פרופ' גבריאל [גבי] קאופמן

חיידקים ונגיפיהם (בקטריופאג'ים, פאג'ים) שורדים הודות להתפתחות מתמדת של אמצעי ההגנה חיידקיים ואמצעי נגד נגיפיים.  "מירוץ חימוש" זה מודגם ע"י השתלשלות אבולוציונית בה אנזים הגבלת DNA restriction) DNA) חיידקי מנוטרל ע"י פפטיד תוצר פאג'ץ  אולם ניטרול  זה מחולל הפעלה של מערכת הגנה חיידקית משנית - האנטיקודון נוקלאז PrrC - שבוקעת את לולאת האנטידוקון של אחד מסוגי ה tRNA.  נזק זה עשוי לבלום  התפתחות  חלקיקי פאג' חדשים ולמנוע לכן את התפשטות ההדבקה לתאים אחרים באוכלוסיה, אולם גם אמצעי הגנה זה מנוטרל, הפעם  ע"י מערכת תיקון tRNA של הפאג'.  אנטיקודון נולקאז חיידקית משוכללת יותר בשם RloC מחוללת נזק שהפאג' אינו מתקן אבל הוא מתגבר בדרך אחרת, באמצעות מולקולת tRNA המשמשת מעין פיתיון שמנטרל את RloC. RloC נבדל מ PrrC גם בכך שהוא מצוייד במתג השתקה-הפעלה פנימי.  מתג זה מגיב לשברי DNA ומאפשר בכך את הפעלת RloC כאשר החיידק בו RloC מקנן מותקף ע"י פאג' שבוקע את ה- DNA התאי. אנו חוקרים את הבקרה ויחסי המבנה-תפקוד של PrrC ו RloC ומתעניינים באפשרות לנצל את RloC כאמצעי לחיסון חיידקים מועילים מפני הדבקת פאג'.

Gabriel Kaufmann – List of publications

Krutkina,E., Klaiman,D., Margalit,T., Jerabek-Willemsen,M. and Kaufmann,G. (2016). Dual nucleotide specificity determinants of an infection aborting anticodon nuclease.  Virology, . In press.

Bitton,L., Klaiman,D. and Kaufmann,G. (2015).  Phage T4-induced DNA breaks activate a tRNA repair-defying anticodon nuclease. Mol. Microbiol., 97, 898-910.

Klaiman,D., Steinfels-Kohn,E., and Kaufmann,G. A DNA break inducer activates the anticodon nuclease RloC and the adaptive immunity in Acinetobacter baylyi ADP1. (2014) Nuceic Acids Res.  42, 328-339.

Klaiman, D., Steinfels-Kohn, E., Krutkina, K., Davidov, E., and Kaufmann, G. (2012). The wobble nucleotide excising anticodon nuclease RloC is governed by the zinc hook and DNA-dependent ATPase of its Rad50-like domain. Nuceic Acids Res. 40, 8568-8578.

Klaiman,D. and Kaufmann,G. (2011). Phage T4-induced dTTP accretion bolsters a tRNase-based host defense. Virol. 414, 97-101.

Kaufmann,G., Davidov,E., Steinfels-Kohn,E., Krutkina,K., Klaiman,D., Margalit,T., Chai-Danino,M., and Kotlyar,A. (2011). RloC: a Translation-Disabling tRNase Implicated in Phage Exclusion during Recovery from DNA Damage. In DNA repair I.Kruman, ed. InTech Open Access Publisher Rijeka, Croatia. pp 21-44.

Davidov,E. and Kaufmann,G. (2008). RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase. Mol. Microbiol. 69, 1560-1574.

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.

Rytkonen,A.K., Hillukkala,T., Vaara,M., Sokka,M., Jokela,M., Sormunen,R., Nasheuer,H.P., Nethanel,T., Kaufmann,G., Pospiech,H., and Syvaoja,J.E. (2006a). DNA polymerase epsilon associates with the elongating form of RNA polymerase II and nascent transcripts. FEBS J. 273, 5535-5549.

Rytkonen,A.K., Vaara,M., Nethanel,T., Kaufmann,G., Sormunen,R., Laara,E., Nasheuer,H.P., Rahmeh,A., Lee,M.Y., Syvaoja,J.E., and Pospiech,H. (2006b). Distinctive activities of DNA polymerases during human DNA replication. FEBS J. 273, 2984-3001

Blanga-Kanfi,S., Amitsur,M., Azem,A., and Kaufmann,G. (2006). PrrC-anticodon nuclease: functional organization of a prototypical bacterial restriction RNase. Nucleic Acids Res. 34, 3209-3219.

