Publications

Here you can find some selected publications (last update: April 2017).
For the full publication list please refer to the PubMed site
.

Gophna, U, Allers T and Marchfelder A, (2017). Finally, archaea get their CRISPR-Cas toolbox. Trends Microbiol, in press


Ma M, Li de la Sierra-Gallay I, Lazar N, Pellegrini O, Durand D, Marchfelder A, Condon C and van Tilbeurgh H (2017) The crystal structure of Trz1, the long form RNase Z from yeast. Nucleic Acids Res, in press


 Maier, L.K., Alkhnbashi, O.S., Backofen, R. and Marchfelder, A. (2017) CRISPR AND SALTY - CRISPR-Cas systems in Haloarchaea. in NAMB (Nucleic Acids and Molecuar Biology) Volume” RNA metabolism and gene expression in Archaea ed. Clouet-d´ Orval, B.; Springer, in press


Stachler, AE, Turgeman-Grott, I, Shtifman Segal, E, Allers, T., Marchfelder, A. and Gophna, U. (2017) High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon. Nucleic Acids Res, in press


Babski J, Haas KA, Näther-Schindler D, Pfeiffer F, Förstner KU, Hammelmann M, Hilker R, Becker A, Sharma CM, Marchfelder A*, Soppa J.* (2016) Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq). BMC Genomics, 17: 629.  * joint corresponding author


Stachler AE and Marchfelder A (2016) Gene Repression in Haloarchaea using the CRISPR (clustered regularly interspaced short palindromic repeats) - Cas I-B system. J Biol Chem, 291: 15226-42


Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H (2015) Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods, 89: 138-48


DB Cass SDB, Haas KA, Stoll B, Alkhnbashi O, Sharma K, Urlaub H, Backofen R, Marchfelder A and Bolt EL (2015) The role of Cas8 in type I CRISPR interference, Bioscience Reports, 35: e00197


Maier, L.K., Dyall-Smith M, Marchfelder A. (2015) The adaptive immune system of Haloferax volcanii, Life, 5: 521-37.


Maier, L.K., Benz, J., Fischer, S., Alstetter, M., Jaschinski, K., Hilker, R., Becker, A., Allers, T., Soppa, J. and Marchfelder, A. (2015) Deletion of the Sm1 encoding motif in the lsm gene result in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells, Biochemie, 117: 129-137


Maier, L.K., Stachler, A., Saunders, S.J., Backofen R and Marchfelder, A. (2015) An Active Immune Defence with a Minimal CRISPR (clustered regularly interspaced short palindromic repeats) RNA and Without the Cas6 Protein. J Biol Chem., 290: 4192-201


Hrle, A., Maier, L.-K., Sharma, K., Ebert, J, R., Basquin, C., Urlaub, H., Marchfelder, A. and Conti, E. (2014) Structural analyses of the CRISPR protein Csc2 reveal the RNA binding interface of the type I-D Cas7 family. RNA Biology, 11: 1072-82


Babski, J., Maier, L.K., Heyer, R., Jaschinski, J., Prasse, D., Jäger, D., Randau, L., Schmitz, R.A., Marchfelder, A. and Soppa, J. (2014) Small regulatory RNAs in Archaea. RNA Biology, 11: 484-93


Jaschinski, K., Babski, J., Lehr, M., Burmester, A., Benz, J., Heyer, R., Dörr, M.,  Marchfelder, A. and Soppa, J. (2014) Generation and phenotyping of a collection of sRNA gene deletion mutants of the haloarchaeon Haloferax volcanii. PlosONE, 9: e90763


Brendel J., Stoll B., Lange S.J., Sharma K., Lenz C., Stachler A.E., Maier L.K., Richter H., Nickel L., Schmitz R.A., Randau L., Allers T., Urlaub H., Backofen R., Marchfelder A. (2014) A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of crRNAs in Haloferax volcanii. J Biol Chem, 289: 7164-7177


Marchfelder, A, Maier, L.-K., Heidrich, N., Pul, Ü. (2013) CRISPR-Cas: das Immunsystem der Prokaryoten. Biologie in unserer Zeit, 43: 158-165


