A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes

Science ◽  
2021 ◽  
Vol 372 (6541) ◽  
pp. 516-520
Author(s):  
Dona Sleiman ◽  
Pierre Simon Garcia ◽  
Marion Lagune ◽  
Jerome Loc’h ◽  
Ahmed Haouz ◽  
...  
Keyword(s):  
Molecular Biology ◽  
Dna Polymerase ◽  
Building Block ◽  
Biosynthetic Pathway ◽  
Viral Dna ◽  
Phage Dna ◽  
Close Relationship ◽  
Purine Pathway

Cells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme condensing aspartate and inosylate in the adenine pathway. PurZ condenses aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2′-deoxyadenylate), which undergoes defumarylation and phosphorylation to give dZTP (2-amino-2′-deoxyadenosine-5′-triphosphate), a substrate for the phage DNA polymerase. Crystallography and phylogenetics analyses indicate a close relationship between phage PurZ and archaeal PurA enzymes. Our work elucidates the biocatalytic innovation that remodeled a DNA building block beyond canonical molecular biology.

scholarly journals Histone H3 Lysine 4 Methylation Marks Postreplicative Human Cytomegalovirus Chromatin

2012 ◽  
Vol 86 (18) ◽  
pp. 9817-9827 ◽  
Author(s):  
Alexandra Nitzsche ◽  
Charlotte Steinhäußer ◽  
Katrin Mücke ◽  
Christina Paulus ◽  
Michael Nevels
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Histone Modification ◽  
Dna Polymerase ◽  
Human Cytomegalovirus ◽  
Viral Genome ◽  
Histone H3 ◽  
Viral Dna ◽  
The Impact ◽  
Preferential Incorporation

In the nuclei of permissive cells, human cytomegalovirus genomes form nucleosomal structures initially resembling heterochromatin but gradually switching to a euchromatin-like state. This switch is characterized by a decrease in histone H3 K9 methylation and a marked increase in H3 tail acetylation and H3 K4 methylation across the viral genome. We used ganciclovir and a mutant virus encoding a reversibly destabilized DNA polymerase to examine the impact of DNA replication on histone modification dynamics at the viral chromatin. The changes in H3 tail acetylation and H3 K9 methylation proceeded in a DNA replication-independent fashion. In contrast, the increase in H3 K4 methylation proved to depend widely on viral DNA synthesis. Consistently, labeling of nascent DNA using “click chemistry” revealed preferential incorporation of methylated H3 K4 into viral (but not cellular) chromatin during or following DNA replication. This study demonstrates largely selective epigenetic tagging of postreplicative human cytomegalovirus chromatin.

scholarly journals Deep-sea vent phage DNA polymerase specifically initiates DNA synthesis in the absence of primers

2017 ◽  
Vol 114 (12) ◽  
pp. E2310-E2318 ◽  
Author(s):  
Bin Zhu ◽  
Longfei Wang ◽  
Hitoshi Mitsunobu ◽  
Xueling Lu ◽  
Alfredo J. Hernandez ◽  
...  
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerase ◽  
Deep Sea ◽  
Phage Dna

scholarly journals Detection and partial genetic characterisation of novel avi- and siadenoviruses in racing and fancy pigeons (Columba livia domestica)

2016 ◽  
Vol 64 (4) ◽  
pp. 514-528 ◽  
Author(s):  
Mónika Z. Ballmann ◽  
Balázs Harrach
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Polymerase ◽  
Nested Pcr ◽  
Columba Livia ◽  
Hexon Gene ◽  
Polymerase Gene ◽  
Viral Dna ◽  
Phylogeny Analysis ◽  
Pcr Targeting