Kaufmann,G. and Nethanel,T. (2004). Did an early version of the eukaryal replisome enable the emergence of chromatin? Prog. Nucleic Acid Res. Mol. Biol. 77, 173-209.

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.

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.

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.

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.

Kaufmann,G. (2000). Anticodon nucleases. Trends Biochem. Sci. 25, 70-74.

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.

Mass,G., Nethanel,T., and Kaufmann,G. (1998). The middle subunit of replication protein A contacts growing RNA-DNA primers in replicating simian virus 40 chromosomes. Mol. Cell Biol. 18, 6399-6407.

Zlotkin,T., Kaufmann,G., Jiang,Y., Lee,M.Y., Uitto,L., Syvaoja,J., Dornreiter,I., Fanning,E., and Nethanel,T. (1996). DNA polymerase epsilon may be dispensable for. EMBO J. 15, 2298-2305.

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.

Shterman,N., Elroy-Stein,O., Morad,I., Amitsur,M., and Kaufmann,G. (1995). Cleavage of the HIV replication primer tRNALys,3 in human cells expressing bacterial anticodon nuclease. Nucleic Acids Res. 23, 1744-1749.

Morad,I., Chapman-Shimshoni,D., Amitsur,M., and Kaufmann,G. (1993). Functional expression and properties of the tRNA(Lys)-specific core anticodon nuclease encoded by Escherichia coli prrC. J. Biol. Chem. 268 , 26842-26849.

Nethanel,T., Zlotkin,T., and Kaufmann,G. (1992). Assembly of simian virus 40 Okazaki pieces from DNA primers is reversibly arrested by ATP depletion. J. Virol. 66, 6634-6640.

Amitsur,M., Morad,I., Chapman-Shimshoni,D., and Kaufmann,G. (1992). HSD restriction-modification proteins partake in latent anticodon nuclease. EMBO J. 11, 3129-3134.

Nethanel,T. and Kaufmann,G. (1990). Two DNA polymerases may be required for synthesis of the lagging DNA strand of simian virus 40. J. Virol. 64, 5912-5918.

Levitz,R., Chapman,D., Amitsur,M., Green,R., Snyder,L., and Kaufmann,G. (1990). The optional E. coli prr locus encodes a latent form of phage T4- induced anticodon nuclease. EMBO J. 9, 1383-1389.

Amitsur,M., Morad,I., and Kaufmann,G. (1989). In vitro reconstitution of anticodon nuclease from components encoded by phage T4 and Escherichia coli CTr5X. EMBO J. 8, 2411-2415.

Nethanel,T., Reisfeld,S., Dinter-Gottlieb,G., and Kaufmann,G. (1988). An Okazaki piece of simian virus 40 may be synthesized by ligation of shorter precursor chains. J. Virol. 62, 2867-2873.

Chapman,D., Morad,I., Kaufmann,G., Gait,M.J., Jorissen,L., and Snyder,L. (1988). Nucleotide and deduced amino acid sequence of stp: the bacteriophage T4 anticodon nuclease gene. J. Mol. Biol. 199, 373-377.

Amitsur,M., Levitz,R., and Kaufmann,G. (1987). Bacteriophage T4 anticodon nuclease, polynucleotide kinase and RNA ligase reprocess the host lysine tRNA. EMBO J. 6, 2499-2503.

Kaufmann,G., David,M., Borasio,G.D., Teichmann,A., Paz,A., Amitsur,M., Green,R., and Snyder,L. (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.

Zannis-Hadjopoulos M, Kaufmann G, Wang SS, Lechner RL, Karawya E, Hesse J, Martin RG. (1985). Properties of some monkey DNA sequences obtained by a procedure that enriches for DNA replication origins. Mol Cell Biol.5, 1621-9

Kaufmann,G. and Amitsur,M. (1985). Host transfer RNA cleavage and reunion in T4-infected Escherichia coli CTr5x. Nucleic. Acids Res. 13, 4333-4341.

Kaufmann,G., Zannis-Hadjopoulos,M., and Martin,R.G. (1985). Cloning of nascent DNA synthesized early in the cell cycle. Mol. Cell. Biol. 5, 721-727.

