Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters

Rhodius, Virgil A.; Segall-Shapiro, Thomas H.; Sharon, Brian D.; Ghodasara, Amar; Orlova, Ekaterina; Tabakh, Hannah; Burkhardt, David H; Clancy, Kevin; Peterson, Todd C.; Gross, Carol A.; Voigt, Christopher A.

doi:10.1038/msb.2013.58

Cited by 161 publications

(238 citation statements)

References 59 publications

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“…Moreover, unlike the housekeeping σs, recognition of the UP element by the α-subunit of RNAP cannot substitute for the -35 motif, although UP elements do enhance expression from weak promoters (80). This observation has been validated for many ECF σs (81). Interestingly, at the time that this σ group was identified, it was noted that the regions of σ implicated in initiating melting and in recognizing the -10 motif (σ regions 2.3-2.4) were highly divergent from housekeeping σs.…”

Section: A Modified Initiation Strategy Allows the Divergent Alternatmentioning

confidence: 86%

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

Feklístov

Sharon

Darst

et al. 2014

Annu. Rev. Microbiol.

410

499

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Transcription initiation is the crucial focal point of gene expression in prokaryotes. The key players in this process, sigma factors (σs), associate with the catalytic core RNA polymerase to guide it through the essential steps of initiation: promoter recognition and opening, and synthesis of the first few nucleotides of the transcript. Here we recount the key advances in σ biology, from their discovery 45 years ago to the most recent progress in understanding their structure and function at the atomic level. Recent data provide important structural insights into the mechanisms whereby σs initiate promoter opening. We discuss both the housekeeping σs, which govern transcription of the majority of cellular genes, and the alternative σs, which direct RNA polymerase to specialized operons in response to environmental and physiological cues. The review concludes with a genome-scale view of the extracytoplasmic function σs, the most abundant group of alternative σs.

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Section: A Modified Initiation Strategy Allows the Divergent Alternatmentioning

confidence: 86%

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

Feklístov

Sharon

Darst

et al. 2014

Annu. Rev. Microbiol.

410

499

View full text Add to dashboard Cite

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“…In the last years, a significant number of ''orthogonal'' (non cross-interacting) transcriptional activators and repressors have been identified and used to construct basic synthetic biological circuits (Rhodius et al 2013;Stanton et al 2014;Nielsen and Voigt 2014). It would therefore be interesting to perform the analysis presented here with transcriptional regulation based on Hill functions.…”

Section: Discussionmentioning

confidence: 99%

Design principles for robust oscillatory behavior

2015

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Oscillatory responses are ubiquitous in regulatory networks of living organisms, a fact that has led to extensive efforts to study and replicate the circuits involved. However, to date, design principles that underlie the robustness of natural oscillators are not completely known. Here we study a three-component enzymatic network model in order to determine the topological requirements for robust oscillation. First, by simulating every possible topological arrangement and varying their parameter values, we demonstrate that robust oscillators can be obtained by augmenting the number of both negative feedback loops and positive autoregulations while maintaining an appropriate balance of positive and negative interactions. We then identify network motifs, whose presence in more complex topologies is a necessary condition for obtaining oscillatory responses. Finally, we pinpoint a series of simple architectural patterns that progressively render more robust oscillators. Together, these findings can help in the design of more reliable synthetic biomolecular networks and may also have implications in the understanding of other oscillatory systems.

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“…MicrobesOnline's operon predictions were used, except in cases in which the analyzed genome was not part of that database. In such cases, ECF-encoding operons were defined, as previously (20), as all consecutive genes adjacent to the ECF factor gene in the same orientation and separated by less than 50 nucleotides. Then, BioProspector (21; http://ai.stanford.edu/ϳxsliu/BioProspector/) was used to identify overrepresented motifs in those sequences, mostly as described previously (20).…”

Section: Methodsmentioning

confidence: 99%

“…In such cases, ECF-encoding operons were defined, as previously (20), as all consecutive genes adjacent to the ECF factor gene in the same orientation and separated by less than 50 nucleotides. Then, BioProspector (21; http://ai.stanford.edu/ϳxsliu/BioProspector/) was used to identify overrepresented motifs in those sequences, mostly as described previously (20). The parameter settings used to search for two-block motifs that may not occur in all input sequences and only on their forward strands were as follows: lengths of the upstream and downstream blocks (W and w, respectively), 5 to 7 nucleotides; minimum distance (g) and maximum distance (G) separating the two blocks, 15 to 19 nucleotides and 16 to 20 nucleotides, respectively.…”

Section: Methodsmentioning

confidence: 99%

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

et al. 2015

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Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies. IMPORTANCEIn the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify, classify, and describe numerous novel and conserved signaling devices. Hence, our work serves as an important resource for any researcher interested in signal transduction of this important bacterial phylum, which contains organisms of ecological, biotechnological, and medical relevance. Bacterial survival critically depends on the ability to swiftly respond to environmental changes. To efficiently monitor the surrounding environment, microbial genomes encode numerous and highly diverse proteins that can sense a given extracellular stimulus, transmit the signal to the cytoplasm, and elicit a proper response. These signal-transducing proteins (STPs) can be divided into three major groups: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function factors (ECFs). The vast majority of STPs in bacteria are 1CSs. These systems are composed of a single protein that contains an input domain, which senses the stimulus, and an output domain, which elicits the response by binding nucleic acids, modifying proteins, or performing an enzymati...

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Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters

Abstract: The interaction specificities of extracytoplasmic function (ECF) sigma (σ) factors with promoters and their negative regulators (anti-σs) were mapped to identify non-crossreacting parts. These orthogonal sets represent a synthetic biology toolbox of genetic switches.

Cited by 161 publications

References 59 publications

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

Design principles for robust oscillatory behavior

Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

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