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  Topic: The Canonical Genetic Code, Resources & arguments< Next Oldest | Next Newest >  

Posts: 36
Joined: May 2002

(Permalink) Posted: May 25 2002,12:35   

Quote (theyeti @ May 23 2002,16:32)
Awhile back I had a discussion about the DI's wacko response to the PBS evolution series here.  Scroll down a few messages.  There are some links to some good recent papers in that thread.  The references are:

Trends in Biochemical Sciences 2001, 26:591-596

Proc Natl Acad Sci U S A 1995 Mar 92:2441-5

J. Biol. Chem., Vol. 276, Issue 10, 6881-6884, March 9, 2001

Annu. Rev. Biochem. 2000. 69:617-650.


Let me add some links to the references

Proc. Natl. Acad. Sci. USA, Vol. 97, Issue 15, 8392-8396, July 18, 2000 Interpreting the universal phylogenetic tree, Carl R. Woese

This article was referenced by others, a few quotes


Archaeal Phylogeny Based on Ribosomal Proteins
Oriane Matte-Tailliez , Céline Brochier , Patrick Forterre and Hervé Philippe

Until recently, phylogenetic analyses of Archaea have mainly been based on ribosomal RNA (rRNA) sequence comparisons, leading to the distinction of the two major archaeal phyla: the Euryarchaeota and the Crenarchaeota. Here, thanks to the recent sequencing of several archaeal genomes, we have constructed a phylogeny based on the fusion of the sequences of the 53 ribosomal proteins present in most of the archaeal species. This phylogeny was remarkably congruent with the rRNA phylogeny, suggesting that both reflected the actual phylogeny of the domain Archaea even if some nodes remained unresolved. In both cases, the branches leading to hyperthermophilic species were short, suggesting that the evolutionary rate of their genes has been slowed down by structural constraints related to environmental adaptation. In addition, to estimate the impact of lateral gene transfer (LGT) on our tree reconstruction, we used a new method that revealed that 8 genes out of the 53 ribosomal proteins used in our study were likely affected by LGT. This strongly suggested that a core of 45 nontransferred ribosomal protein genes existed in Archaea that can be tentatively used to infer the phylogeny of this domain. Interestingly, the tree obtained using only the eight ribosomal proteins likely affected by LGT was not very different from the consensus tree, indicating that LGT mainly brought random phylogenetic noise. The major difference involves organisms living in similar environments, suggesting that LGTs are mainly directed by the physical proximity of the organisms rather than by their phylogenetic proximity

Proc. Natl. Acad. Sci. USA, Vol. 98, Issue 3, 805-808, January 30, 2001 The universal nature of biochemistry  Norman R. Pace

Next reference

Lluís Ribas de Pouplana, Paul Schimmel, Aminoacyl-tRNA synthetases: potential markers of genetic code development, Trends in Biochemical Sciences 26 (10) (2001) pp. 591-596.

Operational RNA code for amino acids in relation to genetic code in evolution.  Ribas de Pouplana, L ... Schimmel P
J Biol Chem 2001 Mar 9;276(10):6881-4.

Some links to research

AMINOACYL-TRNA SYNTHESIS  Annu. Rev. Biochem. 2000 , Vol. 69: 617-650.


Aminoacyl-tRNAs are substrates for translation and are pivotal in determining how the genetic code is interpreted as amino acids. The function of aminoacyl-tRNA synthesis is to precisely match amino acids with tRNAs containing the corresponding anticodon. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an aminoacyl-tRNA synthetase, although intrinsic proofreading and extrinsic editing are also essential in several cases. Recent studies of aminoacyl-tRNA synthesis, mainly prompted by the advent of whole genome sequencing and the availability of a vast body of structural data, have led to an expanded and more detailed picture of how aminoacyl-tRNAs are synthesized. This article reviews current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis.

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