ABSTRACT
Herbivorous insects use detoxification enzymes, including cytochrome P450 monooxygenases, glutathione S-transferases, and carboxy/cholinesterases, to metabolize otherwise deleterious plant secondary metabolites. Whereas Acyrthosiphon pisum (pea aphid) feeds almost exclusively from the Fabaceae, Myzus persicae (green peach aphid) feeds from hundreds of species in more than forty plant families. Therefore, M. persicae as a species would be exposed to a greater diversity of plant secondary metabolites than A. pisum, and has been predicted to require a larger complement of detoxification enzymes. A comparison of M. persicae cDNA and A. pisum genomic sequences is partially consistent with this hypothesis. There is evidence of at least 40% more cytochrome P450 genes in M. persicae than in A. pisum. In contrast, no major differences were found between the two species in the numbers of glutathione S-transferases, and carboxy/cholinesterases. However, given the incomplete M. persicae cDNA data set, the number of identified detoxification genes in this species is likely to be an underestimate.
Subject(s)
Aphids/enzymology , Aphids/genetics , Genome, Insect , Amino Acid Sequence , Animals , Base Sequence , Biotransformation/genetics , Carboxylic Ester Hydrolases/genetics , Carboxylic Ester Hydrolases/metabolism , Cholinesterases/genetics , Cholinesterases/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , DNA Primers/genetics , DNA, Complementary/genetics , Evolution, Molecular , Expressed Sequence Tags , Glutathione Transferase/genetics , Glutathione Transferase/metabolism , Insect Proteins/genetics , Insect Proteins/metabolism , Molecular Sequence Data , Pisum sativum/metabolism , Pisum sativum/parasitology , Phylogeny , Prunus/metabolism , Prunus/parasitology , Sequence Homology, Amino Acid , Species SpecificityABSTRACT
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E. coli, we have observed a direct relationship between cumulative signal phase and reading frame. Based on this observation, we have developed a model that indicates how likely it is for the ribosome to stay in frame throughout the process of elongation. We validate this model by analyzing verified coding sequences in E. coli.
Subject(s)
Escherichia coli Proteins/physiology , Open Reading Frames , Peptide Termination Factors/physiology , RNA, Ribosomal, 16S/chemistry , Ribosomes/physiology , Algorithms , Codon , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Frameshift Mutation , Models, Genetic , Models, Statistical , Models, Theoretical , Nucleic Acid Hybridization , Peptide Termination Factors/metabolism , RNA, Messenger/metabolism , Ribosomes/genetics , Signal Processing, Computer-Assisted , SoftwareABSTRACT
The 16s ribosomal tail end has been conjectured to play an important role in the regulation of protein production and of translation efficiency. Using E. coli K-12 as our model organism, we generate sequences of 13 base pairs as hypothetical ribosome tail ends. We analyzed the distributions of these random hypothetical ribosome tail ends and found the actual E. coli ribosome tail end to be significantly different from a randomly generated ribosome tail in the magnitude of the lock and synchronization signals, and the signal to noise ratio. We then designed and ran a genetic algorithm to optimize hypothetical ribosome tail ends simultaneously for these three signal criteria. We found that the actual E. coli ribosome tail end was among the best by these measures.
