Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

Hu, Wei; Wang, Chengkun; Ji, Liang; Zhang, Tianlong; Hu, Zhixing; Wang, Zhijun; Lan, Wenxian; Li, Fang; Wu, Houming; Ding, Jianping; Wu, Geng; Deng, Zixin; Cao, Chunyang

doi:10.1038/cr.2012.66

Cited by 39 publications

(63 citation statements)

References 16 publications

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“…The genes required for modification ( dndABCDE ; after DNA damage) and restriction ( dndFGH ) have been identified in several hundred bacterial and archaeal genomes (59). The structures and biochemical activities of the DndA (cysteine desulfurase), DndC (phosphoadenosine phosphosulfate reductase), and DndE (DNA-binding protein with a distinct fold) that are directly involved in phosphorothioation have been thoroughly characterized (26, 61, 178, 184). Additionally, it has been shown that DndB is a transcriptional regulator of the dnd operons (57), but the functions of the other genes associated with this system are less clear (177).…”

Section: Innate Immunitymentioning

confidence: 99%

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

283

235

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Evolution of bacteria and archaea involves an incessant arms race against an enormous diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most bacteria and archaea are dedicated to antiparasite defense. The functions of these defense systems follow several distinct strategies, including innate immunity; adaptive immunity; and dormancy induction, or programmed cell death. Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity. Some general principles of function and evolution of defense systems are starting to crystallize, in particular, extensive gain and loss of defense genes during the evolution of prokaryotes; formation of genomic defense islands; evolutionary connections between mobile genetic elements and defense, whereby genes of mobile elements are repeatedly recruited for defense functions; the partially selfish and addictive behavior of the defense systems; and coupling between immunity and dormancy induction/programmed cell death.

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Section: Innate Immunitymentioning

confidence: 99%

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Koonin

Makarova²,

Wolf³

2017

Annu. Rev. Microbiol.

283

235

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“…A DndD homolog in P. fluorescens , SpfD, has ATPase activity possibly related to DNA structure alteration or nicking during PT incorporation 18 . Finally, the DndE structure reveals a tetramer conformer and a possible nicked double strand DNA binding protein 19 .…”

Section: Introductionmentioning

confidence: 99%

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

et al. 2014

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Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. To better understand PT biology, we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: real-time (SMRT) sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 18% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT modification proteins and rule out known R-M mechanisms.

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“…DndC possesses ATP pyrophosphatase activity and shows significant homology to PAPS reductase family proteins (13,16). By comparison, DndD has ATPase activity that is possibly related to DNA nicking during sulfur incorporation, and structural analysis suggests that DndE binds to nicked double-stranded DNA (13,19,20). In some strains, a divergently transcribed cluster, dndFGH, occurs in the vicinity of the dndBCDE operon.…”

mentioning

confidence: 99%

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

Chen

Wang

Chen

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, 6m A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G PS 6m A) dinucleotides in the G PS 6m AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G PS A) motifs per genome, with 6m A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G PS 6m ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G PS ATC) and Dam methyltransferase from E. coli DH10B ( 6m A in G 6m ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed 6m A in all 2,058 G PS ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that 6m A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each.T he emergence of convergent technologies has led to a growing appreciation for the diversity of DNA modifications in microbial epigenetics and restriction-modification (R-M) systems (1-3). DNA methylation, the most extensively studied genetic modification, was originally discovered in bacteria in the context of R-M systems involving a methyltransferase (MTase) that modifies "self" DNA at specific target sites and a cognate restriction endonuclease (REase) that discriminates and destroys unmodified invading DNA (3-5). R-M systems are ubiquitous in prokaryotes and are classified into four types (I, II, III, and IV) based on their molecular structure, sequence recognition, cleavage position, and cofactor requirements (3, 6, 7). However, some MTases exist alone, without an apparent cognate REase partner. These so-called "orphan" MTases include DNA adenine methylase (Dam), which modifies the adenine N-6 in the GATC motif, DNA cytosine methylase (Dcm), which methylates C-5 of the second cytosine in CC(A/T) GG sequences, and cell cycle-regulated methylase (CcrM), which methylates the N-6 of adenine in GANTC (N = A, T, C, or G) (8). Despite the absence of cognate REases, orphan MTases still confer immunity against the virulence of a parasitic R-M complex with the same target sites (9). In addition to defense against bacteriophages and transposons, DNA m...

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Structural insights into DndE from Escherichia coli B7A involved in DNA phosphorothioation modification

Cited by 39 publications

References 16 publications

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes

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