ORFeome explained

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,

1. Book: Ohara . O. . ORFeome Cloning . 10.1007/978-1-60761-232-2_1 . Reverse Chemical Genetics . Methods in Molecular Biology . 577 . 3–9 . 2009 . 978-1-60761-231-5 . 19718504 .
2. Titz B, Rajagopala SV, Goll J, Häuser R, McKevitt MT, Palzkill T, Uetz P . The binary protein interactome of Treponema pallidum--the syphilis spirochete . PLOS ONE . 3 . 5 . e2292 . 2008 . 18509523 . 2386257 . 10.1371/journal.pone.0002292 . 2008PLoSO...3.2292T . Hall . Neil. free .
3. Uetz P, Rajagopala SV, Dong YA, Haas J . From ORFeomes to protein interaction maps in viruses . Genome Research . 14 . 10B . 2029–33 . Oct 2004 . 15489322 . 10.1101/gr.2583304. free .
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 . 10.1128/IAI.73.7.4445-4450.2005 . 0019-9567 . 1168556 . 15972547.
5. Viadas C, Rodríguez MC, García-Lobo JM, Sangari FJ, López-Goñi I . Construction and evaluation of an ORFeome-based Brucella whole-genome DNA microarray . Microbial Pathogenesis . 47 . 4 . 189–95 . Oct 2009 . 19524659 . 10.1016/j.micpath.2009.06.002 .
6. Maier CJ, Maier RH, Virok DP, Maass M, Hintner H, Bauer JW, Onder K . Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae . BMC Genomics . 13 . 632 . 2012 . 23157390 . 3534531 . 10.1186/1471-2164-13-632 . free .
7. Rajagopala SV, Yamamoto N, Zweifel AE, Nakamichi T, Huang HK, Mendez-Rios JD, Franca-Koh J, Boorgula MP, Fujita K, Suzuki K, Hu JC, Wanner BL, Mori H, Uetz P . The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology . BMC Genomics . 11 . 470 . 2010 . 20701780 . 3091666 . 10.1186/1471-2164-11-470 . free .
8. Brettin T, Altherr MR, Du Y, Mason RM, Friedrich A, Potter L, Langford C, Keller TJ, Jens J, Howie H, Weyand NJ, Clary S, Prichard K, Wachocki S, Sodergren E, Dillard JP, Weinstock G, So M, Arvidson CG . Expression capable library for studies of Neisseria gonorrhoeae, version 1.0 . BMC Microbiology . 5 . 50 . 2005 . 16137322 . 1236931 . 10.1186/1471-2180-5-50 . free .
9. Labaer J, Qiu Q, Anumanthan A, Mar W, Zuo D, Murthy TV, Taycher H, Halleck A, Hainsworth E, Lory S, Brizuela L . The Pseudomonas aeruginosa PA01 gene collection . Genome Research . 14 . 10B . 2190–200 . Oct 2004 . 15489342 . 528936 . 10.1101/gr.2482804 .

Staphylococcus aureus^[10] and human herpesviruses^[11]

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