Structural Biophysics of the NusB:NusE Antitermination Complex

Das, Ranabir; Loss, Sandra; Li, Jess; Waugh, David S.; Tarasov, Sergey G.; Wingfield, Paul T.; Byrd, R. Andrew; Altieri, Amanda S.

doi:10.1016/j.jmb.2007.11.022

Cited by 25 publications

(47 citation statements)

References 45 publications

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“…The global structures of isolated NusB (Altieri et al, 2000; Bonin et al, 2004; Das et al, 2008; Gopal et al, 2000) and of NusB in complex with S10 Δloop are very similar (Figure 2A, inset 1; Table S1). S10 Δloop in complex with NusB likewise resembles the structure of S10 in the 30S subunit (Schuwirth et al, 2005) (Figure 2A, inset 2; Table S1).…”

Section: Resultsmentioning

confidence: 84%

“…Helix α1 and an irregular strand, β2, of S10 Δloop bridge the two helical bundles of NusB (contact regions I and II in Figure 2A). The region on NusB contacted by S10 Δloop coincides with NusB residues that show NMR chemical shift changes upon addition of full-length S10 (Das et al, 2008). These observations further corroborate the equivalence of the wt and loop-deleted S10 in transcription.…”

Section: Resultsmentioning

confidence: 99%

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Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

et al. 2008

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Summary Protein S10 is a component of the 30S ribosomal subunit and participates together with NusB protein in processive transcription antitermination. The molecular mechanisms by which S10 can act as a translation or a transcription factor are not understood. We used complementation assays and recombineering to delineate regions of S10 dispensable for antitermination, and determined the crystal structure of a transcriptionally active NusB-S10 complex. In this complex, S10 adopts the same fold as in the 30S subunit and is blocked from simultaneous association with the ribosome. Mass spectrometric mapping of UV-induced crosslinks revealed that the NusB-S10 complex presents an intermolecular, composite and contiguous binding surface for RNAs containing BoxA antitermination signals. Furthermore, S10 overproduction complemented a nusB null phenotype. These data demonstrate that S10 and NusB together form a BoxA-binding module; that NusB facilitates entry of S10 into the transcription machinery; and that S10 represents a central hub in processive antitermination.

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Section: Resultsmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

et al. 2008

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“…The presence of a recognizable AT region, especially the boxA feature, in the leader regions of rrn operons from other microorganisms and the observed conservation of the Nus factors (4,7,14,20) are highly suggestive that RNA polymerase molecules transcribing rrn operons in most, if not all, bacteria are modified by an auxiliary set of proteins that change, or regulate, the transcription elongation properties of the polymerase. It seems reasonable, given its effectiveness in regulating rRNA synthesis, that such an antitermination system in other microorganisms will have the same effect as that seen for E. coli, namely, to confer the ability to read through factordependent terminators and to allow faster transcription than that obtained with unmodified polymerase molecules (1,29,(49)(50)(51).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Comparison of Ribosomal Operon Antitermination Function

