Synonymous codon preferences in bacteriophage T4: A distinctive use of transfer RNAs from T4 and from its host Escherichia coli

Kunisawa, Takashi

doi:10.1016/s0022-5193(05)80725-8

Cited by 43 publications

(27 citation statements)

References 19 publications

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“…In each case, the T4 tRNA recognizes a codon that is relatively minor in E. coli but more frequent in T4 genes. There is no positive correlation between the most abundant amino acids in the T4 proteome and the tRNAs encoded by the phage (591). E. coli-optimal codons are in fact used more frequently for T4 proteins present in large numbers per phage particle (such as in gp23, the major capsid protein), while T4-optimal codons, defined as those recognized by the phage tRNAs, are used more frequently for T4 proteins present in small numbers per phage particle (and probably in weakly expressed genes).…”

Section: Trnasmentioning

confidence: 97%

“…E. coli-optimal codons are in fact used more frequently for T4 proteins present in large numbers per phage particle (such as in gp23, the major capsid protein), while T4-optimal codons, defined as those recognized by the phage tRNAs, are used more frequently for T4 proteins present in small numbers per phage particle (and probably in weakly expressed genes). This may serve to enhance the expression of low-abundance T4 late proteins, whose products are required in larger amounts than the typical low-abundance E. coli protein (590)(591)(592).…”

Section: Trnasmentioning

confidence: 99%

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Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

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703

801

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SUMMARY 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.

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Section: Trnasmentioning

confidence: 97%

Section: Trnasmentioning

confidence: 99%

Bacteriophage T4 Genome

Miller

Kutter

Mosig

et al. 2003

Microbiol Mol Biol Rev

Self Cite

703

801

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“…Similarly, the frequency of AUA codon for Ile in phage genes is about three times as high as that in host genes. From these observations, we can hypothesize that phage tRNAs could serve to supplement host tRNAs present in minor amounts and thus enhance the efficiency of translation of phage genes (Kunisawa, 1992).…”

Section: Trna Usage and Synonymous Codon Usage Of T4mentioning

confidence: 95%

“…The latter idea was put forward following the discovery of phage-encoded tRNAs but this has not been verified. In 1992, the advantage of a phage having its own tRNAs was examined in the light of the synonymous codon-usage data of phage T4 and its host Escherichia coli; the phage tRNA species could serve to supplement the host's isoacceptor tRNA species that are present in minor cellular amounts and recognize those synonymous codons that are rare in the host genes but are frequent in the phage genes (Kunisawa, 1992). At that time, T4 presented a unique example in which complete data on phage-encoded tRNAs were available.…”

Section: Introductionmentioning

confidence: 99%

Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases

Kunisawa

2002

Data Sci. J.

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“…It is intriguing that this genome encodes many extra tRNAs, suggesting that they probably help translation of the host mRNAs or they may be involved in translation of the phage mRNAs (8). Comparative codon usage analysis of B. cereus strains (AH187 and ATCC 14597) and the phage showed different preferences in phenylalanine, asparagine, and serine, explaining a possible role for extra tRNAs in the phage genome.…”

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confidence: 99%

Complete Genome Sequence of Bacillus cereus Bacteriophage BCP78

Lee

Shin

Son

et al. 2012

J Virol

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Bacillus cereus is generally found in soil habitats, and it contaminates a wide variety of foods, causing food poisoning with symptoms such as vomiting and diarrhea. To develop a novel biocontrol agent to inhibit this pathogen, bacteriophage BCP78 belonging to the Siphoviridae family was isolated from a fermented food sample. Here we announce the complete genome sequence of BCP78, which may be useful for understanding its inhibition mechanism against B. cereus, and describe major findings from the genome annotation.

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Synonymous codon preferences in bacteriophage T4: A distinctive use of transfer RNAs from T4 and from its host Escherichia coli

Cited by 43 publications

References 19 publications

Bacteriophage T4 Genome

Bacteriophage T4 Genome

Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases

Complete Genome Sequence of Bacillus cereus Bacteriophage BCP78

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