Publications

2019

Muok, A. R., Y. Deng, V. M. Gumerov, J. E. Chong, J. R. DeRossa, K. Kurniyati, R. Coleman, K. M. Lancaster, C. Li, I. B. Zhulin, and B. R. Crane. 2019. A di-iron protein recruited as an Fe[II] and oxygen sensor for bacterial chemotaxis functions by stabilizing an iron-peroxy species.  Proceedings of the National Academy of Sciences of the USA Jul 3. pii: 201904234. doi: 10.1073/pnas.1904234116. [Epub ahead of print].

Hong, Y., Z. Huang, D-F. Li, B. Ni, C.-Y. Jiang, X.-J. Liu, Y.-J. Hou, W.-S. Yang, D.-C. Wang, I. B. Zhulin, and S.-J. Liu. 2019. Trimeric structure of the ligand-binding domain suggests a mode of communication in bacterial chemoreceptors. Molecular Microbiology Jun 8. doi: 10.1111/mmi.14326. [Epub ahead of print].

Huang Z., Y.H. Wang, H.Z. Zhu, E.P. Andrianova, C.Y. Jiang, D. Li, L. Ma, J. Feng, Z.P. Liu, H. Xiang, I.B. Zhulin, and S.J. Liu. 2019. Cross talk between chemosensory pathways that modulate chemotaxis and biofilm formation. mBio 10: e02876-18.

Liu J., T. Murali, T. Yu, C. Liu, T.A. Sivakumaran, H.N.B. Moseley, I.B. Zhulin, H.L. Weiss, E.B. Durbin, S.R. Ellingson, J. Liu, B. Huang, B.J. Hallahan, C.M. Horbinski, K. Hodges, D.L. Napier, T. Bocklage, J. Mueller, N. Vanderford, D.W. Fardo, C. Wang, and S.M. Arnold. 2019. Characterization of squamous cell lung cancers from Appalachian Kentucky. Cancer Epidemiology, Biomarkers and Prevention 28: 348-356.

2018

Petukh, M., and I. B. Zhulin. 2018. Comparative study of the effect of disease causing and benign mutations in position Q92 on cholesterol binding by the NPC1 N-terminal domain. Proteins 86: 1165-1175.

Melesse, M., J. N. Bembenek, and I. B. Zhulin. 2018. Conservation of the separase regulatory domain. Biology Direct 13: 7.

Ortega, D. R. and I. B. Zhulin. 2018. Phylogenetic and protein sequence analysis of bacterial chemoreceptors. Methods in Molecular Biology 1729: 373-385.

Lu, J. G., J. Bishop, S. Cheyette, I. B. Zhulin, S. Guo, N. Sobreira, and S. E. Brenner. 2018. A novel PRRT2 pathogenic variant in a family with Paroxysmal Kinesigenic Dyskinesia and Benign Familial Infantile Seizures. Cold Spring Harbor Molecular Case Studies 4: a002287.

Cross, K. L., P. Chirania, W. Xiong, C. J. Beall, J, G. Elkins, R, J. Giannone, A, L. Griffen, A. M. Guss, R. L. Hettich, S. S. Joshi, E. M. Morkzan, R. K. Martin, I. B. Zhulin, E. J. Leys, and M, Podar. 2018. Insights into the evolution of host association through the isolation and characterization of a human periodontal pathogen, Desulfobulbus oralis. mBio 9: e02061-17.

2017

Ortega, D. R., A. D. Fleetwood, T. Krell, C. S. Harwood, G. J. Jensen, and I. B. Zhulin. 2017. Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the USA 114: 12809-12814.

Ortega, A., I. B. Zhulin, and T. Krell. 2017. Sensory repertoire of bacterial chemoreceptors. Microbiology and Molecular Biology Reviews 81: e00033-17.

Adebali, O., M. G. Petukh, A. O. Reznik, A. V. Tishkov, A. Upadhyay and I. B. Zhulin. 2017 Class III histidine kinases: a recently accessorized kinase domain in putative modulators of type IV pili based motility. Journal of Bacteriology 199: e00218-17.

Stock, A. M. and I. B. Zhulin. 2017. Two-Component Signal Transduction: a Special Issue in the Journal of Bacteriology. Journal of Bacteriology 199: e00443-17.

