Structure of the Escherichia coli Leucine-responsive Regulatory Protein Lrp Reveals a Novel Octameric Assembly

Rios, Stephanie De Los; Perona, John J.

doi:10.1016/j.jmb.2006.12.032

Cited by 90 publications

(131 citation statements)

References 48 publications

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“…High affinity Ptr2 binding to this UAS stems, at least in part, from its compliance with tight DNA wrapping around the Ptr2 tetramer/octamer, with concomitant bending and narrowing of the minor groove at the dyad centers of the binding sites (Fig. 5C, Vertical Arrows); these are known features of the binding sites of both the bacterial and archaeal Lrp/AsnC family proteins (25)(26)(27)(28)(29)(30). It is therefore likely that these same sequence features also accommodate efficient positioning of histones within the synthetically optimized UAS.…”

Section: Resultsmentioning

confidence: 99%

Transcriptional activation in the context of repression mediated by archaeal histones

Wilkinson

Ouhammouch

Geiduschek

2010

Proc. Natl. Acad. Sci. U.S.A.

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Many archaea (including all the methanogens, nearly all euryarchaeotes, and some crenarchaeotes) use histones as components of the chromatin that compacts their genomes. The archaeal histones are homo-and heterodimers that pair on DNA to form tetrasomes (as the eukaryotic histones H3 and H4 do). The resulting DNA packaging is known to interfere with assembly of the archaeal transcription apparatus at promoters; the ability of transcriptional activation to function in repressive archaeal chromatin has not yet been explored in vitro. Using four of the Methanocaldococcus jannaschii (Mja) histones, we have examined activation of the model Mja rb2 transcription unit by the Mja transcriptional activator Ptr2 in this simplified-chromatin context. Using hydroxyl radical footprinting, we find that the Ptr2-specific rb2 upstream activating site is a preferred histone-localizing site that nucleates histone: DNA-binding radiating from the rb2 promoter. Nevertheless, Ptr2 competes effectively with histones for access to the rb2 promoter and most potently activates transcription in vitro at histone concentrations that extensively coat DNA and essentially silence basal transcription.chromatin | promoter complex | Ptr2 | RNA polymerase | upstream activating site

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Section: Resultsmentioning

confidence: 99%

Transcriptional activation in the context of repression mediated by archaeal histones

Wilkinson

Ouhammouch

Geiduschek

2010

Proc. Natl. Acad. Sci. U.S.A.

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“…Lrp is the closest analog to a eukaryotic histone. Lrp forms octomeric structures around which DNA winds, similarly to DNA wrapping around histones (de los Rios and Perona 2007). HU, IHF, Lrp, DnaA, and IciA are also global transcription regulators (Bouvier et al 1998;Oberto et al 2009;Prieto et al 2012).…”

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confidence: 99%

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

et al. 2015

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The mutagenicity of DNA double-strand break repair in Escherichia coli is controlled by DNA-damage (SOS) and general (RpoS) stress responses, which let error-prone DNA polymerases participate, potentially accelerating evolution during stress. Either base substitutions and indels or genome rearrangements result. Here we discovered that most small basic proteins that compact the genome, nucleoid-associated proteins (NAPs), promote or inhibit mutagenic break repair (MBR) via different routes. Of 15 NAPs, H-NS, Fis, CspE, and CbpA were required for MBR; Dps inhibited MBR; StpA and Hha did neither; and five others were characterized previously. Three essential genes were not tested. Using multiple tests, we found the following: First, Dps, which reduces reactive oxygen species (ROS), inhibited MBR, implicating ROS in MBR. Second, CbpA promoted F9 plasmid maintenance, allowing MBR to be measured in an F9-based assay. Third, Fis was required for activation of the SOS DNA-damage response and could be substituted in MBR by SOS-induced levels of DinB error-prone DNA polymerase. Thus, Fis promoted MBR by allowing SOS activation. Fourth, H-NS represses ROS detoxifier sodB and was substituted in MBR by deletion of sodB, which was not otherwise mutagenic. We conclude that normal ROS levels promote MBR and that H-NS promotes MBR by maintaining ROS. CspE positively regulates RpoS, which is required for MBR. Four of five previously characterized NAPs promoted stress responses that enhance MBR. Hence, most NAPs affect MBR, the majority via regulatory functions. The data show that a total of six NAPs promote MBR by regulating stress responses, indicating the importance of nucleoid structure and function to the regulation of MBR and of coupling mutagenesis to stress, creating genetic diversity responsively.

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“…UPEC Lrp binds to three of the six Lrp binding sites in the pap promoter; binding of proximal sites leads to the pap off state, while binding of distal sites results in the on state (73). Cocrystal structures of Lrp with pap promoter DNA reveal that DNA wraps around and binds to an octameric Lrp complex, reminiscent of the eukaryotic nucleosome-like complex (74)(75)(76). Therefore, Lrp multimerization and DNA topology are crucial for transcriptional regulation, providing a mechanistic rationale for how changes in Lrp concentrations could influence phenotypic variation of symbiotic phenotypes in X. nematophila.…”

Section: Phenotypic Variation In X Nematophilamentioning

confidence: 99%

Ready or Not: Microbial Adaptive Responses in Dynamic Symbiosis Environments

Cao

Goodrich‐Blair

2017

J Bacteriol

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In mutually beneficial and pathogenic symbiotic associations, microbes must adapt to the host environment for optimal fitness. Both within an individual host and during transmission between hosts, microbes are exposed to temporal and spatial variation in environmental conditions. The phenomenon of phenotypic variation, in which different subpopulations of cells express distinctive and potentially adaptive characteristics, can contribute to microbial adaptation to a lifestyle that includes rapidly changing environments. The environments experienced by a symbiotic microbe during its life history can be erratic or predictable, and each can impact the evolution of adaptive responses. In particular, the predictability of a rhythmic or cyclical series of environments may promote the evolution of signal transduction cascades that allow preadaptive responses to environments that are likely to be encountered in the future, a phenomenon known as adaptive prediction. In this review, we summarize environmental variations known to occur in some well-studied models of symbiosis and how these may contribute to the evolution of microbial population heterogeneity and anticipatory behavior. We provide details about the symbiosis between Xenorhabdus bacteria and Steinernema nematodes as a model to investigate the concept of environmental adaptation and adaptive prediction in a microbial symbiosis.

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Structure of the Escherichia coli Leucine-responsive Regulatory Protein Lrp Reveals a Novel Octameric Assembly

Cited by 90 publications

References 48 publications

Transcriptional activation in the context of repression mediated by archaeal histones

Transcriptional activation in the context of repression mediated by archaeal histones

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

Ready or Not: Microbial Adaptive Responses in Dynamic Symbiosis Environments

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