Experts and Doctors on ribosomes in Piscataway, New Jersey, United States

Summary

Locale: Piscataway, New Jersey, United States
Topic: ribosomes

Top Publications

  1. Liu M, Zhang Y, Inouye M, Woychik N. Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit. Proc Natl Acad Sci U S A. 2008;105:5885-90 pubmed publisher
  2. Kozak M. Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene. 2003;318:1-23 pubmed
    ..quot; This compromise would allow the sequences to be used for gene expression studies, for which they sometimes work, without asserting more than has been proven about the mechanism. ..
  3. Kozak M. Lessons (not) learned from mistakes about translation. Gene. 2007;403:194-203 pubmed
    ..I explain why new assays, devised to rule out splicing in tests with dicistronic vectors, are not valid and why experiments with IRESs are not a good way to investigate the mechanism whereby microRNAs inhibit translation. ..
  4. Raveh A, Margaliot M, Sontag E, Tuller T. A model for competition for ribosomes in the cell. J R Soc Interface. 2016;13: pubmed publisher
    ..In addition, we show that increasing the length of an mRNA molecule decreases the production rate of all the mRNAs. ..
  5. Goss Kinzy T, Harger J, Carr Schmid A, Kwon J, Shastry M, Justice M, et al. New targets for antivirals: the ribosomal A-site and the factors that interact with it. Virology. 2002;300:60-70 pubmed
    ..These results suggest that structural features associated with the ribosomal A-site and with the trans-acting factors that interact with it may present a new set of molecular targets for the rational design of antiviral compounds. ..
  6. Mateyak M, Kinzy T. eEF1A: thinking outside the ribosome. J Biol Chem. 2010;285:21209-13 pubmed publisher
    ..A mechanistic understanding of these non-canonical functions of eEF1A will shed light on many important biological questions, including viral-host interaction, subcellular organization, and the integration of key cellular pathways. ..
  7. Xia B, Ke H, Shinde U, Inouye M. The role of RbfA in 16S rRNA processing and cell growth at low temperature in Escherichia coli. J Mol Biol. 2003;332:575-84 pubmed
  8. Inoue K, Alsina J, Chen J, Inouye M. Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli. Mol Microbiol. 2003;48:1005-16 pubmed
    ..These results indicate that Era is involved in 16S rRNA maturation and ribosome assembly. ..
  9. Jones P, Inouye M. The cold-shock response--a hot topic. Mol Microbiol. 1994;11:811-8 pubmed
    ..In addition to E. coli, cold-shock proteins have also been found in other prokaryotic and eukaryotic organisms. ..

