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How Bacterial Chemoreceptors Evolve Novel Ligand Specificities.

Gavira JA, Gumerov VM, Rico-Jiménez M, Petukh M, Upadhyay AA, Ortega A, Matilla MA, Zhulin IB, Krell T.

mBio. 2020 Jan 21;11(1). pii: e03066-19. doi: 10.1128/mBio.03066-19.


MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems.

Gumerov VM, Ortega DR, Adebali O, Ulrich LE, Zhulin IB.

Nucleic Acids Res. 2020 Jan 8;48(D1):D459-D464. doi: 10.1093/nar/gkz988.


A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species.

Muok AR, Deng Y, Gumerov VM, Chong JE, DeRosa JR, Kurniyati K, Coleman RE, Lancaster KM, Li C, Zhulin IB, Crane BR.

Proc Natl Acad Sci U S A. 2019 Jul 23;116(30):14955-14960. doi: 10.1073/pnas.1904234116. Epub 2019 Jul 3.


The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure.

Hong Y, Huang Z, Guo L, Ni B, Jiang CY, Li XJ, Hou YJ, Yang WS, Wang DC, Zhulin IB, Liu SJ, Li DF.

Mol Microbiol. 2019 Sep;112(3):906-917. doi: 10.1111/mmi.14326. Epub 2019 Jun 21.


Cross Talk between Chemosensory Pathways That Modulate Chemotaxis and Biofilm Formation.

Huang Z, Wang YH, Zhu HZ, Andrianova EP, Jiang CY, Li D, Ma L, Feng J, Liu ZP, Xiang H, Zhulin IB, Liu SJ.

mBio. 2019 Feb 26;10(1). pii: e02876-18. doi: 10.1128/mBio.02876-18.


Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky.

Liu J, Murali T, Yu T, Liu C, Sivakumaran TA, Moseley HNB, Zhulin IB, Weiss HL, Durbin EB, Ellingson SR, Liu J, Huang B, Hallahan BJ, Horbinski CM, Hodges K, Napier DL, Bocklage T, Mueller J, Vanderford NL, Fardo DW, Wang C, Arnold SM.

Cancer Epidemiol Biomarkers Prev. 2019 Feb;28(2):348-356. doi: 10.1158/1055-9965.EPI-17-0984. Epub 2018 Oct 30.


Conservation of the separase regulatory domain.

Melesse M, Bembenek JN, Zhulin IB.

Biol Direct. 2018 Apr 27;13(1):7. doi: 10.1186/s13062-018-0210-0.


Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.

Cross KL, Chirania P, Xiong W, Beall CJ, Elkins JG, Giannone RJ, Griffen AL, Guss AM, Hettich RL, Joshi SS, Mokrzan EM, Martin RK, Zhulin IB, Leys EJ, Podar M.

mBio. 2018 Mar 13;9(2). pii: e02061-17. doi: 10.1128/mBio.02061-17.


Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors.

Ortega DR, Zhulin IB.

Methods Mol Biol. 2018;1729:373-385. doi: 10.1007/978-1-4939-7577-8_29.


A novel PRRT2 pathogenic variant in a family with paroxysmal kinesigenic dyskinesia and benign familial infantile seizures.

Lu JG, Bishop J, Cheyette S, Zhulin IB, Guo S, Sobreira N, Brenner SE.

Cold Spring Harb Mol Case Stud. 2018 Feb 1;4(1). pii: a002287. doi: 10.1101/mcs.a002287. Print 2018 Feb.


Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa.

Ortega DR, Fleetwood AD, Krell T, Harwood CS, Jensen GJ, Zhulin IB.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12809-12814. doi: 10.1073/pnas.1708842114. Epub 2017 Nov 13.


Sensory Repertoire of Bacterial Chemoreceptors.

Ortega Á, Zhulin IB, Krell T.

Microbiol Mol Biol Rev. 2017 Oct 25;81(4). pii: e00033-17. doi: 10.1128/MMBR.00033-17. Print 2017 Dec. Review.


Two-Component Signal Transduction: a Special Issue in the Journal of Bacteriology.

Stock AM, Zhulin IB.

J Bacteriol. 2017 Aug 22;199(18). pii: e00443-17. doi: 10.1128/JB.00443-17. Print 2017 Sep 15. No abstract available.


Classic Spotlights: Selected Highlights from the First 100 Years of the Journal of Bacteriology.

