Literature DB >> 34591643

The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases.

Han Altae-Tran1,2,3,4,5, Soumya Kannan1,2,3,4,5, F Esra Demircioglu1,2,3,4,5, Rachel Oshiro1,2,3,4,5, Suchita P Nety1,2,3,4,5, Luke J McKay6,7,8, Mensur Dlakić9, William P Inskeep6,7, Kira S Makarova10, Rhiannon K Macrae1,2,3,4,5, Eugene V Koonin10, Feng Zhang1,2,3,4,5.   

Abstract

IscB proteins are putative nucleases encoded in a distinct family of IS200/IS605 transposons and are likely ancestors of the RNA-guided endonuclease Cas9, but the functions of IscB and its interactions with any RNA remain uncharacterized. Using evolutionary analysis, RNA sequencing, and biochemical experiments, we reconstructed the evolution of CRISPR-Cas9 systems from IS200/IS605 transposons. We found that IscB uses a single noncoding RNA for RNA-guided cleavage of double-stranded DNA and can be harnessed for genome editing in human cells. We also demonstrate the RNA-guided nuclease activity of TnpB, another IS200/IS605 transposon-encoded protein and the likely ancestor of Cas12 endonucleases. This work reveals a widespread class of transposon-encoded RNA-guided nucleases, which we name OMEGA (obligate mobile element–guided activity), with strong potential for developing as biotechnologies.

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Year:  2021        PMID: 34591643      PMCID: PMC8929163          DOI: 10.1126/science.abj6856

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  59 in total

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Authors:  Bernd Zetsche; Jonathan S Gootenberg; Omar O Abudayyeh; Ian M Slaymaker; Kira S Makarova; Patrick Essletzbichler; Sara E Volz; Julia Joung; John van der Oost; Aviv Regev; Eugene V Koonin; Feng Zhang
Journal:  Cell       Date:  2015-09-25       Impact factor: 41.582

Review 2.  The principles of guiding by RNA: chimeric RNA-protein enzymes.

Authors:  Alexander Hüttenhofer; Peter Schattner
Journal:  Nat Rev Genet       Date:  2006-06       Impact factor: 53.242

3.  Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

Authors:  P J Lockhart; A W Larkum; M Steel; P J Waddell; D Penny
Journal:  Proc Natl Acad Sci U S A       Date:  1996-03-05       Impact factor: 11.205

4.  GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments.

Authors:  Stephen M Crotty; Bui Quang Minh; Nigel G Bean; Barbara R Holland; Jonathan Tuke; Lars S Jermiin; Arndt Von Haeseler
Journal:  Syst Biol       Date:  2020-03-01       Impact factor: 15.683

5.  A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins.

Authors:  Steffen Frey; Dirk Görlich
Journal:  J Chromatogr A       Date:  2014-02-19       Impact factor: 4.759

6.  R2R--software to speed the depiction of aesthetic consensus RNA secondary structures.

Authors:  Zasha Weinberg; Ronald R Breaker
Journal:  BMC Bioinformatics       Date:  2011-01-04       Impact factor: 3.169

7.  ViennaRNA Package 2.0.

Authors:  Ronny Lorenz; Stephan H Bernhart; Christian Höner Zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F Stadler; Ivo L Hofacker
Journal:  Algorithms Mol Biol       Date:  2011-11-24       Impact factor: 1.405

8.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Authors:  Donovan H Parks; Michael Imelfort; Connor T Skennerton; Philip Hugenholtz; Gene W Tyson
Journal:  Genome Res       Date:  2015-05-14       Impact factor: 9.043

9.  Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity.

Authors:  Mart Krupovic; Kira S Makarova; Patrick Forterre; David Prangishvili; Eugene V Koonin
Journal:  BMC Biol       Date:  2014-05-19       Impact factor: 7.431

Review 10.  Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.

Authors:  Eugene V Koonin
Journal:  Biol Direct       Date:  2017-02-10       Impact factor: 4.540

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  22 in total

Review 1.  Advancement in CRISPR/Cas9 Technology to Better Understand and Treat Neurological Disorders.

Authors:  Aishika Datta; Deepaneeta Sarmah; Harpreet Kaur; Antra Chaudhary; Namrata Vadak; Anupom Borah; Sudhir Shah; Xin Wang; Pallab Bhattacharya
Journal:  Cell Mol Neurobiol       Date:  2022-06-25       Impact factor: 5.046

2.  Advances in gene editing without residual transgenes in plants.

Authors:  Yubing He; Michael Mudgett; Yunde Zhao
Journal:  Plant Physiol       Date:  2022-03-28       Impact factor: 8.340

3.  The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases.

Authors:  Han Altae-Tran; Soumya Kannan; F Esra Demircioglu; Rachel Oshiro; Suchita P Nety; Luke J McKay; Mensur Dlakić; William P Inskeep; Kira S Makarova; Rhiannon K Macrae; Eugene V Koonin; Feng Zhang
Journal:  Science       Date:  2021-09-09       Impact factor: 47.728

4.  Hypercompact adenine base editors based on transposase B guided by engineered RNA.

Authors:  Do Yon Kim; Yuhee Chung; Yujin Lee; Dongmin Jeong; Kwang-Hyun Park; Hyun Jung Chin; Jeong Mi Lee; Seyeon Park; Sumin Ko; Jeong-Heon Ko; Yong-Sam Kim
Journal:  Nat Chem Biol       Date:  2022-08-01       Impact factor: 16.174

5.  Structure-based evolutionary relationship between IscB and Cas9.

Authors:  Ning Jia; Dinshaw J Patel
Journal:  Cell Res       Date:  2022-10       Impact factor: 46.297

Review 6.  Mammalian genome innovation through transposon domestication.

Authors:  Andrew J Modzelewski; Johnny Gan Chong; Ting Wang; Lin He
Journal:  Nat Cell Biol       Date:  2022-08-25       Impact factor: 28.213

Review 7.  Structural biology of CRISPR-Cas immunity and genome editing enzymes.

Authors:  Joy Y Wang; Patrick Pausch; Jennifer A Doudna
Journal:  Nat Rev Microbiol       Date:  2022-05-13       Impact factor: 78.297

8.  icaR and icaT are Ancient Chromosome Genes Encoding Substrates of the Type III Secretion Apparatus in Shigella flexneri.

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Review 9.  New Editing Tools for Gene Therapy in Inherited Retinal Dystrophies.

Authors:  Juliette Pulman; José-Alain Sahel; Deniz Dalkara
Journal:  CRISPR J       Date:  2022-05-03

Review 10.  CRISPR-based genome editing through the lens of DNA repair.

Authors:  Tarun S Nambiar; Lou Baudrier; Pierre Billon; Alberto Ciccia
Journal:  Mol Cell       Date:  2022-01-20       Impact factor: 17.970

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