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==Examples==
==Examples==

===Universally conserved genes===
The most highly conserved genes are those that can be found in all organisms. These mainly comprise of the [[ncRNA]]s and proteins required for [[Transcription (biology)|transcription]] and [[Translation (biology)|translation]], which are assumed to have been conserved from the [[last universal common ancestor]] of all life.<ref>{{cite journal|last1=Isenbarger|first1=Thomas A.|last2=Carr|first2=Christopher E.|last3=Johnson|first3=Sarah Stewart|last4=Finney|first4=Michael|last5=Church|first5=George M.|last6=Gilbert|first6=Walter|last7=Zuber|first7=Maria T.|last8=Ruvkun|first8=Gary|title=The Most Conserved Genome Segments for Life Detection on Earth and Other Planets|journal=Origins of Life and Evolution of Biospheres|date=14 October 2008|volume=38|issue=6|pages=517–533|doi=10.1007/s11084-008-9148-z}}</ref>


===Ultra-conserved elements===
===Ultra-conserved elements===

Revision as of 07:06, 10 December 2017

Compare sequence motifs and protein domains.
A sequence alignment of mammalian histone proteins
Sequences are the amino acids for residues 120-180 of the proteins. Residues that are conserved across all sequences are highlighted in grey. Below the protein sequences is a key denoting conserved sequence (*), conservative mutations (:), semi-conservative mutations (.), and non-conservative mutations ( ).[1]

In evolutionary biology, conserved sequences are similar or identical sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences) or within a genome (paralogous sequences). Conservation indicates that a sequence has been maintained by natural selection.

A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. Examples of highly conserved sequences include the include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst Eukaryotes, and the tmRNA in Bacteria.

History

See also: History of molecular evolution

The discovery of the role of DNA in inheritance, and observations by Frederick Sanger of variation between animal insulins in 1949,[2] prompted early molecular biologists to study taxonomy from a molecular perspective.[3][4] Studies in the 1960’s used DNA hybridization and protein cross-reactivity techniques to measure similarity between known orthologous proteins, such as hemoglobin[5] and Cytochrome C.[6] In 1965, Émile Zuckerkandl and Linus Pauling introduced the concept of the molecular clock,[7] proposing that steady rates of mutation could be used to estimate the time since two organisms diverged. While initial phylogenies closely matched the fossil record, observations that some genes appeared to evolve at different rates led to the development of theories of molecular evolution.[8][9] Margaret Dayhoff's 1966 comparison of ferrodoxin sequences showed that natural selection would act to conserve and optimise protein sequences essential to life.[10]

Mechanisms

See also: Natural selection and Neutral theory of molecular evolution

Over many generations, nucleic acid sequences in the genome of an evolutionary lineage can gradually change or erode over time due to random mutations and deletions.[11][12] Sequences may also recombine or be deleted due to chromosomal rearrangements. Conserved sequences are sequences which persist in the genome despite such forces, and have slower rates of mutation than the background mutation rate. [13]

Conservation can occur in coding and non-coding nucleic acid sequences. The extent to which a sequence is conserved can be affected by its function and robustness to mutation, varying selection pressures, population size and genetic drift. Many functional sequences are also modular, containing regions which may be subject to independent selection pressures, such as protein domains.

Nucleic acid and protein sequences

Highly conserved DNA sequences are thought to have functional value. The role for many of these highly conserved non-coding DNA sequences is not understood. A common notation to denote the level of sequence conservation is used by the clustal alignment programs. Below a set of aligned sequences, residue columns are indicated as fully conserved (*), containing only conservative mutations (:), semi-conservative mutations (.), and non-conservative mutations ( ).[14]

Examples

Universally conserved genes

The most highly conserved genes are those that can be found in all organisms. These mainly comprise of the ncRNAs and proteins required for transcription and translation, which are assumed to have been conserved from the last universal common ancestor of all life.[15]

