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Unusual Activity of a Chlamydomonas TET/JBP Family Enzyme.

Aravind L, Balasubramanian S, Rao A.

Biochemistry. 2019 Sep 3;58(35):3627-3629. doi: 10.1021/acs.biochem.9b00609. Epub 2019 Aug 22. No abstract available.


The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis.

Zhang C, Hung YH, Rim HJ, Zhang D, Frost JM, Shin H, Jang H, Liu F, Xiao W, Iyer LM, Aravind L, Zhang XQ, Fischer RL, Huh JH, Hsieh TF.

Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17563-17571. doi: 10.1073/pnas.1907290116. Epub 2019 Aug 13.


Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome.

Boulias K, Toczydłowska-Socha D, Hawley BR, Liberman N, Takashima K, Zaccara S, Guez T, Vasseur JJ, Debart F, Aravind L, Jaffrey SR, Greer EL.

Mol Cell. 2019 Aug 8;75(3):631-643.e8. doi: 10.1016/j.molcel.2019.06.006. Epub 2019 Jul 3.


Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.

Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH.

Nat Struct Mol Biol. 2019 Jul;26(7):607-612. doi: 10.1038/s41594-019-0246-6. Epub 2019 Jun 24.


Evidence based interventions and implementation gaps in control of tuberculosis: A systematic review in low and middle-income countries with special focus on India.

Indira Krishnan AK, Mini GK, Aravind LR.

Indian J Tuberc. 2019 Apr;66(2):268-278. doi: 10.1016/j.ijtb.2019.04.006. Epub 2019 Apr 11. Review.


Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives.

Burroughs AM, Glasner ME, Barry KP, Taylor EA, Aravind L.

J Biol Chem. 2019 Jun 28;294(26):10211-10235. doi: 10.1074/jbc.RA119.007595. Epub 2019 May 15.


Antimicrobial Peptides, Polymorphic Toxins, and Self-Nonself Recognition Systems in Archaea: an Untapped Armory for Intermicrobial Conflicts.

Makarova KS, Wolf YI, Karamycheva S, Zhang D, Aravind L, Koonin EV.

MBio. 2019 May 7;10(3). pii: e00715-19. doi: 10.1128/mBio.00715-19.


Deciphering the Role of a SLOG Superfamily Protein YpsA in Gram-Positive Bacteria.

Brzozowski RS, Huber M, Burroughs AM, Graham G, Walker M, Alva SS, Aravind L, Eswara PJ.

Front Microbiol. 2019 Apr 5;10:623. doi: 10.3389/fmicb.2019.00623. eCollection 2019.


The Origin and Evolution of Release Factors: Implications for Translation Termination, Ribosome Rescue, and Quality Control Pathways.

Burroughs AM, Aravind L.

Int J Mol Sci. 2019 Apr 23;20(8). pii: E1981. doi: 10.3390/ijms20081981. Review.


Retraction Note: Vibrio parahaemolyticus RhsP represents a widespread group of pro-effectors for type VI secretion systems.

Jiang N, Tang L, Xie R, Li Z, Burkinshaw B, Liang X, Sosa D, Aravind L, Dong T, Zhang D, Zheng J.

Nat Commun. 2019 Mar 15;10(1):1277. doi: 10.1038/s41467-019-09094-0.


Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile Elements.

Krishnan A, Burroughs AM, Iyer LM, Aravind L.

iScience. 2018 Nov 30;9:192-208. doi: 10.1016/j.isci.2018.10.017. Epub 2018 Oct 23.


Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost.

Matteoli FP, Passarelli-Araujo H, Reis RJA, da Rocha LO, de Souza EM, Aravind L, Olivares FL, Venancio TM.

BMC Genomics. 2018 Oct 16;19(1):750. doi: 10.1186/s12864-018-5130-y.


Vibrio parahaemolyticus RhsP represents a widespread group of pro-effectors for type VI secretion systems.

Jiang N, Tang L, Xie R, Li Z, Burkinshaw B, Liang X, Sosa D, Aravind L, Dong T, Zhang D, Zheng J.

Nat Commun. 2018 Sep 25;9(1):3899. doi: 10.1038/s41467-018-06201-5. Retraction in: Nat Commun. 2019 Mar 15;10(1):1277.


Loss of the Spinocerebellar Ataxia type 3 disease protein ATXN3 alters transcription of multiple signal transduction pathways.