Zannis-Hadjopoulos M, Kaufmann G, Martin RG. (1984).  Mammalian DNA enriched for replication origins is enriched for snap-back sequences.  J Mol Biol. 179, 577-86.

Dinter-Gottlieb,G. and Kaufmann,G. (1983). Aphidicolin arrest irreversibly impairs replicating SV40 chromosomes. J. Biol. Chem. 258, 3809-3812.

David,M., Borasio,G.D., and Kaufmann,G. (1982). T4 bacteriophage-coded polynucleotide kinase and RNA ligase are involved in host tRNA alteration or repair. Virol. 123, 480-483.

David,M., Borasio,G.D., and Kaufmann,G. (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.

Kaufmann,G. and Falk,H.H. (1982). An oligoribonucleotide polymerase from SV40-infected cells with properties of a primase. Nucleic. Acids Res. 10, 2309-2321.

Dinter-Gottlieb,G. and Kaufmann,G. (1982). Uncoupling of SV40 tsA replicon activation from DNA chain elongation by temperature shifts and aphidicolin arrest. Nucleic Acids Res. 10, 763-773.

Kaufmann,G. (1981). Characterization of initiator RNA from replicating simian virus 40 DNA synthesized in isolated nuclei. J. Mol. Biol. 147, 25-39.

Kaufmann,G., Choder,M., and Groner,Y. (1980). Synthesis of carrier-free beta-32P-nucleosides-triphosphate in almost quantitative yields. Anal. Biochem. 109, 198-202.

David,M., Vekstein,R., and Kaufmann G (1979). RNA ligase reaction products in plasmolyzed Escherichia coli cells infected by T4 bacteriophage. Proc. Natl. Acad. Sci. USA 76, 5340-5344.

DePamphilis ML, Anderson S, Bar-Shavit R, Collins E, Edenberg H, Herman T, Karas B, Kaufmann G, Krokan H, Shelton E, Su R, Tapper D, Wassarman PM. (1979) Replication and structure of simian virus 40 chromosomes. Cold Spring Harb Symp Quant Biol  43, Pt 2, 679-92

Kaufmann,G., Bar-Shavit,R., and DePamphilis,M.L. (1978). Okazaki pieces grow opposite to the replication fork direction during simian virus 40 DNA replication. Nucleic. Acids Res. 5, 2535-2545.

Anderson S, Kaufman G, DePamphilis ML. (1977). RNA primers in SV40 DNA replication: identification of transient RNA-DNA covalent linkages in replicating DNA. Biochemistry. 1977 Nov 15;16(23):4990-8

Kaufmann,G., Anderson,S., and DePamphilis,M.L. (1977). RNA primers in simian virus 40 DNA replication: distribution of 5' terminal oligoribonucleotides in nascent DNA. J. Mol. Biol. 111, 549-568.

Kaufmann,G. and Kallenbach,N.R. (1975). Determination of recognition sites of T4 RNA ligase on the 3'-OH and 5' -P termini of polyribonucleotide chains. Nature 254, 452-454.

Kaufmann,G. and Littauer,U.Z. (1974). Covalent joining of phenylalanine transfer ribonucleic acid half- molecules by T4 RNA ligase. Proc. Natl. Acad. Sci. U. S. A. 71, 3741-3745.

Kaufmann,G., Klein,T., and Littauer,U.Z. (1974). T4 RNA ligase: substrate chain length requirements. FEBS Lett. 46, 271-275.

Kaufmann,G., Grosfeld,H., and Littauer,U.Z. (1973). Stepwise phosphorolysis with polynucleotide phosphorylase: a novel method for sequence analysis of oligoribonucleotides. FEBS Lett. 31, 47-52.

Kaufmann,G., Firdkin,M., Zutra,A., and Littauer,U.Z. (1971). Monofunctional substrates of polynucleotide phosphorylase. The monoaddition of 2'(3')-O-isovaleryl-nucleoside diphosphate to an initiator oligonucleotide. Eur. J. Biochem. 24, 4-11.

Kaufmann,G. and Littauer,U.Z. (1970). Phosphorolysis of aminoacyl-tRNA by polynucleotide phosphorylase from Escherichia coli . Eur. J. Biochem. 12, 85-92.

Kaufmann,G. and Littauer,U.Z. (1969). Deoxyadenosine diphosphate as substrate for polynucleotide phosphorylase from Escherichia coli. FEBS Lett. 4, 79-83.