Terry Platt

Transcription termination factor rho is an RNA-DNA helicase

E. coli rho factor can unwind a short RNA-DNA duplex in vitro. The duplex is formed between a polylinker sequence at the 3 end of RNA derived from the rho-dependent terminator trp t and the complementary sequence in a single-strand DNA molecule. Release of trp t RNA from the duplex requires nucleoside triphosphate hydrolysis by rhos NTPase activity and is dependent on rho recognition of the RNA that is 5 to the RNA-DNA duplex region. The direction of helix unwinding appears to be 5 to 3 along the RNA molecule. These characteristics now account for how the RNA-binding and RNA-dependent NTP hydrolysis activities of rho may participate directly in transcription termination. Our results suggest that NTP hydrolysis is utilized to help unwind the RNA-DNA duplex at the 3 end of a nascent transcript, facilitating RNA release from the DNA template.

Rho and RNA: models for recognition and response

Escherichia coli Rho factor Is required for termination of transcription at certain sites by RNA polymerase. Binding to unstructured cytosine‐containing RNA target sites, subsequent RNA‐dependent ATP hydrolysis, and an RNA‐DNA helicase activity that presumably facilitates termination, are considered essential for Rho function. Yet the RNA recognition elements have remained elusive, the parameters relating RNA binding to ATPase activation have been obscure, and the mechanistic steps that integrate Rhos characteristics with its termination function in vitro and in vivo have been largely undefined. Recent work offers new insights into these interactions with results that are both surprising and satisfying in the context of Rhos emerging structure. These include the requirements for binding and ATPase activation by a variety of RNA substrates, dynamic analyses of Rho tracking, helicase and termination activity, and the participation of a new factor (NusG) that interacts with Rho. Models for Rho function are considered in the light of these recent revelations.

An innovative selection and training program for problem‐based learning (PBL) workshop leaders in biochemistry*

We describe here a novel and effective structure to support the replacement of traditional recitation sections in a large upper level biochemistry course with small student‐led problem‐based learning (PBL) groups (“workshops”) that employ a cooperative learning approach. This is part of an ongoing campus‐wide effort to establish and maintain such workshops as a viable and integral component of many undergraduate courses at the University of Rochester. In biochemistry, for each workshop group of 8–10 students, we rely on a student leader, usually recruited from the previous years pool of top students, whose function is both to guide and to inspire the group effort. A crucial component of our approach is that these leaders participate in a semester‐long credit‐bearing training course co‐taught by the course instructors and an educational specialist. In this course, leaders review the preceding and upcoming weeks workshops and study selected aspects of learning theory, group dynamics, and diversity training. Overall our workshop leaders feel that they benefit substantially from this training by improving their pedagogical skills in the context of biochemistry, by putting theories about group leadership and learning into practice, and by solidifying their working biochemical knowledge. We believe that the important features of implementing our model (the incorporation of a problem‐based learning approach into a student‐led small group format) are: 1) the teamwork as co‐equals between the course instructors and the educational specialists, 2) the concurrent iterative training of the workshop leaders in a credit‐bearing course of study, 3) the built‐in leader turnover (normally a frustrating occurrence) as a beneficial component of the course, and 4) the enthusiasm and commitment to biochemistry displayed to current students by their peer leaders.

Sustaining Change in Upper Level Courses: Peer-Led Workshops in Organic Chemistry and Biochemistry.

Our peer-led collaborative learning groups, called Workshops, have now had extended success in ntwo upper-level courses in chemistry and biochemistry. These Workshops are in turn supported by na third upper-level course for training peer-leaders. Our data confirm that the initial positive nresults from the introduction of Workshops in organic chemistry and in biochemistry have been nmaintained over time and over changes in course instructor. In addition, training upper-level nWorkshop leaders has contributed substantially to the self-sustaining character of our program. nThese longitudinal results have been accompanied by the lateral spread of Workshops into other ncourses and departments. The concurrent development of mutually reinforcing partnerships among nfaculty, staff and students has supported these changes. Complementary adjustments in ninstitutional practice, and the recent establishment here of a Center for Workshop Education now nprovide a formal framework to foster the continuing promise of our Workshop program.

Structure and Function of Rho Factor and Its Role in Transcription Termination

One step in the regulation of gene expression that can be controlled by a variety of mechanisms is the transcription of messenger RNA from the DNA template. It is becoming increasingly apparent that an important aspect of such regulation involves transcription termination and its control. Termination sites at the ends of genes or operons provide a signal for RNA polymerase to cease transcribing, thus defining the 3’ end of the primary transcript. Termination signals that reside at other positions in the transcript can also regulate gene expression through the effects of attenuation, retroregulation, and polarity [for reviews see 1,2]. One class of transcription termination events utilized by Escherichia coli and various bacteriophages is dependent upon the action of a protein factor called rho, which participates in the recognition of and response to certain termination sites. Though little is understood about the RNA sequence or structural elements required for rho recognition, a great deal has been learned recently about the structure of rho protein itself. This review will focus on the molecular architecture of rho protein with an emphasis on its domain structure, the interaction of each domain with its substrate, and the interactions between domains that are required for catalysis of transcription termination.