Zeng L, Zhang D, McLoughlin HS, Zalon AJ, Aravind L, Paulson HL.

PLoS One. 2018 Sep 19;13(9):e0204438. doi: 10.1371/journal.pone.0204438. eCollection 2018.


TCRβ-expressing macrophages induced by a pathogenic murine malaria correlate with parasite burden and enhanced phagocytic activity.

Oakley MS, Chorazeczewski JK, Aleshnick M, Anantharaman V, Majam V, Chawla B, Myers TG, Su Q, Okoth WA, Takeda K, Akue A, KuKuruga M, Aravind L, Kumar S.

PLoS One. 2018 Jul 25;13(7):e0201043. doi: 10.1371/journal.pone.0201043. eCollection 2018.


Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo-like domains from bacteria and eukaryotes.

Kaur G, Iyer LM, Subramanian S, Aravind L.

Sci Rep. 2018 Apr 18;8(1):6196. doi: 10.1038/s41598-018-24467-z.


Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes.

Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ.

Nature. 2018 May;557(7705):446-451. doi: 10.1038/s41586-018-0022-5. Epub 2018 Apr 9.


Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys.

Holland SJ, Berghuis LM, King JJ, Iyer LM, Sikora K, Fifield H, Peter S, Quinlan EM, Sugahara F, Shingate P, Trancoso I, Iwanami N, Temereva E, Strohmeier C, Kuratani S, Venkatesh B, Evanno G, Aravind L, Schorpp M, Larijani M, Boehm T.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3211-E3220. doi: 10.1073/pnas.1720871115. Epub 2018 Mar 19.


Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity.

Krishnan A, Iyer LM, Holland SJ, Boehm T, Aravind L.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):E3201-E3210. doi: 10.1073/pnas.1720897115. Epub 2018 Mar 19.


Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria.

Ravi J, Anantharaman V, Aravind L, Gennaro ML.

Antonie Van Leeuwenhoek. 2018 May;111(5):753-760. doi: 10.1007/s10482-018-1053-5. Epub 2018 Feb 27.


Structure-function analysis of manganese exporter proteins across bacteria.

Zeinert R, Martinez E, Schmitz J, Senn K, Usman B, Anantharaman V, Aravind L, Waters LS.

J Biol Chem. 2018 Apr 13;293(15):5715-5730. doi: 10.1074/jbc.M117.790717. Epub 2018 Feb 13.


CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog.

Pusapati GV, Kong JH, Patel BB, Krishnan A, Sagner A, Kinnebrew M, Briscoe J, Aravind L, Rohatgi R.

Dev Cell. 2018 Jan 22;44(2):271. doi: 10.1016/j.devcel.2018.01.002. No abstract available.


Inferring joint sequence-structural determinants of protein functional specificity.

Neuwald AF, Aravind L, Altschul SF.

Elife. 2018 Jan 16;7. pii: e29880. doi: 10.7554/eLife.29880.


CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog.

Pusapati GV, Kong JH, Patel BB, Krishnan A, Sagner A, Kinnebrew M, Briscoe J, Aravind L, Rohatgi R.

Dev Cell. 2018 Jan 8;44(1):113-129.e8. doi: 10.1016/j.devcel.2017.12.003. Epub 2017 Dec 28. Erratum in: Dev Cell. 2018 Jan 22;44(2):271.


A Nonhemolytic Group B Streptococcus Strain Exhibits Hypervirulence.

Gendrin C, Vornhagen J, Armistead B, Singh P, Whidbey C, Merillat S, Knupp D, Parker R, Rogers LM, Quach P, Iyer LM, Aravind L, Manning SD, Aronoff DM, Rajagopal L.

J Infect Dis. 2018 Mar 5;217(6):983-987. doi: 10.1093/infdis/jix646.


O-GlcNAcylation destabilizes the active tetrameric PKM2 to promote the Warburg effect.

Wang Y, Liu J, Jin X, Zhang D, Li D, Hao F, Feng Y, Gu S, Meng F, Tian M, Zheng Y, Xin L, Zhang X, Han X, Aravind L, Wei M.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13732-13737. doi: 10.1073/pnas.1704145115. Epub 2017 Dec 11.


Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease.

Kweon SM, Zhu B, Chen Y, Aravind L, Xu SY, Feldman DE.

Cell Rep. 2017 Oct 10;21(2):482-494. doi: 10.1016/j.celrep.2017.09.055.


