PVC superphylum
{{Short description|Obsolete superphylum of bacteria}}
{{automatic taxobox
| name = PVC
| image = ChlamydiaTrachomatisEinschlusskörperchen.jpg
| image_caption = Chlamydia trachomatis
| classification_status = obsolete
| taxon = PVC superphylum
| authority =
| subdivision_ranks = Phyla
| subdivision = Chlamydiota
| synonyms = Planctobacteria Cavalier-Smith, 1987{{cite journal | last1 = Cavalier-Smith | first1 = T | year = 1987 | title = The origin of eukaryote and archaebacterial cells | journal = Annals of the New York Academy of Sciences | volume = 503 | issue = 1 | pages = 17–54 | doi=10.1111/j.1749-6632.1987.tb40596.x | pmid=3113314| bibcode = 1987NYASA.503...17C | s2cid = 38405158 }}
}}
The PVC is an obsolete superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota.{{cite journal |last1=Rivas-Marín |first1=Elena |last2=Devos |first2=Damien P. |title=The Paradigms They Are a-Changin': past, present and future of PVC bacteria research |journal=Antonie van Leeuwenhoek |pages=785–799 |language=en |doi=10.1007/s10482-017-0962-z |date=1 June 2018|volume=111 |issue=6 |pmid=29058138 |pmc=5945725 }} Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wall twice. It has been hypothesised that a member of the PVC clade might have been the host cell in the endosymbiotic event that gave rise to the first proto-eukaryotic cell.{{cite journal|last1=Forterre|first1=Patrick|title=A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong|journal=Research in Microbiology|date=January 2011|volume=162|issue=1|pages=77–91|doi=10.1016/j.resmic.2010.10.005|pmid=21034817|doi-access=free}}{{cite journal|last1=Baum|first1=David A|last2=Baum|first2=Buzz|title=An inside-out origin for the eukaryotic cell|journal=BMC Biology|date=28 October 2014|volume=12|issue=1|pages=76|doi=10.1186/s12915-014-0076-2|pmid=25350791|pmc=4210606 |doi-access=free }}
Cavalier-Smith calls the same group Planctobacteria and considers it a phylum. However, this is not followed by the larger scientific community.{{cite book |series=Bergey's Manual of Systematic Bacteriology|volume=4|title=The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes|editor=George M. Garrity |author1=Krieg, N.R. |author2=Ludwig, W. |author3=Whitman, W.B. |author4=Hedlund, B.P. |author5=Paster, B.J. |author6=Staley, J.T. |author7=Ward, N. |author8=Brown, D. |author9=Parte, A. |publisher=Springer|location= New York |edition= 2nd|isbn=978-0-387-95042-6 |pages=908 |url=https://www.springer.com/life+sciences/book/978-0-387-95042-6 |date=November 24, 2010| orig-year =1984(Williams & Wilkins)|id=British Library no. GBA561951}} In the Cavalier-Smith bacterial megaclassification, it is within the bacterial Gracilicutes infra-kingdom and comprises the phyla Chlamydiota, Lentisphaerota, Planctomycetota, Verrucomicrobiota.{{Cite journal| last1 = Cavalier-Smith| first1 = T| title = The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification| journal = International Journal of Systematic and Evolutionary Microbiology| volume = 52| issue = Pt 1| pages = 7–76| year = 2002| pmid = 11837318| doi=10.1099/00207713-52-1-7| doi-access = free}}{{cite journal |author=Cavalier-Smith T |title=Rooting the tree of life by transition analyses |journal=Biol. Direct |volume=1 |issue= 1|pages=19 |year=2006 |pmid=16834776 |pmc=1586193 |doi=10.1186/1745-6150-1-19 |url=http://www.biology-direct.com/content/1//19 |doi-access=free }}
{{cladogram
|align=none
|title=PVC superphylum{{Cite journal
| last1 = Rappe | first1 = M. S.
| last2 = Giovannoni | first2 = S. J.
| title = The Uncultured Microbial Majority
| journal = Annual Review of Microbiology
| volume = 57
| pages = 369–394
| year = 2003
| pmid = 14527284
| doi = 10.1146/annurev.micro.57.030502.090759
| last1 = Woese | first1 = C. R.
| title = Bacterial evolution
| journal = Microbiological Reviews
| volume = 51
| issue = 2
| pages = 221–271
| year = 1987
| doi = 10.1128/MMBR.51.2.221-271.1987
| pmid = 2439888
| pmc = 373105
| last1 = Wagner | first1 = M.
