Bacteriophage Mu genome sequence: Analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus

Journal of Molecular Biology

Volumn 317, Issue 3, 2002, Pages 337-359

  Morgan, Gregory J ^a   Hatfull, Graham F ^a   Casjens, Sherwood ^b   Hendrix, Roger W ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Bacteriophage evolution; Bacteriophage Mu; Comparative genome analysis; Genome sequence; Prophage

Indexed keywords

PROTEIN; PROTEINASE;

ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; BACTERIOPHAGE MU; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; DEINOCOCCACEAE; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENETIC SIMILARITY; GENOME ANALYSIS; GENOME SIZE; HAEMOPHILUS; HOST; MOLECULAR EVOLUTION; MOSAICISM; MULTIGENE FAMILY; NEISSERIA; NONHUMAN; PRIORITY JOURNAL; PROPHAGE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES COMPARISON;

BACTERIOPHAGE LAMBDA; DEINOCOCCUS; ENTEROBACTERIA PHAGE MU; HAEMOPHILUS; NEISSERIA;

EID: 0036299014     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2002.5437     Document Type: Article

References (144)

1. Bacteriophage-induced mutation in E. coli
2. Phage Mu: An overview
3. "Muprints" of the lac operon demonstrate physiological control over the randomness of in vivo transposition
4. Bacteriophage Mu-1: A tool to transpose and to localize bacterial genes
5. In vivo genetic engineering: The Mu mediated transposition of chromosomal DNA segments onto transmissible plasmids
6. Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements
7. Regulation of bacteriophage Mu transposition
8. Transposition of phage Mu DNA
9. Transpositional recombination: Mechanistic insights from studies of Mu and other elements
10. Studies on a "jumping gene machine": Higher-order nucleoprotein complexes in Mu DNA transposition
11. Structure of the bacteriophage Mu transposase core: A common structural motif for DNA transposition and retroviral integration
12. Heteroduplex structures of bacteriophage Mu DNA
13. Characterization of the inhomogeneous DNA in virions of bacteriophage Mu by DNA reannealing kinetics
14. Ends of bacteriophage mu DNA
15. The relationship of two invertible segments in bacteriophage Mu and Salmonella typhimurium DNA
16. Invertible DNA determines host specificity of bacteriophage Mu
17. Purification and characterization of the unusual deoxynucleoside, alpha- N-(9-beta-D-2′-deoxyribofuranosylpurin-6-yl)glycinamide, specified by the phage Mu modification function
18. + cells can be attributed to its ability to bind hemimethylated Pmom promoter DNA
19. Transcription activation by the bacteriophage Mu Mor protein: Analysis of promoter mutations in Pm identifies a new region required for promoter function
20. Regulation of the bacteriophage Mu gem operon
21. Rec dependence of Mu transposition from P22-transduced fragments
22. Construction of gene-targeting vectors: A rapid Mu in vitro DNA transposition-based strategy generating null, potentially hypomorphic, and conditional alleles
23. A chromosomal expression vector for Escherichia coli based on the bacteriophage Mu
24. An efficient DNA sequencing strategy based on the bacteriophage Mu in vitro DNA transposition reaction
25. Bacteriophage Mu as a genetic tool to study Erwinia amylovora pathogenicity and hypersensitive reaction on tobacco
26. The structure of the contractile sheath of bacteriophage Mu
27. Involvement of the invertible G segment in bacteriophage Mu tail fiber biosynthesis
28. Morphogenetic structures present in lysates of amber mutants of bacteriophage Mu
29. Structure of the mutator phage Mu-1 of Escherichia coli
30. Genetic analysis of diaminopimelic acid- and lysine-requiring mutants of Escherichia coli
31. Electron microscopic evidence for linear insertion of bacteriophage Mu-1 in lysogenic bacteria
32. Mu-1 bacteriophage DNA
33. Analysis of bacteriophage Mu and lambda-Mu hybrid DNAs by specific endonucleases
34. Comparative analysis of invertible DNA in phage genomes
35. Bacteriophage Mu Mor protein requires sigma 70 to activate the Mu middle promoter
36. Regulatory factors acting at the bacteriophage Mu middle promoter
37. Inversion of the G DNA segment of phage Mu controls phage infectivity
38. The mom gene of bacteriophage Mu: A unique regulatory scheme to control a lethal function
39. Translational stimulation: RNA sequence and structure requirements for binding of Com protein
