Masayori Inouye Professor UMDNJ Dept. Biochemistry 675 Hoes Lane Piscataway. NJ 08854 (732) 235-4540 FAX - 4783 inouye@umdnj.edu

Molecular biology of cellular adaptation to stresses

Cold-shock Adaptation - When E. coli cells are exposed to low temperatures. a number of cytoplasmic proteins (cold-shock proteins) are specifically induced. Among them. CspA. CspB and CsrA have been extensively studied in our laboratory. Our data indicate that CsrA is a new ribosomal protein which functions as an ATP-dependent RNA helicase to unwind stable secondary structure in mRNAs formed at low temperatures. CspA is an RNA chaperone which prevents the formation of secondary structures in mRNA. and CspB is a DNA chaperone which plays an important role in transcription as well as in DNA replication.

Osmoregulation and Transmembrane Signal Transduction - Adaptive responses of E. coli to medium osmolarity provides an ideal system in which to study signal transduction across the membrane as well as the transcriptional regulation of two porin genes (ompF and ompC) by a transcriptional factor (OmpR). Its function is modulated by a transmembrane signal transducer (EnvZ) which functions not only as kinase but also as phosphatase for OmpR.

Molecular Biology of Aging - One of the major causes of aging is known to be oxidative damage due to various oxidants produced during respiration. We have constructed transgenic mice overexpressing human glutathione peroxidases and superoxide dismutase to study oxidative stress on aging and the effect of antioxidant enzymes on radical-generation chemicals and carcinogens.

Development of Myxococcus xanthus - M. xanthus is a Gram-negative bacterium which can undergo cellular differentiation upon nutrient starvation. M. xanthus provides an excellent system in which to study the morphogenesis and molecular mechanism of control of gene expression during development. Attempts are being made to characterize several development-specific proteins. including a number of eukaryotic-like protein serine/threonine kinases.

GTP Metabolism - GTP plays key roles in various cellular functions. We are investigating a number of GTP-associated proteins in E. coli such as Era (an essential GTP-binding protein of unknown function). EF-Tu. and nucleoside diphosphate kinase.

Protein Folding - We are attempting to decipher the precise process of protein folding by molecular genetic as well as biochemical approaches using pro-subtilisin as a model system. In this system the propeptide of 77 amino acid residues functions as an intramolecular chaperone which is essential for the folding of active subtilisin.

Bacterial Retroelements - About 10% of the natural population of E. coli contain a highly diverse retroelement called 'retron'. which is responsible for the production of a peculiar RNA-DNA complex (msDNA). We are attempting to determine the biological function of the retron. the biosynthetic mechanism of msDNA. and to search for its origin.

Selected Publications

Shimazu T, Degenhardt K, Nur-E-Kamal A, Zhang J, Yoshida T, Zhang Y, Mathew R, White E, Inouye M. (2007) NBK/BIK antagonizes MCL-1 and BCL-XL and activates BAK-mediated apoptosis in response to protein synthesis inhibition. Genes Dev. 21(8):929-41.

Falzon L, Patel S, Chen YJ, Inouye M. (2007) Autotomic behavior of the propeptide in propeptide-mediated folding of prosubtilisin E. J Mol Biol. 366(2):494-503.

Suzuki M, Roy R, Zheng H, Woychik N, Inouye M. (2006) Bacterial bioreactors for high yield production of recombinant protein. J Biol Chem. 281(49):37559-65.

Inouye M. (2006) The discovery of mRNA interferases: implication in bacterial physiology and application to biotechnology. J Cell Physiol. 209(3):670-6. Review.

Inouye M. (2006) Signaling by transmembrane proteins shifts gears. Cell. 126(5):829-31.

Hwang J, Inouye M. (2006) The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli. Mol Microbiol. 61(6):1660-72.

Falzon L, Suzuki M, Inouye M. (2006) Finding one of a kind: advances in single-protein production. Curr Opin Biotechnol. 17(4):347-52.

Inoue K, Chen J, Tan Q, Inouye M. (2006) Era and RbfA have overlapping function in ribosome biogenesis in Escherichia coli. J Mol Microbiol Biotechnol. 11(1-2):41-52.

Yoshida T. Qin L. Egger LA. Inouye M. (2006) Transcription Regulation of ompF and ompC by a single transcription factor. OmpR. J Biol Chem. 281(25):17114-23.

Zhang Z. Emanetoglu NW. Saraf G. Chen Y. Wu P. Zhong J. Lu Y. Chen J. Mirochnitchenko O. Inouye M. (2006) DNA immobilization and SAW response in ZnO nanotips grown on LiNbO3 substrates. IEEE Trans Ultrason Ferroelectr Freq Control. 53(4):786-92.

Mineno J. Okamoto S. Ando T. Sato M. Chono H. Izu H. Takayama M. Asada K. Mirochnitchenko O. Inouye M. Kato I. (2006) The expression profile of microRNAs in mouse embryos. Nucleic Acids Res. Mar 31;34(6):1765-71.

