Genomic Evolution of 11 Type Strains within Family Planctomycetaceae

Guo, Min; Zhou, Qian; Zhou, Yizhuang; Yang, L.; Liu, Tianxiang; Yang, Jing; Chen, Yanling; Su, Longxiang; Xu, Jin; Chen, Jing; Liu, Feng; Chen, Jiapeng; Dai, Wenkui; Ni, Peixiang; Fang, Chengxiang

doi:10.1371/journal.pone.0086752

Cited by 21 publications

(17 citation statements)

References 56 publications

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“…In a second step, we employed comparative genomics to analyse planctomycetal genomes with respect to genes required for PG synthesis. Taking the assumed large evolutionary divergence of Planctomycetes into account, we used methods apt to deal with evolutionarily more distant sequences, and analysed entire planctomycetal genomes employing dynamic queries and position-specific iterative BLAST searches 17 (see Supplementary Note 2 for details). Thus, contrary to a previous study that reported the absence of genes required for PG synthesis in some planctomycetal genomes 17 , we found that all the analysed species harbour essential genes for PG synthesis ( Supplementary Tables 1 and 2 , Supplementary Data 1-4 and Supplementary Discussion ).…”

Section: Resultsmentioning

confidence: 99%

“…The postulation of a proteinaceous cell wall dates back three decades 10 and has been passed on since then. Despite its conceptual importance, the cell wall composition of Planctomycetes has been rarely addressed experimentally 11 16 17 . However, recent reports on penicillin sensitivity of anammox Planctomycetes questioned their lack of a PG cell wall 18 .…”

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confidence: 99%

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Planctomycetes do possess a peptidoglycan cell wall

Jeske

Schüler

Schümann³

et al. 2015

Nat Commun

154

127

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Most bacteria contain a peptidoglycan (PG) cell wall, which is critical for maintenance of shape and important for cell division. In contrast, Planctomycetes have been proposed to produce a proteinaceous cell wall devoid of PG. The apparent absence of PG has been used as an argument for the putative planctomycetal ancestry of all bacterial lineages. Here we show, employing multiple bioinformatic methods, that planctomycetal genomes encode proteins required for PG synthesis. Furthermore, we biochemically demonstrate the presence of the sugar and the peptide components of PG in Planctomycetes. In addition, light and electron microscopic experiments reveal planctomycetal PG sacculi that are susceptible to lysozyme treatment. Finally, cryo-electron tomography demonstrates that Planctomycetes possess a typical PG cell wall and that their cellular architecture is thus more similar to that of other Gram-negative bacteria. Our findings shed new light on the cellular architecture and cell division of the maverick Planctomycetes.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Planctomycetes do possess a peptidoglycan cell wall

Jeske

Schüler

Schümann³

et al. 2015

Nat Commun

154

127

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“…A genome sequence-based phylogeny with the same branching order but less bootstrapping support (probably because a restricted set of genes was used) was recently reported by Gou et al . [ 88 ].…”

Section: Insights From the Genome Sequencementioning

confidence: 99%

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

Scheuner

Tindall

et al. 2014

Stand in Genomic Sci

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Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

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“…102 entries in May 2017). The genomes that were affiliated to Planctomycetes phylum (as predicted by PhyloPhlAn) and had a genome completeness (as estimated by CheckM) [17] higher than 10% were merged with the above-mentioned RefSeq release. Prior to inclusion in RefSeq, 13 genomes (that lacked annotation) were annotated using Prokka [18].…”

Section: Supplementary Materials and Methodsmentioning

confidence: 99%