Deborah A. Steege

Professor of Biochemistry

Research interests include Gene Function and Regulation, Nucleic Acids Biochemistry, RNA Biochemistry.

Contact Information

Office Number: (919) 684-4098

e-mail steege@biochem.duke.edu

Lab Location

Education

• Ph.D. (Yale University, 1974)

Research Interests

We are interested in the sequence and structural features of RNA that mediate regulation of gene expression. Our emphasis is on controls of gene expression at steps after initiation of transcription, which are increasingly recognized as important means of regulation. The general objective is to address current and fundamental questions in translation and mRNA processing/decay. At present, we are working on a set of genes encoded by polycistronic mRNAs but expressed at markedly different levels from the same mRNA molecule. One issue under study is the processing of these mRNAs by the host cell machinery for mRNA decay. Messenger RNA (Fig. 1) decay is proving an important parameter that determines levels of gene expression and permits rapid responses to cellular signalling events, but until recent accelerated progress, has been the slowest of the principal gene regulatory processes to be worked out. Key discoveries in the field have been that polyadenylation promotes bacterial mRNA decay and that several important enzymes of decay are associated in a high molecular weight complex called the degradosome. We have recently shown that polyadenylation occurs at a later step of decay rather than an initiating step as had been believed. Polyadenylation now appears to have an important role in maintaining the momentum of exonucleolytic degradation on mRNAs. We have also determined that our set of mRNAs illustrate wave of endonucleolytic decay mediated by the degradosome that is the predominant pathway for decay of bacterial mRNAs. Because these abundant mRNAs reflect the major activity on the decay machinery in the cell, we anticipate that further work will yield a much clearer understanding of the mechanism of mRNA decay. We plan also to follow the localization of the decay machinery in the cell.

A second issue that has been under investigation longterm is the coupling of translation of genes encoded on polycistronic mRNAs, which are widespread in bacterial systems. Past work has focused on the mechanisms of translational coupling and determining how coupling is used either to coordinate expression of two adjacent genes or to downregulate expression from one to the next. Until now the principal general perception about coupling has always been that translation of the proximal gene functions in one of several ways as a positive factor that facilitates or increases the efficiency of downstream translation. In our recent work, (Fig. 2) however, we discovered a gene pair in which the upstream gene was translated at very high levels, yet the activity transmitted to the downstream gene was unexpectedly low, about one percent of upstream translation. The basis for the inefficient coupling emerged when coupling efficiency was found to increase as the upstream translation level was decreased systematically. The results demonstrate that in this gene pair, upstream translation functions in an unprecedented way as a negative factor to actually limit downstream expression. Our evidence indicates that translation in excess of an optimal level in an upstream gene can interfere with coupling in the intercistronic junction. It remains to be established to what extent interference between genes at the translational level may have functioned as a selective force in determining the structures and organization of polycistronic gene clusters in bacterial genomes.

Lab Members

Selected Publications

Yu J. S., Kokoska RJ, Khemici V, Steege DA. (2007) In-frame overlapping genes: the challenges for regulating gene expression. Mol Microbiol. Feb; 63(4):1158-72. (Abstract)

Yu, J. S., S. Madison-Antenucci and D.A. Steege (2001). Translation at higher than an optimal level interferes with coupling at an intercistronic junction. Mol. Microbiol. 821- 834. (Abstract)

Steege, D.A. (2000) Emerging features of mRNA decay in bacteria. RNA 6, 1079-1090. (Abstract)

Goodrich, A.F. and D.A. Steege (1999) Roles of polyadenylation and nucleolytic cleavage in the filamentous phage mRNA processing and decay pathways in Escherichia coli. RNA 5, 972-985. (Abstract)

Kokoska, R.J. and D.A. Steege (1998). Appropriate expression of filamentous phage f1 DNA replication genes II and X requires RNase E-dependent processing and separate mRNAs. J. Bacteriol. 180, 3245-3249. (Abstract)

S. Madison-Antenucci and D. A. Steege (1998) “Translation limits synthesis of an assembly-initiating coat protein of filamentous phage IKe.” J Bacteriol 3:464-72. (Abstract)

M. D. Stump, S. Madison-Antenucci, R. J. Kokoska and D. A. Steege (1997) “Filamentous phage IKe mRNAs conserve form and function despite divergence in regulatory elements.” J Mol Biol 1:51-65. (Abstract)