Armitage, J. P., A. Becker, P. J. Christie, P. A. J. de Boer, V. J. DiRita, R. L. Gourse, T. M. Henkin, W. Margolin, W. W. Metcalf, C. W. Mullineaux, G. A. O’Toole, J. S. Parkinson, O. Schneewind, T. J. Silhavy, A. M. Stock, and I. B. Zhulin. 2017. Classic Spotlights: Selected highlights from the first 100 years of the Journal of Bacteriology. Journal of Bacteriology 199: e00062-17.

Zhulin, I. B. 2017. By staying together, two genes keep the motor running. Structure 25: 214-215.

Adebali, O. and I. B. Zhulin. 2017. Aquerium: a web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. Proteins 85: 72-77.

2016

Zhulin, I.B. 2016. Classic spotlight: Genetics of Escherichia coli chemotaxis. Journal of Bacteriology 198: 3041.

Day, C. J., R. M. King, L. K. Shewell, G. Tram, T. Najnin, L. E. Hartley-Tassell, J. C. Wilson, A. D. Fleetwood, I. B. Zhulin and V. Korolik. 2016. A direct-sensing galactose chemoreceptor recently evolved in invasive strains of Campylobacter jejuni. Nature Communications 7: 13206.

Zhulin, I. B. 2016. Classic spotlight: 16S rRNA redefines microbiology. Journal of Bacteriology 198: 2764-2765.

Adebali, O., A.O. Reznik, D.S. Ory, and I.B. Zhulin. 2016. Establishing precise evolutionary history of a gene improves predicting disease causing missense mutations. Genetics in Medicine 18: 1029-1036.

Upadhyay, A., A.D. Fleetwood, O. Adebali, R.D. Finn, and I.B. Zhulin. 2016. Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes. PLoS Computational Biology 12: e1004862.

Buensuceso. R., Y. Nguyen, K. Zhang, M. Daniel-Ivad, S. Sugiman-Marangos, A. D. Fleetwood, I. B. Zhulin, M. S. Junop, P. L. Howell, and L. L. Burrows. 2016. The conserved TPR-containing C-terminal domain of Pseudomonas aeruginosa FimV is required for its cAMP-dependent and independent functions. Journal of Bacteriology 198: 2263-2274.

Ortega, D.R. and I.B. Zhulin. 2016. Evolutionary genomics suggests that CheV is an additional adaptor for accommodating specific chemoreceptors within the chemotaxis signaling complex. PLoS Computational Biology 12: e1004723.

Wang, X., A.K. Pandey, M K. Mulligan, E.G. Williams, K. Mozhui, Z. Li, V. Jovaisaite, L.D. Quarles, Z. Xiao, J. Huang, J.A. Capra, Z. Chen, W.L. Taylor, L. Bastarache, X. Niu, K.S. Pollard, D.C. Ciobanu, A.O. Reznik, A.V. Tishkov, I.B. Zhulin, J. Peng, S.F. Nelson, J.C. Denny, J. Auwerx, L. Lu, and R.W. Williams. 2016. Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications 7: 10464.

2015

Adebali, O., D.R. Ortega, and I.B. Zhulin. 2015. CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics 31: 1475-1477.

Zhulin, I.B. 2015. Databases for microbiologists. Journal of Bacteriology 197: 2458-2467.

Wisniewski-Dye, F., B. Drogue, S. Borland, C. Prigent-Combaret, K. Borziak, I.B. Zhulin, L. Lozano,V. Gonzalez, and P. Mavingui. 2015. Core and accessory genomes of the diazotroph Azospirillum. In: Biological Nitrogen Fixation, volume 1, First Edition. Frans J. de Brujn (ed.), John Wiley & Sons, Inc.

2014

Ulirch, L.E., and I.B. Zhulin. 2014. SeqDepot: a streamlined database of protein sequences and precomputed features. Bioinformatics 30: 295-297.

Krishnan, B., S.E. Thomas, H. Yamada, R. Yan, I.B. Zhulin, and B.D. McKee. 2014. Sisters Unbound is required for meiotic centromeric cohesion in Drosophila melanogaster. Genetics 198: 947-965.

2013

Ortega, D.R., C. Yang, P. Ames, J. Baudry, J.S. Parkinson, and I.B. Zhulin. 2013. A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nature Communications 4: 2881.

van Kessel, J.C., L.E. Ulrich, I.B. Zhulin, and B.L. Bassler. 2013. Analysis of activator and repressor functions reveals the requirements for transcriptional control by LuxR, the master regulator of quorum sensing in Vibrio harveyi. mBio 4: 00378-13.

