Prof. Gabriel Kaufmann
Ph.D.: Weizmann Institute of Science , 1972
Phone: (Office) +972-3-6426213
(Lab ) +972-3-6409067
(Home) +972-3-6496273
Fax (Office) +972-3-6406834
E-mail: Gabika@tauex.tau.ac.il
Room#: Sherman, Room 615


Research Interests

Suicidal, phage-excluding tRNases PrrC and RloC

Loss of a single tRNA species suffices to block translation, arrest growth and eventually cause cell death (1).  Microbial organisms accomplish this feat using nucleases that target tRNA's Achilles heel.  These anticodon nucleases (ACNases) exclude phage, kill competing cells and may provide other, yet unknown advantages.

We focus on the suicidal, phage-excluding ACNase PrrC (1, 2) and its less familiar paralog RloC (3). PrrC is silenced in uninfected E. coli by the associated type I DNA restriction nuclease EcoprrI and unleashed during phage T4 infection by the T4-encoded anti-DNA restriction factor Stp (Fig. 1).

The resulting incision of tRNALys could block phage protein synthesis and contain the infection but T4 tRNA repair enzymes counteract the damage.  Currently we study how EcoprrI, Stp and two different nucleotides recognized by PrrC's ABC ATPase-like N-domain regulate the ACNase.

Fig. 1. The anticodon nuclease PrrC: silencing, activation and phage rebuttal. PrrC (green oval) is kept inactive before infection by the associated type I DNA restriction-modification enzyme EcoprrI (red ensemble).  During phage T4 infection the phage-encoded peptide Stp, an intended inhibitor of EcoprrI's DNA restriction activates the latent PrrC tRNase.  The resultant incision of tRNALys is counteracted by T4-encoded 3'-phosphatase/5'-polynucleotide kinase (Pnk) and RNA ligase 1 (Rli).

RloC seems to be a more sophisticated version of PrrC, judged from two of its distinct properties.  First, RloC excises its substrate's wobble nucleotide, a lesion likely to impede phage reversal and render RloC a more potent antiviral device than PrrC (3). 

Second, RloC's complex regulatory domain (Fig. 2) resembles Rad50 and related DNA repair proteins endowed with DNA bridging activity (3, 6).  RloC's DNA bridging activity (Fig. 3) impacts its ACNase function in a significant way (3). These facts, taken with the transient inactivation of type I DNA restriction enzymes following DNA damage (7), underlie a model where RloC wards off phage escaping DNA restriction during recovery from DNA damage (3). This model is currently tested.

The above examples of RNA repair and, possibly, repair avoidance could be considered isolated cases where lack of a suitable DNA template precludes replenishment of the damaged RNA by transcription. Nonetheless, various types of cellular RNA repair have popped up recently: RNA polymerases proofread their transcripts (8), an RNA methylase removes toxic methyl groups (9) and a cellular repair-modification complex prevents re-cleavage of the RNA it mends (10). These findings hint that RNA repair figures in cell biology more than previously appreciated.     


fig2

Fig. 2.  A. Domain alignment of PrrC and RloC (3-5). ATPase and ACNase domains are respective pink or green rectangles; RloC's predicted coiled coil (CC) grey, the interrupting gap in pink and the zinc-hook motif in yellow. Dashed lines connect shared motifs. B. Cartoon of RloC's expected mode of DNA bridging [adapted from Rad50's (6)]. The CC/ZH protrusions bridge DNA molecules tethered to ATPase head domains (pink ovals) by coordinating zinc ions at the ZH dimerization interfaces (yellow circles)

Fig. 3. AFM imaging of RloC DNA bridging activity. AFM image of plasmid pUC19 (A) and its complex with RloC-E696A (B).  The molecules were deposited on mica and visualized by AFM.  RloC is seen as bright spots that bridge distant regions of the DNA (in collaboration with D. Zikich and A. Kotlyar, TAU Department of Biochemistry).

