Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes

Abstract

Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction. With genomes under 1 Mbp in size, most Mollicutes species retain the capacity to replicate and grow autonomously. The major goal of this work was to identify the minimal set of proteins that can sustain ribosome biogenesis and translation of the genetic code in these bacteria. Using the experimentally validated genes from the model bacteria Escherichia coli and Bacillus subtilis as input, genes encoding proteins of the core translation machinery were predicted in 39 distinct Mollicutes species, 33 of which are culturable. The set of 260 input genes encodes proteins involved in ribosome biogenesis, tRNA maturation and aminoacylation, as well as proteins cofactors required for mRNA translation and RNA decay. A core set of 104 of these proteins is found in all species analyzed. Genes encoding proteins involved in post-translational modifications of ribosomal proteins and translation cofactors, post-transcriptional modifications of t+rRNA, in ribosome assembly and RNA degradation are the most frequently lost. As expected, genes coding for aminoacyl-tRNA synthetases, ribosomal proteins and initiation, elongation and termination factors are the most persistent (i.e. conserved in a majority of genomes). Enzymes introducing nucleotides modifications in the anticodon loop of tRNA, in helix 44 of 16S rRNA and in helices 69 and 80 of 23S rRNA, all essential for decoding and facilitating peptidyl transfer, are maintained in all species. Reconstruction of genome evolution in Mollicutes revealed that, beside many gene losses, occasional gains by horizontal gene transfer also occurred. This analysis not only showed that slightly different solutions for preserving a functional, albeit minimal, protein synthetizing machinery have emerged in these successive rounds of reductive evolution but also has broad implications in guiding the reconstruction of a minimal cell by synthetic biology approaches.

Bacillus subtilis exhibits MnmC-like tRNA modification activities

“…In fact, MnmE and MnmG have been included in the minimal set of proteins required for a functional translation apparatus in bacteria [12]. By contrast, putative orthologs of the E. coli bi-functional MnmC protein are conserved only in γ-proteobacteria and a few members of other bacterial classes, although orthologs of a single domain have been identified in several genomes [13].…”

An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast

“…Interestingly, all tRNA molecules feature post-transcriptional chemical modifications, some of which are highly conserved throughout all domains of life (Grosjean 2009;Grosjean et al 2014). To date, ∼110 RNA modifications have been reported, and among the 42 tRNA species found in yeast, 25 modifications occur at 36 individual nucleotide positions (Phizicky and Hopper 2010).…”

The Blueprint of a Minimal Cell: MiniBacillus

“…More strongly conserved genes were preferred over less conserved genes. In this respect, gene conservation and essentiality in genome-reduced Mycoplasma and other mollicutes species and the inclusion of genes in the genome of M. mycoides JCVI-syn3.0 had a high priority (8,10,42).…”

“…Finally, we decided to include the nano-RNase NrnA, which degrades and thus recycles bi-and oligoribonucleotides (71). This enzyme is conserved in all groups of mollicutes despite their significant genome reduction (42). This strong conservation is suggestive of an important function and justifies the inclusion of this protein in the minimal cell.…”