Julius B. Lucks/Bibliography/Sanger-JMolBiol-1982

Notes on [1]

• many cases translation terminators and initiators overlap
  • ATGA, TGA terminates, ATG initiates
    • hypothesis: translational coupling - ribosome can initiate at the start site after termination more efficiently than a free ribosome
• in the whole left arm, CTA (minor leucine tRNA) is absent
  • 'Possibly, at the late stages of infection CUA becomes a limiting codon so that the structural proteins can be synthesized at the expense of other proteins of the bacteriophage or host that contains CUA codons. Such a situation could be achieved if the CUA tRNA was inactivated by one of the late proteins of lambda and it would be interesting to know if this is indeed the case. In this connection, Yudelevich (1971) [2] has shown that a different leucine tRNA, which recognizes the codon CUG, is split into two fragments by an enzyme produced by bacteriophage T4 when it infects the cell.'
  • The distribution of other rare codons in genes of the left arm suggest that they may have a controlling function on the relative amounts of proteins produced.
• good discussion of the 'shotgun' sequencing technique - very thorough
  • sonication to produce random DNA fragments - making clones with the fragments - screening the clones for desired sequence region, and then sequencing those clones
  • sonication better than restriction enzyme digests because the latter are too specific to give a desired number of useful clones
• initial data acquisition very fast, but started to get redundancy - turned to more directed sequencing once about 90% done
• target specific sequences by using hybridization probes to select clones from a random mixture
• analyzed codon frequencies in genes by tabulating frequencies
  • It appears that the distribution of codons differs in the different transcription units of lambda.
  • mentions GC-rich left arm and AT-rich right arm
• mentions left arm proteins made in very different amounts, but from same transcript
  • the varying yeild of proteins is probably due to differences in translation
    • mentions codon usage of rare tRNAs - proteins produced in smaller amounts have more rare codons
• detailed discussion of Shine-Dalgarno sequences for each ORF

Bibliography

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1. Notes