Distribution and preservation of the components of the engulfment. What is beyond representative genomes?

Abstract

Engulfment requires the coordinated, targeted synthesis and degradation of peptidoglycan at the leading edge of the engulfing membrane to allow the mother cell to completely engulf the forespore. Proteins such as the DMP and Q:AH complexes in Bacillus subtilis are essential for engulfment, as are a set of accessory proteins including GerM and SpoIIB, among others. Experimental and bioinformatic studies of these proteins in bacteria distinct from Bacillus subtilis indicate that fundamental differences exist regarding the organization and mechanisms used to successfully perform engulfment. As a consequence, the distribution and prevalence of the proteins involved in engulfment and other proteins that participate in different sporulation stages have been studied using bioinformatic approaches. These works are based on the prediction of orthologs in the genomes of representative Firmicutes and have been helpful in tracing hypotheses about the origin and evolution of sporulation genes, some of which have been postulated as sporulation signatures. To date, an extensive study of these signatures outside of the representative Firmicutes is not available. Here, we asked whether phyletic profiles of proteins involved in engulfment can be used as signatures able to describe the sporulation phenotype. We tested this hypothesis in a set of 954 Firmicutes, finding preserved phyletic profiles defining signatures at the genus level. Finally, a phylogenetic reconstruction based on non-redundant phyletic profiles at the family level shows the non-monophyletic origin of these proteins due to gain/loss events along the phylum Firmicutes.

Conservation and Evolution of the Sporulation Gene Set in Diverse Members of the Firmicutes

“…show patterns of extensive loss of sporulation genes. Consistent with the previous observations (59,60), they both lack seven of the nine genes of the SpoIIQ-SpoIIIA complex, retaining only SpoIIQ and SpoIIIAH components. Further, they both lack such widely conserved sporulation genes as spoIIID, bofA, cotQ, safA, yabQ, ypeB, yyaC, yyaD, sleL (yyaH), and gerW (ytfJ) (Table S2, Table S4).…”

“…The Erysipelotrichia members C. innocuum and E. ramosum retain only the spoIIIAH and spoIIQ genes. In addition, they possess SpoIVFB and GerM, but lack SpoIIB and SpoIVFA (Table S2, Figure S5B, C), see also reference (60). Six members of the family Planococcaceae show stronger conservation of the SpoIIQ-SpoIIIA complex: in addition to SpoIIIAH and SpoIIQ, they retain SpoIIIAC, SpoIIIAE, and SpoIIIAG components (Fig.…”

The benzoyl-CoA pathway serves as a genomic marker to identify the oxygen requirements in the degradation of aromatic hydrocarbons

“…We used this information to search for orthologous sequences of BCLs in bacterial genomes. To this end, we used an approach developed by our group ( Martinez-Amador et al, 2019 ; Soto-Avila et al, 2021 ), in which the first step was the identification of Pfam domains found in the PfamA database ( Mistry et al, 2021 ), whose matrices were used to inspect the amino acid sequences of proteomes downloaded from the KEGG database. Once the Pfam domains were identified, we constructed protein architectures.…”

“…These pathways are often arranged as operons ( Egland et al, 1995 ; Porter and Young, 2014 ; Arnold et al, 2021 ). Therefore, instead of considering three upstream and downstream genes, as proposed in our previous work ( Martinez-Amador et al, 2019 ; Soto-Avila et al, 2021 ), we extended the inspection of genes in the genomic context to 10 upstream and 10 downstream genes from the BCL. The protein architectures and the Pfam accession numbers of the genes represented in the genomic context are shown in Supplementary Table S1 .…”

“…The protein architectures and the Pfam accession numbers of the genes represented in the genomic context are shown in Supplementary Table S1 . As in our previous work ( Martinez-Amador et al, 2019 ; Soto-Avila et al, 2021 ), for these proteins, we retained hits with an e -value cutoff ≤0.001.…”