φ29 Family of phages

Microbiology and Molecular Biology Reviews

Volumn 65, Issue 2, 2001, Pages 261-287

  Meijer, W J J ^a   Horcajadas, J A ^a   Salas, M ^a  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; DNA POLYMERASE; HYDROLASE; PEPTIDOGLYCAN; PROTEIN P16; PHAGE PHI29 PROTEIN P6; VIRUS DNA; VIRUS PROTEIN; VIRUS RNA;

BACTERIAL GENE; BACTERIOPHAGE; CARBOXY TERMINAL SEQUENCE; DNA PACKAGING; GENE CASSETTE; GENE REPLICATION; GENE SEQUENCE; NONHUMAN; OPEN READING FRAME; OPERON; PROMOTER REGION; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN SYNTHESIS; REVIEW; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; ARTICLE; BACILLUS; BACILLUS PHAGE; CHEMISTRY; DNA REPLICATION; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; VIROLOGY;

BACTERIA (MICROORGANISMS); BACTERIOPHAGE PHI29; UNIDENTIFIED BACTERIOPHAGE;

AMINO ACID SEQUENCE; BACILLUS; BACILLUS PHAGES; BASE SEQUENCE; DNA REPLICATION; DNA, VIRAL; MOLECULAR SEQUENCE DATA; RNA, VIRAL; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 0034973586     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.65.2.261-287.2001     Document Type: Review

References (229)

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2. Phage φ29 protein p6 is in a monomer-dimer equilibrium that shifts to higher association states at the millimolar concentrations found in vivo
3. Identification of residues within two regions involved in self-association of viral histone-like protein p6 from phage φ29
4. Tailed bacteriophages: The order Caudovirales
5. Role of RNA in bacteriophage φ29 DNA packaging
6. Structure of Bacillus subtilis bacteriophage φ29 and the length of φ29 deoxyribonucleic acid
7. Analysis of bacteriophage φ29 gene function: Protein synthesis in suppressor-sensitive mutant infection of Bacillus subtilis
8. Analysis of gene function in Bacillus subtilis bacteriophage φ29
9. Morphogenesis of bacteriophage φ29
10. Protease-sensitive transfection of Bacillus subtilis with bacteriophage GA-1 DNA: A probable case of heterologous transfection
11. Purification, crystallization and initial X-ray analysis of the head-tail connector of bacteriophage φ29
12. Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging
13. Characterization of the dual start motif of a class II holin gene
14. In vitro transcription of bacteriophage φ29 DNA: Inhibition of early promoters by the viral replication protein p6
15. Characterization of a new prokaryotic transcriptional activator and its DNA recognition site
16. In vivo transcription of bacteriophage φ29 DNA: Transcription initiation sites
17. In vivo transcription of bacteriophage φ29 DNA: Transcription termination
18. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
19. Nucleotide sequence of the right early region of Bacillus phage φ15 and comparison with related phages: Reorganization of gene 17 during evolution
20. A conserved 3′-5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases
21. The highly conserved amino acid sequence Tyr-Gly-Asp-Thr-Asp-Ser in α-like DNA polymerases is required by phage φ29 DNA polymerase for protein-primed initiation and polymerization
22. Morphogenesis of bacteriophage φ29 of Bacillus subtilis: Oriented and quantized in vitro packaging of DNA protein gp3
23. In vitro assembly of the Bacillus subtilis bacteriophage φ29
24. DNA-independent deoxynucleotidylation of the φ29 terminal protein by the φ29 DNA polymerase
25. Highly efficient DNA synthesis by the phage φ29 DNA polymerase. Symmetrical mode of DNA replication
26. Replication of phage φ29 DNA in vitro: Role of the viral protein p6 in initiation and elongation
27. Terminal protein-primed DNA amplification
28. + ions on φ29 DNA-protein p3 replication: Formation of a complex between the terminal protein and the DNA polymerase
29. Characterization and purification of a phage φ29-encoded DNA polymerase required for the initiation of replication
30. Replication of phage φ29 DNA with purified terminal protein and DNA polymerase: Synthesis of full length DNA
31. Bacteriophage φ29 DNA polymerase