Borziak, K., A.D. Fleetwood, and I.B. Zhulin. 2013. Chemoreceptor gene loss and acquisition via horizontal gene transfer in Escherichia coli. Journal of Bacteriology 195: 3596-3602.

Ortega, D.R., G. Mo, K. Lee, H. Zhou, J. Baudry, F.W. Dahlquist, and I.B. Zhulin. 2013. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. PLoS Computational Biology 9: e1003337.

Li, X., A.D. Fleetwood, C. Bayas, A.M. Bilwes, D.R. Ortega, J.J. Falke, I.B. Zhulin, and B.R. Crane. 2013. The 3.2 A resolution structure of a Receptor:CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays. Biochemistry 52: 3852-3865.

Cashman, D., D.R. Ortega, I.B. Zhulin, and J. Baudry. 2013. Homology modeling of the CheW coupling protein of the chemotaxis signaling complex. PLoS One 8: e70705.

2012

Rekapalli, B., K. Wuichet, G.D. Peterson, and I.B. Zhulin. 2012. Dynamics of domain coverage of the protein sequence universe. BMC Genomics 13: 634.

Sukharnikov, L.O., M. Alahuhta, R. Brunecky, A. Upadhyay, M.E. Himmel, V.L. Lunin, and I.B. Zhulin. 2012. Sequence, structure and evolution of cellulases in the glycosyl hydrolase family 48.  Journal of Biological Chemistry 287: 41068-41077.

2011

Wisniewski-Dyé, F., K. Borziak, G. Khalsa-Moyers, G. Alexandre, L.O. Sukharnikov, K. Wuichet, G.B. Hurst, W.H. McDonald, J.S. Robertson, V. Barbe, A. Calteau, Z. Rouy, S. Mangenot, C. Prigent-Combaret, P. Normand, M. Boyer, P. Siguier, Y. Dessaux, C. Elmerich, G. Condemine, G. Krishnen, I. Kennedy, A.H. Paterson, V. González, P. Mavingui and I.B. Zhulin. 2011 Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genetics 7: e1002430.

Sukharnikov, L.O., B.J. Cantwell, M. Podar and I.B. Zhulin. 2011. Cellulases: ambiguous non-homologous enzymes in a genomic perspective. Trends in Biotechnology 29: 473-479.

2010

Wuichet, K., B.J. Cantwell and I.B. Zhulin. 2010. Evolution and phyletic distribution of two component signal transduction systems. Current Opinion in Microbiology 13: 219-225.

Wuichet, K. and I.B. Zhulin. 2010. Origins and diversification of a complex signal transduction system in prokaryotes. Science Signaling 3: ra50.

Xie, Z., L.E. Ulrich, I.B. Zhulin and G. Alexandre. 2010. A PAS-domain containing chemoreceptor couples dynamic changes in metabolism with chemotaxis. Proceedings of the National Academy of Sciences of the USA 107: 2235-2240.

Ulrich, L.E. and I.B. Zhulin. 2010. The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Nucleic Acids Research 38: D401-D407.

2009

Briegel, A., D. R. Ortega, E. I. Tocheva, K. Wuichet, Z. Li, S. Chen, A. Mueller, C. Iancu, G. Murphy, M. Dobro, I.B. Zhulin and G. J. Jensen. 2009. Universal architecture of bacterial chemoreceptor arrays. Proceedings of the National Academy of Sciences of the USA 106: 17181-17186.

Anderson, I., L. Dharmarajan, J. Rodriguez, I. Porat, L. E. Ulrich, J. G. Elkins, K. Mavromatis, H. Sun, M. Land, A. Lapidus, S. Lucas, A. Copeland, H. Huber, I. B. Zhulin, W. Whitman, B. Mukhopadhyay, and N. Kyrpides. 2009. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics 10: 145.

Zhulin, I. B. 2009. It is computation time for bacteriology! Journal of Bacteriology 191: 20-22.

Rekapalli, B., C. Halloy, and I. B. Zhulin. 2009. HSP-HMMER: a tool for protein domain identification on a large scale. Proceedings of the 24th ACM Symposium on Applied Computing, Honolulu, Hawaii: 766-770.

Elliott, K. T., I. B. Zhulin, J. A. Stuckey, and V. J. DiRita. 2009. Conserved residues in the HAMP domain define a new family of proposed bipartite energy taxis receptors. Journal of Bacteriology 191: 375-387.

