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Education:

• B.S. 1961 Chemistry Technical University, Hannover, Germany
• Dr. rer. nat. 1967 Organic/Biochemistry Technical University, Munich, Germany
• Postdoctoral Purdue University

Overview

Ulfert received a B.S. degree equivalent in chemistry from the Technical University Hannover, Germany in 1961 and the Dr. rer. nat. in organic chemistry-biochemistry from Technical University Munich, Germany in 1967. He held a postdoctoral position at the School of Pharmacy at Purdue University and was appointed to its faculty in 1969. He spent a sabbatical year at the Department of Genetics at the John Innes Institute, Norwich, England studying Streptomyces genetics with Prof. D.A. Hopwood in 1976-77. He joined the Wisconsin faculty as a Professor of Pharmaceutical Biochemistry in 1981. In 1990-91 he was a visiting scientist at Institut Pasteur, Paris, France studying protein expression patterns in Streptomyces with Prof. J.E. Davies. He has published in the areas of alkaloid and antibiotic biosynthesis, mode of action of antibiotics, enzymology and Streptomyces DNA amplification. Since 1994 his research has concentrated on RNA-related topics. He seeks molecular modeling confirmation for his hypothesis on the evolution of a primordial genetic apparatus and for his theory on the mechanism of present-day protein biosynthesis.

The proposed primordial genetic apparatus may have been constituted by a variety of replication-proficient mRNAs carrying ANU (N=A,C,G,U) codons and four replication-proficient primordial tRNA precursors carrying ANU anticodons. These tRNA precursors may have become joined to specific amino acids - when these were present in the form of the respective Leuchs anhydrides - at extant 3' CCA ends upon formation of a pseudoknot between the CCA ends and precursor tRNA UUANUGG anticodon loop sequences. This implemented/established the following primordial anticodon-amino acid relationships: AAU-Ile/Leu, AGU-Thr/Ser, AUU-Asn/Asp and ACU-AGBA (±-amino-³ guanidino-butyric acid)/Arg, with many of these still being valid today.

Present-day protein biosynthesis is proposed to depend on a process, named discriminative coaxial in-phase anticodon-codon docking (DCIPACD), whereby ribosomes present a codon as an A-RNA minihelix and promote its interaction with an incoming anticodon/tRNA by directing the anticodon to follow a coaxial and in phase approach while assuming an A-RNA minihelix conformation. This fosters facile formation of cognate anticodon-codon complexes without any tRNA rearrangement in the tRNA anticodon stem-loop region. Ribosomes can avoid via DCIPACD detrimental G-U and U-G pairings involving the first and second codon positions as well as other mismatches. It has also been proposed that ribosomes oscillate between two different states, one of which is characterized by an ~ 90 Angstrom gap in the area between the small bacterial ribosomal protein S12 and the large bacterial ribosomal protein L14 located on the small and large ribosomal subunits, respectively. Conversely, when the ribosome is in the closed state - presently well known form X-ray studies - this distance is 15.8 Angstroms.

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We have reported DNA amplification dependent on an 8.8 kb sequence, designated as AUD-Sar 1, in the native host Streptomyces achromogenes subsp. rubradiris and in Streptomyces lividans, into which this amplification system can be transferred.

The hypothesis on the evolution of a simple genetic apparatus is based on the premise that primordial evolution had a firm physicochemical foundation. It postulates precise interactions of the side chains of the amino acids Asn (Asp), ±-amino-³ guanidino-butyric acid (Arg), Ile (Leu) and Thr (Ser) with the Watson-Crick surface of the second base of the ANU anticodons AUU, ACU, AAU, and AGU, respectively. The hypothesis also makes the prediction that evolutionarily even earlier RNA molecules carrying stem loop structures resembling the tRNA anticodon arms of the postulated tRNA precursors were able to initiate self-replication within the anticodon loop opposite the two Gs of the loop UUANUGG sequences and that this feature allowed them to gain predominance among early extant RNA species. Furthermore, it is postulated that a physical basis existed for ANN stop anticodon (UNN codon) formation/assignment which facilitated, later during evolution, the emergence/assignment of the present-day stop codons UAA, UAG and UGA.