32. Relating structure to function in φ29 DNA polymerase
33. Structural and functional analysis of temperature-sensitive mutants of the phage φ29 DNA polymerase
34. 390 are affected in dNTP binding
35. 2SLYP is critical for synthetic activities
36. 3NSxYG" is involved in template-primer binding and dNTP selection
37. Primer-terminus stabilization at the φ29 DNA polymerase active site: Mutational analysis of conserved motif KxY
38. A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type φ29 DNA polymerase
39. The isolation and morphology of some new bacteriophages specific for Bacillus and Acetobacter species
40. Compartmentalization of phage φ29 DNA replication: Interaction between the primer terminal protein and the membrane-associated protein p1
41. Initiation of bacteriophage φ29 DNA replication in vivo: Assembly of a membrane-associated multiprotein complex
42. Polymerization of bacteriophage φ29 replication protein p1 into protofilament sheets
43. In vitro replication of bacteriophage PRD1 DNA. Characterization of the protein-primed initiation site
44. Assembly of Bacillus subtilis phage φ29. I. Mutants in the cistrons coding for the structural proteins
45. Order of assembly of the lower collar and the tail proteins of Bacillus subtilis bacteriophage φ29
46. A-RNA polymerase-dependent promoters
47. Pleiotropic effect of protein p6 on the viral cycle of bacteriophage φ29
48. Replication slippage of different DNA polymerases is inversely related to their strand displacement efficiency
49. Three-dimensional reconstruction of the connector of bacteriophage φ29 at 1.8 nm resolution
50. Bacillus subtilis phage φ29; characterization of gene products and functions
51. A precursor of the neck appendage protein of B. subtilis phage φ29
52. Structural localization of the proteins of the head to tail connecting region of bacteriophage φ29
53. Bacteriophage connectors: Structural features of a DNA translocating motor
54. Structure of the head-tail connector of bacteriophage φ29
55. 2+-induced conformational change of packaging RNA for procapsid recognition and binding during phage φ29 DNA encapsidation
56. Sequential action of six virus-encoded DNA-packaging RNAs during phage φ29 genomic DNA translocation
57. Sequence requirements for hand-in hand interaction in formation of RNA dimers and hexamers to gear φ29 DNA translocation motor
58. The organization of replication and transcription
59. Bacteriophage φ29 early protein p17 is conditionally required for the first rounds of viral DNA replication
60. Structure -function analysis of 3′→5′-exonuclease of DNA polymerases
61. 122, a single-stranded DNA ligand for 3′-5′ exonucleolysis, is required to interact with the terminal protein
62. Processive proofreading and the spatial relationship between polymerase and exonuclease active sites of bacteriophage φ29 DNA polymerase
63. An invariant lysine residue is involved in catalysis at the 3′-5′ exonuclease active site of eukaryotic-type DNA polymerases
64. Primer-terminus stabilization at the 3′-5′ exonuclease active site of φ29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases
65. Mutational analysis of φ29 DNA polymerase residues acting as ssDNA ligands for 3′-5′ exonucleolysis
66. Characterization of an RNA-binding domain in the bacteriophage φ29 connector
67. Role of the amino-terminal domain of bacteriophage φ29 connector in DNA binding and packaging
68. An aspartic acid residue in TPR-1, a specific region of protein -priming DNA polymerases, is required for the functional interaction with primer terminal protein
69. Functional interactions between a phage histone-like protein and a transcriptional factor in regulation of φ29 early-late transcriptional switch
70. Replication of recombinant φ29 DNA molecules in Bacillus subtilis protoplasts
71. In vitro evolution of terminal protein-containing genomes
72. Fidelity of φ29 DNA polymerase. Comparison between protein-primed initiation and DNA polymerization
73. 3′→5′ exonuclease active site of φ29 DNA polymerase. Evidence favoring a metal ion-assisted reaction mechanism
