Conserved Signature Indel

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Example of a sequence alignment of different CSIs from taxon X. Dots mark identical amino acids to the uppermost sequence.

Conserved signature inserts and deletions (in English 'conserved characteristic indels', CSI) are indels in conserved protein-coding DNA sequences . They are used in biochemistry and genetics as markers to determine the degree of relationship between different species .

properties

CSI belong to the Indels and occur rarely compared to SNP . The CSIs differ little between two species and almost not within one species. Therefore, they can be used to determine the relationship between different species and to create a phylogenetic tree . As an alternative to family tree analysis using CSI, the SNPs of the 16S rRNA are usually compared.

Group-specific CSI

Some CSIs are group-specific and are characteristic of the taxon in question , as they appear in all representatives of a group and not in other groups. The original indel of a taxon-specific CSI probably appeared before the split in the last common ancestor .

Multi-group or mainline CSI

Main line CSI

Multi-group CSI (synonymous main line CSI) are CSI that occur in several phyla , but not in individual phyla. These include B. a CSI of 150-180 amino acids in gyrase B at position 529-751, which occurs in various Proteobacteria , Chlamydiaceae , Planctomycetes and Aquificales , but not in other bacterial phyla or archaea . Another major line CSI of about 100 amino acids is in protein RpoB at position 919-1058 and occurs in Proteobacteria, Bacteroidetes-Chlorobi , Chlamydiaceae, Planctomycetes, and Aquificales. In vertebrates there is a CSI in the protein Bcl2l10 .

Applications

  • CSI-based relationships within the Thermotogae

  • CSI-based relationships between two archaean phyla

  • CSI-based relationships within the Pasteurella family

Among other things, CSIs were used to differentiate the genus Thermotogae from other bacteria and the individual strains from one another.

Individual evidence

  1. ^ SL Baldauf: Animals and Fungi are Each Other's Closest Relatives: Congruent Evidence from Multiple Proteins . In: Proceedings of the National Academy of Sciences . 90, No. 24, 1993. doi : 10.1073 / pnas.90.24.11558 . PMID 8265589 . PMC 48023 (free full text).
  2. ↑ a b c d Radhey S. Gupta: Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes . In: Microbiology and Molecular Biology Reviews . 62, No. 4, 1998, pp. 1435-91. PMID 9841678 . PMC 98952 (free full text).
  3. ↑ Radhey S. Gupta, Emma Griffiths: Critical Issues in Bacterial Phylogeny . In: Theoretical Population Biology . 61, No. 4, 2002, pp. 423-34. doi : 10.1006 / tpbi.2002.1589 . PMID 12167362 .
  4. ↑ Ania M. Cutiño-Jiménez, Marinalva Martins-Pinheiro, Wanessa C. Lima, Alexander Martín-Tornet, Osleidys G. Morales, Carlos FM Menck: Evolutionary placement of Xanthomonadales based on conserved protein signature sequences . In: Molecular Phylogenetics and Evolution . 54, No. 2, 2010, pp. 524-34. doi : 10.1016 / j.ympev.2009.09.026 . PMID 19786109 .
  5. ^ A b Antonis Rokas, Peter WH Holland: Rare genomic changes as a tool for phylogenetics . In: Trends in Ecology & Evolution . 15, No. 11, 2000. doi : 10.1016 / S0169-5347 (00) 01967-4 . PMID 11050348 .
  6. ↑ James R. Brown, Christophe J. Douady, Michael J. Italia, William E. Marshall, Michael J. Stanhope: Universal trees based on large combined protein sequence data sets . In: Nature Genetics . 28, No. 3, 2001, pp. 281-5. doi : 10.1038 / 90129 . PMID 11431701 .
  7. ^ T Cavalier-Smith: The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification . In: International Journal of Systematic and Evolutionary Microbiology . 52, No. 1, 2002, pp. 7-76. PMID 11837318 .
  8. ↑ FD Ciccarelli, T Doerks, C Von Mering, CJ Creevey, B Snel, P Bork: Toward Automatic Reconstruction of a Highly Resolved Tree of Life . In: Science . 311, No. 5765, 2006, pp. 1283-7. doi : 10.1126 / science.1123061 . PMID 16513982 .
  9. ↑ V. Daubin, M Gouy, G Perrière: A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a core of Genes sharing a common history . In: Genome Research . 12, No. 7, 2002, pp. 1080-90. doi : 10.1101 / gr.187002 . PMID 12097345 . PMC 186629 (free full text).
  10. ↑ Jonathan A. Eisen: The RecA Protein as a Model Molecule for Molecular Systematic Studies of Bacteria: Comparison of Trees of RecAs and 16S rRNAs from the Same Species . In: Journal of Molecular Evolution . 41, No. 6, 1995, pp. 1105-23. doi : 10.1007 / bf00173192 . PMID 8587109 . PMC 3188426 (free full text).
  11. ↑ E. Griffiths, RS Gupta: Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae . In: Microbiology . 153, No. 8, 2007. doi : 10.1099 / mic.0.2007 / 009118-0 . PMID 17660429 .
  12. ↑ Radhey S. Gupta: Evolutionary relationships among photosynthetic bacteria . In: Photosynthesis Research . 76, No. 1-3, 2003, pp. 173-83. doi : 10.1023 / A: 1024999314839 . PMID 16228576 .
  13. ↑ Emma Griffiths, Radhey S. Gupta: Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales . In: International Microbiology . 7, No. 1, 2004, pp. 41-52. PMID 15179606 .
  14. ↑ V. Gaget, p Gribaldo, N. Tandeau de Marsac: At rpoB signature sequence Provides unique resolution for the molecular typing of cyanobacteria. In: International journal of systematic and evolutionary microbiology. Volume 61, Pt 1 January 2011, pp. 170-183, ISSN  1466-5034 . doi : 10.1099 / ijs.0.019018-0 . PMID 20190018 .
  15. ↑ Y. Guillemin, A. Cornut-Thibaut, G. Gillet, F. Penin, A. Aouacheria: Characterization of unique signature sequences in the divergent maternal protein Bcl2l10. In: Molecular biology and evolution. Volume 28, Number 12, December 2011, pp. 3271-3283, ISSN  1537-1719 . doi : 10.1093 / molbev / msr152 . PMID 21705382 .
  16. ↑ Radhey S. Gupta, Vaibhav Bhandari: Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups . In: Antonie van Leeuwenhoek . 100, No. 1, 2011, pp. 1-34. doi : 10.1007 / s10482-011-9576-z . PMID 21503713 .