Li GY. Zhang Y. Chan MC. Mal TK. Hoeflich KP. Inouye M. Ikura M. (2006) Characterization of dual substrate binding sites in the homodimeric structure of Escherichia coli mRNA interferase MazF. J Mol Biol. 357(1):139-50.

Foronjy RF. Mirochnitchenko O. Propokenko O. Lemaitre V. Jia Y. Inouye M. Okada Y. D'Armiento JM. (2006) Superoxide dismutase expression attenuates cigarette smoke- or elastase-generated emphysema in mice. Am J Respir Crit Care Med. 173(6):623-31.

Hong M. Xu W. Yoshida T. Tanaka K. Wolff DJ. Zhou F. Inouye M. You G. (2005) Human organic anion transporter hOAT1 forms homooligomers. J Biol Chem. 280(37):32285-90.

Jiang W. Prokopenko O. Wong L. Inouye M. Mirochnitchenko O. (2005) IRIP. a new ischemia/reperfusion-inducible protein that participates in the regulation of transporter activity. Mol Cell Biol. 25(15):6496-508.

Zhang Y. Zhu L. Zhang J. Inouye M. (2005) Characterization of ChpBK. an mRNA interferase from Escherichia coli. J Biol Chem. 280(28):26080-8.

Sone M. Falzon L. Inouye M. (2005) The role of tryptophan residues in the autoprocessing of prosubtilisin E. Biochim Biophys Acta. 1749(1):15-22.

Suzuki M. Zhang J. Liu M. Woychik NA. Inouye M. (2005) Single protein production in living cells facilitated by an mRNA interferase. Mol Cell. 18(2):253-61.

Acton TB. Gunsalus KC. Xiao R. Ma LC. Aramini J. Baran MC. Chiang YW. Climent T. Cooper B. Denissova NG. Douglas SM. Everett JK. Ho CK. Macapagal D. Rajan PK. Shastry R. Shih LY. Swapna GV. Wilson M. Wu M. Gerstein M. Inouye M. Hunt JF. Montelione GT. (2005) Robotic cloning and Protein Production Platform of the Northeast Structural Genomics Consortium. Methods Enzymol. 394:210-43.

Zhang Y. Zhang J. Hara H. Kato I. Inouye M. (2005) Insights into the mRNA cleavage mechanism by MazF. an mRNA interferase. J Biol Chem. 280(5):3143-50.

Phadtare S. Inouye M. wild-type and cold-sensitive. quadruple-csp-deletion strains of Escherichia coli. J Bacteriol. (2004) Genome-wide transcriptional analysis of the cold shock response in 186(20):7007-14.

Inouye M. Ke H. Yashio A. Yamanaka K. Nariya H. Shimamoto T. Inouye S. (2004) Complex formation between a putative 66-residue thumb domain of bacterial reverse transcriptase RT-Ec86 and the primer recognition RNA. J Biol Chem. 279(49):50735-42.

Khorchid A. Inouye M. Ikura M. (2005) Structural characterization of Escherichia coli sensor histidine kinase EnvZ: the periplasmic C-terminal core domain is critical for homodimerization.
Biochem J. 385(Pt 1):255-64.

Zhu Y. Inouye M. (2004) The HAMP linker in histidine kinase dimeric receptors is critical for symmetric transmembrane signal transduction. J Biol Chem. 279(46):48152-8.

Inouye M. Phadtare S. (2004) Cold shock response and adaptation at near-freezing temperature in microorganisms. Sci STKE. 2004(237):pe26.

Qing G. Ma LC. Khorchid A. Swapna GV. Mal TK. Takayama MM. Xia B. Phadtare S. Ke H. Acton T. Montelione GT. Ikura M. Inouye M. (2004) Cold-shock induced high-yield protein production in Escherichia coli. Nat Biotechnol. 22(7):877-82.

Qing G. Xia B. Inouye M. (2003) Enhancement of translation initiation by A/T-rich sequences downstream of the initiation codon in Escherichia coli. J Mol Microbiol Biotechnol. 6(3-4):133-44.

Zhang J. Zhang Y. Zhu L. Suzuki M. Inouye M. (2004) Interference of mRNA function by sequence-specific endoribonuclease PemK. J Biol Chem. 279(20):20678-84.

Phadtare S. Inouye M. Severinov K. (2004) The mechanism of nucleic acid melting by a CspA family protein. J Mol Biol. 337(1):147-55.

Phadtare S. Severinov K. Inouye M. (2003) Assay of transcription antitermination by proteins of the CspA family. Methods Enzymol. 371:460-71.

Zhang Y. Zhang J. Hoeflich KP. Ikura M. Qing G. Inouye M. (2003) MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol Cell. 12(4):913-23.

Phadtare S. Hwang J. Severinov K. Inouye M. (2003) CspB and CspL. thermostable cold-shock proteins from Thermotoga maritima. Genes Cells. 8(10):801-10.