74. Taxonomy, classification and nomenclature of viruses
75. Role of the DNA/membrane complex in prokaryotic DNA replication
76. Plasmid replication and partition in Escherichia coli: Is the cell membrane the key?
77. A new protein domain for binding to DNA through the minor groove
78. Activation of replication origins in φ29-related phages requires the recognition of initiation proteins to specific nucleoprotein complexes
79. Assembly of the tail protein of the Bacillus subtilis phage φ29
80. Template requirements for initiation of phage φ29 DNA replication in vitro
81. The bacteriophage φ29 DNA polymerase, a proofreading enzyme
82. Site-directed mutagenesis in the DNA linking site of bacteriophage φ29 terminal protein: Isolation and characterization of a Ser232Thr mutant
83. Nucleotide sequence of Bacillus phage φ29 genes 14 and 15: Homology of gene 15 with other phage lysozymes
84. The complete sequence of the Bacillus phage φ29 right early region
85. Structural and functional comparative study of the complexes formed by viral φ29, Nf and GA-1 SSB proteins with DNA
86. Differential functional behavior of viral φ29, Nf, and GA-1 SSB proteins
87. Specific recognition of parental terminal protein by DNA polymerase for initiation of protein-primed DNA replication
88. Molecular function of the dual-start motif in the λ S holin
89. RNA dependence of the bacteriophage φ29 DNA packaging ATPase
90. The bacteriophage φ29 packaging proteins supercoil the DNA ends
91. Zur struktur von bakteriophagen aus enzym-produzierenden Bacillus kulturen
92. Crystallographic analysis reveals the 12-fold symmetry of the bacteriophage φ29 connector particles
93. Characterization of the small RNA of the bacteriophage φ29 DNA packaging machine
94. A small viral RNA is required for in vitro packaging of bacteriophage φ29 DNA
95. Regulation of the phage φ29 prohead shape and size by the portal vertex
96. A defined system for in vitro packaging of DNA-gp3 of the Bacillus subtilis bacteriophage φ29
97. Initiation events in in vitro packaging of bacteriophage φ29 DNA-p3
98. Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage φ29
99. Inter-RNA interaction of phage φ29 pRNA to form a hexameric complex for viral DNA transportation
100. Assembly of phage φ29 genome with viral protein p6 into a compact complex
101. Mechanism of stimulation of DNA replication by bacteriophage φ29 single-stranded DNA-binding protein p5
102. Analysis of replicative intermediates produced during bacteriophage φ29 DNA replication in vitro
103. Cloning and template activity of the origins of replication of phage φ29 DNA
104. Signals in the φ29 DNA-terminal protein template for the initiation of phage φ29 DNA replication
105. Analysis of gene function of bacteriophage φ29 of Bacillus subtilis: Identification of cistrons essential for viral assembly
106. A -dependent promoter sequences: Evidence for extended contact between RNA polymerase and upstream promoter DNA
107. Symmetry mismatch and DNA packaging in large bacteriophages
108. Bacteriophage DNA packaging: RNA gears in a DNA transport machine
109. Location of the serine residue involved in the linkage between the terminal protein and the DNA of φ29
110. In vitro synthesis of late bacteriophage φ29 RNA
111. G
112. Topology of the components of the DNA packaging machinery in the phage φ29 prohead
113. DNA base composition, susceptibility to bacteriophages, and interspecific transformation as criteria for classification in the genus Bacillus
114. Functional characterization of the genes coding for the terminal protein and DNA polymerase from bacteriophage GA-1. Evidence for a sliding-back mechanism during protein-primed GA-1 DNA replication
115. 82 are recognition elements of the replication origins
116. The RGD sequence in phage φ29 terminal protein is required for interaction with φ29 DNA polymerase
117. The structure of replicating DNA molecules of Bacillus subtilis phage φ29
118. DNA replication in bacteriophage φ29: The requirement of a viral-specific product for association of φ29 DNA with the cell membrane of Bacillus amyloliquefaciens
119. The structural basis of nuclear function
120. Assembly of Bacillus subtilis phage φ29.2. Mutants in the cistrons coding for the non-structural proteins
121. Function and structure relationships in DNA polymerases
122. Transcription of the genome of bacteriophage φ29: Isolation and mapping of the major early mRNA synthesized in vivo and in vitro
123. Constitutive function of a positively regulated promoter reveals new sequences essential for activity
124. Dissociation of the protein primer and DNA polymerase after initiation of adenovirus DNA replication
125. A precursor terminal protein -trinucleotide intermediate during initiation of adenovirus DNA replication: Regeneration of molecular ends in vitro by a jumping back mechanism
126. The orderly, in vitro emergence of DNA from bacteriophage φ29 particles
127. The minus 35 recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at the "extended minus 10" promoters
