Biology:ORFeome

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In, molecular genetics, an ORFeome refers to the complete set of open reading frames (ORFs) in a genome. The term may also be used to describe a set of cloned ORFs.[1] ORFs correspond to the protein coding sequences (CDS) of genes. ORFs can be found in genome sequences by computer programs such as GENSCAN and then amplified by PCR. While this is relatively trivial in bacteria the problem is non-trivial in eukaryotic genomes because of the presence of introns and exons as well as splice variants.

Use in research

The usage of complete ORFeomes reflects a new trend in biology that can be succinctly summarized as omics. ORFeomes are used for the study of protein-protein interactions,[2][3] protein microarrays, the study of antigens,[4] and other fields of study.

Cloned ORFeomes

Complete ORF sets have been cloned for a number of organisms including Brucella melitensis,[5] Chlamydia pneumoniae,[6] Escherichia coli,[7] Neisseria gonorrhoeae,[8] Pseudomonas aeruginosa,[9] Schizosaccharomyces pombe, Staphylococcus aureus[10] and human herpesviruses[11]

A partial human ORFeome has also been produced.[12][13]

References

  1. ↑ Ohara, O. (2009). "ORFeome Cloning". Reverse Chemical Genetics. Methods in Molecular Biology. 577. pp. 3–9. doi:10.1007/978-1-60761-232-2_1. ISBN 978-1-60761-231-5. 
  2. ↑ Hall, Neil, ed (2008). "The binary protein interactome of Treponema pallidum--the syphilis spirochete". PLOS ONE 3 (5): e2292. doi:10.1371/journal.pone.0002292. PMID 18509523. Bibcode: 2008PLoSO...3.2292T.  open access
  3. ↑ "From ORFeomes to protein interaction maps in viruses". Genome Research 14 (10B): 2029–33. Oct 2004. doi:10.1101/gr.2583304. PMID 15489322. 
  4. ↑ McKevitt, Matthew; Brinkman, Mary Beth; McLoughlin, Melanie; Perez, Carla; Howell, Jerrilyn K.; Weinstock, George M.; Norris, Steven J.; Palzkill, Timothy (2005-07-01). "Genome scale identification of Treponema pallidum antigens". Infection and Immunity 73 (7): 4445–4450. doi:10.1128/IAI.73.7.4445-4450.2005. ISSN 0019-9567. PMID 15972547. 
  5. ↑ "Construction and evaluation of an ORFeome-based Brucella whole-genome DNA microarray". Microbial Pathogenesis 47 (4): 189–95. Oct 2009. doi:10.1016/j.micpath.2009.06.002. PMID 19524659. 
  6. ↑ "Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae". BMC Genomics 13: 632. 2012. doi:10.1186/1471-2164-13-632. PMID 23157390. 
  7. ↑ "The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology". BMC Genomics 11: 470. 2010. doi:10.1186/1471-2164-11-470. PMID 20701780. 
  8. ↑ "Expression capable library for studies of Neisseria gonorrhoeae, version 1.0". BMC Microbiology 5: 50. 2005. doi:10.1186/1471-2180-5-50. PMID 16137322. 
  9. ↑ "The Pseudomonas aeruginosa PA01 gene collection". Genome Research 14 (10B): 2190–200. Oct 2004. doi:10.1101/gr.2482804. PMID 15489342. 
  10. ↑ "The ORFeome of Staphylococcus aureus v 1.1". BMC Genomics 9: 321. 2008. doi:10.1186/1471-2164-9-321. PMID 18605992. 
  11. ↑ Sun, Ren, ed (Sep 2009). "Evolutionarily conserved herpesviral protein interaction networks". PLOS Pathogens 5 (9): e1000570. doi:10.1371/journal.ppat.1000570. PMID 19730696. 
  12. ↑ "hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes". Genomics 89 (3): 307–15. Mar 2007. doi:10.1016/j.ygeno.2006.11.012. PMID 17207965. 
  13. ↑ http://horfdb.dfci.harvard.edu/ Human ORFeome 2011 Release



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