Comparative genomic analysis of mollicutes with and without a chaperonin system

Abstract

The GroE chaperonin system, which comprises GroEL and GroES, assists protein folding in vivo and in vitro. It is conserved in all prokaryotes except in most, but not all, members of the class of mollicutes. In Escherichia coli, about 60 proteins were found to be obligatory clients of the GroE system. Here, we describe the properties of the homologs of these GroE clients in mollicutes and the evolution of chaperonins in this class of bacteria. Comparing the properties of these homologs in mollicutes with and without chaperonins enabled us to search for features correlated with the presence of GroE. Interestingly, no sequence-based features of proteins such as average length, amino acid composition and predicted folding/disorder propensity were found to be affected by the absence of GroE. Other properties such as genome size and number of proteins were also found to not differ between mollicute species with and without GroE. Our data suggest that two clades of mollicutes re-acquired the GroE system, thereby supporting the view that gaining the system occurred polyphyletically and not monophyletically, as previously debated. Our data also suggest that there might have been three isolated cases of lateral gene transfer from specific bacterial sources. Taken together, our data indicate that loss of GroE does not involve crossing a high evolutionary barrier and can be compensated for by a small number of changes within the few dozen client proteins.

Omnipresent Maxwell's demons orchestrate information management in living cells

“…Three major types that act in synergy are (almost) always simultaneously present: chaperonin GroES/GroEL (Yan et al, 2018), molecular chaperone DnaK/DnaJ/GrpE (Uchida and Kanemori, 2018) and disaggregase ClpB (Sugita et al, 2018). As seen in the minimal genomes of B. aphidicola or M. mycoides Syn3.0 (Schwarz et al, 2018), the presence of at least two of them is essential for life. When cells require ironsulfur centres, a further set of specific chaperones, HscAB, may also be required (Table 1).…”

Reconciling the controversy regarding the functional importance of bullet- and football-shaped GroE complexes

“…Next, we analyzed the distributions of folding rates of homologs of the 57 obligatory GroEL substrates in mollicutes (27), a class of bacteria that includes both organisms with a chaperonin system and (the only known) organisms without a chaperonin system. The distribution of folding rates of the 155 homologs of GroEL substrates in mollicutes with a chaperonin system was also found to be bimodal ( Fig.…”

“…The list of GroEL homologs from mollicutes was taken from Ref. 27. PSIPRED (24) was used to predict the secondary structure of all of the proteins in this study.…”

Synonymous and non‐synonymous codon substitutions can alleviate dependence on GroEL for folding

“…Databases . The DHFR protein sequences of 13 mollicute species containing GroEL (GroEL + ) and 20 species lacking GroEL (GroEL − ) (Schwarz et al, 2018 ) were downloaded from EMBL‐EBI UniProt database ( https://www.uniprot.org/ ), based on their accession ID. The proteins were then mapped to their nucleotide level accession ID, using a dedicated python script, and all the nucleotide sequences were downloaded in a fasta format.…”

“…Databases. The DHFR protein sequences of 13 mollicute species containing GroEL (GroEL + ) and 20 species lacking GroEL (GroEL À ) (Schwarz et al, 2018) were downloaded from EMBL-EBI UniProt database (https://www. uniprot.org/), based on their accession ID.…”