Ultra-conserved elements

Sequences that are highly similar or identical across multiple species are termed ultra-conserved elements or UCEs. UCEs were first discovered in vertebrates,[16] and have subsequently been identified within various taxonomic groupings.[17] While the origin and function of UCEs are poorly understood,[18] they have been used to investigate deep-time divergences in amniotes,[19] insects, [20] and between animals and plants. [21]

GERP scores

A GERP (Genomic Evolutionary Rate Profiling) score measures evolutionary conservation of genetic sequences across species.[22] There is a relationship between a sequence's GERP score and the proportion of variant alleles within that sequence. As the GERP score of a sequence increases, variation within that sequence becomes more rare. A higher GERP signifies a highly conserved sequence, where alteration is harmful, so adverse variants would reduce the fitness of the organism and be selected against.

Biological role

Sequences are only likely to be highly conserved through geological time if they are required for basic cellular functions (such as coding for vital enzymes), stability, embryonic development, reproduction. Sequence similarity is used as evidence of structural and functional conservation, and evolutionary relationships between sequences. Consequently, functional elements are frequently identified by searching for conserved sequences in a genome.

Conservation of protein-coding sequences leads to the presence of identical amino acid residues at analogous regions of the protein structure and hence similar function. Conservative mutations alter amino acids to similar chemically residues and so may still not affect the protein's function. Among the most highly conserved sequences are the active sites of enzymes and the binding sites of protein receptors.[citation needed]

Conserved non-coding sequences do not encode protein, but often harbour cis-regulatory elements, including the evo-devo gene toolkit. Some deletions of highly conserved sequences in humans (hCONDELs) and other organisms have been suggested to be a potential cause of the anatomical and behavioural differences between humans and other mammals.[23][24] The TATA promoter sequence is an example of a highly conserved DNA sequence found in most eukaryotes.[25]

Applications

The research of conserved genetic sequences is extremely beneficial to the scientific community. The detection of similar sequences across diverse species’ genomes can provide useful information regarding the evolutionary history of these species. Additionally, the examination of conserved sequences can aid medical research. By identifying rare alleles within conserved sequences, information can be compiled and used to assess risk of disease among humans. Genome-wide association studies (GWAS) compare various alleles across the human genome and their association with risk for a particular diseases or ailments.[citation needed]