Stoll, B., Maier, L.-K., Lange, S. J., Brendel, J., Fischer, S., Backofen, R. and Marchfelder, A. (2013) Requirements for a successful defence reaction by the CRISPR/Cas type I-B system. Biochem. Soc. Trans., 41: 1444-1448


Marchfelder, A. (2013) A Sophisticated Defense System: CRISPR-Cas. RNA Biology, 10: 665-658


Maier, L.-K., Lange, S. J., Stoll, B., Haas, K. A., Fischer, S., Fischer, E.,  Duchardt-Ferner, E., Wöhnert, J., Backofen, R. and Marchfelder, A. (2013) Essential requirements to detect and degrade invaders. RNA Biology, 10: 865-874


Skowronek, E., Grzechnik, P., Späth, B., Rösch, S., Marchfelder, A. and Kufel, J. (2013) Pathways for 3’ processing of yeast tRNAs involve tRNase Z, Rex1 and Rrp6. RNA, 20: 115-130


Maier LK, Fischer S, Stoll B, Brendel J, Pfeiffer F, Dyall-Smith M, Marchfelder A. (2013) The ring of confidence: a haloarchaeal CRISPR/Cas system. Biochem. Soc. Trans., 41: 374-378


Schnattinger, T., Schöning, U., Marchfelder, A., Kestler, H. (2013) RNA-Pareto: Interactive Analysis of Pareto-optimal RNA Sequence-Structure Alignments. Bioinformatics, 29: 3102-4


Englert, M., Späth, B., Schiffer, S., Rösch, S., Beier, H. and Marchfelder, A. (2013) Use of RNA affinity matrices for the isolation of RNA-binding proteinsin Handbook of RNA Biochemistry eds. Hartmann, R. K., Bindereif, A., Schön, A. and Westhof, E.; Wiley VCH, Weinheim


Maier LK, Fischer S, Stoll B, Brendel J, Pfeiffer F, Dyall-Smith M, Marchfelder A. (2012) The immune system of halophilic archaea. Mobile Genetic Elements, 2: 1-5


Fischer S, Maier LK, Stoll B, Brendel J, Fischer E, Pfeiffer F, Dyall-Smith M, Marchfelder A. (2012) An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA. J Biol Chem, 287: 33351-63


Heyer, R., Dörr, M., Jellen-Ritter, A., Späth, B., Babski, J., Jaschinski, K., Soppa, J. and Marchfelder, A. (2012) High throughput sequencing reveals a plethora of small RNAs including tRNA derived fragments in Haloferax volcanii. RNA Biology, 9: 1011-1018


Marchfelder, A., Fischer, S., Brendel, J., Stoll, B., Maier, L.-K., Jäger, D., Prasse, D., Plagens,A., Schmitz, R.A. and Randau, L. (2012) Small RNAs for Defence and Regulation in Archaea. Extremophiles, 16: 685-696


Schmitz-Streit, R., Jäger, D. , Jellen-Ritter, A., Babski, J., Soppa, J. and Marchfelder, A. (2011) Archaea employ small RNAs as regulators, in Regulatory RNAs in Prokaryotes eds Hess, W.R. and Marchfelder, A., Springer Verlag, Wien, pp 131-145


Fischer, S., Benz, J., Späth, B., Maier, LK., Straub, J., Granzow, M., Raabe, M., Urlaub, H., Hoffmann, J., Brutschy, B., Allers, T., Soppa, J., and Marchfelder, A. (2010) The archaeal Lsm protein binds to small RNAs, J Biol Chem, 285: 34429-34438


Barbezier, N., Canino, G., Rodor, J., Jobet, E., Saez-Vasquez, J., Marchfelder, A. and Echeverría, M. (2009) Processing of a dicistronic tRNA-snoRNA precursor: combined analysis in vitro and in vivo reveals alternate pathways and coupling to assembly of snoRNP. Plant Phys, 150: 1598- 1610


Canino, G., Bocian, E., Barbezier, N., Echeverria, M.,Forner, J., Binder, S. and Marchfelder, A. (2009) The four tRNase Z enzymes encoded in Arabidopsis have distinct features. Plant Phys, 150: 1494-1502


