How RNA Polymerases Initiate Transcription: the Work of Michael J. Chamberlin

Studies of Ribonucleic Acid Chain Initiation by Escherichia coli Ribonucleic Acid Polymerase Bound to T7 Deoxyribonucleic Acid. I. An Assay for the Rate and Extent of Ribonucleic Acid Chain Initiation (Mangel, W. F., and Chamberlin, M. J. (1974) J. Biol. Chem. 249, 2995–3001)

Studies of Ribonucleic Acid Chain Initiation by Escherichia coli Ribonucleic Acid Polymerase Bound to T7 Deoxyribonucleic Acid. II. The Effect of Alterations in Ionic Strength on Chain Initiation and on the Conformation of Binary Complexes (Mangel, W. F., and Chamberlin, M. J. (1974) J. Biol. Chem. 249, 3002–3006)

Studies of Ribonucleic Acid Chain Initiation by Escherichia coli Ribonucleic Acid Polymerase Bound to T7 Deoxyribonucleic Acid. III. The Effect of Temperature on Ribonucleic Acid Chain Initiation and on the Conformation of Binary Complexes (Mangel, W. F., and Chamberlin, M. J. (1974) J. Biol. Chem. 249, 3007–3013)

Michael John Chamberlin was born in 1937 in Chicago, Illinois. He attended Harvard University, where he was mentored by Journal of Biological Chemistry (JBC) Classics author John Edsall (1). He received his A.B. in 1959 and went to Stanford University to work with JBC Classics author Paul Berg (2). After earning his Ph.D. in 1963, Chamberlin remained in California and became an Assistant Professor of Virology at the University of California, Berkeley. He was promoted to Associate Professor of Molecular Biology in 1967, Associate Professor of Biochemistry in 1971, and Professor in 1973. Chamberlin was also Vice Chairman of the Department of Biochemistry at Berkeley from 1983 to 1988, after which he became Professor of Biochemistry and Molecular Biology. He retired in 1999 and remains at Berkeley as an Emeritus Professor.

Chamberlin is probably best known for his work on how RNA polymerases initiate and terminate transcription. In 1974 he published a series of three papers in the JBC that resulted in a model for RNA chain initiation by RNA polymerase. These three papers have been reprinted here as JBC Classics. Prior to publishing these papers, Chamberlin had already determined that the sequence of steps leading to the initiation of transcription involves the binding of RNA polymerase to DNA, location of a specific promoter, and finally, RNA chain initiation (3–7).

In the first paper in the series, Chamberlin explains the assay he used to measure the rate and extent of RNA chain initiation by Escherichia coli RNA polymerase. The assay is based on the ability of the antibiotic rifampicin to specifically inhibit the initiation of RNA synthesis. Rifampicin does not block the binding of RNA polymerase to the DNA template, but rather it interferes with the formation of the first phosphodiester bond in the RNA chain. Thus, the antibiotic is inhibitory only prior to RNA chain initiation. By exposing binary complexes of RNA polymerase and T7 DNA to a mixture of rifampicin and the four ribonucleoside triphosphates, Chamberlin was able to create a competition between inactivation of the enzyme by the antibiotic and RNA chain initiation. Because the second order rate constant for rifampicin attack on enzyme in binary complexes with T7 DNA was known, Chamberlin was able to determine the intrinsic rate and extent of RNA chain initiation by measuring the fraction of binary complexes inactivated by rifampicin. Using the assay, Chamberlin determined that chain initiation took place with an apparent first order rate constant of 3.0 s^–1 (t_½ = 0.23 s) and that the fraction of polymerase molecules able to initiate production of an RNA chain depends on the amount of σ subunit in the enzyme preparation.⇓

In the second Classic, Chamberlin uses his assay to study the effect of ionic strength on RNA chain initiation and binary complex formation. He found that essentially all enzymes in complexes formed at low salt concentrations could initiate an RNA chain rapidly at the T7 early promoter region. However, enzymes in binary complexes formed in high salt concentrations could not rapidly initiate chain formation. From these observations Chamberlin proposed that RNA polymerase could exist in two types of binary complexes, the equilibrium of which was affected by alterations in the salt concentration of the solution. He called these states the “rapid starting complex” (RS complex), from which rapid RNA chain initiation could occur, and the “non-starting complex” (I complex), in which RNA polymerase is either at a site or in a conformation from which RNA chain initiation cannot occur or occurs very slowly.

In the final JBC Classic, Chamberlin looks at the effect of temperature on chain initiation and the formation of binary complexes, again using his assay. He discovered that the effects of temperature on transcription were similar to those of ionic strength. While alterations in the temperature had a detectable but modest effect on the rapid rate of RNA chain initiation by RNA polymerase in binary complexes, the temperature of the solution in which binary complexes were formed dramatically affected the fraction of enzyme that could rapidly initiate an RNA chain. These data further confirmed Chamberlin's two-complex theory and allowed him to propose a model for the two kinds of binary complexes. He postulated that “the I complex involves RNA polymerase bound at the promoter region, but that the DNA helix in this region remains in a helical conformation. In the RS complex, a limited strand separation (six to seven base pairs) has occurred in this region of the DNA helix which allows the enzyme access to the base pairing residues of the DNA template.” Chamberlin's model remains today, although his RS complex has since been renamed the “open complex” and the I complex is now the “closed complex.”

Chamberlin's many honors include election to the National Academy of Sciences, the American Academy of Arts and Sciences, and the American Academy of Microbiology. He was also the recipient of the 1974 Charles Pfizer Award from the American Chemical Society and the 2001 Monie A. Ferst Award from Sigma Xi. Chamberlin has served on several editorial boards including those of the Journal of Biological Chemistry and Biochemistry.