Arnvig¹,

Zeng

Quan

et al. 2008

J Bacteriol

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Transcription antitermination in the ribosomal operons of Escherichia coli results in the modification of RNA polymerase by specific proteins, altering its basic properties. For such alterations to occur, signal sequences in rrn operons are required as well as individual interacting proteins. In this study we tested putative rrn transcription antitermination-inducing sequences from five different bacteria for their abilities to function in E. coli. We further examined their response to the lack of one known rrn transcription antitermination protein from E. coli, NusB. We monitored antitermination activity by assessing the ability of RNA polymerase to read through a factor-dependent terminator. We found that, in general, the closer the regulatory sequence matched that of E. coli, the more likely there was to be a successful antitermination-proficient modification of the transcription complex. The rrn leader sequences from Pseudomonas aeruginosa, Bacillus subtilis, and Caulobacter crescentus all provided various levels of, but functionally significant antitermination properties to, RNA polymerase, while those of Mycobacterium tuberculosis and Thermotoga maritima did not. Possible RNA folding structures of presumed antitermination sequences and specific critical bases are discussed in light of our results. An unexpected finding was that when using the Caulobacter crescentus rrn leader sequence, there was little effect on terminator readthrough in the absence of NusB. All other hybrid antitermination system activities required this factor. Possible reasons for this finding are discussed.Transcription antitermination is a ubiquitous mechanism used in the regulation of gene expression in bacteriophages, bacteria, viruses, and possibly also archaea and eukaryotes (12,22). Antitermination circumvents termination events, leading to increased expression of the genes for which it is used. In addition to regulation by other sophisticated mechanisms, transcription of the seven rRNA operons of Escherichia coli is also regulated by transcription antitermination (29, 41). Efficient and balanced synthesis of the three rRNA species, 16S, 23S, and 5S, depends on an antitermination mechanism that modifies the transcription elongation complex into a form that efficiently expresses the entire operon (24,38,39). The antitermination event is signaled by an RNA element, the antitermination site (AT site), consisting of sequences designated boxB, boxA, and boxC. Antitermination requires the association of proteins NusA, NusB, and NusG, as well as ribosomal proteins, with the transcription elongation complex (28,37,46,47). Both the proteins and the AT site reveal sequence homologies across even distantly related species of bacteria (4). For example, examination of rrn leader and spacer regions from widely differing bacteria in the general location of the E. coli AT sequences reveals that AT features are readily recognized on the basis of sequence elements alone. Thus, although only E. coli and Mycobacterium tuberculosis AT sites have been...

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“…The NusB component of the NusB. NusE (S10) dimer is thought to bind to the BoxA motif shown in italics (Das et al ., 2008). …”

Section: Figurementioning

confidence: 99%

Physiology of Mycobacteria

Cook

Berney

Gebhard

et al. 2009

Advances in Microbial Physiology

159

112

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Mycobacterium tuberculosis is a prototrophic, metabolically flexible bacterium that has achieved a spread in the human population that is unmatched by any other bacterial pathogen. The success of M. tuberculosis as a pathogen can be attributed to its extraordinary stealth and capacity to adapt to environmental changes throughout the course of infection. These changes include: nutrient deprivation, hypoxia, various exogenous stress conditions and, in the case of the pathogenic species, the intraphagosomal environment. Knowledge of the physiology of M. tuberculosis during this process has been limited by the slow growth of the bacterium in the laboratory and other technical problems such as cell aggregation. Advances in genomics and molecular methods to analyse the M. tuberculosis genome have revealed that adaptive changes are mediated by complex regulatory networks and signals, resulting in temporal gene expression coupled to metabolic and energetic changes. An important goal for bacterial physiologists will be to elucidate the physiology of M. tuberculosis during the transition between the diverse conditions encountered by M. tuberculosis. This review covers the growth of the mycobacterial cell and how environmental stimuli are sensed by this bacterium. Adaptation to different environments is described from the viewpoint of nutrient acquisition, energy generation and regulation. To gain quantitative understanding of mycobacterial physiology will require a systems biology approach and recent efforts in this area are discussed. “It is now 100 years since the first mycobacterium was isolated by Hansen (1874). Somewhat ironically, this was the leprosy bacillus, Mycobacterium leprae, which even today is still resisting all attempts to cultivate it in the laboratory. The tubercle bacillus, M. tuberculosis was not discovered until eight years later (Koch, 1882) and this has remained an object of intensive investigation ever since. The widespread interest in the mycobacteria of course stems from the diseases they cause and, lest it be imagined that tuberculosis is a disease which has now been largely conquered and that leprosy is of relatively rare occurrence, current estimates for the number of case of tuberculosis and leprosy in the world today are 20,000,000 and 11,000,000, respectively (Bechelli and Dominguez, 1972). The annual estimated mortality rate is equally dramatic, namely 3,000,000 (World Health Organization, 1974). Also causing unease is the continuing isolation from tubercular patients of strains already resistant to one or more chemotherapeutic agent”. C. Ratledge (1976).

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Structural Biophysics of the NusB:NusE Antitermination Complex

Cited by 25 publications

References 45 publications

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

Structural and Functional Analysis of the E. coli NusB-S10 Transcription Antitermination Complex

Evolutionary Comparison of Ribosomal Operon Antitermination Function

Physiology of Mycobacteria

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