bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and <i>Escherichia coli</i>

Shahmuradov, Ilham A.; Razali, Rozaimi Mohamad; Bougouffa, Salim; Radovanović, Aleksandar; Bajic, Vladimir B.

doi:10.1093/bioinformatics/btw629

Cited by 75 publications

(69 citation statements)

References 43 publications

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“…We created a simple model which incorporates four features related to promoter function. We calculated the maximum position weight matrix (PWM) score using motifs from bTSSfinder (Shahmuradov et al , 2017) for both the -10 and -35 core promoter motifs. We scanned the -10 and -35 PWM individually and took the max score at any position using scoring functions from the Bioconductor package Biostrings (Pagès et al , 2017) .…”

Section: Simple Model With Promoter Featuresmentioning

confidence: 99%

Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

Urtecho

Insigne

Tripp

et al. 2020

Preprint

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Despite decades of intense genetic, biochemical, and evolutionary characterizations of bacterial promoters, we still lack the basic ability to identify or predict transcriptional activities of promoters using primary sequence. Even in simple, well-characterized organisms such as E. coli there is little agreement on the number, location, and strength of promoters. Here, we use a genomically-encoded massively parallel reporter assay to perform the first full characterization of autonomous promoter activity across the E. coli genome. We measure promoter activity of >300,000 sequences spanning the entire genome and precisely map 2,228 promoters active in rich media. We show that antisense promoters have a profound effect on global transcription and how codon usage has adapted to encode intragenic promoters. Furthermore, we perform a scanning mutagenesis of 2,057 promoters to uncover regulatory sequences responsible for regulating promoter activity. Finally, we show that despite these large datasets and modern machine learning algorithms, the task of predicting promoter activity from primary sequence sequence is still challenging.

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Section: Simple Model With Promoter Featuresmentioning

confidence: 99%

Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

Urtecho

Insigne

Tripp

et al. 2020

Preprint

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“…Promoter prediction was performed via web analysis tools BPROM (Salamov and Solovyevand, 2011) and bTSSfinder (Shahmuradov et al, 2017) using their default settings and full length sequences for ϕX174 (Genbank No. NC_001422.1).…”

Section: Methodsmentioning

confidence: 99%

A high-resolution map of bacteriophage øX174 transcription

Logel

Jaschke

2020

Preprint

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Bacteriophage øX174 is a model virus for studies across the fields of structural biology, genetics, gut microbiome, and synthetic biology, but did not have a high-resolution transcriptome until this work. In this study we used next-generation sequencing to measure the RNA produced from øX174 while infecting its host E. coli C. We broadly confirm the past transcriptome model while revealing several interesting deviations from previous knowledge. Additionally, we measure the strength of canonical øX174 promoters and terminators and discover both a putative new promoter that may be activated by heat shock sigma factors, as well as rediscover a controversial Rho-dependent terminator. We also provide evidence for the first antisense transcription observed in the Microviridae family, identify two promoters that may be involved in generating this transcriptional activity, and discuss possible reasons why this RNA may be produced.

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“…After primary assessment and selection of the top 25% (eight) candidates, the intergenic regions containing putative promoters were assessed by prediction software to search for features potentially indicative of efficient gene expression in D. radiodurans. The motif-finding tool, MEME, and promoter prediction software such as BPROM (Softberry), bTSSfinder (E. coli type setting), and Neural Network Promoter Prediction (prokaryote setting, minimum promoter score 0.8) were used to search for motifs indicative of promoter regions within the selected candidate promoters (41)(42)(43). Putative promoter regions were also assessed by BLAST to search for conservation across other taxa.…”

Section: Methodsmentioning

confidence: 99%

Discovery and Characterization of NativeDeinococcus radioduransPromoters for Tunable Gene Expression

Chen

Sherman

Chu

et al. 2019

Appl Environ Microbiol

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The potential utilization of extremophiles as a robust chassis for metabolic engineering applications has prompted interest in the use of Deinococcus radiodurans for bioremediation efforts, but current applications are limited by the lack of availability of genetic tools, such as promoters. In this study, we used a combined computational and experimental approach to identify and screen 30 predicted promoters for expression in D. radiodurans using a fluorescent reporter assay. The top eight candidates were further characterized, compared to currently available promoters, and optimized for engineering through minimization for use in D. radiodurans. Of these top eight, two promoter regions, PDR_1261 and PrpmB, were stronger and more consistent than the most widely used promoter sequence in D. radiodurans, PgroES. Furthermore, half of the top eight promoters could be minimized by at least 20% (to obtain final sequences that are approximately 24 to 177 bp), and several of the putative promoters either showed activity in Escherichia coli or were D. radiodurans specific, broadening the use of the promoters for various applications. Overall, this work introduces a suite of novel, well-characterized promoters for protein production and metabolic engineering in D. radiodurans. IMPORTANCE The tolerance of the extremophile, Deinococcus radiodurans, to numerous oxidative stresses makes it ideal for bioremediation applications, but many of the tools necessary for metabolic engineering are lacking in this organism compared to model bacteria. Although native and engineered promoters have been used to drive gene expression for protein production in D. radiodurans, very few have been well characterized. Informed by bioinformatics, this study expands the repertoire of well-characterized promoters for D. radiodurans via thorough characterization of eight putative promoters with various strengths. These results will help facilitate tunable gene expression, since these promoters demonstrate strong and consistent performance compared to the current standard, PgroES. This study also provides a methodology for high-throughput promoter identification and characterization using fluorescence in D. radiodurans. The promoters identified in this study will facilitate metabolic engineering of D. radiodurans and enable its use in biotechnological applications ranging from bioremediation to synthesis of commodity chemicals.R ecent work regarding the biological engineering of extremophiles has increased interest in their use as a robust chassis for metabolic engineering. The appeal of using extremophiles in various applications is largely due to their ability to survive conditions toxic to traditional engineering strains. One extremophile considered attractive is Deinococcus radiodurans, a Gram-positive bacteria known for its tolerance to ionizing radiation, heavy metal exposure, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens (1-3). In the context of its applications in bioremediation,

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bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli

Cited by 75 publications

References 43 publications

Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

A high-resolution map of bacteriophage øX174 transcription

Discovery and Characterization of NativeDeinococcus radioduransPromoters for Tunable Gene Expression

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