See also

References

  1. ^ "Clustal FAQ #Symbols". Clustal. Retrieved 8 December 2014.
  2. ^ Sanger, F. (24 September 1949). "Species Differences in Insulins". Nature. 164 (4169): 529–529. doi:10.1038/164529a0.
  3. ^ Marmur, J; Falkow, S; Mandel, M (October 1963). "New Approaches to Bacterial Taxonomy". Annual Review of Microbiology. 17 (1): 329–372. doi:10.1146/annurev.mi.17.100163.001553.
  4. ^ Pace, N. R.; Sapp, J.; Goldenfeld, N. (17 January 2012). "Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life". Proceedings of the National Academy of Sciences. 109 (4): 1011–1018. doi:10.1073/pnas.1109716109.
  5. ^ Zuckerlandl, Emile; Pauling, Linus B. (1962). "Molecular disease, evolution, and genetic heterogeneity". Horizons in Biochemistry: 189–225.
  6. ^ Margoliash, E (October 1963). "PRIMARY STRUCTURE AND EVOLUTION OF CYTOCHROME C". Proc Natl Acad Sci U S A. 50 (4): 672–679.
  7. ^ Zuckerkandl, E; Pauling, LB (1965). "Evolutionary Divergence and Convergence in Proteins". Evolving Genes and Proteins: 96–166. doi:10.1016/B978-1-4832-2734-4.50017-6.
  8. ^ Marmur, J; Falkow, S; Mandel, M (October 1963). "New Approaches to Bacterial Taxonomy". Annual Review of Microbiology. 17 (1): 329–372. doi:10.1146/annurev.mi.17.100163.001553.
  9. ^ Pace, N. R.; Sapp, J.; Goldenfeld, N. (17 January 2012). "Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life". Proceedings of the National Academy of Sciences. 109 (4): 1011–1018. doi:10.1073/pnas.1109716109.
  10. ^ Eck, R. V.; Dayhoff, M. O. (15 April 1966). "Evolution of the Structure of Ferredoxin Based on Living Relics of Primitive Amino Acid Sequences". Science. 152 (3720): 363–366. doi:10.1126/science.152.3720.363.
  11. ^ Kimura, M (17 February 1968). "Evolutionary Rate at the Molecular Level". Nature. 217 (5129): 624–626. doi:10.1038/217624a0.
  12. ^ King, J. L.; Jukes, T. H. (16 May 1969). "Non-Darwinian Evolution". Science. 164 (3881): 788–798. doi:10.1126/science.164.3881.788.
  13. ^ Kimura, M; Ohta, T (1974). "On Some Principles Governing Molecular Evolution" (PDF). Proc Natl Acad Sci USA. 71 (7): 2848–2852. PMC 388569.
  14. ^ "Clustal FAQ #Symbols". Clustal. Retrieved 8 December 2014.
  15. ^ Isenbarger, Thomas A.; Carr, Christopher E.; Johnson, Sarah Stewart; Finney, Michael; Church, George M.; Gilbert, Walter; Zuber, Maria T.; Ruvkun, Gary (14 October 2008). "The Most Conserved Genome Segments for Life Detection on Earth and Other Planets". Origins of Life and Evolution of Biospheres. 38 (6): 517–533. doi:10.1007/s11084-008-9148-z.
  16. ^ Bejerano, G. (28 May 2004). "Ultraconserved Elements in the Human Genome". Science. 304 (5675): 1321–1325. doi:10.1126/science.1098119.
  17. ^ Siepel, A. (1 August 2005). "Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes". Genome Research. 15 (8): 1034–1050. doi:10.1101/gr.3715005.
  18. ^ Harmston, N.; Baresic, A.; Lenhard, B. (11 November 2013). "The mystery of extreme non-coding conservation". Philosophical Transactions of the Royal Society B: Biological Sciences. 368 (1632): 20130021–20130021. doi:10.1098/rstb.2013.0021.
  19. ^ Faircloth, B. C.; McCormack, J. E.; Crawford, N. G.; Harvey, M. G.; Brumfield, R. T.; Glenn, T. C. (9 January 2012). "Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales". Systematic Biology. 61 (5): 717–726. doi:10.1093/sysbio/sys004.
  20. ^ Faircloth, Brant C.; Branstetter, Michael G.; White, Noor D.; Brady, Seán G. (May 2015). "Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera". Molecular Ecology Resources. 15 (3): 489–501. doi:10.1111/1755-0998.12328.
  21. ^ Reneker, J.; Lyons, E.; Conant, G. C.; Pires, J. C.; Freeling, M.; Shyu, C.-R.; Korkin, D. (10 April 2012). "Long identical multispecies elements in plant and animal genomes". Proceedings of the National Academy of Sciences. 109 (19): E1183–E1191. doi:10.1073/pnas.1121356109.
  22. ^ Genomic Evolutionary Rate Profiling at Sidow Lab
  23. ^ McLean, Cory Y.; et al. (10 March 2011). "Human-specific loss of regulatory DNA and the evolution of human-specific traits". Nature. 471 (7337): 216–219. doi:10.1038/nature09774. PMC 3071156. PMID 21390129.
  24. ^ Gross, Liza (September 2007). "Are "Ultraconserved" Genetic Elements Really Indispensable?". PLOS Biology. 5 (9): e253. doi:10.1371/journal.pbio.0050253. PMC 1964769. PMID 20076686.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  25. ^ Patikoglou, G. A.; Kim, J. L.; Sun, L.; Yang, S.-H.; Kodadek, T.; Burley, S. K. (15 December 1999). "TATA element recognition by the TATA box-binding protein has been conserved throughout evolution". Genes & Development. 13 (24): 3217–3230. doi:10.1101/gad.13.24.3217. PMC 317201. PMID 10617571.

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