DNA replication of single-stranded Escherichia coli DNA phages

Baas, Pieter

doi:10.1016/0167-4781(85)90096-x

Cited by 84 publications

(38 citation statements)

References 136 publications

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“…Moriya et al have shown that PdG is an effective block to replication when incorporated into singlestranded vectors (8). Incorporation of adducts that are strong blocks to replication into the (Ϫ)-strand of M13MB102 could lead to an apparent shift in template utilization because of the consecutive rather than bidirectional mechanism of strand replication employed by M13 genomes (29). Once the lesion is bypassed during the initial stage of DNA replication, the (ϩ)-strand released can be rapidly copied to a duplex.…”

Section: Discussionmentioning

confidence: 99%

Repair of Propanodeoxyguanosine by Nucleotide Excision Repair in Vivo and in Vitro

Johnson

Fink

Marnett

1997

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 99%

Repair of Propanodeoxyguanosine by Nucleotide Excision Repair in Vivo and in Vitro

Johnson

Fink

Marnett

1997

Journal of Biological Chemistry

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“…The gene V protein stabilizes singlestranded DNA (ssDNA) during phage replication, and shifts the synthesis of phage DNA from double-stranded form to single-stranded form, in the. later stage of phage infection, by preventing the synthesis of the complementary DNA strand (14,18,19,(23)(24)(25)..The gene V protein also binds selectively to the 5' operator sequence of the gene II mRNA of phage fl and represses the translation of the gene II protein (26-29). The gene V protein binds to ssDNA with high affinity and cooperatively (19,30,31).…”

mentioning

confidence: 99%

Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry.

Cheng

Harms²,

Goudreau³

et al. 1996

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

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The binding stoichiometry of gene V protein from bacteriophage ft to several oligonucleotides was studied using electrospray ionization-mass spectrometry (ESI-MS). Using mild mass spectrometer interface conditions that preserve noncovalent associations in solution, gene V protein was observed as dimer ions from a 10 mM NH4OAc solution.Addition of oligonucleotides resulted in formation of proteinoligonucleotide complexes with stoichiometry of approximately four nucleotides (nt) per protein monomer. A 16-mer oligonucleotide gave predominantly a 4:1 (protein monomer: oligonucleotide) complex while oligonucleotides shorter than 15 nt showed stoichiometries of 2:1. Stoichiometries and relative binding constants for a mixture of oligonucleotides were readily measured using mass spectrometry. The binding stoichiometry of the protein with the 16-mer oligonucleotide was measured independently using size-exclusion chromatography and the results were consistent with the mass spectrometric data. These results demonstrate, for the first time, the observation and stoichiometric measurement of proteinoligonucleotide complexes using ESI-MS. The sensitivity and high resolution of ESI-MS should make it a useful tool in the study of protein-DNA interactions.Protein-DNA interactions are involved in many cellular processes and thus are fundamentally important for the functioning of biological systems. The stoichiometry of binding is an important characteristic of protein-DNA interactions. Determination of binding stoichiometries can be difficult when there are mixed stoichiometries present in a sample or when molecular mass (Mr) differences between possible alternative stoichiometries are small (1). Mass spectrometry (MS) is the most accurate method for Mr measurement, and thus is potentially useful for accurate determination of protein-DNA binding stoichiometry. However, the application of MS to the direct characterization of protein-DNA complexes has been precluded due to the difficulty of transferring these complexes intact from solution into the mass spectrometer using conventional ionization methods. Electrospray ionization (ESI) allows ionization of non-volatile samples from solution and the development of this technique has greatly expanded the application of mass spectrometry in the analysis of biomolecules (2-5). Recently, a number of groups have reported observations of specific noncovalent complexes of biomolecules from solution using ESI-MS (6-11). These reports prompted us to investigate the application of this technique to intact protein-DNA noncovalent complexes.We chose gene V protein from bacteriophage fl for our study due to its well characterized structure (12-16) and the extensive studies on the DNA binding stoichiometry and cooperatively (17)(18)(19)(20)(21)(22). The gene V protein stabilizes singlestranded DNA (ssDNA) during phage replication, and shifts the synthesis of phage DNA from double-stranded form to single-stranded form, in the. later stage of phage infection, by preventing the synthesis of th...

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“…Gene V protein coats the single-stranded DNA (ssDNA) intermediate in bacteriophage fl DNA replication, forming an ordered superhelical protein-DNA complex (1,(5)(6)(7)(8). This protein-DNA complex facilitates packaging of the ssDNA into new phage particles.…”

mentioning

confidence: 99%

Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.

Skinner

Zhang

Leschnitzer

et al. 1994

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

105

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The crystal structure of the dimeric gene V protein of bacteriophage fl was determined using multiwavelength anomalous diffraction on the selenomethioninecontaining wild-type and isoleucine-47 methionine mutant proteins with x-ray diffraction data phased to 2.5 A resolution.The structure of the wild-type protein has been refined to an R factor of 19.2% using native data to 1.8 A resolution. The structure of the gene V protein was used to obtain a model for the protein portion of the gene V protein-single-stranded DNA complex.Gene V protein of bacteriophage fltt is a member of a class of proteins involved in DNA replication that bind to singlestranded nucleic acids with high affinity and cooperativity but little sequence specificity (1-4). Gene V protein coats the single-stranded DNA (ssDNA) intermediate in bacteriophage fl DNA replication, forming an ordered superhelical protein-DNA complex (1,(5)(6)(7)(8). This protein-DNA complex facilitates packaging of the ssDNA into new phage particles. Gene V protein also binds with some specificity to a translational operator sequence on phage fl gene II mRNA (9-12).The gene V protein provides a general model for proteinssDNA interactions that are strong, yet not sequencespecific. Gene V protein binding to single-stranded nucleic acids and to oligonucleotides has been studied using chemical modification, spectroscopic techniques, and mutagenesis (13-24). The structure of the protein-ssDNA complex has been studied using electron microscopy and solution scattering methods and is found to consist of a regular left-handed superhelix in which the gene V protein dimers are arrayed on the outside of the superhelix and the ssDNA strands are inside (8,25). The structure of the gene V protein is also of interest because its small size and the large number of mutants available have made it a useful model for determining effects ofamino acid substitutions on protein stability and function (23,26,27).A model for the crystal structure of the wild-type (WT) gene V protein has been reported (28), but recent NMR studies have demonstrated that the positions of amino acids involved in the segments of antiparallel (-structure are not compatible with those in the model (21), and a new determination of the structure was necessary. The multiwavelength anomalous diffraction (MAD) technique (29) was ideally suited for this purpose, as the WT gene V protein contains two methionine residues (Met-1 and Met-77) that might be substituted in vivo in Escherichia coli by selenomethionine. Here we report the determination of the gene V protein structure using the MAD technique, the refinement of the structure using x-ray diffraction data on the WT gene V proteinAt and a model for protein-protein contacts in the gene V protein-ssDNA superhelical complex. MATERIALS AND METHODSModeling of the Protein Portion of Gene V Protein-ssDNA Complex. The gene V protein dimer was placed with its internal two-fold axis of symmetry perpendicular to the axis of the superhelix to be generated and Phe-73 pointing ei...

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DNA replication of single-stranded Escherichia coli DNA phages

Cited by 84 publications

References 136 publications

Repair of Propanodeoxyguanosine by Nucleotide Excision Repair in Vivo and in Vitro

Repair of Propanodeoxyguanosine by Nucleotide Excision Repair in Vivo and in Vitro

Direct measurement of oligonucleotide binding stoichiometry of gene V protein by mass spectrometry.

Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.

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