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Items: 1 to 50 of 345

1.

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.

2.

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.

PMID:
29632312
3.

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.

4.

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.

5.

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.

PMID:
29488183
6.

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.

PMID:
29440394
7.

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.

8.

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.

9.

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.

10.

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.

PMID:
29244079
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

PMID:
28518157
17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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/j.sbi.2016.06.016. Epub 2016 Jul 8. No abstract available.

24.

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.

25.

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.

26.

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].

27.

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.

28.

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.

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.

30.
31.

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.

32.

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.

33.

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.

34.

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.

35.
36.

Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis.

Burroughs AM, Aravind L.

Front Genet. 2014 Dec 23;5:424. doi: 10.3389/fgene.2014.00424. eCollection 2014.

37.

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Chavez L, Huang Y, Luong K, Agarwal S, Iyer LM, Pastor WA, Hench VK, Frazier-Bowers SA, Korol E, Liu S, Tahiliani M, Wang Y, Clark TA, Korlach J, Pukkila PJ, Aravind L, Rao A.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):E5149-58. doi: 10.1073/pnas.1419513111. Epub 2014 Nov 18.

38.

Multiple enzymatic activities of ParB/Srx superfamily mediate sexual conflict among conjugative plasmids.

Maindola P, Raina R, Goyal P, Atmakuri K, Ojha A, Gupta S, Christie PJ, Iyer LM, Aravind L, Arockiasamy A.

Nat Commun. 2014 Oct 31;5:5322. doi: 10.1038/ncomms6322.

39.

Selection of the lamprey VLRC antigen receptor repertoire.

Holland SJ, Gao M, Hirano M, Iyer LM, Luo M, Schorpp M, Cooper MD, Aravind L, Mariuzza RA, Boehm T.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14834-9. doi: 10.1073/pnas.1415655111. Epub 2014 Sep 16.

40.

Genomic donor cassette sharing during VLRA and VLRC assembly in jawless vertebrates.

Das S, Li J, Holland SJ, Iyer LM, Hirano M, Schorpp M, Aravind L, Cooper MD, Boehm T.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14828-33. doi: 10.1073/pnas.1415580111. Epub 2014 Sep 16.

41.

Editorial overview: Sequences and topology: sequences, structures, genomes and populations.

Aravind L, Orengo CA.

Curr Opin Struct Biol. 2014 Jun;26:vii-viii. doi: 10.1016/j.sbi.2014.06.005. Epub 2014 Jul 23. No abstract available.

PMID:
25088012
42.

The natural history of ADP-ribosyltransferases and the ADP-ribosylation system.

Aravind L, Zhang D, de Souza RF, Anand S, Iyer LM.

Curr Top Microbiol Immunol. 2015;384:3-32. doi: 10.1007/82_2014_414. Review.

PMID:
25027823
43.

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.

44.

Resilience of biochemical activity in protein domains in the face of structural divergence.

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

Curr Opin Struct Biol. 2014 Jun;26:92-103. doi: 10.1016/j.sbi.2014.05.008. Epub 2014 Jun 19. Review.

45.

CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems.

Makarova KS, Anantharaman V, Grishin NV, Koonin EV, Aravind L.

Front Genet. 2014 Apr 30;5:102. doi: 10.3389/fgene.2014.00102. eCollection 2014.

46.

An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent aggregation.

Castaing JP, Lee S, Anantharaman V, Ravilious GE, Aravind L, Ramamurthi KS.

FEMS Microbiol Lett. 2014 Sep;358(2):145-53. doi: 10.1111/1574-6968.12452. Epub 2014 May 20.

47.

The Knickkopf DOMON domain is essential for cuticle differentiation in Drosophila melanogaster.

Shaik KS, Wang Y, Aravind L, Moussian B.

Arch Insect Biochem Physiol. 2014 Jun;86(2):100-6. doi: 10.1002/arch.21165. Epub 2014 Apr 10.

PMID:
24723222
48.

A TET homologue protein from Coprinopsis cinerea (CcTET) that biochemically converts 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine.

Zhang L, Chen W, Iyer LM, Hu J, Wang G, Fu Y, Yu M, Dai Q, Aravind L, He C.

J Am Chem Soc. 2014 Apr 2;136(13):4801-4. doi: 10.1021/ja500979k. Epub 2014 Mar 25.

49.
50.

Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.

Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L.

BMC Bioinformatics. 2014 Mar 19;15:75. doi: 10.1186/1471-2105-15-75.

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