Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Combined Automated Annotation using Multiple IEA Methods
Bend induced by the phage phi 29 transcriptional activator in the viral late promoter is required for activation.
-
p4 binds the A3 promoter between -50 and -100 relative to the transcription start site, at an intrinsically curved inverted-repeat site whose curvature it increases, and the bend is required for activation.
"Protein p4 binds to a region of the A3 promoter, located between nucleotides -50 and -100 relative to the transcription start site, that presents a sequence-directed curvature."
Bacillus subtilis phage phi29. Characterization of gene products and functions.
-
The 1976 screen identified a single cistron required for final lysis of the infected bacteria, whose mutants lyse late but yield a normal or larger burst when lysed artificially - the phenotype of a holin null, and one that a late-transcription mutant cannot have.
"A cistron, probably involved in the final lysis of the infected bacteria, has been found."
-
The same paper's other mutant class, the six genes that fail to synthesise phage DNA, does not include gene 4; those rows were distributed correctly across genes 1, 2, 3, 6 and 17.
"Mutants in six genes do not synthesize phage DNA."
Activation and repression of transcription at two different phage phi29 promoters are mediated by interaction of the same residues of regulatory protein p4 with RNA polymerase.
-
One p4 surface, the domain containing Arg120, both activates A3 and represses A2c through contact with RNA polymerase; which outcome occurs depends on where p4 sits relative to the enzyme at each promoter.
"Therefore, the contact between protein p4 and RNAP through the protein p4 domain containing Arg120 can activate or repress transcription, depending on the promoter."
-
Activation of A3 works by stabilising RNA polymerase at the promoter as a closed complex, that is, at the initiation step.
"Activation involves stabilization of RNA polymerase (RNAP) at the A3 promoter as a closed complex and is mediated by interaction between RNAP and a small domain of protein p4 in which residue Arg120 plays an essential role."
Protein p4 represses phage phi 29 A2c promoter by interacting with the alpha subunit of Bacillus subtilis RNA polymerase.
-
Repression of A2c is at promoter clearance, not at polymerase binding or initiation: the polymerase binds and forms an initiated complex but never reaches elongation.
"Regulatory protein p4 from Bacillus subtilis phage phi 29 represses the strong viral A2c promoter (PA2c) by preventing promoter clearance; it allows RNA polymerase to bind to the promoter and form an initiated complex, but the elongation step is not reached."
-
The p4 partner is the C-terminal domain of the polymerase alpha subunit: p4 forms a complex with purified wild-type alpha but not with alpha lacking its last 15 residues.
"Protein p4 could form a complex at PA2c with purified wild-type alpha subunit, but not with a deletion mutant lacking the 15 C-terminal residues."
Mechanism for the switch of phi29 DNA early to late transcription by regulatory protein p4 and histone-like protein p6.
-
A gene-4 nonsense mutant fails at the switch in vivo: early transcription from A2b and A2c keeps rising through infection and A3 transcripts are almost undetectable.
"In bacteria harbouring a nonsense mutant in gene 4, transcription from promoters A2b and A2c increases steadily during infection while the transcripts arising from promoter A3 are almost undetectable"
-
A3 cannot be used by the host polymerase unaided, lacking a -35 element, whereas A2b and A2c are bound directly.
"RNAP binds to promoters A2c and A2b, but not to promoter A3 that lacks a"
-
At A2b the p4-p6 complex displaces RNA polymerase from the promoter, removing the polymerase footprint.
"Concomitantly, the RNAP-derived hypersensitive band at promoter A2b disappeared (band at"
The phi29 transcriptional regulator contacts the nucleoid protein p6 to organize a repression complex.
-
p4 and p6 bind cooperatively over the approximately 200 bp interval between A3 and A2c, and stable assembly of that complex requires a contact between p6 and the p4 C-terminus, so p4 defines the phase and boundaries of the p6 filament.
"We show that stable assembly of this complex requires interaction between protein p6 and the C-terminus of protein p4."
The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA.
-
p4 is a homodimer with a unique alpha/beta fold whose N-terminal beta-turn N-hooks enter the major groove and make base-specific contacts, reaching two major-groove areas three helical turns apart across a strongly curved 41 bp A3-site DNA.
"The two N-hooks enter the major groove of the double helix, establishing base-specific contacts."
-
The lysis proteins are made in the late phase, alongside the structural and morphogenesis proteins, so they lie downstream of the promoter p4 activates.
"The synthesis of DNA replication proteins and p4 takes place in the early phase, while structural, morphogenesis, and lysis proteins are synthesized in the late phase."
Molecular interactions and protein-induced DNA hairpin in the transcriptional control of bacteriophage ø29 DNA.
-
phi29 transcription is carried out entirely by the host Bacillus subtilis sigma-A RNA polymerase; the phage contributes regulators, not polymerase or sigma subunits.
"Phage Ø29 gene expression is directed by the Bacillus subtilis σA-RNAP"
-
The late genes, which include the morphogenesis and cell lysis genes, are expressed from a single promoter, A3.
"Genes coding for structural proteins and for proteins involved in morphogenesis and cell lysis, centered in the genome, are coded in the complementary DNA strand and are transcribed at later times of infection."
-
Suppressor-sensitive mutants in early genes 4 and 6 have impaired transcription in a non-suppressor host.
"suppressor-sensitive mutants in early genes 4 and 6 have impaired transcription when they infect a non-suppressor host"
The missing link in phage lysis of gram-positive bacteria: gene 14 of Bacillus subtilis phage phi 29 encodes the functional homolog of lambda S protein.
-
The phi29 gene product required for efficient lysis of Bacillus subtilis is gp14, which behaves as a holin: expressed alone in E. coli it kills without lysing, and expressed together with a murein hydrolase it lyses.
"Phage phi 29 gene 14, the product of which is required for efficient lysis of Bacillus subtilis, was cloned in Escherichia coli."
Nucleotide sequence of Bacillus phage phi 29 genes 14 and 15: homology of gene 15 with other phage lysozymes.
-
The suppressor-sensitive allele in the phi29 lysis gene region is sus14(1241), in gene 14; gene 15 was characterised by sequence and encodes a lysozyme homologous to the P22 and T4 enzymes.
"The g14 open reading frame (ORF) was confirmed by sequencing a sus14(1241) mutant."
Dual translational start motif evolutionarily conserved in the holin gene of Bacillus subtilis phage phi 29.
-
Gene 14 encodes the phi29 holin function and gene 15, downstream of it, the lysozyme; gene 14 uses a dual translational start giving a holin and an inhibitory longer species.
"The 131-codon gene 14 of Bacillus subtilis phage phi 29 encodes the holin function, whereas the downstream gene 15 codes for a lysozyme."