Protein coding palindromes in Rickettsia:
A unique mechanism to create novel protein sequences
Ogata H. (1), Monchois V. (1), Audic S.(1), Coutard B. (1),
Byrne D. (1), Fournier P.-E. (2), Renesto P. (2), Raoult D. (2),
Abergel C. (1), Claverie J.-M. (1);
(1) Information Genetique &
Structurale, CNRS UMR1889, Marseille, France.
(2) Unite des Rickettsies, Universite de la Mediterranee,
CNRS UMR6020, IFR48, Marseille, France.
Mobile palindromic sequences are usually confined in the intergenic
regions of bacterial genomes. However, Rickettsia appears to be a unique
exception in this respect. In the genome of R. conorii, we identified 3
families of palindromic sequences (RPE-1, 2 and 3) exhibiting a high
frequency of insertions into ORFs [1]. Most of these altered ORFs
correspond to proteins with essential functions in other microbes.
Predicted locations of the RPEs are always compatible with the protein
3-D fold and function. RT-PCR experiments have demonstrated the
retention of the RPE nucleotide sequences within the transcript for
3 genes. Using in vivo E. coli expression, we verified that the RPE
sequences in 4 R. conorii ORFs are indeed translated, and retained
in the final proteins [2]. Furthermore the enzymatic activity was
confirmed for one ORF (guanylate kinase) harboring the RPE peptides
at its N-terminus. The RPE encoded peptide retained in Rickettsia
proteins is thus probably a compact domain. The insertion of the RPEs
appears random in respect of the ORFs functions, and of the coding
versus non-coding regions. Several RPEs were found even in RNA coding genes.
The sequence of RPEs evolves faster than other regions of the genes.
Thus the RPEs appear to represent a previously unknown class of
mobile elements that recurrently supplies new coding sequences in Rickettsia.
Characterization of 3-D structures of the RPE-containing proteins as
well as the accumulation of more bacterial genome sequences must lead
to better appreciation of the significance of this phenomenon
in the origin and evolution of proteins.
[1] Ogata et al.: Science, 290, 347-350, 2000;
Science, 291, 252-253, 2001; Science, 293,
2093-2098, 2001; 2002 (submitted).
[2] Monchois et al.: 2002 (submitted).
Molecular Evolution - Evolution, Genomics, Bioinformatics
Jointly organized by ISME and SMBE
(June 13-16, 2002, Sorrento - Naples - Italy)