MOODS: fast search for position weight matrix matches in DNA sequences

Korhonen, Janne H.; Martinmäki, Petri; Pizzi, Cinzia; Rastas, Pasi; Ukkonen, Esko

doi:10.1093/bioinformatics/btp554

Cited by 172 publications

(144 citation statements)

References 12 publications

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“…The consensus binding sequence and position frequency matrix were obtained for OpaR (33) and AphA (55). The position frequency matrix was then used to identify potential binding sites using the MOODS (Motif Occurrence Detection Suite) algorithm (version 1.0.2.1) (84,85). The upstream intergenic sequence for the first gene of each operon was obtained from the NCBI database and used to identify putative binding sites.…”

Section: Methodsmentioning

confidence: 99%

Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus

et al. 2017

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Quorum sensing (QS) is a process by which bacteria alter gene expression in response to cell density changes. In Vibrio species, at low cell density, the sigma 54-dependent response regulator LuxO is active and regulates the two QS master regulators AphA, which is induced, and OpaR, which is repressed. At high cell density the opposite occurs: LuxO is inactive, and therefore OpaR is induced while AphA is repressed. In Vibrio parahaemolyticus, a significant enteric pathogen of humans, the roles of these regulators in pathogenesis are less known. We examined deletion mutants of luxO, opaR, and aphA for in vivo fitness using an adult mouse model. We found that the luxO and aphA mutants were defective in colonization compared to levels in the wild type. The opaR mutant did not show any defect in vivo. Colonization was restored to wild-type levels in a luxO opaR double mutant and was also increased in an opaR aphA double mutant. These data suggest that AphA is important and that overexpression of opaR is detrimental to in vivo fitness. Transcriptome sequencing (RNA-Seq) analysis of the wild type and luxO mutant grown in mouse intestinal mucus showed that 60% of the genes that were downregulated in the luxO mutant were involved in amino acid and sugar transport and metabolism. These data suggest that the luxO mutant has a metabolic disadvantage, which was confirmed by growth pattern analysis using phenotype microarrays. Bioinformatics analysis revealed OpaR binding sites in the regulatory region of 55 carbon transporter and metabolism genes. Biochemical analysis of five representatives of these regulatory regions demonstrated direct binding of OpaR in all five tested. These data demonstrate the role of OpaR in carbon utilization and metabolic fitness, an overlooked role in the QS regulon.KEYWORDS Vibrio parahaemolyticus, carbon metabolism, intestinal colonization, quorum sensing V ibrio parahaemolyticus is the leading cause of bacterial seafood-borne gastroenteritis worldwide, resulting in mild to severe inflammatory gastroenteritis (1-5). The completed genome sequence of V. parahaemolyticus RIMD2210633, an O3:K6 serotype associated with pandemic disease, demonstrated the presence of two type III secretion systems (T3SS-1 and T3SS-2), one on each chromosome, which led to the identification of several effector proteins associated with inflammatory diarrhea (6-8). Studies have shown that T3SS-2 is the major contributing factor to enterotoxicity and that inflammatory diarrhea and intestinal epithelium cell disruption are dependent upon a functional T3SS-2 (9-12).Much less is known about how V. parahaemolyticus initially colonizes and survives within the host gastrointestinal tract. This lack of knowledge is in part due to a lack of animal models to study colonization and infection in vivo. The development of a streptomycin-pretreated adult mouse model that removes microbiota colonization resistance and allows V. parahaemolyticus to colonize has uncovered a number of

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Section: Methodsmentioning

confidence: 99%

Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus

et al. 2017

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“…Transcription factor motifs in ChIP-seq peak regions were detected using MOODS 52 . The motif thresholds were defined based on P < 0.0001).…”

Section: Mathematical Aspects Of Linear Estimation Methods (Efilter)mentioning

confidence: 99%

Uniform, optimal signal processing of mapped deep-sequencing data

et al. 2013

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“…Peak sequences (±75 bp from the peak summit) were then extracted from the UCSC hg19 build of the human genome using the twobitreader package (available on PyPI). Occurrences of motifs were found using analyze.py (seriesoftubes), which relies on MOODS [54] for efficiency. JASPAR [55] motifs MA0144.1 and MA0099.2 were used to find STAT3 and AP1 sites, respectively.…”

Section: Gbr To Gene Assignmentmentioning

confidence: 99%

Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes

et al. 2014

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Background: Glucocorticoid receptor (GR) is a hormone-activated, DNA-binding transcriptional regulatory factor that controls inflammation, metabolism, stress responses, and other physiological processes. In vitro, GR binds as an inverted dimer to a motif consisting of two imperfectly palindromic 6 bp half sites separated by 3 bp spacers. In vivo, GR employs different patterns of functional surfaces of GR to regulate different target genes. The relationships between GR genomic binding and functional surface utilization have not been defined.

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MOODS: fast search for position weight matrix matches in DNA sequences

Cited by 172 publications

References 12 publications

Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus

Quorum Sensing Regulators Are Required for Metabolic Fitness in Vibrio parahaemolyticus

Uniform, optimal signal processing of mapped deep-sequencing data

Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes

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