2008

Fredrickson, J. K., M.F. Romine, A. S. Beliaev, J. M. Auchtung, M. E. Driscoll, T. S. Gardner, K. H. Nealson, A. L. Osterman, G. Pinchuk, J. L. Reed, D. A. Rodionov, J. L. Rodrigues, D. A. Saffarini, M. H. Serres, A. M Spormann, I. B. Zhulin, and J. M. Tiedje. 2008. Towards environmental systems biology of Shewanella. Nature Reviews Microbiology 6: 592-603.

Werner, R. M., L. E. Taylor 2nd, B. Henrissat, L. Hauser, M. Land, P. M. Coutinho, C. Rancurel, E. H. Saunders, A. G. Longmire, H. Zhang, E. A. Bayer, H. J. Gilbert, F. Larimer, I. B. Zhulin, N. A. Ekborg, R. Lamed, P. M. Richardson, I. Borovok, and S. Hutcheson. 2008. Complete genome sequence of the complex carbohydrate-degrading marine bacterium Saccharophagus degradans strain 2-40 T. PLoS Genetics 4: e1000087.

Anderson, I., J. Rodriguez, D. Susanti, I. Porat, C. Reich, L. E. Ulrich, J. Elkins, K. Mavromatis, A. Lykidis, E. Kim, L.S. Thompson, M. Nolan, M. Land, A. Copeland, A. Lapidus, S. Lucas, C. Detter, P. Richardson, I. B. Zhulin, W. Whitman, B. Mukhopadhyav, C. Woese and N. Kyrpides. 2008. Genome sequence of the Crenarchaeal hyperthermophile Thermofilum pendens reveals an unprecedented loss of biosynthetic pathways in a free-living organism. Journal of Bacteriology 190: 2957-2965.

Belas, R., I. B. Zhulin and Z. Yang. 2008. Bacterial sensing and motility: sure bets. Journal of Bacteriology 190: 1849-1856.

2007

Alexander, R.P. and I.B. Zhulin. 2007. Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors. Proceedings of the National Academy of Sciences of the USA 104: 2885-2890.

Borziak, K. and I.B. Zhulin. 2007. FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes. Bioinformatics 23: 2518-2521.

Ulrich, L.E and I.B. Zhulin. 2007. MiST: a Microbial Signal Transduction database. Nucleic Acids Research 35: D386-D390.

Wuichet, K., R.P. Alexander, and I.B. Zhulin. 2007. Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Methods in Enzymology 422: 3-31.

2006

Chain, P.S.G., V.J. Denef, K. Konstantinidis, L.M.Vergez, L. Agullo, V.L.Reyes, L. Hauser, M. Cordova, L. Gomez, M. Gonzalez, M. Land, V. Lao, F. Larimer, J.J. LiPuma, E. Mahenthiralingam, S.A. Malfatti, C.J. Marx, J.J. Parnell, A. Ramette, P. Richardson, M. Seeger, D. Smith, T. Spilker, W.J. Sul, T.V. Tsoi, L.E. Ulrich, I.B. Zhulin, and J.M. Tiedje. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 M bp genome shaped for versatility. Proceedings of the National Academy of Sciences of the USA 103: 15280-15287.

Alexandre G. and I.B. Zhulin. 2006. Chemotaxis in soil diazotrophs: survival and adaptive response. In Associative and Endophytic Nitrogen-fixing Bacteria and Cyanobacterial Associations. C. Elmerich and W.E. Newton, Eds. Springer, pp. 73-84.

2005

Ulrich, L.E., E.V. Koonin and I.B. Zhulin. 2005. One-component regulators dominate signal transduction in prokaryotes. Trends in Microbiology 13: 52-56.

Ulrich, L.E. and I.B. Zhulin. 2005. Four-helical bundle: a ubiquitous sensory module in prokaryotic signal transduction. Bioinformatics 21 Suppl 3: iii45-iii48.

Wu, M., Q. Ren, A. S. Durkin, S. C. Daugherty, L. M. Brinkac, R. J. Dodson, R. Madupu, S. A. Sullivan, J. F. Kolonay, W. Nelson, L. J. Tallon, K. M. Jones, L. E. Ulrich, J. M. Gonzalez, I. B. Zhulin, F. T. Robb and J. A. Eisen. 2005. Life in hot carbon monoxide: the complete genome sequence of Carboxydothermus hydrogenoformans Z-2901. PLoS Genetics 1: e65.