40. Evolution of dsDNA tailed-bacteriophage genomes
41. Control mechanisms in dsDNA bacteriophage assembly
42. Phage evolution and speciation
43. Evolutionary relationships among diverse bacteriophages and prophages: All the world's a phage
44. The origins and ongoing evolution of viruses
45. Comparative genomics of lactococcal phages: Insight from the complete genome sequence of Lactococcus lactis phage BK5-T
46. Nucleotide sequence of bacteriophage lambda DNA
47. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7:Shiga toxin as a phage late-gene product
48. Sequence analysis of Stx2-converting phage VT2-Sa shows a great divergence in early regulation and replication regions
49. Isolation and characterization of APSE-1, a bacteriophage infecting the secondary endosymbiont of Acyrthosiphon pisum
50. Genomic sequence and analysis of the atypical temperate bacteriophage N15
51. Genomic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages
52. Sequence of the genome of Salmonella bacteriophage P22
53. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages
54. Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak
55. The complete genome sequence of Escherichia coli K-12
56. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
57. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12
58. DNA sequences of the tail fiber genes of bacteriophage P2: Evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages
59. The late-expressed region of the temperate coliphage 186 genome
60. The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: Implications for phage evolution and horizontal gene transfer via bacteriophages
61. The complete nucleotide sequence of bacteriophage HP1 DNA
62. Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain
63. Cloning and characterization of bacteriophage-like DNA from Haemophilus somnus homologous to phages P2 and HP1
64. Genome structure of mycobacteriophage D29: Implications for phage evolution
65. Genome organization and characterization of mycobacteriophage Bxb1
66. Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae
67. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491
68. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58
69. Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1
70. Genetic characterization of Mu-like bacteriophage D108
71. Vibrio cholerae conjugative plasmid pSJ15 contains transposable prophage dVcA1
72. Pseudomonas aeruginosa phages whose DNA structure is similar to the DNA structure of phage Mu 1. III. The isolation and analysis of the hybrid phages D3112 and B39: Localization of the immunity region and of certain genetic factors
73. Multiplicity of the integration sites of Mu-like bacteriophages into Pseudomonas aeruginosa chromosome and plasmids
74. Pseudomonas aeruginosa transposable bacteriophages D3112 and B3 require pili and surface growth for adsorption
75. Cryptic transposable phages of Pseudomonas aeruginosa
76. Differentiation between Campylobacter hyoilei and Campylobater coli using genotypic and phenotypic analyses
77. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
78. Cloning of a unique sequence specific to isolates of type B:2 Pasteurella multocida
79. Development of a PCR test based on a gene region associated with the pathogenicity of Pasteurella multocida serotype B:2, the causal agent of haemorrhagic septicaemia in Asia
80. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
81. The site-specific recombinase encoded by pinD in Shigella dysenteriae is due to the presence of a defective Mu prophage
82. DNA sequencing with chain-terminating inhibitors
83. GeneMark: Parallel gene recognition for both strands
84. The current status and portability of our sequence handling software
85. The 3′-terminal sequence of Escherichia coli: 16 S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites
86. Temperature-sensitive mutations in the bacteriophage Mu c repressor locate a 63-amino-acid DNA-binding domain
87. Frameshift mutations in the bacteriophage Mu repressor gene can confer a trans-dominant virulent phenotype to the phage
88. Phage lysozymes
89. Delineation of the virulence-related locus (vrl) of Dichelobacter nodosus
90. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
91. Shape and DNA packaging activity of bacteriophage SPP1 procapsid: Protein components and interactions during assembly