Armitage JP, Becker A, Christie PJ, de Boer PAJ, DiRita VJ, Gourse RL, Henkin TM, Margolin W, Metcalf WW, Mullineaux CW, O'Toole GA, Parkinson JS, Schneewind O, Silhavy TJ, Stock AM, Zhulin IB.

J Bacteriol. 2017 Jun 13;199(13). pii: e00062-17. doi: 10.1128/JB.00062-17. Print 2017 Jul 1. No abstract available.


Class III Histidine Kinases: a Recently Accessorized Kinase Domain in Putative Modulators of Type IV Pilus-Based Motility.

Adebali O, Petukh MG, Reznik AO, Tishkov AV, Upadhyay AA, Zhulin IB.

J Bacteriol. 2017 Aug 22;199(18). pii: e00218-17. doi: 10.1128/JB.00218-17. Print 2017 Sep 15.


By Staying Together, Two Genes Keep the Motor Running.

Zhulin IB.

Structure. 2017 Feb 7;25(2):214-215. doi: 10.1016/j.str.2017.01.005.


Call for Original Research Papers for a Special Collection in Journal of Bacteriology: Two-Component Signal Transduction.

Stock AM, Zhulin IB.

J Bacteriol. 2016 Dec 28;199(2). pii: e00748-16. doi: 10.1128/JB.00748-16. Print 2017 Jan 15. No abstract available.


Classic Spotlight: Genetics of Escherichia coli Chemotaxis.

Zhulin IB.

J Bacteriol. 2016 Oct 21;198(22):3041. Print 2016 Nov 15. No abstract available.


A direct-sensing galactose chemoreceptor recently evolved in invasive strains of Campylobacter jejuni.

Day CJ, King RM, Shewell LK, Tram G, Najnin T, Hartley-Tassell LE, Wilson JC, Fleetwood AD, Zhulin IB, Korolik V.

Nat Commun. 2016 Oct 20;7:13206. doi: 10.1038/ncomms13206.


Classic Spotlight: 16S rRNA Redefines Microbiology.

Zhulin IB.

J Bacteriol. 2016 Sep 22;198(20):2764-5. doi: 10.1128/JB.00616-16. Print 2016 Oct 15. No abstract available.


The Conserved Tetratricopeptide Repeat-Containing C-Terminal Domain of Pseudomonas aeruginosa FimV Is Required for Its Cyclic AMP-Dependent and -Independent Functions.

Buensuceso RN, Nguyen Y, Zhang K, Daniel-Ivad M, Sugiman-Marangos SN, Fleetwood AD, Zhulin IB, Junop MS, Howell PL, Burrows LL.

J Bacteriol. 2016 Jul 28;198(16):2263-74. doi: 10.1128/JB.00322-16. Print 2016 Aug 15.


Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.

Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB.

PLoS Comput Biol. 2016 Apr 6;12(4):e1004862. doi: 10.1371/journal.pcbi.1004862. eCollection 2016 Apr.


Establishing the precise evolutionary history of a gene improves prediction of disease-causing missense mutations.

Adebali O, Reznik AO, Ory DS, Zhulin IB.

Genet Med. 2016 Oct;18(10):1029-36. doi: 10.1038/gim.2015.208. Epub 2016 Feb 18.


Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex.

Ortega DR, Zhulin IB.

PLoS Comput Biol. 2016 Feb 4;12(2):e1004723. doi: 10.1371/journal.pcbi.1004723. eCollection 2016 Feb.


Joint mouse-human phenome-wide association to test gene function and disease risk.

Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW.

Nat Commun. 2016 Feb 2;7:10464. doi: 10.1038/ncomms10464.


Databases for Microbiologists.

Zhulin IB.

J Bacteriol. 2015 Aug 1;197(15):2458-67. doi: 10.1128/JB.00330-15. Epub 2015 May 26. Review.


CDvist: a webserver for identification and visualization of conserved domains in protein sequences.

Adebali O, Ortega DR, Zhulin IB.

Bioinformatics. 2015 May 1;31(9):1475-7. doi: 10.1093/bioinformatics/btu836. Epub 2014 Dec 18.


Sisters unbound is required for meiotic centromeric cohesion in Drosophila melanogaster.

Krishnan B, Thomas SE, Yan R, Yamada H, Zhulin IB, McKee BD.

Genetics. 2014 Nov;198(3):947-65. doi: 10.1534/genetics.114.166009. Epub 2014 Sep 5.


A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors.

Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB.

Nat Commun. 2013;4:2881. doi: 10.1038/ncomms3881.


Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein.

Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB.

