Related papers: Genes Preferring Non-AUG Start Codons in Bacteria
Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae.…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
The tendencies described in this work were revealed in the course of examination of adenine and uracil distribution in the mRNA encoding sequence. The study also discusses the usage of codons occupied by the amino acid arginine in the table…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic…
While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many…
The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of…
The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivate E. coli dihydrofolate reductase…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
The previously formulated model for the evolution of the genetic code was shown to clarify why base triplets of some precursor amino acids differ by a single base from product amino acid codons, while others show less homology. First, the…
This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Statistical analysis of bacteria genomes texts has been performed on the basis of 20 complete genomes origin from Genebank. It has been revealed that the word ranked distributions are quite well approximated by logarithmic law. Results…