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Microbiology and Molecular Biology Reviews, March 2003, p. 86-156, Vol. 67, No. 1
1092-2172/03/$08.00+0     DOI: 10.1128/MMBR.67.1.86-156.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Bacteriophage T4 Genome{dagger}

Eric S. Miller,1* Elizabeth Kutter,2 Gisela Mosig,3,{ddagger} Fumio Arisaka,4 Takashi Kunisawa,5 and Wolfgang Rüger6

Department of Microbiology, North Carolina State University, Raleigh, North Carolina 27695-7615,1 The Evergreen State College, Olympia, Washington 98505,2 Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232,3 Department of Molecular and Cellular Assembly, Tokyo Institute of Technology, Yokohama 226-8501,4 Department of Applied Biological Sciences, Science University of Tokyo, Noda 278-8510, Japan,5 Faculty for Biology, Ruhr-University-Bochum, 44780 Bochum, Germany6

Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth.

* Mailing address: Department of Microbiology, North Carolina State University, Raleigh, NC 27696-7615. Phone: (919) 515-7922. Fax: (919) 515-7867. E-mail: eric_miller{at}ncsu.edu.

{dagger} Dedicated to the memory of Gisela Mosig, our friend, colleague, and mentor.

{ddagger} Deceased.

Microbiology and Molecular Biology Reviews, March 2003, p. 86-156, Vol. 67, No. 1
1092-2172/03/$08.00+0     DOI: 10.1128/MMBR.67.1.86-156.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



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