More Information

Publications42

  1. Choi W, Yamaguchi Y, Lee J, Jang K, Inouye M, Kim S, et al. Translation-dependent mRNA cleavage by YhaV in Escherichia coli. FEBS Lett. 2017;591:1853-1861 pubmed publisher
    ..From these results, we conclude that YhaV is a ribosome-dependent toxin that cleaves mRNA in a translation-dependent manner. ..
  2. Jones P, Mitta M, Kim Y, Jiang W, Inouye M. Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli. Proc Natl Acad Sci U S A. 1996;93:76-80 pubmed
    ..Therefore, the requirement for CsdA in derepression of heat-shock protein synthesis is a cold shock-induced function possibly mediated by destabilization of secondary structures previously identified in the rpoH mRNA. ..
  3. Kinzy S, Caban K, Copeland P. Characterization of the SECIS binding protein 2 complex required for the co-translational insertion of selenocysteine in mammals. Nucleic Acids Res. 2005;33:5172-80 pubmed
    ..Based on these results, we propose a revised model for selenocysteine incorporation where SBP2 remains ribosome bound except during selenocysteine delivery to the ribosomal A-site. ..
  4. Oh W, Wu C, Kim S, Facchinetti V, Julien L, Finlan M, et al. mTORC2 can associate with ribosomes to promote cotranslational phosphorylation and stability of nascent Akt polypeptide. EMBO J. 2010;29:3939-51 pubmed publisher
    ..Thus, mTORC2 can function cotranslationally by phosphorylating residues in nascent chains that are critical to attain proper conformation. Our findings reveal that mTOR links protein production with quality control. ..
  5. Wei Y, Zheng X. Nutritional control of cell growth via TOR signaling in budding yeast. Methods Mol Biol. 2011;759:307-19 pubmed publisher
    ..By using budding yeast as a model, recent studies began to elucidate the complexity of the TOR signaling pathway. ..
  6. Kozak M. Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proc Natl Acad Sci U S A. 1990;87:8301-5 pubmed
    ..This may be relevant to recent reports of adventitious upstream initiation events at non-AUG codons in some vertebrate mRNAs that have structure-prone, G + C-rich leader sequences. ..
  7. Caban K, Copeland P. Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes. J Biol Chem. 2012;287:10664-73 pubmed publisher
  8. Carr Schmid A, Pfund C, Craig E, Kinzy T. Novel G-protein complex whose requirement is linked to the translational status of the cell. Mol Cell Biol. 2002;22:2564-74 pubmed
    ..Thus, Hbs1p and Dom34p may function together to help directly or indirectly facilitate the expression either of specific mRNAs or under certain cellular conditions. ..
  9. Sharp J, Cruz J, Raman S, Inouye M, Husson R, Woychik N. Growth and translation inhibition through sequence-specific RNA binding by Mycobacterium tuberculosis VapC toxin. J Biol Chem. 2012;287:12835-47 pubmed publisher
    ..Therefore, the activity of VapC-mt4 is mechanistically distinct from other TA toxins because it appears to primarily inhibit translation through selective, stable binding to RNA. ..
  10. Gonzalez Flores J, Gupta N, Demong L, Copeland P. The selenocysteine-specific elongation factor contains a novel and multi-functional domain. J Biol Chem. 2012;287:38936-45 pubmed publisher
    ..We propose a model where the SBP2/SECIS complex activates eEFSec by directing functional interactions between Domain IV and the ribosome to promote Sec-tRNA(Sec) binding and accommodation into the ribosomal A-site. ..
  11. Prysak M, Mozdzierz C, Cook A, Zhu L, Zhang Y, Inouye M, et al. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol. 2009;71:1071-87 pubmed publisher
  12. Xia B, Etchegaray J, Inouye M. Nonsense mutations in cspA cause ribosome trapping leading to complete growth inhibition and cell death at low temperature in Escherichia coli. J Biol Chem. 2001;276:35581-8 pubmed
    ..Our system may offer a novel means to study sequence or structural elements involved in the translation of the cspA mRNA and may also be utilized to regulate bacterial growth at low temperature. ..
  13. Huang Y, Swapna G, Rajan P, Ke H, Xia B, Shukla K, et al. Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli. J Mol Biol. 2003;327:521-36 pubmed
    ..coli operon. Structural and functional similarities between RbfA, NusA, and other bacterial type II KH domains suggest previously unsuspected evolutionary relationships between these cold-shock associated proteins...
  14. Harger J, Meskauskas A, Dinman J. An "integrated model" of programmed ribosomal frameshifting. Trends Biochem Sci. 2002;27:448-54 pubmed
  15. Kozak M. A second look at cellular mRNA sequences said to function as internal ribosome entry sites. Nucleic Acids Res. 2005;33:6593-602 pubmed
    ..The practice of calling even very weak results 'positive' is one of the problems discussed herein. The extremely low efficiency of putative IRESs is inconsistent with their postulated biological roles.' ..
  16. Pittman Y, Kandl K, Lewis M, Valente L, Kinzy T. Coordination of eukaryotic translation elongation factor 1A (eEF1A) function in actin organization and translation elongation by the guanine nucleotide exchange factor eEF1Balpha. J Biol Chem. 2009;284:4739-47 pubmed publisher
    ..The consequences of the overlapping functions in this eEF1A domain and its unique differences from the bacterial homologs provide a novel function for eEF1Balpha to balance the dual roles in actin bundling and protein synthesis. ..
  17. Yamaguchi Y, Park J, Inouye M. Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet. 2011;45:61-79 pubmed publisher