| last2 = Horn | first2 = M.
| doi = 10.1016/j.copbio.2006.05.005
| title = The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
| journal = Current Opinion in Biotechnology
| volume = 17
| issue = 3
| pages = 241–249
| year = 2006
| pmid = 16704931
|caption=
|cladogram=
{{clade
|label1=PVC
|1={{clade
|2={{clade
|1={{clade
|2=Omnitrophica}}
|2={{clade
|1=Chlamydiota
|2={{clade
|2={{clade
|2=Verrucomicrobiota}}}}}}}}}}}}}}
Molecular signatures
Planctomycetota, Verrucomicrobiota, and Chlamydiota in the traditional molecular phylogeny view are considered as phyla and also cluster together in the PVC superphylum, along with the candidate phyla Omnitrophica{{cite web|url=https://www.uniprot.org/taxonomy/67812|title=Taxonomy - Candidatus Omnitrophica (PHYLUM)|publisher=UniProt}} (previously OP3) and the Poribacteria.{{Cite journal | last1 = Wagner | first1 = M. | last2 = Horn | first2 = M. | doi = 10.1016/j.copbio.2006.05.005 | title = The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance | journal = Current Opinion in Biotechnology | volume = 17 | issue = 3 | pages = 241–249 | year = 2006 | pmid = 16704931 }} An important molecular marker in the form of a conserved signature protein has been found to be consistently shared by PVC members, with the exception of Poribacteria. The conserved signature protein may be a marker that represents a synapomorphic quality and a means to distinguish this bacterial group. In 2014, studies have characterized this protein and it has been attributed to play an important housekeeping function in DNA/RNA binding.{{cite journal |vauthors=Lagkouvardos I, Jehl MA, Rattei T, Horn M |title= Signature protein of the PVC superphylum |journal=Appl Environ Microbiol |volume=80|issue=2|pages=440–445 |date=2014|pmid=24185849 |doi=10.1128/AEM.02655-13|pmc=3911108|bibcode= 2014ApEnM..80..440L }} This observation not only provides a means to demarcate the PVC superphylum, but it supports strongly supports an evolutionary relationship shared by this clade that is distinct from other bacteria.{{cite journal |vauthors=Gupta RS, Bhandari V, Naushad HS |title=Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships |journal=Front Microbiol |volume=3 |pages=327 |year=2012 |pmid=23060863 |pmc=3444138 |doi=10.3389/fmicb.2012.00327 |doi-access=free }}{{cite journal |vauthors=Gupta RS |title=Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification |journal= FEMS Microbiol Rev |volume=40|issue=4|pages=520–53 |date=2016|pmid=27279642 |doi=10.1093/femsre/fuw011 |doi-access=free }}
Conserved signature indels (CSIs) have also been found specific for the Planctomycetota, Verrucomicrobiota, and Chlamydiota that distinguish each respective phylum from one another, and from other bacteria.{{cite journal |vauthors=Gupta RS, Naushad S, Chokshi C, Griffiths E, Adeolu M |title=A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia |journal=Antonie van Leeuwenhoek |volume=108 |issue=3 |pages=765–781 |year=2015 |pmid=26179278 |doi=10.1007/s10482-015-0532-1|s2cid=17099157 }} A three-amino-acid insert in the RNA polymerase protein RpoB has been found that is shared by all sequenced Verrucomicrobia, Chlamydiae, and Lentisphaerae species. The CSI is absent from neighbouring Planctomycetes' and Poribacteria, suggesting common ancestry among the groups for which the CSI is specific.
Additional lines of evidence for the existence of this clade have been found.{{cite journal |vauthors=Wagner M, Horn M |title=The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance |journal=Curr. Opin. Biotechnol. |volume=17 |issue=3 |pages=241–9 |year=2006 |pmid=16704931 |doi=10.1016/j.copbio.2006.05.005 }}{{cite journal |vauthors=Kamneva OK, Liberles DA, Ward NL |title=Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method |journal=Genome Biol Evol |volume=2 |pages=870–86 |year=2010 |pmid=21048002 |pmc=3000692 |doi=10.1093/gbe/evq071 }} These include the presence of membrane coat-like proteins, tubulin, sterol synthesis, and the presence of condensed DNA.
Notes
{{Reflist|group=note}}