Caryophanaceae
| Caryophanaceae | |
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| Family: | Caryophanaceae Peshkoff, 1939
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Bhargavea | |
The Caryophanaceae is a family of Gram-positive bacteria. In 2020, the now defunct familyPlanococcaceae was merged into Caryophanaceae to rectify a nomenclature anomaly.[1] The type genus of this family is Caryophanon.[2]
The family Planococcacae was validly published in 1949, however it contained within it another family level taxonomic rank, the family Caryophanaceae, which was validly published in 1939.[3] According the the International Code of Nomenclature of Prokaryotes (ICNP), the name Caryophanacaeae has higher priority than Planococcaceae because of its earlier publication.[3] Therefore, the emended family retained the name Caryophanaceae.
The name Caryophanaceae is derived from the Latin term Caryophanon, referring the type genus of the family and the suffix "-aceae", an ending used to denote a family. Together, Caryophanaceae refers to a family whose nomenclatural type is the genus Caryophanon.[1]
Biochemical Characteristics[1]
Cells from members of the family Caryophanaceae can be cocci or rods, sometimes forming filaments or trichomes. Most species are strictly aerobic heterotrophs, although some are also facultatively aerobes. Cells are generally motile by flagella or gliding and they may or may not form endospores. Most species are catalase-positive and oxidase positive or negative.
Historical Systematics and Current Taxonomy
Caryophanaceae, as of 2021, contains 19 validly published genera.[2]
In addition to the nomenclature anomaly, Caryophanaceae also encompassed over 100 species that had varying morphology/biochemical characteristics, demonstrating that they were phylogenetically unrelated.[4] The original assignment of species into the family Caryophanaceae was largely based on 16S rRNA genome sequence analyses, which is known to have low discriminatory power and the results of which changes depends on the algorithm and organism information used. Despite this, the analyses still exhibited polyphyletic branching, indicating the presence of distinct subgroups within the family.[4]
In 2020, Gupta and Patel proposed the emendation of Caryophanaceae, specifically the unification with Planoccocacae, the proposal of 3 new genera as well as the transfer of a number of misclassified species into the appropriate genera.[1] The changes were proposed based on various phylogenetic trees constructed based on multiple large datasets of protein sequences and the identification of unique molecular markers known as conserved signatures indels in multiple proteins.[1]
Molecular signatures
Members of this family can be reliably distinguished from all other bacteria through molecular markers known as conserved signature indels (CSIs). CSIs are found in conserved regions in genes and proteins of a group of organisms and flanked on both sides by highly conserved sequences, ensuring reliable sequence alignment and their dependability as a molecular marker.[5] These specific insertions and deletions result from rare genetic changes in a common ancestor and are passed down vertically to descendants of the ancestor.[5] CSIs can also serve as a basis for developing diagnostic methods for pathogenic species.[6][7]
13 CSIs were identified for this family in the proteins phenylalanine–tRNA ligase subunit alpha, chaperonin GroEL, ribosome maturation factor RimP, BrxA/BrxB family bacilliredoxin, RNA methyltransferase, Rhomboid family intramembrane serine protease, ATP- dependent Clp protease ATP-binding subunit, DNA-directed RNA polymerase subunit beta, Chorismate synthase, Stage IV sporulation protein A, peptidase, KinB-signaling pathway activation protein, and DUF423 domain-containing protein.[1] These CSIs can be used to identify additional species belonging to Caryophanacaeae through in-silico or other experimental methods.
References
- ^ a b c d e f Gupta, Radhey S.; Patel, Sudip (2020-01-14). "Robust Demarcation of the Family Caryophanaceae (Planococcaceae) and Its Different Genera Including Three Novel Genera Based on Phylogenomics and Highly Specific Molecular Signatures". Frontiers in Microbiology. 10. doi:10.3389/fmicb.2019.02821. ISSN 1664-302X.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ a b "Family: Caryophanaceae". lpsn.dsmz.de. Retrieved 2021-06-05.
- ^ a b Tindall, B. J. (2019-08-01). "When treated as heterotypic synonyms the names Caryophanaceae Peshkoff 1939 (Approved Lists 1980) and Caryophanales Peshkoff 1939 (Approved Lists 1980) have priority over the names Planococcaceae Krasil'nikov 1949 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980) and Bacillales Prévot 1953 (Approved Lists 1980), respectively". International Journal of Systematic and Evolutionary Microbiology. 69 (8): 2187–2195. doi:10.1099/ijsem.0.003354. ISSN 1466-5026.
- ^ a b Ludwig, Wolfgang; Schleifer, Karl‐Heinz; Whitman, William B. (2015-09-14). "Planococcaceae". Bergey's Manual of Systematics of Archaea and Bacteria: 1–1. doi:10.1002/9781118960608.fbm00116.
- ^ a b Naushad, Hafiz Sohail; Lee, Brian; Gupta, Radhey S. (2014-02-01). "Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria". International Journal of Systematic and Evolutionary Microbiology. 64 (Pt_2): 366–383. doi:10.1099/ijs.0.054213-0. ISSN 1466-5026.
- ^ Wong, Shirley Y.; Paschos, Athanasios; Gupta, Radhey S.; Schellhorn, Herb E. (2014-10-07). "Insertion/deletion-based approach for the detection of Escherichia coli O157:H7 in freshwater environments". Environmental Science & Technology. 48 (19): 11462–11470. doi:10.1021/es502794h. ISSN 1520-5851. PMID 25166281.
- ^ Ahmod, Nadia Z.; Gupta, Radhey S.; Shah, Haroun N. (2011-12-01). "Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group". Journal of Microbiological Methods. 87 (3): 278–285. doi:10.1016/j.mimet.2011.08.015. ISSN 1872-8359. PMID 21907250.
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