Characterization and Evolution of Cell Division and Cell Wall Synthesis Genes in the Bacterial Phyla Verrucomicrobia , Lentisphaerae , Chlamydiae , and Planctomycetes and Phylogenetic Comparison with rRNA Genes

Abstract

In the past, studies on the relationships of the bacterial phyla Planctomycetes, Chlamydiae, Lentisphaerae, and Verrucomicrobia using different phylogenetic markers have been controversial. Investigations based on 16S rRNA sequence analyses suggested a relationship of the four phyla, showing the branching order Planctomycetes, Chlamydiae, Verrucomicrobia/Lentisphaerae. Phylogenetic analyses of 23S rRNA genes in this study also support a monophyletic grouping and their branching order-this grouping is significant for understanding cell division, since the major bacterial cell division protein FtsZ is absent from members of two of the phyla Chlamydiae and Planctomycetes. In Verrucomicrobia, knowledge about cell division is mainly restricted to the recent report of ftsZ in the closely related genera Prosthecobacter and Verrucomicrobium. In this study, genes of the conserved division and cell wall (dcw) cluster (ddl, ftsQ, ftsA, and ftsZ) were characterized in all verrucomicrobial subdivisions (1 to 4) with cultivable representatives (1 to 4). Sequence analyses and transcriptional analyses in Verrucomicrobia and genome data analyses in Lentisphaerae suggested that cell division is based on FtsZ in all verrucomicrobial subdivisions and possibly also in the sister phylum Lentisphaerae. Comprehensive sequence analyses of available genome data for representatives of Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes strongly indicate that their last common ancestor possessed a conserved, ancestral type of dcw gene cluster and an FtsZ-based cell division mechanism. This implies that Planctomycetes and Chlamydiae may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with Verrucomicrobia.

The AlternativeTranslational Profile That Underlies the Immune-Evasive State of Persistence in Chlamydiaceae Exploits Differential Tryptophan Contents of the Protein Repertoire

“…7. The 16-gene assemblage given across the top of the middle panel and denoted the "ancestral sequence" has been called the dcw (division and cell wall) cluster (105). The strong conservation of gene order has been suggested to implicate the cotranslational assembly of many dcw gene products (90).…”

“…The strong conservation of gene order has been suggested to implicate the cotranslational assembly of many dcw gene products (90). The common ancestor of the Verrucomicrobia, Lentisphaerae, Chlamydiae, and Planctomycetes "superphylum" has been proposed to have had a dcw cluster (mraZ (105). If this was so, then the following changes occurred to yield the contemporary gene organization of the pathogenic chlamydiae: (i) mraZ has been lost, (ii) a hypothetical gene has replaced ftsL, (iii) the ancestral operon has been split between murE and murF to yield the two clusters shown in the bottom and middle panels of Fig.…”

“…This "Ca. Protochlamydia amoebophila" fusion may have originated from a higher plant source via LGT (105).…”

The 1st EMBO workshop on PVC bacteria—Planctomycetes–Verrucomicrobia–Chlamydiae superphylum: Exceptions to the bacterial definition?

“…planctomycetes species) is now amply supported (Gupta et al 2012;Hou et al 2008;Kamneva et al 2010;Pilhofer et al 2008;Wagner and Horn 2006).…”

“…The inference that those organisms form a natural group was initially based on 16S rRNA phylogenetic analysis (Wagner and Horn 2006). However, since then it has been recovered by a range of further analyses and has become increasingly accepted as a valid taxonomic grouping (Gupta et al 2012;Hou et al 2008;Kamneva et al 2010;Pilhofer et al 2008;Pol et al 2007;Fuerst 2013). …”