Distribution and frequencies of post-transcriptional modifications in tRNAs

<div><p>Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.</p></div

Reconstruction of the evolution of translation-related gene set in mollicutes.

<p>Ancestral gene content at each node of the phylogenetic tree was inferred using the posterior probabilities calculated from the birth-and death model implemented in the COUNT program. Genes gained and lost are framed and highlighted with colors corresponding to gene categories, respectively. Very similar results were obtained using Wagner parsimony method with a gain penalty of 4. The phylogenetic tree was inferred using the maximum likelihood method from the concatenated multiple alignments of 79 proteins encoded by genes present at one copy in each genome. The phylogenetic groups are indicated: S for Spiroplasma, H for Hominis, P for Pneumoniae and AAP. The non-cultivated <i>Mollicutes</i> are framed by a red dashed line.</p

Total number of proteins involved in translation for each <i>Mollicutes</i> species.

<p>The number of proteins involved in translation for each <i>Mollicutes</i> species was tabulated in reference to the number found for the two model bacteria <i>E. coli</i> (Ec) and <i>B. subtilis</i> (Bs). The numbering of species is the same as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen-1004363-g001" target="_blank">Figure 1</a>. The data corresponding to non-cultivated <i>Mollicutes</i> are framed with a red dashed line as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen-1004363-g001" target="_blank">Figure 1</a>. The horizontal blue dashed line indicates 104, which correspond to the core of translation proteins shared by all <i>Mollicutes.</i></p

The minimal set of proteins for a functional translation apparatus in the 39 <i>Mollicutes</i> species.

<p>The acronyms of the 129 selected translation proteins in <i>Mollicutes</i> are divided in 2 parts: in A (left part), the 104 core proteins present in all <i>Mollicutes</i> analyzed are listed, while in B (right part) 25 additional proteins supposed to complement the 104 core protein are indicated. The acronyms and corresponding color code for the boxes are as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen-1004363-g001" target="_blank"><b>Figures 1</b></a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen-1004363-g003" target="_blank"><b>3</b></a> and the corresponding names are given in <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen.1004363.s007" target="_blank">Table S2</a></b>). When the acronym in bold black letters is followed by one red asterisk, the proteins are absent in the non culturable <i>M. suis</i> and when followed by two red stars proteins are absent in the 3 hemoplasmas and/or the phytoplasmas (all these are present in panel B only). All numbers in brackets within boxes correspond to those indicated in part D of <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen-1004363-g001" target="_blank">Figure 1</a>. Acronyms indicated in red correspond to proteins that are found in <i>B. subtilis</i> and not in <i>E. coli</i>. The various types of translation-associated RNAs are indicated in small blue boxes. In the cases of tRNA and rRNA modification enzymes, the type of nucleotide modification and their positions in RNA as identified in <i>E. coli</i> are also given. Modified nucleotides m⁷G and m¹A carries a positive charge at neutral pH (indicated by a +). XY means that either protein X or protein Y is found in mollicutes. However because of their overlapping functions or analogous specificities, the common essential function is preserved in all the 39 <i>Mollicutes</i> analyzed. The indication ‘n-RNases (15)’ means that one ancestral gene has been duplicated several times independently and each mollicute contain 1 to up 4 exemplars (they were however counted for one enzyme in our statistic). The average G+C % content in genome of the 39 <i>Mollicutes</i> analyzed is 27.6 varying from 21.4 in <i>Ca</i>. Phytoplasma mali to up to 40.0 in <i>M. pneumoniae</i> (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen.1004363.s006" target="_blank">Table S1</a>).</p

Genes coding for proteins implicated in translation in <i>Mollicutes.</i>

<p>Using queries from <i>E. coli</i> (<i>Ec</i>) and from <i>B. subtilis</i> (<i>Bs</i>), the presence of homologous proteins was searched in 39 <i>Mollicutes</i> genomes (see list of selected species below part B of the figure). This figure corresponds to the raw data given in <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen.1004363.s008" target="_blank">Table S3</a></b>. The results were grouped into three panels: conserved core of genes involved in translation (A), genes lost in some species only (B) and genes absent in all <i>Mollicutes</i> species (C). In panels A and C, only data concerning <i>Ec</i> and <i>Bs</i> are shown. In part B, the selected species clustered according to the 4 phylogenetic groups; Spiroplasma, Hominis, Pneumoniae and AAP <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen.1004363-Johansson1" target="_blank">[25]</a>. The queries, of which names of corresponding acronyms are given in <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen.1004363.s007" target="_blank">Table S2</a></b>, are ordered from top to bottom, first according to the highest number of occurences and second according to the 7 protein categories following this sequence: ribosomal proteins, tRNA aminoacylation, rRNA modifications, tRNA modifications, ribosome assembly, translation and RNA processing. The different categories are color coded as shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004363#pgen-1004363-t001" target="_blank"><b>Table 1</b></a> and below part C of the figure. The presence or absence of a given gene in a <i>Mollicutes</i> species is indicated by “1” in a grey background or by “0” in a white background, respectively. The 17 genes missing in some of the non-cultivated <i>Mollicutes</i> are indicated within a dashed-red box. The total number of genes in each category is indicated in panel D.</p

Genes coding for proteins implicated in the biosynthesis and functions of translation machinery in model bacteria.

<p>Ec: Escherichia coli.</p><p>Bs: Bacillus subtilis.</p

Evaluation of THUMPα secondary structure elements by circular dichroïsm

<p><b>Copyright information:</b></p><p>Taken from "THUMP from archaeal tRNA:mG10 methyltransferase, a genuine autonomously folding domain"</p><p>Nucleic Acids Research 2006;34(9):2483-2494.</p><p>Published online 10 May 2006</p><p>PMCID:PMC1459410.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The molar ellipticity was calculated on the basis of exact amino acid composition of recombinant THUMPα product. Signal of 8.48 μM purified protein in 10 mM Tris/HCl buffer (pH 8.0) is shown in red while k2D estimation is shown in blue. Secondary structures predictions by different methods available via the GeneSilico metaserver () gave on the average 44% of α-helices and 21% of β-sheets. The content of α-helices is overestimated by the predictions (or alternatively, the CD measurements may underestimate it)