Studies seeking support for the proposed DCIPACD process during protein synthesis have been carried out via computerized molecular modeling. These studies revealed that it is possible to place the shoulder of the 30S ribosome into the left crown area of the 50S ribosomal subunit with attendant loss of close contact of the loop region of 16S ribosomal RNA helix 44 with the 50S subunit and movement of helix H76-78 and protein L1 as well as centrally located crown components of the 50S subunit out of the way. This 30S subunit placement creates S12/L14-gapped ribosomes. Such ribosomes may arise first during the initiation phase of translation followed by closing of the ribosome upon binding of an ±&alpha-tRNA prior to the first translocation step. S12-L14-gapped ribosomes may subsequently be re-generated via the action of ATPases - RbbA in bacteria, EF3 in fungi and ribosome-bound ATPases in eukaryotic systems - thus permitting the next incoming cognate ±&alpha-tRNA to dock via the DCIPACD process. Most recently, it has been shown that the process of rescuing a stalled bacterial ribosome via the activity of a molecule named tmRNA (transfer-messenger RNA) and a protein named SmpB (small protein B) can be modeled with S12-L14 gapped ribosomes.

Selected Poster Abstracts:
All abstracts listed below were presented at meetings organized by the RNA Society. The RNA Society considers abstracts as personal communications - they are available upon request.

• "Hypothetical conformational basis for early UNN stop codons (ANA stop anticodons)." Poster 301-First Annual Meeting of the RNA Society, 1996, Madison, WI
• "The Hirsh UGA suppressor, E. coli tRNATrp(CCA)G24A and related suppressors may present their anticodons with a small counterclockwise twist that modulates coaxial in-phase anticodon-codon docking." Poster 389-Fifth Annual Meeting of the RNA Society, 2000, Madison, WI
• "S12/L14-gapped ribosomes and bound ATPases are vital in translation initiation/elongation/termination - a hypothesis." Poster 699-Eighth Annual Meeting of the RNA Society, 2003, Vienna, Austria
• "Modeling S12/L14-gapped ribosome formation by docking a crown-altered 50S subunit with a 30S subunit carrying fMet-tRNA×IF2×GTP bound to IF1 and an initiation codon." Poster 399-Eighth Annual Meeting of the RNA Society, 2003, Vienna, Austria
• "Modeling discriminative coaxial-in phase anticodon-codon docking involving EF-Ts×aa-tRNA×EF-Tu×GTP or Sec-tRNA×SelB×GTP complexes and S12/L14-gapped ribosomes." Poster 324-Eighth Annual Meeting of the RNA Society, 2003, Vienna, Austria
• "Modeling functional docking of structurally characterized bacterial/eukaryotic release factors RF2/eRF1 to S12/L14-gapped and, upon release factor refolding, closed ribosomes." Poster 325-Eighth Annual Meeting of the RNA Society, 2003, Vienna, Austria
• "Modeling functional ribosomal 30S A site docking of SmpB of Ala-tmRNASmpB units as an anticodon arm mimic." Poster 592-Tenth Annual Meeting of the RNA Society, 2003, Banff, Canada

Highlighted Publications:

• U. Hornemann, X.Y. Zhang and C.J. Otto, "Transferable Streptomyces DNA amplification and coamplification of foreign DNA sequences," J. Bacteriol., 175, 1126-1133 (1993).
• U. Hornemann, and X.Y. Zhang, "Transferable Streptomyces DNA amplification – an example of involvement of an ori site," Biotechnologya, 7/8, 120-125 (1995). Meeting report written for: Proceedings of the Ninth Symposium on the Biology of Actinomycetes, Moscow, 1994.
• O.M. Cholewa and U. Hornemann, "Laminated dialysis cassette," BioTechniques, 25, 212 (1998).