information is stored within DNA, which is embedded in a dynamic nucleoprotein complex, called chromatin. The integrity of DNA is inescapably and continuously threatened by spontaneous and induced alterations to its basic structure. DNA itself is unstable and undergoes hydrolysis, which creates abasic sites and causes deamination [1]. Furthermore, cellular metabolic processes such as oxidative respiration produce oxygen radicals and other reactive molecules, which damage DNA [2]. Finally, exposure to environmental sources such as solar UV irradiation, × radiation, and numerous chemicals induces DNA injuries.DNA damage interferes with vital processes such as transcription and replication, which may cause cells to die or senesce, thus contributing to aging [3]. Replication of damaged DNA templates severely affects the fidelity of the polymerases, and may result in permanent mutations or chromosomal aberrations, which are at the basis of malignant transformation. Genetic erosion and its consequences are neutralized by a variety of DNA repair and associated DNA-damage signaling pathways, collectively called the DNA-damage response (DDR) [3-6]. In this review, we will focus on three repair pathways which are among the best characterized with regard to their repair mechanisms and interactions with chromatin: nucleotide excision repair (NER), which removes helix-distorting intra-strand lesions, and homologous recombination (HR) and non-homologous end-joining (NHEJ), both of which repair double-strand breaks (DSBs).All DNA-associated processes, such as transcription, replication, recombination, and DNA repair, are for a large part regulated by the chromatin structure [7,8]. Because this nucleoprotein complex limits the ability of other proteins to interact with DNA, the chromatin structure needs to be modified to facilitate efficient access to DNA. In
ATP-Dependent Chromatin Remodeling by Cockayne Syndrome Protein B and NAP1-Like Histone Chaperones Is Required for Efficient Transcription-Coupled DNA Repair  [PDF]
Iltaeg Cho equal contributor,Pei-Fang Tsai equal contributor,Robert J. Lake,Asjad Basheer,Hua-Ying Fan
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003407
Abstract: The Cockayne syndrome complementation group B (CSB) protein is essential for transcription-coupled DNA repair, and mutations in CSB are associated with Cockayne syndrome—a devastating disease with complex clinical features, including the appearance of premature aging, sun sensitivity, and numerous neurological and developmental defects. CSB belongs to the SWI2/SNF2 ATP–dependent chromatin remodeler family, but the extent to which CSB remodels chromatin and whether this activity is utilized in DNA repair is unknown. Here, we show that CSB repositions nucleosomes in an ATP–dependent manner in vitro and that this activity is greatly enhanced by the NAP1-like histone chaperones, which we identify as new CSB–binding partners. By mapping functional domains and analyzing CSB derivatives, we demonstrate that chromatin remodeling by the combined activities of CSB and the NAP1-like chaperones is required for efficient transcription-coupled DNA repair. Moreover, we show that chromatin remodeling and repair protein recruitment mediated by CSB are separable activities. The collaboration that we observed between CSB and the NAP1-like histone chaperones adds a new dimension to our understanding of the ways in which ATP–dependent chromatin remodelers and histone chaperones can regulate chromatin structure. Taken together, the results of this study offer new insights into the functions of chromatin remodeling by CSB in transcription-coupled DNA repair as well as the underlying mechanisms of Cockayne syndrome.
CLONING AND CHARACTERIZATION OF THE GENE(ahr) ENCODING ATP-DEPENDENT DNA HELICASE REP FROM VIBRIO ALGINOLYTICUS STRAIN HY9901
溶藻弧菌HY9901 ahr基因克隆与序列分析

CAI Shuang-Hu,WU Zao-He,JIAN Ji-Chang,LU Yi-Shan,
蔡双虎
,吴灶和,简纪常,鲁义善

水生生物学报 , 2008,
Abstract: A 1.2 kb internal fragment of the ATP-dependent DNA helicase rep gene from Vibrio alginolyticus strain HY9901 was amplified by PCR with designed primers and the unknown flanking sequences of 5'-and 3'-ends of the ahr gene were characterized by using inverse PCR and nested PCR. Sequence analysis showed the ahr gene contained a 2016 bp ORF encoding 671 amino acids. Compared with uther relevant vibrios,the deduced amino acid sequence of the ATP-dependent DNA helicase rep precursor from Vibrio alginolyticus strain HY9901 possesses very high similarity with them.