128. Localization of bacterial DNA polymerase: Evidence for a factory model of replication
129. The attachment of the bacterial chromosome to the membrane
130. Phage taxonomy and classification
131. In vitro initiation of pneumococcal phage Cp-1 DNA replication occurs at the third 3′ nucleotide of the linear template: A stepwise sliding-back mechanism
132. Characterization of the phage φ29 protein p5 as a single-stranded DNA binding protein. Function in φ29 DNA-protein p3 replication
133. Dynamic relocalization of phage φ29 DNA during replication and the role of the viral protein p16.7
134. Characterization of the bacteriophage φ29-encoded protein p16.7: A membrane protein involved in phage DNA replication
135. In vitro transcription of bacteriophage φ29 DNA. Correlation between in vitro and in vivo promoters
136. In vivo transcription of bacteriophage φ29 DNA early and late promoter sequences
137. Genetic analysis of bacteriophage φ29 of Bacillus subtilis: Integration and mapping of reference mutants of two collections
138. The protein covalently linked to the 5′ termini of the DNA of Bacillus subtilis phage φ29 is involved in the initiation of DNA replication
139. Transcription activation by phage φ29 protein p4 is mediated by interaction with the α subunit of Bacillus subtilis RNA polymerase
140. Substitution of the C-terminal domain of the Escherichia coli RNA polymerase α subunit by that from Bacillus subtilis makes the enzyme responsive to a Bacillus subtilis transcriptional activator
141. Transcriptional activator of phage φ29 late promoter: Mapping of residues involved in interaction with RNA polymerase and in DNA bending
142. Residues of the Bacillus subtilis phage φ29 transcriptional activator required both to interact with RNA polymerase and to activate transcription
143. Initiation of φ29 DNA replication occurs at the second 3′ nucleotide of the linear template: A sliding-back mechanism for protein-primed DNA replication
144. 2GR
145. Protein-primed DNA replication: A transition between two modes of priming by a unique DNA polymerase
146. Transcription activation or repression by phage φ29 protein p4 depends on the strength of the RNA polymerase-promoter interactions
147. Transcription regulation in Bacillus subtilis phage φ29: Expression of the viral promoters throughout the infection cycle
148. Activation and repression of transcription at two different phage φ29 promoters are mediated by interaction of the same residues of regulatory protein p4 with RNA polymerase
149. Protein p4 represses phage φ29 A2c promoter by interacting with the α subunit of Bacillus subtilis RNA polymerase
150. Nucleotide sequence that signal the initiation of transcription and translation in Bacillus subtilis
151. Suppressor-sensitive mutants and genetic map of Bacillus subtilis bacteriophage φ29
152. The bacteriophage φ29 head-tail connector imaged at high resolution with the atomic force microscope in buffer solution
153. Morphogenesis of bacteriophage φ29 of Bacillus subtilis: Preliminary isolation and characterization of intermediate particles of the assembly pathway
154. Organization of DNA into foci during replication
155. Phage φ29 regulatory protein p4 stabilizes the binding of the RNA polymerase to the late promoter in a process involving direct protein-protein contacts
156. Bacteriophage Nf DNA region controlling late transcription: Structural and functional homology with bacteriophage φ29
157. DNA-protein complex in circular DNA from phage φ29
158. Deletions at the N-terminus of bacteriophage φ29 protein p6: DNA binding and activity in φ 29 DNA replication
159. Nucleotide sequence of the right early region of Bacillus subtilis phage PZA completes the 19366-bp sequence of PZA genome. Comparison with the homologous sequence of phage φ29
160. Overproduction and purification of protein p6 of Bacillus subtilis phage φ29: Role in the initiation of DNA replication
161. Bacteriophage B103: Complete DNA sequence of its genome and relationship to other Bacillus phages
162. Molecular phylogeny of φ29-like phages and their evolutionary relatedness to other protein-primed replicating phages and other phages hosted by Gram-positive bacteria
163. Transcription initiation at the Escherichia coli galactose operon promoters in the absence of the normal -35 region
164. Characterization, overproduction and purification of the product of gene 1 of Bacillus subtilis phage φ29
165. Interaction of the bacteriophage φ29 protein p6 with double-stranded DNA
166. Head-neck connecting protein in phage φ29
167. Morphogenesis of bacteriophage φ29 of Bacillus subtilis: Mapping and functional analysis of the head fiber gene
168. Transcription activation and repression by interaction of a regulator with the α subunit of RNA polymerase: The model of phage φ29 protein p4
169. A DNA curvature can substitute phage φ29 regulatory protein p4 when acting as a transcriptional repressor
170. Bend induced by phage φ29 transcriptional activator in the viral late promoter is required for activation
171. Cloning and purification of a unique lysozyme produced by Bacillus phage φ29
