Movatterモバイル変換

[0]ホーム
URL:

Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
Thehttps:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

NIH NLM Logo
Log inShow account info
Access keysNCBI HomepageMyNCBI HomepageMain ContentMain Navigation
pubmed logo
Advanced Clipboard
User Guide

Full text links

Atypon full text link Atypon Free PMC article
Full text links

Actions

Share

.2014 Jan;80(2):440-5.
doi: 10.1128/AEM.02655-13. Epub 2013 Nov 1.

Signature protein of the PVC superphylum

Affiliations

Signature protein of the PVC superphylum

Ilias Lagkouvardos et al. Appl Environ Microbiol.2014 Jan.

Abstract

The phyla Planctomycetes, Verrucomicrobia, Chlamydiae, Lentisphaerae, and "Candidatus Omnitrophica (OP3)" comprise bacteria that share an ancestor but show highly diverse biological and ecological features. Together, they constitute the PVC superphylum. Using large-scale comparative genome sequence analysis, we identified a protein uniquely shared among all of the known members of the PVC superphylum. We provide evidence that this signature protein is expressed by representative members of the PVC superphylum. Its predicted structure, physicochemical characteristics, and overexpression in Escherichia coli and gel retardation assays with purified signature protein suggest a housekeeping function with unspecific DNA/RNA binding activity. Phylogenetic analysis demonstrated that the signature protein is a suitable phylogenetic marker for members of the PVC superphylum, and the screening of published metagenome data indicated the existence of additional PVC members. This study provides further evidence of a common evolutionary history of the PVC superphylum and presents a unique case in which a single protein serves as an evolutionary link among otherwise highly diverse members of major bacterial groups.

PubMed Disclaimer

Figures

FIG 1
FIG 1
Features of the PVC superphylum SP. (A) Conservation of the SP amino acid sequence. A sequence logo based on a MUSCLE alignment of all of the known SPs generated by WebLogo 3 is shown (28, 48). The overall height of the alignment positions indicates sequence conservation, while the height of each symbol indicates the relative frequency of each amino acid at the respective position. Symbol colors reflect amino acid chemical properties. Highly conserved positions can be observed along the complete length of the alignment, with a longer conserved region in the middle, corresponding to a predicted α-helix. (B) Predicted secondary and tertiary structures of representative SPs compared to those of small DNA/RNA binding proteins of E. coli. Predictions were performed with I-TASSER (49) (i to iii) and the QUARK server (50) (iv to vi). Structures: i and iv, SP of Protochlamydia amoebophila. UWE25 (GenBank/EMBL/DDBJ accession number YP_008052); ii and v, SP of V. spinosum (WP_009960041); iii and vi, SP of R. baltica (KF733603); vii, E. coli ribosomal protein L30 (Protein Data Bank accession number 2AW4); viii, E. coli DNA binding protein H-NS (Protein Data Bank accession number 1HNS); ix, E. coli histone like protein HU (Protein Data Bank accession number 1MUL). Pink, alpha-helix; yellow, beta-sheet; blue, turn; gray, unstructured. Independently of the software, a central alpha-helix is predicted for all of the SPs. The SP of all of the Planctomycetes shows a C-terminal lysine-rich extension that forms additional secondary-structure elements. (C) Nucleic acid mobility retardation by SP of R. baltica and P. amoebophila. Agarose gel i, retardation assay with sheared genomic DNA. Lanes: 1, molecular size markers; 2, empty; 3, genomic DNA with GST-tagged SP of R. baltica, 4: GST-tagged SP of R. baltica without DNA; 5, genomic DNA only. Agarose gel ii, retardation assay with purified total RNA. Lanes: 1 and 5, molecular size markers; 2, RNA only; 3, RNA with GST-tagged SP of R. baltica; 4, RNA with GST-tagged SP of P. amoebophila; 6, RNA with GST only. Arrows indicate bands representing the 16S and 23S rRNAs, respectively. (Bottom agarose gel) retardation assay with PCR products. Lanes: 1, molecular size markers; 2, only PCR product; 3 to 7, PCR product with increasing concentrations of GST-tagged SP of P. amoebophila; 8, PCR product with GST only. The same molecular size marker was used in all of the experiments, and fragment sizes in base pairs are shown on the left. The retardation assays suggest unspecific binding of SP to DNA and RNA.
FIG 2
FIG 2
Evolutionary relationships of all of the known PVC superphylum SPs and their metagenomic homologs. The environmental origin of SPs is color coded at the tips of the tree for metagenomic sequences but not for SPs originating from complete genome sequences. An approximate maximum-likelihood tree is shown; nodes with less than 70% support are collapsed.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Wagner M, Horn M. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17:241–249. 10.1016/j.copbio.2006.05.005 - DOI - PubMed
    1. Pilhofer M, Rappl K, Eckl C, Bauer AP, Ludwig W, Schleifer KH, Petroni G. 2008. 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. J. Bacteriol. 190:3192–3202. 10.1128/JB.01797-07 - DOI - PMC - PubMed
    1. Griffiths E, Gupta RS. 2007. Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 153:2648–2654. 10.1099/mic.0.2007/009118-0 - DOI - PubMed
    1. Kamneva OK, Knight SJ, Liberles DA, Ward NL. 2012. Analysis of genome content evolution in PVC bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol. Evol. 4:1375–1390. 10.1093/gbe/evs113 - DOI - PMC - PubMed
    1. Gupta RS, Bhandari V, Naushad HS. 2012. Molecular signatures for the PVC clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of bacteria provide insights into their evolutionary relationships. Front. Microbiol. 3:327. 10.3389/fmicb.2012.00327 - DOI - PMC - PubMed

Publication types

MeSH terms

Substances

Associated data

Related information

Grants and funding

LinkOut - more resources

Full text links
Atypon full text link Atypon Free PMC article
Cite
Send To

NCBI Literature Resources

MeSHPMCBookshelfDisclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

[8]ページ先頭
©2009-2025 Movatter.jp