Up to now, only a single adenovirus (AdV) isolate seemingly specific for pigeons, hence named pigeon AdV-1 (PiAdV-1), has been characterised at DNA sequence level. In the present work, the prevalence and diversity of AdVs occurring in domestic pigeon were examined by a survey performed on randomly collected samples using a very efficient, consensus nested PCR targeting the viral DNA polymerase gene. The newly detected viruses were characterised by sequencing and phylogeny analysis. Amplification of additional genome fragments was attempted by the use of several other PCR methods aiming at the hexon gene. During a 4-year survey, samples from dead or live, healthy pigeons originating from 27 lofts were examined in Hungary. Almost 50% of the samples (48 out of 97) proved to be positive for AdV. Sequence analysis revealed the presence of four hitherto unknown pigeon AdV types. PiAdV-1 was also identified in one sample. Two novel viruses named PiAdV-2 and -3 were found to belong to the genus Aviadenovirus, and two other novel types (PiAdV-4 and -5) to the genus Siadenovirus. This is the first report on the occurrence of siadenoviruses in birds belonging to the order Columbiformes. Approximately two-thirds of the PiAdV-2 genome was sequenced and analysed.

scholarly journals The Phage φ29 Membrane Protein p16.7, Involved in DNA Replication, Is Required for Efficient Ejection of the Viral Genome

2007 ◽  
Vol 189 (15) ◽  
pp. 5542-5549 ◽  
Author(s):  
Martín Alcorlo ◽  
Víctor González-Huici ◽  
José M. Hermoso ◽  
Wilfried J. J. Meijer ◽  
Margarita Salas
Keyword(s):  
Dna Replication ◽  
Membrane Protein ◽  
Second Step ◽  
Host Proteins ◽  
Viral Dna ◽  
Dna Ejection ◽  
Phage Dna ◽  
Ejection Mechanism ◽  
The Right

ABSTRACT It is becoming clear that in vivo phage DNA ejection is not a mere passive process. In most cases, both phage and host proteins seem to be involved in pulling at least part of the viral DNA inside the cell. The DNA ejection mechanism of Bacillus subtilis bacteriophage φ29 is a two-step process where the linear DNA penetrates the cell with a right-left polarity. In the first step ∼65% of the DNA is pushed into the cell. In the second step, the remaining DNA is actively pulled into the cytoplasm. This step requires protein p17, which is encoded by the right-side early operon that is ejected during the first push step. The membrane protein p16.7, also encoded by the right-side early operon, is known to play an important role in membrane-associated phage DNA replication. In this work we show that, in addition, p16.7 is required for efficient execution of the second pull step of DNA ejection.

scholarly journals UV- and MMS-induced mutagenesis of lambdaO(am)8 phage under nonpermissive conditions for phage DNA replication.

2003 ◽  
Vol 50 (4) ◽  
pp. 921-939 ◽  
Author(s):  
Joanna Krwawicz ◽  
Anna Czajkowska ◽  
Magdalena Felczak ◽  
Irena Pietrzykowska
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Excision Repair ◽  
Protein S ◽  
Dna Lesions ◽  
E Coli ◽  
Phage Dna ◽  
Induced Mutagenesis ◽  
C Proteins ◽  
Inducible Protein

Mutagenesis in Escherichia coli, a subject of many years of study is considered to be related to DNA replication. DNA lesions nonrepaired by the error-free nucleotide excision repair (NER), base excision repair (BER) and recombination repair (RR), stop replication at the fork. Reinitiation needs translesion synthesis (TLS) by DNA polymerase V (UmuC), which in the presence of accessory proteins, UmuD', RecA and ssDNA-binding protein (SSB), has an ability to bypass the lesion with high mutagenicity. This enables reinitiation and extension of DNA replication by DNA polymerase III (Pol III). We studied UV- and MMS-induced mutagenesis of lambdaO(am)8 phage in E. coli 594 sup+ host, unable to replicate the phage DNA, as a possible model for mutagenesis induced in nondividing cells (e.g. somatic cells). We show that in E. coli 594 sup+ cells UV- and MMS-induced mutagenesis of lambdaO(am)8 phage may occur. This mutagenic process requires both the UmuD' and C proteins, albeit a high level of UmuD' and low level of UmuC seem to be necessary and sufficient. We compared UV-induced mutagenesis of lambdaO(am)8 in nonpermissive (594 sup+) and permissive (C600 supE) conditions for phage DNA replication. It appeared that while the mutagenesis of lambdaO(am)8 in 594 sup+ requires the UmuD' and C proteins, which can not be replaced by other SOS-inducible protein(s), in C600 supE their functions may be replaced by other inducible protein(s), possibly DNA polymerase IV (DinB). Mutations induced under nonpermissive conditions for phage DNA replication are resistant to mismatch repair (MMR), while among those induced under permissive conditions, only about 40% are resistant.

