Repressor Proteins

This chapter explores the data collected on the importance of bacteriophages to the ecology of the earth's polar regions. It examines the numbers of phage-like particles that have been observed in the ecosystems and their importance in regulating bacterial numbers and the food chain of the extreme oligotrophic environments. To understand the potential impact of bacteriophages on polar ecosystems, it is first necessary to understand the different life choices of phages and how environmental factors are known to affect them. Perhaps not surprisingly, these data suggest that bacteriophages are an important shunt in carbon cycling in the Antarctic regions as well as in the Arctic. Unlike many other studies, the authors conclude that neither bacteriovores nor bacteriophages are important regulators of bacterial numbers but that numbers are regulated by algae blooms and other factors that affect bacterial growth. Pseudolysogeny was first defined by Baess in 1971. In his review, pseudolysogeny was identified as a phage-host interaction in which the phage, following infection of the host, elicits an unstable, nonproductive response. Thus any study that enumerates total virus-like particles (VLPs) must be tempered with the understanding that not all will be infective. The data obtained in this study support the hypothesis that bacteriophages are of quantifiable significance in the carbon-flow cycle of Antarctic oligotrophic lakes. Few researchers have investigated bacteriophages in both the Arctic and Antarctic in the same study. Phylogenetic analysis of their data revealed five previously uncharacterized subgroups of T4-like bacteriophages in many environments, including the Arctic samples.

Promoter escape is the process that an initiated RNA polymerase (RNAP) molecule undergoes to achieve the initiation-elongation transition. Having made this transition, an RNAP molecule would be relinquished from its promoter hold to perform productive (full-length) transcription. Prior to the transition, this process is accompanied by abortive RNA formation—the amount and pattern of which is controlled by the promoter sequence information. Qualitative and quantitative analysis of abortive/productive transcription from several Escherichia coli promoters and their sequence variants led to the understanding that a strong (RNAP-binding) promoter is more likely to be rate limited (during transcription initiation) at the escape step and produce abortive transcripts. Of the two subelements in a promoter, the PRR (the core Promoter Recognition Region) was found to set the initiation frequency and the rate-limiting step, while the ITS (the Initial Transcribed Sequence region) modulated the ratio of abortive versus productive transcription. The highly abortive behavior of E. coli RNAP could be ameliorated by the presence of Gre (transcript cleavage stimulatory) factor(s), linking the first step in abortive RNA formation by the initial transcribing complexes (ITC) to RNAP backtracking. The discovery that translocation during the initiation stage occurs via DNA scrunching provided the source of energy that converts each ITC into a highly unstable "stressed intermediate." Mapping all of the biochemical information onto an X-ray crystallographic structural model of an open complex gave rise to a plausible mechanism of transcription initiation. The chapter concludes with contemplations of the kinetics and thermodynamics of abortive initiation-promoter escape.

This chapter states that initial rates of β-galactosidase production were very similar with and without inducer. The author thinks it is safe to say that this PaJaMa experiment provided the basis and frame of reference for further studies on the mechanism of enzyme regulation. The PaJaMa experiment is the basis of a historical-philosophical study of the nature of discovery by Kenneth Schaffner, who interviewed the individuals involved and reconstructed a composite of what happened. From the PaJaMa studies on the molecular nature of induction—proposed to be the effects of interaction of a lactose-related inducer with the repressor protein, which initiates a quite different process of gene expression—Jacques Monod became interested in how a small molecule can modify a protein’s function. The author says that the time spent by him in Monod’s laboratory was certainly one of the most remarkable of his career, as he learned there of the great power of genetics in combination with biochemistry.

The most universally known and the most often misquoted is "Whatever is true for E. coli is true for an elephant." Jacques Monod's faith in the universality of the laws and mechanisms of biology contrasting with his provocative attitude of apparent cynicism in front of the great problems of "the secrets of life" was fascinating to those of us who surrounded him. Monod showed with Melvin Cohn that the kinetic parameters as well as the immunochemical properties of β-galactosidase did not change when a variety of inducers were utilized with the inducible strain or compared to the enzyme of the constitutive mutants, where no inducer was used. The rapid regulatory switches pointed toward an unstable intermediate embodying the genetic information between gene and protein. The intermediate, called "the messenger," soon became the messenger RNA, (mRNA). The progress of translation is independent of both the termination of the transcription and the survival of the initial end of mRNA. The survival of the initiating end of mRNA is independent of the intracellular concentration of inducer and largely, although not completely, independent of transcription. The mRNA is polycistronic and stays probably as a single piece for the major part of its functional lifetime. At the steady state of all processes, the polycistronic mRNA is, however, seldom integral. The major part of it should be pieces: some unfinished, some already missing the initiating end, some devoid of both, still growing on one side while losing the other side at the same speed.

This chapter focuses on the different molecular mechanisms two model luminous bacteria, Vibrio fischeri (a symbiont) and V. harveyi (a free-living microbe), use for regulating lux expression. Expression of luminescence in most bacteria is tightly regulated by the density of the population. In V. fischeri, the regulatory genes involved in density-dependent control of luminescence are adjacent to the luxCDABEG operon encoding the luciferase enzymes. The regulatory genes that control luminescence in V. harveyi are different from those of V. fischeri. One complementation group of V. harveyi dim mutants could be restored to full light production by a family of recombinant cosmids containing a subset of common restriction fragments. Initial HAI-1 and HAI-2 signal recognition by LuxN and LuxQ could activate a series of phosphotransfer reactions. Two-component circuits have been characterized in which a single protein contains both a sensor kinase and a response regulator domain (similar to LuxN and LuxQ) and a second protein contains both a response regulator domain and a DNA binding motif (similar to LuxO). The differences between the regulatory circuits controlling density-dependent expression of luminescence in V. fischeri and V. harveyi are striking. Subsequent mutations and gene duplications and rearrangements generated new and multiple autoinducers, receptivities, and regulatory connections, finally resulting in a bacterium with the properties of V. harveyi.