References 

      1.   G. Kaufmann, Trends Biochem. Sci. 25, 70 (2000).

      2.   S. Blanga-Kanfi, M. Amitsur, A. Azem, G. Kaufmann, Nucleic Acids Res. 34, 3209 (2006).

      3.   E. Davidov, G. Kaufmann, Mol. Microbiol. 69, 1560 (2008).

      4.   H. Masaki, T. Ogawa, Biochimie 84, 433 (2002).

      5.   J. Lu, B. Huang, A. Esberg, M. J. Johansson, A. S. Bystrom, RNA. 11, 1648 (2005).

      6.   K. P. Hopfner et al., Nature 418, 562 (2002).

      7.   G. W. Blakely, N. E. Murray, Mol. Microbiol. 60, 883 (2006).

      8.   D. Wang et al., Science 324, 1203 (2009).

      9.   P. A. Aas et al., Nature 421, 859 (2003).

             10.   C. M. Chan, C. Zhou, R. H. Huang, Science 326, 247 (2009).

Selected Publications

ANTICODON NUCLEASE
  1. Davidov, E. and Kaufmann, G. (2008) RloC: a wobble nucleotide excising and zinc responsive bacterial tRNase. Mol. Microbiol. 69:1560:1574.  e-format
  2. Klaiman, D., Amitsur, M., Blanga-Kanfi,S., Chai, M., Davis, D.R., and Kaufmann, G. (2007).  Parallel dimerization of a PrrC-anticodon nuclease region implicated in tRNALys recognition. Nucleic Acids Res. 35:4704-4714. e-format
  3. Blanga-Kanfi, S., Amitsur,M. Azem,A. and Kaufmann, G. (2006). PrrC-anticodn nuclease:functional organization of a prototypical bacterial restriction RNase. Nucleic Acids Res. 34: 3209-3219. e-format
  4. Amitsur, M., Benjamin, S., Rosner, R., Chapman-Shimshoni, D., Meidler, R., Blanga, S. and Kaufmann, G. (2003). Bacteriophage T4-encoded Stp can be replaced as activator of anticodon nuclease by a normal host cell metabolite. Mol. Microbiol. 50, 129-143. e-format
  5. Jiang,Y., Blanga,S., Amitsur,M., Meidler,R., Krivosheyev,E., Sundaram,M., Bajji,A.C., Davis,D.R., and Kaufmann,G. (2002). Structural features of tRNALys favored by anticodon nuclease as inferred from reactivities of anticodon stem and loop substrate analogs. J. Biol. Chem. 277, 3836-3841. e-format
  6. Jiang,Y., Meidler,R., Amitsur,M., and Kaufmann,G. (2001). Specific Interaction between Anticodon Nuclease and the tRNA(Lys) Wobble Base. J. Mol. Biol. 305, 377-388. e-format
  7. Kaufmann,G. (2000). Anticodon nucleases. Trends Biochem. Sci. 25, 70-74. e-format
  8. Meidler,R., Morad,I., Amitsur,M., Inokuchi,H., and Kaufmann,G. (1999). Detection of Anticodon Nuclease Residues Involved in tRNALys Cleavage Specificity. J. Mol. Biol. 287, 499-510. e-format
  9. Penner,M., Morad,I., Snyder,L., and Kaufmann,G. (1995). Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems. J. Mol. Biol. 249, 857-868. e-format  
  10. Shterman, N., O. Elroy-Stein, I. Morad, M. Amitsur, and G. Kaufmann. (1995). Cleavage of the HIV replication primer tRNALys3 in human cells expressing bacterial anticodon nuclease. Nucleic Acids. Res. 23:1744-1749. e-format
  11. Morad, I., D. Chapman-Shimshoni, M. Amitsur, and G. Kaufmann. (1993). Functional expression and properties of the tRNA(Lys)-specific core anticodon nuclease encoded by Escherichia coli prrC. J. Biol. Chem. 268:26842-26849. e-fomrat  
  12. Amitsur, M., I. Morad, D. Chapman-Shimshoni, and G. Kaufmann. (1992). HSD restriction-modification proteins partake in latent anticodon nuclease. EMBO J. 11:3129-3134 e-format
  13. Levitz, R., D. Chapman, M. Amitsur, R. Green, L. Snyder, and G. Kaufmann. (1990). The optional E. coli prr locus encodes a latent form of phage T4-induced anticodon nuclease. EMBO J. 9:1383-1389 e-format
  14. Amitsur, M., I. Morad, and G. Kaufmann. (1989). In vitro reconstitution of anticodon nuclease from components encoded by phage T4 and Escherichia coli CTr5X. EMBO J. 8:2411-2415 e-format
  15. Amitsur, M., R. Levitz, and G. Kaufmann. 1987. Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 6:2499-2503 e-format
  16. Chapman. D., Morad, I., Kaufmann, G., Gait, M.J., Jorissen, L., Snyder,L. (1988) Nucleotide and deduced amino acid sequence of stp: the bacteriophage T4 anticodon nuclease gene. J.Mo. Biol. 199(2):373-7 e-format
  17. Kaufmann, G., M. David, G. D. Borasio, A. Teichmann, A. Paz, M. Amitsur, R. Green, and L. Snyder. (1986). Phage and host genetic determinants of the specific anticodon-loop cleavages in bacteriophage T4 infected Escherichia coli CTr5X. J. Mol. Biol. 188:15-22
  18. David, M., G. D. Borasio, and G. Kaufmann. (1982). T4 bacteriophage-coded polynucleotide kinase and RNA ligase are involved in host tRNA alteration or repair. Virology 123:480-483
  19. David, M., G. D. Borasio, and G. Kaufmann. (1982). Bacteriophage T4-induced anticodon-loop nuclease detected in a host strain restrictive to RNA ligase mutants. Proc. Natl. Acad. Sci. U. S. A. 79:7097-7101. e-format