PLoS Comput Biol. 2013;9(11):e1003337. doi: 10.1371/journal.pcbi.1003337. Epub 2013 Nov 14.


SeqDepot: streamlined database of biological sequences and precomputed features.

Ulrich LE, Zhulin IB.

Bioinformatics. 2014 Jan 15;30(2):295-7. doi: 10.1093/bioinformatics/btt658. Epub 2013 Nov 13.


Homology modeling of the CheW coupling protein of the chemotaxis signaling complex.

Cashman DJ, Ortega DR, Zhulin IB, Baudry J.

PLoS One. 2013 Aug 7;8(8):e70705. doi: 10.1371/journal.pone.0070705. eCollection 2013.


Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli.

Borziak K, Fleetwood AD, Zhulin IB.

J Bacteriol. 2013 Aug;195(16):3596-602. doi: 10.1128/JB.00421-13. Epub 2013 Jun 7.


The 3.2 Å resolution structure of a receptor: CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays.

Li X, Fleetwood AD, Bayas C, Bilwes AM, Ortega DR, Falke JJ, Zhulin IB, Crane BR.

Biochemistry. 2013 Jun 4;52(22):3852-65. doi: 10.1021/bi400383e. Epub 2013 May 23.


Dynamics of domain coverage of the protein sequence universe.

Rekapalli B, Wuichet K, Peterson GD, Zhulin IB.

BMC Genomics. 2012 Nov 16;13:634. doi: 10.1186/1471-2164-13-634.


Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48.

Sukharnikov LO, Alahuhta M, Brunecky R, Upadhyay A, Himmel ME, Lunin VV, Zhulin IB.

J Biol Chem. 2012 Nov 30;287(49):41068-77. doi: 10.1074/jbc.M112.405720. Epub 2012 Oct 10.


Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments.

Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, González V, Mavingui P, Zhulin IB.

PLoS Genet. 2011 Dec;7(12):e1002430. doi: 10.1371/journal.pgen.1002430. Epub 2011 Dec 22.


Cellulases: ambiguous nonhomologous enzymes in a genomic perspective.

Sukharnikov LO, Cantwell BJ, Podar M, Zhulin IB.

Trends Biotechnol. 2011 Oct;29(10):473-9. doi: 10.1016/j.tibtech.2011.04.008. Epub 2011 Jun 16.


Origins and diversification of a complex signal transduction system in prokaryotes.

Wuichet K, Zhulin IB.

Sci Signal. 2010 Jun 29;3(128):ra50. doi: 10.1126/scisignal.2000724.


PAS domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis.

Xie Z, Ulrich LE, Zhulin IB, Alexandre G.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2235-40. doi: 10.1073/pnas.0910055107. Epub 2010 Jan 19.


Evolution and phyletic distribution of two-component signal transduction systems.

Wuichet K, Cantwell BJ, Zhulin IB.

Curr Opin Microbiol. 2010 Apr;13(2):219-25. doi: 10.1016/j.mib.2009.12.011. Epub 2010 Feb 3. Review.


The MiST2 database: a comprehensive genomics resource on microbial signal transduction.

Ulrich LE, Zhulin IB.

Nucleic Acids Res. 2010 Jan;38(Database issue):D401-7. doi: 10.1093/nar/gkp940. Epub 2009 Nov 9.


Universal architecture of bacterial chemoreceptor arrays.

Briegel A, Ortega DR, Tocheva EI, Wuichet K, Li Z, Chen S, Müller A, Iancu CV, Murphy GE, Dobro MJ, Zhulin IB, Jensen GJ.

Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17181-6. doi: 10.1073/pnas.0905181106. Epub 2009 Sep 23.


The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota.

Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N.

BMC Genomics. 2009 Apr 2;10:145. doi: 10.1186/1471-2164-10-145.


It is computation time for bacteriology!

Zhulin IB.

J Bacteriol. 2009 Jan;191(1):20-2. doi: 10.1128/JB.01491-08. Epub 2008 Oct 31. No abstract available.


Conserved residues in the HAMP domain define a new family of proposed bipartite energy taxis receptors.

Elliott KT, Zhulin IB, Stuckey JA, DiRita VJ.

J Bacteriol. 2009 Jan;191(1):375-87. doi: 10.1128/JB.00578-08. Epub 2008 Oct 24.


Towards environmental systems biology of Shewanella.

Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM.

Nat Rev Microbiol. 2008 Aug;6(8):592-603. doi: 10.1038/nrmicro1947. Epub 2008 Jul 7. Review.


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