Multifunctional Involvement of a C2H2 Zinc Finger Protein (PbZfp) in Malaria Transmission, Histone Modification, and Susceptibility to DNA Damage Response.

Gopalakrishnan AM, Aly ASI, Aravind L, Kumar N.

MBio. 2017 Aug 29;8(4). pii: e01298-17. doi: 10.1128/mBio.01298-17.


Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects.

Ribeiro L, Tobias-Santos V, Santos D, Antunes F, Feltran G, de Souza Menezes J, Aravind L, Venancio TM, Nunes da Fonseca R.

PLoS Genet. 2017 Jul 3;13(7):e1006868. doi: 10.1371/journal.pgen.1006868. eCollection 2017 Jul.


Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements.

Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L.

J Bacteriol. 2017 Jul 11;199(15). pii: e00245-17. doi: 10.1128/JB.00245-17. Print 2017 Aug 1.


Erratum: THEMIS enhances TCR signaling and enables positive selection by selective inhibition of the phosphatase SHP-1.

Choi S, Warzecha C, Zvezdova E, Lee J, Argenty J, Lesourne R, Aravind L, Love PE.

Nat Immunol. 2017 May 18;18(6):705. doi: 10.1038/ni0617-705c. No abstract available.


Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts.

Burroughs AM, Kaur G, Zhang D, Aravind L.

Cell Cycle. 2017 Jun 3;16(11):1093-1103. doi: 10.1080/15384101.2017.1315494. Epub 2017 Apr 25.


A conserved NAD+ binding pocket that regulates protein-protein interactions during aging.

Li J, Bonkowski MS, Moniot S, Zhang D, Hubbard BP, Ling AJ, Rajman LA, Qin B, Lou Z, Gorbunova V, Aravind L, Steegborn C, Sinclair DA.

Science. 2017 Mar 24;355(6331):1312-1317. doi: 10.1126/science.aad8242.


THEMIS enhances TCR signaling and enables positive selection by selective inhibition of the phosphatase SHP-1.

Choi S, Warzecha C, Zvezdova E, Lee J, Argenty J, Lesourne R, Aravind L, Love PE.

Nat Immunol. 2017 Apr;18(4):433-441. doi: 10.1038/ni.3692. Epub 2017 Feb 27. Erratum in: Nat Immunol. 2017 May 18;18(6):705.


Molecular Markers of Radiation Induced Attenuation in Intrahepatic Plasmodium falciparum Parasites.

Oakley MS, Verma N, Zheng H, Anantharaman V, Takeda K, Gao Y, Myers TG, Pham PT, Mahajan B, Kumar N, Sangweme D, Tripathi AK, Mlambo G, Aravind L, Kumar S.

PLoS One. 2016 Dec 2;11(12):e0166814. doi: 10.1371/journal.pone.0166814. eCollection 2016.


The mechanism of force transmission at bacterial focal adhesion complexes.

Faure LM, Fiche JB, Espinosa L, Ducret A, Anantharaman V, Luciano J, Lhospice S, Islam ST, Tréguier J, Sotes M, Kuru E, Van Nieuwenhze MS, Brun YV, Théodoly O, Aravind L, Nollmann M, Mignot T.

Nature. 2016 Nov 24;539(7630):530-535. doi: 10.1038/nature20121. Epub 2016 Oct 5.


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. Epub 2016 Aug 17. Review.


Editorial overview: Sequences and topology: Protein function - synthesizing information from sequence, structure and disorder.

Meiering EM, Aravind L.

Curr Opin Struct Biol. 2016 Jun;38:vii-ix. doi: 10.1016/ Epub 2016 Jul 8. No abstract available.


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. Epub 2016 Apr 8.


Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification.

Iyer LM, Zhang D, Aravind L.

Bioessays. 2016 Jan;38(1):27-40. doi: 10.1002/bies.201500104. Epub 2015 Dec 12. Review.


Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

Mesquita RD, Vionette-Amaral RJ, Lowenberger C, Rivera-Pomar R, Monteiro FA, Minx P, Spieth J, Carvalho AB, Panzera F, Lawson D, Torres AQ, Ribeiro JM, Sorgine MH, Waterhouse RM, Montague MJ, Abad-Franch F, Alves-Bezerra M, Amaral LR, Araujo HM, Araujo RN, Aravind L, Atella GC, Azambuja P, Berni M, Bittencourt-Cunha PR, Braz GR, Calderón-Fernández G, Carareto CM, Christensen MB, Costa IR, Costa SG, Dansa M, Daumas-Filho CR, De-Paula IF, Dias FA, Dimopoulos G, Emrich SJ, Esponda-Behrens N, Fampa P, Fernandez-Medina RD, da Fonseca RN, Fontenele M, Fronick C, Fulton LA, Gandara AC, Garcia ES, Genta FA, Giraldo-Calderón GI, Gomes B, Gondim KC, Granzotto A, Guarneri AA, Guigó R, Harry M, Hughes DS, Jablonka W, Jacquin-Joly E, Juárez MP, Koerich LB, Lange AB, Latorre-Estivalis JM, Lavore A, Lawrence GG, Lazoski C, Lazzari CR, Lopes RR, Lorenzo MG, Lugon MD, Majerowicz D, Marcet PL, Mariotti M, Masuda H, Megy K, Melo AC, Missirlis F, Mota T, Noriega FG, Nouzova M, Nunes RD, Oliveira RL, Oliveira-Silveira G, Ons S, Orchard I, Pagola L, Paiva-Silva GO, Pascual A, Pavan MG, Pedrini N, Peixoto AA, Pereira MH, Pike A, Polycarpo C, Prosdocimi F, Ribeiro-Rodrigues R, Robertson HM, Salerno AP, Salmon D, Santesmasses D, Schama R, Seabra-Junior ES, Silva-Cardoso L, Silva-Neto MA, Souza-Gomes M, Sterkel M, Taracena ML, Tojo M, Tu ZJ, Tubio JM, Ursic-Bedoya R, Venancio TM, Walter-Nuno AB, Wilson D, Warren WC, Wilson RK, Huebner E, Dotson EM, Oliveira PL.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14936-41. doi: 10.1073/pnas.1506226112. Epub 2015 Nov 16. Erratum in: Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):E1415-6. Lange, Angela B [added]; Orchard, Ian [added].


Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling.

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

Nucleic Acids Res. 2015 Dec 15;43(22):10633-54. doi: 10.1093/nar/gkv1267. Epub 2015 Nov 20.


Transcription factors, chromatin proteins and the diversification of Hemiptera.

Vidal NM, Grazziotin AL, Iyer LM, Aravind L, Venancio TM.

Insect Biochem Mol Biol. 2016 Feb;69:1-13. doi: 10.1016/j.ibmb.2015.07.001. Epub 2015 Jul 29.


Expression, Purification, and Biological Characterization of Babesia microti Apical Membrane Antigen 1.

Moitra P, Zheng H, Anantharaman V, Banerjee R, Takeda K, Kozakai Y, Lepore T, Krause PJ, Aravind L, Kumar S.

Infect Immun. 2015 Oct;83(10):3890-901. doi: 10.1128/IAI.00168-15. Epub 2015 Jul 20.


DNA Methylation on N6-Adenine in C. elegans.

Greer EL, Blanco MA, Gu L, Sendinc E, Liu J, Aristizábal-Corrales D, Hsu CH, Aravind L, He C, Shi Y.

Cell. 2015 May 7;161(4):868-78. doi: 10.1016/j.cell.2015.04.005. Epub 2015 Apr 30.


The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element.

Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS, Storz G.

Mol Cell. 2015 Mar 19;57(6):1099-1109. doi: 10.1016/j.molcel.2015.01.035.


Whole exome sequencing identifies the TNNI3K gene as a cause of familial conduction system disease and congenital junctional ectopic tachycardia.

Xi Y, Honeywell C, Zhang D, Schwartzentruber J, Beaulieu CL, Tetreault M, Hartley T, Marton J, Vidal SM, Majewski J, Aravind L; Care4Rare Canada Consortium, Gollob M, Boycott KM, Gow RM.

Int J Cardiol. 2015 Apr 15;185:114-6. doi: 10.1016/j.ijcard.2015.03.130. Epub 2015 Mar 11. No abstract available.


Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide.

Samanovic MI, Tu S, Novák O, Iyer LM, McAllister FE, Aravind L, Gygi SP, Hubbard SR, Strnad M, Darwin KH.

Mol Cell. 2015 Mar 19;57(6):984-994. doi: 10.1016/j.molcel.2015.01.024. Epub 2015 Feb 26.


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