92. Bacteriophage HK97 head assembly: A protein ballet
93. Discovery of the tail tube gene of bacteriophage Mu and sequence analysis of the sheath and tube genes
94. Bacteriophage Mu head assembly
95. Structural polypeptides and products of late genes of bacteriophage Mu: Characterization and functional aspects
96. Bacteriophage Mu T mutants are defective in synthesis of the major head polypeptide
97. Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome
98. Some general questions about movable elements and their implications
99. The Mu gem operon: Its role in gene expression, recombination and cell cycle
100. The GemA protein of phage Mu and the GyrB gyrase subunit of Escherichia coli: The search for targets and interactions leading to the reversion of Mu-induced mutations
101. Replacement of the bacteriophage Mu strong gyrase site and effect on Mu DNA replication
102. A DNA gyrase-binding site at the center of the bacteriophage Mu genome is required for efficient replicative transposition
103. Isolation of conditional defective mutants of temperate phage Mu-1 and deletion mapping of the Mu-1 prophage
104. Polypeptides encoded by the early region of bacteriophage Mu synthesized in minicells of Escherichia coli
105. Prophage deletion mapping of bacteriophage Mu-1
106. Specific binding of Mu repressor to DNA
107. Sequence of the left end of Mu
108. Interactions between the repressor and the early operator region of bacteriophage Mu
109. The molecular cloning of the immunity region of phage Mu
110. A novel class of winged helix-turn-helix protein: The DNA-binding domain of Mu transposase
111. Characterization of the lysogenic repressor (c) gene of the Pseudomonas aeruginosa transposable bacteriophage D3112
112. Regulation and expression of the mom gene
113. The DNA modification function of temperate phage Mu-1
114. Com, the phage Mu mom translational activator, is a zinc-binding protein that binds specifically to its cognate mRNA
115. The zinc coordination site of the bacteriophage Mu translational activator protein, Com
116. Mu-like prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens
117. Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae
118. A programmed translational frameshift is required for the synthesis of a bacteriophage lambda tail assembly protein
119. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa consortium of the organization for nucleotide sequencing and analysis
120. Bacterial evolution
121. Site-specific recombination in bacteriophage Mu: Characterization of binding sites for the DNA invertase Gin
122. The DNA invertase Gin of phage Mu: Formation of a covalent complex with DNA via a phosphoserine at amino acid position 9
123. Shiga toxins even when different are encoded at identical positions in the genomes of related temperate bacteriophages
124. Isolation of Shigella sonnei lysogenic for a bacteriophage encoding gene for production of Shiga toxin
125. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
126. Structural analysis of phage-borne stx genes and their flanking sequences in Shiga toxin-producing Escherichia coli and Shigella dysenteriae type 1 strains
127. Spontaneous tandem amplification and deletion of the shiga toxin operon in Shigella dysenteriae 1
128. Arrangement and functional identification of genes in the regulatory region of lambdoid phage H-19B, a carrier of a Shiga-like toxin
129. Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain
130. The evolution of Mu
131. Selfish operons: Horizontal transfer may drive the evolution of gene clusters
132. Evolution of the lambdoid phages
133. Molecular genetics of bacteriophage P22
134. DNA inversion regions Min of plasmid p15B and Cin of bacteriophage P1: Evolution of bacteriophage tail fiber genes
135. Phase variation: Evolution of a controlling element
136. Conserved sequence patterns in phages Mu and lambda DNA
137. Mycobacteriophage TM4: Genome structure and gene expression
138. The complete genome sequence of the Streptomyces temperate phage φC31: Evolutionary relationships to other viruses
139. Improved strategy for large scale DNA sequencing using DNase I cleavage for generating random subclones
140. Comparison of left-end DNA sequences of bacteriophages Mu and D108
141. Characterization of the Pseudomonas aeruginosa transposable phage D3112 (corrected) left-end regulatory region