172. Families of proteins forming transmembrane channels
173. Protein-priming of DNA replication
174. Bacillus phage φ29
175. Mechanism of initiation of linear DNA replication in prokaryotes
176. Characterization of a protein covalently linked to the 5′ termini of the DNA of Bacillus subtilis phage φ29
177. Terminal protein priming of DNA replication: Bacteriophage φ29 as a model system
178. Mechanisms for priming DNA synthesis
179. Replication and transcription of bacteriophage φ29
180. Head fibers of bacteriophage φ29
181. A novel kinetic analysis to calculate nucleotide affinity of proofreading DNA polymerases. Application to φ29 DNA polymerase fidelity mutants
182. Role of the first aspartate residue of the "YxDTDS" motif of φ29 DNA polymerase as a metal ligand during both TP-primed and DNA-primed DNA synthesis
183. The putative coiled coil domain of the φ29 terminal protein is a major determinant involved in recognition of the origin of replication
184. Phage φ29 protein p6: A viral histone-like protein
185. Superhelical path of the DNA in the nucleoprotein complex that activates the initiation of phage φ29 DNA replication
186. Signals at the bacteriophage φ29 DNA replication origins required for protein p6 binding and activity
187. A novel nucleoprotein complex at a replication origin
188. Characterization of Bacillus subtilis bacteriophage. II. Isolation and morphology of phage Nf and properties of its DNA
189. The role of the host cell membrane in the replication and morphogenesis of bacteriophages
190. Structure of the bacteriophage φ29 DNA packaging motor
191. Site-directed mutagenesis at the Exo III motif of φ29 DNA polymerase: Overlapping structural domains for the 3′-5′' exonuclease and strand-displacement activities
192. Complex formation between phage φ29 single-stranded DNA binding protein and DNA
193. Helix-destabilizing activity of φ29 single-stranded DNA binding protein: Effect on the elongation rate during strand displacement DNA replication
194. RNA polymerase binding sites and transcription map of the DNA of Bacillus subtilis phage φ29
195. The missing link in phage lysis of Gram-positive bacteria: Gene 14 of Bacillus subtilis phage φ29 encodes the functional homolog of lambda S protein
196. Gene 1, one of the dna genes of bacteriophage φ29, represses other dna genes through binding to mRNA
197. Inhibition of protein synthesis from DNA replication genes by the product of gene 1, a dna gene of Bacillus subtilis phage φ29
198. Assembly of a tailed bacterial virus and its genome release studied in three dimensions
199. Dual translational start motif evolutionary conserved in the holin gene of Bacillus subtilis phage φ29
200. Morphogenesis of bacteriophage φ29 of Bacillus subtilis: Cleavage and assembly of the neck appendage protein
201. Probing the structure of monomers and dimers of the bacterial virus φ29 hexamer RNA complex by chemical modification
202. Complete inhibition of virion assembly in vivo with mutant pRNA essential for phage φ29 DNA packaging
203. Role of the "YxGG/A" motif of φ29 DNA polymerase in protein-primed replication
204. Analysis of φ29 DNA polymerase by partial proteolysis: Binding of terminal protein in the double-stranded DNA channel
205. A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases
206. φ29 DNA polymerase requires the N-terminal domain to bind terminal protein and DNA primer substrates
207. Supercoiled DNA wraps around the bacteriophage φ29 head-tail connector
208. Domain architecture of the bacteriophage φ29 connector protein
209. The three-dimensional structure of a DNA translocating machine at 10 Å resolution
210. Structure of viral connectors and their function in bacteriophage assembly and DNA packaging
211. RNA-mediated specificity of DNA packaging into hybrid preheads
212. Adsorption of bacteriophage φ29 to Bacillus subtilis through the neck appendages of the viral particle
213. Nucleotide sequence of the late region of Bacillus phage φ29 completes the 19285-bp sequence of φ29. Comparison with the homologous sequence of phage PZA
214. The -16 region of Bacillus subtilis and other gram-positive bacterial promoters
215. HOLINS: The protein clocks of bacteriophage infections
216. Modulation of in vivo and in vitro transcription of bacteriophage φ29 early genes
217. Comparative studies on the small Bacillus bacteriophages
218. Nucleotide sequences at the termini of φ29 DNA
219. Nucleotide sequence analysis of DNA replication origins of the small bacteriophages: Evolutionary relationships
220. Terminal proteins and short inverted terminal repeats of the small Bacillus bacteriophage genomes
221. Nucleotide sequence of the major early region of bacteriophage φ29
222. Phages will out: Strategies of host cell lysis
223. Bacteriophage lysis: Mechanism and regulation
224. Holins: Form and function in bacteriophage lysis
225. Functional domains in the bacteriophage φ29 terminal protein for interaction with the φ29 DNA polymerase and with DNA
226. Function of hexameric RNA in packaging of bacteriophage φ29 DNA in vitro