A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

Abstract

The cell cycle is a fundamental process that has been extensively studied in bacteria. However, many of its components and their interactions with machineries involved in other cellular processes are poorly understood. Furthermore, most knowledge relies on the study of a few models, but the real diversity of the cell division apparatus and its evolution are largely unknown. Here, we present a massive in-silico analysis of cell division and associated processes in around 1,000 genomes of the Firmicutes, a major bacterial phylum encompassing models (i.e. Bacillus subtilis, Streptococcus pneumoniae, and Staphylococcus aureus), as well as many important pathogens. We analyzed over 160 proteins by using an original approach combining phylogenetic reconciliation, phylogenetic profiles, and gene cluster survey. Our results reveal the presence of substantial differences among clades and pinpoints a number of evolutionary hotspots. In particular, the emergence of Bacilli coincides with an expansion of the gene repertoires involved in cell wall synthesis and remodeling. We also highlight major genomic rearrangements at the emergence of Streptococcaceae. We establish a functional network in Firmicutes that allows identifying new functional links inside one same process such as between FtsW (peptidoglycan polymerase) and a previously undescribed Penicilin-Binding Protein or between different processes, such as replication and cell wall synthesis. Finally, we identify new candidates involved in sporulation and cell wall synthesis. Our results provide a previously undescribed view on the diversity of the bacterial cell cycle, testable hypotheses for further experimental studies, and a methodological framework for the analysis of any other biological system.

Keywords: Bacteria; Firmicutes; cell cycle; cell division; evolution; evolutionary scenario; functional link; phylogenomics; phylogeny.

Fig. 1.

Taxonomic distribution of CDAP protein families. (A) Size of protein families corresponding to CDAP proteins. Each line corresponds to either a monogenetic or a multigenetic family. More precisely, 40 CDAP protein families are monogenic, while 136 belong to 63 multigenic families. Families of multigenic families that do not correspond to CDAP are in grey, while other colours correspond to CDAP protein families. Name of the CDAP families are provided on the left. (B) Taxonomic distribution (presence/absence) of CDAP proteins in the 304 studied firmicutes species. The protein families are classified by cognate CDAP (see supplementary table S1, Supplementary Material online). Nodes on the phylogeny (and thus branch lengths) are ordered according to their relative dating proposed by Phylobayes. The coloured strip corresponds to family taxonomic rank (see supplementary fig.S1, Supplementary Material online).

Fig. 2.

Evolutionary events that have impacted the 176 CDAP protein families during the diversification of Firmicutes.(A) Events inferred with the phylogenetic profile approach. (C) Events inferred with the reconciliation approach. Circles at branches correspond to inferred events. Their size is proportional to the number of events. Colors correspond to the type of evolutionary events: green = acquisitions, red = losses, blue = duplications, yellow = HGT, Pink = homologue replacements. Branches identified as hotspots are indicated by arrows. Colours associated to branch names correspond to the dominating type of events. (B) Distribution per branch of the number of events inferred with phylogenetic profiles. (D) Distribution per branch of the number of events inferred with reconciliation.

Fig. 3.

Evolution of CDAP gene clusters during the diversification of Firmicutes. (A) gene clusters inferred at the root of Firmicutes. Color of family names corresponds to the CDAP (blue: cell division, pink: elongation, yellow: cell wall, green: Z-ring localization, violet: chromosomal segregation, cyan: chromosome replication, orange: sporulation, blue-green: capsule synthesis, grey: peripherical). (B) Evolutionary event affecting gene clusters. Circles at branches correspond to inferred events. Their size is proportional to the number of events. Colors correspond to the type of evolutionary events: green = creations, red = disruptions, and pink = modifications. Branches identified as hotspots are indicated by arrows. Colors associated to branch names correspond to the dominating type of events. (C) Distribution of the number of events per branch.

Fig. 4.

Correlation network of CDAP proteins. Nodes represent CDAP protein families. They are colored according to their cognate CDAP. Edges represent the 2% highest Z-scores between pairs of CDAP protein families (see Material and methods). The color and the width of edges correspond to the strength of the Z-score. Main correlation clusters are indicated in grey. Families without any significative link with another family are not shown (Alr, ClpX, FtsK, LeuS, LysA, LysA(P1), LytB, MurI, MurZ, NudF, PbpA(P1), RecA, RodZ, ValS, XerS, ZapA).

Fig. 5.

Mapping of correlation index of CDAP proteins and potential candidates. The heatmap represents the similarity between taxonomic distributions of studied CDAP protein families (top) and proteins families from firmicutes proteomes with the most similar taxonomic distribution (left). These proteins represent potential CDAP candidate families. The names of the leaves correspond to the major annotation of the family. The color of the squares corresponds to the strength of correlation (white = 0, black = 1). Three clusters are highlighted in color (blue and yellow correspond to sporulation clusters, green correspond to Bacilli cluster). New candidates are indicated in red, protein families highlighted elsewhere in grey (Traag et al. 2013).