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RNA damage in biological conflicts and the diversity of responding RNA repair systems.

Burroughs AM, Aravind L.

Nucleic Acids Res. 2016 Oct 14;44(18):8525-8555.


A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts.

Hammani K, Takenaka M, Miranda R, Barkan A.

Nucleic Acids Res. 2016 May 19;44(9):4278-88. doi: 10.1093/nar/gkw270.


Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors.

Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L.

Nucleic Acids Res. 2016 May 5;44(8):3513-33. doi: 10.1093/nar/gkw221.


When the Scaffold Cannot Be Ignored: The Role of the Hydrophobic Core in Ligand Binding and Specificity.

Koulechova DA, Tripp KW, Horner G, Marqusee S.

J Mol Biol. 2015 Oct 9;427(20):3316-26. doi: 10.1016/j.jmb.2015.08.014.


A conserved glutamate residue in the C-terminal deaminase domain of pentatricopeptide repeat proteins is required for RNA editing activity.

Hayes ML, Dang KN, Diaz MF, Mulligan RM.

J Biol Chem. 2015 Apr 17;290(16):10136-42. doi: 10.1074/jbc.M114.631630.


A new family of secreted toxins in pathogenic Neisseria species.

Jamet A, Jousset AB, Euphrasie D, Mukorako P, Boucharlat A, Ducousso A, Charbit A, Nassif X.

PLoS Pathog. 2015 Jan 8;11(1):e1004592. doi: 10.1371/journal.ppat.1004592.


Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.

Fu CJ, Sheikh S, Miao W, Andersson SG, Baldauf SL.

Genome Biol Evol. 2014 Aug 21;6(9):2240-57. doi: 10.1093/gbe/evu180.


Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata.

Oldenkott B, Yamaguchi K, Tsuji-Tsukinoki S, Knie N, Knoop V.

RNA. 2014 Oct;20(10):1499-506. doi: 10.1261/rna.045575.114.


Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics.

Aravind L, Burroughs AM, Zhang D, Iyer LM.

Cold Spring Harb Perspect Biol. 2014 Jul 1;6(7):a016063. doi: 10.1101/cshperspect.a016063. Review.


Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.

Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR.

Nat Biotechnol. 2014 Jan;32(1):71-5. doi: 10.1038/nbt.2778.


New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing.

Burroughs AM, Ando Y, Aravind L.

Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):141-81. doi: 10.1002/wrna.1210. Review.


Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.

Hayes ML, Giang K, Berhane B, Mulligan RM.

J Biol Chem. 2013 Dec 20;288(51):36519-29. doi: 10.1074/jbc.M113.485755.


A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes.

Schallenberg-RĂ¼dinger M, Lenz H, Polsakiewicz M, Gott JM, Knoop V.

RNA Biol. 2013;10(9):1549-56. doi: 10.4161/rna.25755.


Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA.

Iyer LM, Zhang D, Burroughs AM, Aravind L.

Nucleic Acids Res. 2013 Sep;41(16):7635-55. doi: 10.1093/nar/gkt573.


Rhs proteins from diverse bacteria mediate intercellular competition.

Koskiniemi S, Lamoureux JG, Nikolakakis KC, t'Kint de Roodenbeke C, Kaplan MD, Low DA, Hayes CS.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7032-7. doi: 10.1073/pnas.1300627110.


Bacterial contact-dependent growth inhibition.

Ruhe ZC, Low DA, Hayes CS.

Trends Microbiol. 2013 May;21(5):230-7. doi: 10.1016/j.tim.2013.02.003. Review.

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