Update on the Keio collection of Escherichia coli single‐gene deletion mutants
| Autor: | Miki Hasegawa, Barry L. Wanner, Kenji Nakahigashi, Yae Touda, Mihoko Yoshino, Satoko Kinjyo, Toru Nakayashiki, Yuki Takai, Hitomi Dose, Hirotada Mori, Natsuko Yamamoto, Tomoko Nakamichi, Akemi Furubayashi, Masaru Tomita, Kirill A. Datsenko |
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| Jazyk: | angličtina |
| Rok vydání: | 2009 |
| Předmět: |
DNA
Bacterial Pseudogene DNA Mutational Analysis Mutant Biology Polymerase Chain Reaction General Biochemistry Genetics and Molecular Biology Open Reading Frames Gene Duplication Correspondence Databases Genetic Coding region ORFS Insertion sequence Gene Sequence Deletion Genetics Escherichia coli K12 General Immunology and Microbiology Applied Mathematics Gene Expression Regulation Bacterial Open reading frame Computational Theory and Mathematics GenBank General Agricultural and Biological Sciences Information Systems |
| Zdroj: | Molecular Systems Biology |
| ISSN: | 1744-4292 |
| Popis: | Mol Syst Biol. 5: 335 The Keio collection (Baba et al , 2006) has been established as a set of single‐gene deletion mutants of Escherichia coli K‐12. These mutants have a precisely designed deletion from the second codon from the seventh to the last codon of each predicted ORF. Further information is available at http://sal.cs.purdue.edu:8097/GB7/index.jsp or http://ecoli.naist.jp/. The distribution is now being handled by the National Institute of Genetics of Japan (http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp). To date more than 4 million samples have been distributed worldwide. As we described earlier (Baba et al , 2006), gene amplification during construction is likely to have led to a small number of mutants with genetic duplications. The design of the Keio deletions was based on annotations that are now outdated. Of 4288 ORFs targeted, mutants were obtained for 3985 (Baba et al , 2006). Re‐annotation based on highly accurate sequencing of E. coli K‐12 (Hayashi et al , 2006) led to changing many coding regions and the total number of ORFs to 4296, including pseudogenes (Riley et al , 2006) (Supplementary Table I). The recent E. coli K‐12 MG1655 GenBank record (U0096, released in December 2008) has an additional 97 ORFs (exclusive of the ORFs in IS elements, Supplementary Table II) that were not targeted. Of these 4214 annotated ORFs, 4186 were targeted for deletion and 28 were not (Supplementary Table III), which resulted in the isolation of two independent mutants for 3864 targeted ORFs. No deletion was found for 299 ORFs, which are candidates for essential genes. Deletions were also isolated for 23 other ORFs; however, re‐annotation led to re‐classification of these ORFs as ‘split ORFs’, because their coding … |
| Databáze: | OpenAIRE |
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