DNA REPLICATION

  1. Rytkönen A,K., Hillukkala, T., Vaara, M., Sokka, M., Jokela, M., Sormunen, R., Nasheuer, H.P., Nethanel, T., Kaufmann, G., Pospiech, H., Syväoja. J.E. (2006). DNA polymerase epsilon associates with the elongating form of RNA polymerase II and nascent transcripts.  FEBS J. 273:5535-49. e-format
  2. Rytkönen, A.K,, Vaara, M., Nethanel, T., Kaufmann, G., Sormunen, R., Läärä, E., Nasheuer, H.P., Rahmeh, A., Lee, M.Y., Syväoja, J.E., Pospiech, H. (2006). Distinctive activities of DNA polymerases during human DNA replication. FEBS J. 2006 273:2984-3001. e-format
  3. Kaufmann,G. and Nethanel, N. (2004). Did an early version of the eukaryal replisome enable the emergence of chromatin? Progress in Nucleic Acids Res. Mol.Biol. 77:173-209. e-format
  4. Mass,G., Nethanel,T., Lavrik,O.I., Wold,M.S., and Kaufmann,G. (2001). Replication protein A modulates its interface with the primed DNA template during RNA-DNA primer elongation in replicating SV40 chromosomes. Nucleic Acids Res. 29, 3892-3899. e-format
  5. Mass,G., Nethanel,T., and Kaufmann,G. (1998). The middle subunit of replication protein A contacts RNA-DNA primers within replicating SV40 chromosomes. Mol. Cell. Biol. 18, 6399-6410. e-format
  6. Zlotkin,T., Kaufmann,G., Jiang,Y., Lee,M.Y.W.T., Uitto,L., Syvaoja,J., Dornreiter,I., Fanning,E., and Nethanel,T. (1996). DNA polymerase epsilon may be dispensable for SV40- but not cellular-DNA replication. EMBO Journal 15, 2298-2305. e-format
  7. Nethanel, T., T. Zlotkin, and G. Kaufmann. (1992). Assembly of simian virus 40 Okazaki pieces from DNA primers is reversibly arrested by ATP depletion. J. Virol. 66:6634-6640 e-format
  8. Nethanel, T. and G. Kaufmann. (1990). Two DNA polymerases may be required for synthesis of the lagging DNA strand of simian virus 40. J. Virol. 64:5912-5918 e-format
  9. Nethanel, T., S. Reisfeld, G. Dinter-Gottlieb, and G. Kaufmann. (1988). An Okazaki piece of simian virus 40 may be synthesized by ligation of shorter precursor chains. J. Virol. 62:2867-2873 e-format

Courses

Graduate course
The RNA World – The discovery of catalytic RNA rekindled interest in the hypothesis that RNA preceded in the evolution both DNA and translated proteins. This discovery contributed also important paradigms for studying RNA's structure-function relationships. The past two decades witnessed the elucidation of the structure and catalytic mechanisms of virtually all known natural ribozymes, culminating in the spectacular elucidation of the ribosome crystal structure.  Other, artificial ribozymes, selected in test-tube evolution experiments enriched the repertory of RNA catalyzed reactions, lending credence to the hypothesis that the early life was based on RNA genomes and catalytic RNA phenotype. However, whether RNA was the first genetic molecule and alone drove RNA World's metabolism is uncertain.  Parallel developments revealed the existence of numerous non-coding RNAs that play key roles in gene regulation and genome stability.  The course, focuses on evolutionary, structural and functional aspects of RNA.  It is taught by the organizer, participating students and guest speakers who are experts in relevant fields.  Guest speakers in former years included Prof. Gil Ast (Tel Aviv University), Dr. Assaf Aharoni (Weizmann Institute), Prof. Nayef Jarrous (Hebrew University Medical School), Prof. Shula Michaeli (Bar-Ilan University), Prof. Gadi Schuster (Haifa Technion), Dr. Noam Shomron (Tel Aviv University), Prof. Scott Strobel (Yale University) and Prof. Ada Yonath (Weizmann Institute). 


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