Comparative 3-D Modeling of tmRNA

BMC Molecular Biology

Table 1 Phylogenetic distribution of tmRNA features

Phylogenetic Group	MLD	pk1	pk2	pk3	pk4	Other
Thermophilic Oxygen Reducers
Thermatogales
Green Non-sulfur & Bacteria elatives
Flexibacter Cytophaga Bacteroides
Green Sulfur Bacteria
Planctomyces & elatives
Cyanobacteria				1	1,2	3
Plastids				-	-
Mitochondria	-	-	-	-	-
Fibrobacter/Acidobacter & elatives
Spirochetes & elatives
Proteobacteria, alpha			4		5	3
Proteobacteria, beta			6			3
Proteobacteria, gamma			6
Proteobacteria, delta
Proteobacteria, epsilon
Fusobacteria
Gram Positive Bacteria

The tRNA-like domain (TLD), mRNA-like domain (MLD), and the four pseudoknots pk1 to pk4 are shown on the top. Other features peculiar to a phylogenetic group are in the right column. White fields indicate the presence, dashes the absence of a feature. Numbers suggest the following structural features: (1) certain Cyanobacteria lack these pseudoknots. (2) One-chain cyanobacterial tmRNAs contain two smaller tandem pseudoknots named pk4a and 4b. (3) The tmRNAs of some species in this group consist of two basepaired molecules [14, 21]. (4) The genus Ricketsia and its relatives lack pk2. (5) pk4 of the alpha-Proteobacteria has been reduced to a single helix (named helix 11). (6) Some species in this group contain an additional helix (helix 6d).

ISSN: 1471-2199