Straub, J., Brenneis, M., Jellen-Ritter, A., Heyer, R., Soppa, J. and Marchfelder, A. (2009) Small RNAs in haloarchaea: Identification, differential expression and biological function. RNA Biology, 6, 281-292


Hölzle, A., Fischer, S., Heyer, R., Schütz, S., Zacharias, M., Walther, P., Allers, T. and Marchfelder, A. (2008) Maturation of the 5S rRNA 5´ end is catalysed in vitro by the endonuclease tRNase Z in the archaeon Haloferax volcanii. RNA, 14: 928-37


Klug, G., Evguenieva-Hackenberg, E., Omer, A.D., Dennis, P.P. and Marchfelder, A. (2007) RNA processing. in Archaea: Molecular Cell Biology ed. Cavicchioli, R., ASM press, pp 158-174


Späth, B., Kirchner, S., Vogel, A., Schubert, S., Meinlschmidt, P., Aymanns, S., Nezzar, J. and Marchfelder, A. (2005) Analysis of the functional modules of the tRNA 3' endonuclease (tRNase Z). J Biol Chem, 280: 35440-35447


Dubrovsky, E. B., Dubrovskaya, V. A., Levinger, L., Schiffer, S. and Marchfelder, A. (2004) Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3´ ends in vivo. Nucleic Acids Res, 32: 255-262


Pellegrini, O., Nezzar, J., Marchfelder, A., Putzer, H. and Condon, C. (2003) Endonucleolytic processing of CCA-less tRNA precursors by RNase Z in Bacillus subtilis. EMBO J, 22: 4534-4543


Kruszka, K., Barneche, F., Guyot, R., Ailhas, J., Meneau, I., Schiffer, S., Marchfelder, A. and Echeverría, M. (2003) Plant dicistronic tRNA-snoRNA genes: a new mode of expression of the small nucleolar RNAs processed by RNase Z. EMBO J, 22: 621-632


Schiffer, S., Rösch, S. and Marchfelder, A. (2002) Assigning a function to a conserved group of proteins: The tRNA 3´ processing enzymes. EMBO J 21: 2769-2777


Schierling, K., Rösch, S., Rupprecht, R., Schiffer, S. and Marchfelder, A. (2002) tRNA 3´ end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii. J Mol Biol 316: 893-900


Schürer, H., Schiffer, S., Marchfelder, A. and Mörl, M. (2001) This is the end: Processing, editing and repair at the tRNA 3´-terminus. Biol Chem 382: 1147-1156


Schiffer, S., Helm, M., Théobald-Dietrich, A., Giége, R. and Marchfelder, A. (2001) The plant tRNA 3´ processing enzyme has a broad substrate spectrum. Biochemistry 40: 8264-8272


Mörl, M. and Marchfelder, A. (2001) The final cut: the importance of tRNA 3´ processing. EMBO Rep 2: 17-20


Mayer, M., Schiffer, S. and Marchfelder, A. (2000) tRNA 3´ processing in plants: nuclear and mitochondrial activities differ. Biochemistry 39: 2096-2105


Kunzmann, A., Brennicke, A. and Marchfelder, A. (1998) 5´ end maturation and RNA editing have to precede tRNA 3´ processing in plant mitochondria. Proc Natl Acad Sci, USA 95: 108-113


Marchfelder, A., Clayton, D. A. and Brennicke, A. (1998) The gene for ribosomal protein L7A-1 in S. pombe contains an intron after the initiation codon. Biochim Biophys Acta 1397: 146-150


Marchfelder, A. (1996) Plant mitochondrial RNase P. Mol Biol Rep 22: 151-156


Marchfelder, A., Brennicke, A. and Binder, S. (1996) RNA editing is required for efficient excision of tRNAPhe from precursors in plant mitochondria. J Biol Chem 271: 1898-1903


Marchfelder, A., Schuster, W. and Brennicke, A. (1990) In vitro processing of mitochondrial and plastid derived tRNA precursors in a plant mitochondrial extract. Nucleic Acids Res, 18: 1401-1406


Koepke, AKE and Marchfelder, A. (1988) Sequencing proteins of low availability - gene cloning of ribosomal-protein genes from archaebacterium Methanococcus vannielii. J Protein Chem, 7: 253