2004

Alexandre, G. and I.B. Zhulin. 2004. Ecological role of energy taxis. FEMS Microbiology Reviews 28: 113-126.

Zhulin, I.B. 2004. Digging with experimental pick and computational shovel: a new addition to the histidine kinase superfamily. Journal of Bacteriology 186: 267-269.

2003

Mazzag, B., I.B. Zhulin and A. Mogilner. 2003. Model of bacterial band formation in aerotaxis. Biophysical Journal 85: 3558-3574.

Phillips-Greer, S.E., Alexandre, G., Taylor, B.L. and I.B. Zhulin. 2003. Aer and Tsr guide Escherichia coli in spatial gradients of oxidizable substrates. Microbiology 149: 2661-2667.

Wuichet, K. and I.B. Zhulin. 2003. Molecular evolution of sensory domains in cyanobacterial chemoreceptors. Trends in Microbiology 11: 200-203.

Shu, C.J., L.E. Ulrich and I.B. Zhulin. 2003. The NIT domain: a predicted nitrate responsive module in bacterial sensory receptors. Trends in Biochemical Sciences  28: 121-124.

Alexandre, G. and I. B. Zhulin. 2003. Different evolutionary constraints on CheW and CheY proteins revealed by heterologous expression studies and protein sequence analysis. Journal of Bacteriology  185: 544-552.

Zhulin, I.B., A. Nikolskaya and M. Y. Galperin. 2003. Common sensory domains in transmembrane receptors for diverse signal transduction pathways in Bacteria and Archaea. Journal of Bacteriology 185: 285-294.

2002

Perelygin, A.A., S.V. Scherbik, I.B. Zhulin, B.M. Stockman, Y. Li and M.A. Brinton. 2002. Positioning cloning of the murine flavivirus resistance gene. Proceedings of the National Academy of Sciences of the USA 99: 9322-9327.

Shu, C.J. and I.B. Zhulin. 2002. ANTAR: an RNA-binding domain in transcription antitermination regulatory proteins. Trends in Biochemical Sciences 27: 3-5.

Hauwaerts, D., G. Alexandre, S. Das, J. Vanderleyden and I.B. Zhulin. 2002. A major chemotaxis gene cluster in Azospirillum brasilense and relationships between chemotaxis operons in α-proteobacteria. FEMS Microbiology Letters 208: 61-67.

Aizawa, S.-I., I. B. Zhulin, L. Marquez-Magana and G. W. Ordal. 2002. Chemotaxis and Motility, 437-452. In A. L. Sonenshein et al. (Ed.). Bacillus subtilis and Its Closest Relatives: from Genes to Cells. ASM Press, Washington, DC.

Shiomi, D., I. B. Zhulin, M. Homma and I. Kawagishi. 2002. Dual recognition of the bacterial chemoreceptor by chemotaxis-specific domains of the CheR methyltransferase. Journal of Biochemical Chemistry 277: 42325-42333.

Sun, X., I. Zhulin and R. M. Wartell. 2002. Predicted structure and phyletic distribution of the RNA binding protein Hfq. Nucleic Acids Research 30: 3662-3671.

2001

Zhulin, I. B. 2001. The superfamily of chemotaxis transducers: from physiology to genomics and back. Advances in Microbial Physiology 45: 157-198.

Iyer, L. M., L. Aravind, P. Bork, K. Hoffmann, A. R. Mushegian, I. B. Zhulin, and E. V. Koonin. Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biology 2: research0051.1-0051.11.

Alexandre, G. and I. B. Zhulin. 2001. More than one way to sense chemicals. Journal of Bacteriology 183: 4681-4686.

Kirby, J. R., C. J. Kristich, M. M. Saulmon, L. F. Garrity, I. B. Zhulin, and G. W. Ordal. 2001. CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis. Molecular Microbiology 42: 573-585.

Mougel, C. and I. B. Zhulin. 2001. CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends in Biochemical Sciences 26: 582-584.

2000

Alexandre, G., S. E. Greer, and I. B. Zhulin. 2000. Energy taxis is the dominant behavior in Azospirillum brasilense. Journal of Bacteriology 182: 6042-6048.

Zhulin, I. B. 2000. A novel phototaxis receptor hidden in the cyanobacterial genome. Journal of Molecular Microbiology and Biotechnology 2: 491-493.

Alexandre, G., and I. B. Zhulin. 2000. Laccases are widespread in bacteria. Trends in Biotechnology 18: 41-42.