Enzymes involved in DNA ligation and end-healing in the radioresistant bacterium Deinococcus radiodurans
Melanie Blasius, Rebecca Buob, Igor V Shevelev, Ulrich Hubscher
BMC Molecular Biology , 2007, DOI: 10.1186/1471-2199-8-69
Abstract: In this report, we describe the cloning and expression of a Deinococcus radiodurans DNA ligase in Escherichia coli. This enzyme efficiently catalyses DNA ligation in the presence of Mn(II) and NAD+ as cofactors and lysine 128 was found to be essential for its activity. We have also analysed a predicted second DNA ligase from Deinococcus radiodurans that is part of a putative DNA repair operon and shows sequence similarity to known ATP-dependent DNA ligases. We show that this enzyme possesses an adenylyltransferase activity using ATP, but is not functional as a DNA ligase by itself. Furthermore, we identified a 5'-polynucleotide kinase similar to human polynucleotide kinase that probably prepares DNA termini for subsequent ligation.Deinococcus radiodurans contains a standard bacterial DNA ligase that uses NAD+ as a cofactor. Its enzymatic properties are similar to E. coli DNA ligase except for its preference for Mn(II) as a metal cofactor. The function of a putative second DNA ligase remains unclear, but its adenylyltransferase activity classifies it as a member of the nucleotidyltransferase family. Characterization of another protein from the same operon revealed a 5'-polynucleotide kinase with a possible role in DNA strand-break repair.Deinococcus radiodurans (D. radiodurans) exhibits an extraordinary resistance to ionizing radiation. Ionizing radiation generates a variety of DNA damages, including many types of base damages as well as single-strand and double-strand breaks, the latter being the most lethal damage for a living cell. D. radiodurans can survive irradiation up to 5,000 Gy without measurable loss of viability, and it seems likely that this resistance is based on mechanisms that ensure limited DNA and protein degradation and provide an efficient and accurate DNA strand-break repair [1]. High intracellular levels of Mn(II) protect proteins and allow fast repair of damaged DNA after irradiation [2,3]. Prokaryotes can repair double-strand breaks by homolog
Inactivating UBE2M Impacts the DNA Damage Response and Genome Integrity Involving Multiple Cullin Ligases  [PDF]
Scott Cukras, Nicholas Morffy, Takbum Ohn, Younghoon Kee
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0101844
Abstract: Protein neddylation is involved in a wide variety of cellular processes. Here we show that the DNA damage response is perturbed in cells inactivated with an E2 Nedd8 conjugating enzyme UBE2M, measured by RAD51 foci formation kinetics and cell based DNA repair assays. UBE2M knockdown increases DNA breakages and cellular sensitivity to DNA damaging agents, further suggesting heightened genomic instability and defective DNA repair activity. Investigating the downstream Cullin targets of UBE2M revealed that silencing of Cullin 1, 2, and 4 ligases incurred significant DNA damage. In particular, UBE2M knockdown, or defective neddylation of Cullin 2, leads to a blockade in the G1 to S progression and is associated with delayed S-phase dependent DNA damage response. Cullin 4 inactivation leads to an aberrantly high DNA damage response that is associated with increased DNA breakages and sensitivity of cells to DNA damaging agents, suggesting a DNA repair defect is associated. siRNA interrogation of key Cullin substrates show that CDT1, p21, and Claspin are involved in elevated DNA damage in the UBE2M knockdown cells. Therefore, UBE2M is required to maintain genome integrity by activating multiple Cullin ligases throughout the cell cycle.
Footprint traversal by ATP-dependent chromatin remodeler motor  [PDF]
Ashok Garai,Jesrael Mani,Debashish Chowdhury
Quantitative Biology , 2011, DOI: 10.1103/PhysRevE.85.041902
Abstract: ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require accessibility of specific segments of DNA which are packaged as chromatin. The basic unit of chromatin is a nucleosome where 146 bp $\sim$ 50 nm of a double stranded DNA (dsDNA) is wrapped around a spool formed by histone proteins. The helical path of histone-DNA contact on a nucleosome is also called "footprint". We investigate the mechanism of footprint traversal by a CRE that translocates along the dsDNA. Our two-state model of a CRE captures effectively two distinct chemical (or conformational) states in the mechano-chemical cycle of each ATP-dependent CRE. We calculate the mean time of traversal. Our predictions on the ATP-dependence of the mean traversal time can be tested by carrying out {\it in-vitro} experiments on mono-nucleosomes.
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