Xia B. Ke H. Shinde U. Inouye M. (2003) The role of RbfA in 16S rRNA processing and cell growth at low temperature in Escherichia coli. J Mol Biol. 332(3):575-84.

Zhang J. Zhang Y. Inouye M. (2003) Characterization of the interactions within the mazEF addiction module of Escherichia coli. J Biol Chem. 278(34):32300-6.

Cai SJ. Inouye M. (2003) Spontaneous subunit exchange and biochemical evidence for trans-autophosphorylation in a dimer of Escherichia coli histidine kinase (EnvZ). J Mol Biol. 329(3):495-503.

Qin L. Cai S. Zhu Y. Inouye M. (2003) Cysteine-scanning analysis of the dimerization domain of EnvZ. an osmosensing histidine kinase. J Bacteriol. 185(11):3429-35.

Inoue K. Alsina J. Chen J. Inouye M. (2003) Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era. an essential GTPase in Escherichia coli. Mol Microbiol. 48(4):1005-16.

Cai SJ. Khorchid A. Ikura M. Inouye M. Probing catalytically essential domain orientation in histidine kinase EnvZ by targeted disulfide crosslinking. J Mol Biol. (2003) 328(2):409-18.

Zhu Y. Inouye M. (2003) Analysis of the role of the EnvZ linker region in signal transduction using a chimeric Tar/EnvZ receptor protein. Tez1. J Biol Chem. 278(25):22812-9.

Zhang J. Zhang Y. Inouye M. (2003) Thermotoga maritima MazG protein has both nucleoside triphosphate pyrophosphohydrolase and pyrophosphatase activities. J Biol Chem. 278(24):21408-14.

Huang YJ. Swapna GV. Rajan PK. Ke H. Xia B. Shukla K. Inouye M. Montelione GT. (2003) Solution NMR structure of ribosome-binding factor A (RbfA). a cold-shock adaptation protein from Escherichia coli. J Mol Biol. 327(2):521-36.

Yoshida. T.. Cai. S.-J.. Inouye. M. (2002) Interaction of EnvZ. a sensory histidine kinase. with phosphorylated OmpR. the cognate response regulator. Mol. Micro. 46(5):1283-94.

Yoshida. T.. Qin. L. and Inouye. M. (2002) Formation of the stoichiometric complex of EnvZ. a histidine kinase. with its response regulator. OmpR. Mol. Micro. 46(5):1273-82.

Zhang. J. and Inouye. M. (2002) MazG. a Nucleoside Triphosphate Pyrophosphohydrolase. interacts with Era. an essential GTPase in Escherichia coli. J. Bacteriol. 184:5323-5329.

Zhu. Y. and Inouye. M. (2002) The role of the G2 box. a conserved motif in histidine kinase superfamily. in modulating the function of EnvZ. Mol. Micro. 45:653-63.

Chen. J. Acton. T.B.. Basu. S.K.. Montelione. G.T. and Inouye. M. (2002) Enhancement of the solubility of proteins overexpressed in Escherichia coli by heat shock. J. Mol. Microbiol. Biotechno. 4:519-524.

Phadtare. S.. Kato. I. and Inouye. M. (2002) DNA microarray analysis of the expression profile of Escherichia coli in response to treatment with 4,5-Dihydroxy-2-Cyclopenten-1-One. J. Bacteriol. 84:6725-6729.

Inouye. M.. Dutta. R. and Zhu. Y. (2002) Regulation of Porins in Escherichia coli by the Osmosensing Histidine Kinase/Phosphatase EnvZ. In: Histidine Kinases. (ed. M. Inouye). Academic Press. NY. 25-46.

Phadtare. S.U.. Inouye. M. and Severinov. K. (2002) The nucleic acid melting activity of Escherichia coli CspE is critical for transcription antitermination and cold-acclimation of cells. J. Biol. Chem. 277:7239-45.

Yamanaka. K.. Shimamoto. T.. Inouye. S. and Inouye. M. (2002) Retrons. Mobile DNA II (N.L. Craig et. al. Editors) ASM Press. 784-795.

Inoue. K.. Chen. J.. Kato. I. and Inouye. M. (2002) Specific growth inhibition by acetate of an Escherichia coli strain expressing Era-dE. a dominant negative era mutant. J. Mol. Microbiol. Biotechnol. 4:379-388.

Cai. S.J. and Inouye. M. (2002) EnvZ-OmpR interaction and osmoregulation in Escherichia coli. J. Biol. Chem 277:24155-61.

Xia. B.. Ke. H.. Jiang. W. and Inouye. M. (2002) The Cold Box stem-loop proximal to the 5' -end of the Escherichia coli cspA gene stabilizes its mRNA at low temperature J. Biol. Chem. 277:6005-11.

Phadtare. S. and Inouye. M. (2002) Cold Shock. Encyclopedia of Environmental Microbiology. John Wiley & Sons. Inc. 885-895.