Bacteriophage T4 Gene Expression

National Institute Of Diabetes And Digestive And Kidney Diseases

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Abstract

A lytic phage has a limited window of time to enter the host, replicate its DNA, generate phage bodies, package genomes within phage heads, and lyse the cell. Consequently, phage gene expression requires maximum efficiency. Because of this, phage models, such as that of bacteriophage T4, have provided excellent models systems for understanding mechanisms of transcription regulation. For T4, a temporal pattern of expression generates three classes of T4 transcripts: early, middle, and late. Transcription control begins immediately after infection of the host Escherichia coli when a protein present within the phage head (Alt) is injected into the host along with the phage DNA. Alt ADP-ribosylates specific residues within host RNA polymerase (RNAP), and this chemical modification provides an advantage for T4 early promoters over host promoters. For middle transcription T4 uses two phage-encoded factors (MotA and AsiA) to reconfigure the primary specificity subunit of RNAP, sigma70, generating a remodeled sigma that is specific for T4 middle promoters. T4 DNA is modified by a glucosylated, hydroxymethyl moiety on each cytosine base, and MotA binds much more tightly to this modified DNA than to the host unmodified DNA. This difference in affinity ensures that MotA cannot be soaked up by pieces of the partially digested host DNA as T4 nucleases destroy the host chromosome. In addition, the multiple strong contacts between AsiA and sigma70-RNAP and among MotA, sigma70, and a DNA sequence present in the middle promoters (MotA box) generate a robust transcription complex, specific for the T4 template. In late transcription, T4 replaces sigma70 with 2 phage proteins (Gp55 and Gp33), which constitute a sigma that is specific for the late promoters. RNAP containing this new sigma works with the late activator, Gp45. Interestingly, Gp45 is also the sliding clamp of the DNA replication complex that is needed to clamp DNA polymerase to its template as DNA polymerase moves along the DNA. The additional connection of Gp45 with RNA polymerase generates a highly processive late transcription complex that slides 1-dimenionally along the DNA, a mechanism that is much more efficient than a 3-dimensional promoter search. Gp45 also ties the expression of late genes encoding morphological proteins to the amount of replicated DNA, ensuring cost-effective use of resources. An overview of the entire process reveals that T4 succeeds by simply maximizing the bacterial system of using alternative sigma factors for RNAP under different conditions. In middle transcription AsiA and MotA together with sigma70 create a chimera sigma with a different upstream sequence preference. In late transcription, Gp55 and Gp33 create a new sigma, with a new consensus sequence. Thus, T4 represents a paradigm for this process, and the lessons from T4 should be remembered as the transcriptional takeover mechanisms of as yet uncharacterized phage are investigated in the future. Our lab has spent many years using genetics, biochemistry, and structural analyses to elucidate the protein-protein and protein-DNA contacts involved in the middle transcription complex. To summarize this work, we have written an extensive review that was recently published.