scholarly journals Cycle Sequencing of Filamentous Phage DNA Using a Biotinylated Primer and ΔTaq DNA Polymerase

BioTechniques ◽  
1997 ◽  
Vol 23 (1) ◽  
pp. 125-127 ◽  
Author(s):  
Jianping Qiu ◽  
Huanying Zhou ◽  
Joseph F. Aceto ◽  
Thomas Kieber-Emmons
Keyword(s):  
Dna Polymerase ◽  
Filamentous Phage ◽  
Cycle Sequencing ◽  
Phage Dna

Micromethod for phosphonoformate inhibition assay of hepatitis B viral DNA polymerase.

1984 ◽  
Vol 30 (4) ◽  
pp. 549-552 ◽  
Author(s):  
H J Lin ◽  
P C Wu ◽  
C L Lai ◽  
W Chak
Keyword(s):  
Hepatitis B ◽  
Dna Polymerase ◽  
Specific Activity ◽  
Sample Volume ◽  
Inhibition Assay ◽  
Viral Dna ◽  
Good Discrimination ◽  
Human Dna ◽  
Nucleotide Incorporation ◽  
B Virus

Abstract A micromethod for the specific measurement of hepatitis B viral DNA polymerase in serum is presented, based on the phosphonoformate inhibition assay (J Med Virol 12: 61-70, 1983). In the micromethod, sample volume is reduced to 120 microL and the ultracentrifugation step is eliminated. The method allows good discrimination between serum infected with hepatitis B virus and uninfected serum. The cutoff value for rate of nucleotide incorporation, based on assays of 41 serum specimens negative for hepatitis B serological markers, was about 15 nU/L (90th percentile). Serum containing hepatitis B surface and antigens exhibited rates of phosphonoformate-inhibitive nucleotide incorporation of 150 (SD 150) nU/L, with an upper 90th percentile range of 17 to 667 nU/L (n = 41). The micromethod makes use of commercially available [32P]dCTP (specific activity about 7000 kCi/mol). 125I-labeled dCTP was found to be unsuitable for this assay. Human DNA polymerases in serum are detected by this method but are excluded from the phosphonoformate-inhibitive fraction.

In vitro reconstitution of the biosynthetic pathway of 3-hydroxypicolinic acid

2019 ◽  
Vol 17 (3) ◽  
pp. 454-460 ◽  
Author(s):  
Xuan Yun ◽  
Qian Zhang ◽  
Meinan Lv ◽  
Hai Deng ◽  
Zixin Deng ◽  
...  
Keyword(s):  
Natural Products ◽  
Building Block ◽  
Biosynthetic Pathway ◽  
In Vitro Reconstitution ◽  
Important Building Block

Four enzymes direct the biosynthesis of 3-hydroxypicolinic acid, an important building block of bacterial natural products.

scholarly journals YMDD motif in hepatitis B virus DNA polymerase influences on replication and lamivudine resistance: A study byin vitrofull-length viral DNA transfection

Hepatology ◽  
1999 ◽  
Vol 29 (3) ◽  
pp. 939-945 ◽  
Author(s):  
Suzane Kioko Ono-Nita ◽  
Naoya Kato ◽  
Yasushi Shiratori ◽  
Tsutomu Masaki ◽  
Keng-Hsin Lan ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Dna Polymerase ◽  
Dna Transfection ◽  
Lamivudine Resistance ◽  
Viral Dna ◽  
Hepatitis B Virus Dna ◽  
B Virus ◽  
Ymdd Motif
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