    ..The elucidation of their cellular function and regulation is thus crucial for our understanding of bacterial physiology under various stress conditions. ..
  18. Tolbert M, Morgan C, Pollum M, Crespo Hernandez C, Li M, Brewer G, et al. HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation. J Mol Biol. 2017;429:2841-2858 pubmed publisher
    ..Thus, this work provides key details into how an EV71 IRES structure adapts to hijack a cellular protein, and it suggests that the SLII domain is a potential target for antiviral therapy. ..
  19. Sasikumar A, Kinzy T. Mutations in the chromodomain-like insertion of translation elongation factor 3 compromise protein synthesis through reduced ATPase activity. J Biol Chem. 2014;289:4853-60 pubmed publisher
    ..The chromodomain-like insertion is, therefore, vital to eEF3 function and may be targeted for developing novel antifungal drugs. ..
  20. Hwang J, Inouye M. The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli. Mol Microbiol. 2006;61:1660-72 pubmed
    ..We propose that Der plays a pivotal role in ribosome biogenesis possibly through interaction with rRNA or rRNA/r-protein complex. ..
  21. Hurley J, Woychik N. Bacterial toxin HigB associates with ribosomes and mediates translation-dependent mRNA cleavage at A-rich sites. J Biol Chem. 2009;284:18605-13 pubmed publisher
  22. Donovan J, Caban K, Ranaweera R, Gonzalez Flores J, Copeland P. A novel protein domain induces high affinity selenocysteine insertion sequence binding and elongation factor recruitment. J Biol Chem. 2008;283:35129-39 pubmed publisher
    ..We propose a model in which SECIS binding induces a conformational change in SBP2 that recruits eEFSec, which in concert with the Sec incorporation domain gains access to the ribosomal A site. ..
  23. Inoue K, Chen J, Tan Q, Inouye M. Era and RbfA have overlapping function in ribosome biogenesis in Escherichia coli. J Mol Microbiol Biotechnol. 2006;11:41-52 pubmed
    ..We propose that Era and RbfA have an overlapping function that is essential for ribosome biogenesis, and that RbfA becomes dispensable only at high temperatures because Era can complement its function only at higher temperatures. ..
  24. Doss Pepe E, Chen L, Madura K. Alpha-synuclein and parkin contribute to the assembly of ubiquitin lysine 63-linked multiubiquitin chains. J Biol Chem. 2005;280:16619-24 pubmed
  25. Cui Y, Dinman J, Kinzy T, Peltz S. The Mof2/Sui1 protein is a general monitor of translational accuracy. Mol Cell Biol. 1998;18:1506-16 pubmed
    ..Taken together, these results suggest that Mof2p/Sui1p functions as a general modulator of accuracy at both the initiation and elongation phases of translation. ..
  26. Jiang W, Fang L, Inouye M. Complete growth inhibition of Escherichia coli by ribosome trapping with truncated cspA mRNA at low temperature. Genes Cells. 1996;1:965-76 pubmed
    ..LACE may provide a novel approach to the development of a new antibiotic. ..
  27. Hou Y, Yaskowiak E, March P. Carboxyl-terminal amino acid residues in elongation factor G essential for ribosome association and translocation. J Bacteriol. 1994;176:7038-44 pubmed
    ..We propose that all of these mutations are present in a domain that is essential for ribosome association and that GTP hydrolysis was deficient as a secondary consequence of impaired binding to 70S ribosomes. ..
  28. Tsang C, Zheng X. Opposing role of condensin and radiation-sensitive gene RAD52 in ribosomal DNA stability regulation. J Biol Chem. 2009;284:21908-19 pubmed publisher
    ..In contrast, deletion of RAD52 restores cell viability under the same conditions. These results reveal an opposing role of condensin and Rad52 in the control of rDNA stability under nutrient starvation conditions. ..
  29. Zhang Y, Inouye M. RatA (YfjG), an Escherichia coli toxin, inhibits 70S ribosome association to block translation initiation. Mol Microbiol. 2011;79:1418-29 pubmed publisher
    ..Here we demonstrate that RatA is a new E. coli toxin, which effectively blocks the translation initiation step. We propose that this toxin of previously unknown function be renamed as RatA (Ribosome association toxin A). ..
  30. Caban K, Kinzy S, Copeland P. The L7Ae RNA binding motif is a multifunctional domain required for the ribosome-dependent Sec incorporation activity of Sec insertion sequence binding protein 2. Mol Cell Biol. 2007;27:6350-60 pubmed
    ..5-kDa protein-U4 snRNA complex strongly supports a two-site model for L7Ae domain function within SBP2. These results provide evidence that the SBP2-ribosome interaction is essential for Sec incorporation. ..
  31. Caban K, Copeland P. Size matters: a view of selenocysteine incorporation from the ribosome. Cell Mol Life Sci. 2006;63:73-81 pubmed
    ..The role of the ribosome in this process is emphasized along with a detailed analysis of kinkturn structures present in the ribosome and the L7Ae RNA-binding motif present in SBP2 and other proteins. ..
  32. Jao D, Chen K. Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex. J Cell Biochem. 2006;97:583-98 pubmed
  33. Fingerman I, Nagaraj V, Norris D, Vershon A. Sfp1 plays a key role in yeast ribosome biogenesis. Eukaryot Cell. 2003;2:1061-8 pubmed
    ..This suggests that regulation of genes containing RRPEs is dependent upon Sfp1 but that Sfp1 may not directly bind to these conserved promoter elements; rather, activation may occur through an indirect mechanism. ..