Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

doi:10.1186/1745-6150-1-28

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Baranov PV
Vestergaard B
Hamelryck T
Gesteland RF
Nyborg J
Atkins JF

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Hamelryck T
Gesteland RF
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Hypothesis

Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

Pavel V Baranov¹^,2 , Bente Vestergaard³^,4 , Thomas Hamelryck⁵ , Raymond F Gesteland¹ , Jens Nyborg³^{^} and John F Atkins¹^,2

¹Bioscience Institute, University College Cork, Cork, Ireland

²Department of Human Genetics, University of Utah, 15N 2030E, Salt Lake City, UT84112-5330, USA

³Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark

⁴Department of Medicinal Chemistry, Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark

⁵Bioinformatics center, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, Building 10, 2100 Copenhagen, Denmark

author email corresponding author email^Deceased

Biology Direct 2006, 1:28doi:10.1186/1745-6150-1-28


Published:	13 September 2006

Additional files

Additional File 1:

ClustalW alignment of RF codon sequences in the nexus format. The names of the sequences are given in the following format: RF2_MC_003919.fna – where RF2 – is the name of the factor (either RF1, RF2 or RFH), MC_003919 indicates an accession number (substitute M with N to get an accession number), it also indicates a name of a fasta file from NCBI ftp site which was used in this study, e.g. NC_003919.fna. Note that sequences corresponding to RF2 genes expressed via ribosomal frameshift were modified by deletion of one nucleotide in the frameshift site to correct for ORF disruption.

Format: NEX Size: 1.4MB Download file

Additional File 2:

Saved MEGA3 tree session corresponding to a tree shown in Fig. 3. Names are the same as in the 1. However, the number of sequences is different, since the trees were reconstructed based on corresponding amino acid alignment and only one member from a group of redundant protein sequences was used for phylogenetic reconstruction.

Format: MTS Size: 1.2MB Download file