DOOR 2.0: presenting operons and their functions through dynamic and integrated views

Mao, Xizeng; Ma, Qin; Zhou, Chunkui; Chen, Xin; Zhang, Hanyuan; Yang, Jincai; Mao, Feng; Wei, Lai; Xu, Ying

doi:10.1093/nar/gkt1048

Cited by 151 publications

(187 citation statements)

References 23 publications

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“…Pilus subunits and the associated sortases necessary for assembly are oriented in a predicted operon ( Fig. 2A) under the control of a single promoter (Database of Prokaryotic Operons, version 2.0; http:// csbl.bmb.uga.edu/DOOR/ [36]). We measured the transcript levels of the genes encoding an ancillary protein (spyM3_0098, cbp) and the backbone protein (spyM3_0100, tee3) from cells of MGAS10870 and the isogenic carrier mutant (MGAS10870 liaS R135G ) following treatment with bacitracin (1.0 g/ml, 60 min) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Increased Pilus Production Conferred by a Naturally Occurring Mutation Alters Host-Pathogen Interaction in Favor of Carriage in Streptococcus pyogenes

et al. 2017

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Studies of the human pathogen group A Streptococcus (GAS) define the carrier phenotype to be an increased ability to adhere to and persist on epithelial surfaces and a decreased ability to cause disease. We tested the hypothesis that a single amino acid change (Arg135Gly) in a highly conserved sensor kinase (LiaS) of a poorly defined GAS regulatory system contributes to a carrier phenotype through increased pilus production. When introduced into an emm serotype-matched invasive strain, the carrier allele (the gene encoding the LiaS protein with an arginine-toglycine change at position 135 [liaS R135G ]) recapitulated a carrier phenotype defined by an increased ability to adhere to mucosal surfaces and a decreased ability to cause disease. Gene transcript analyses revealed that the liaS mutation significantly altered transcription of the genes encoding pilus in the presence of bacitracin. Elimination of pilus production in the isogenic carrier mutant decreased its ability to colonize the mouse nasopharynx and to adhere to and be internalized by cultured human epithelial cells and restored the virulence phenotype in a mouse model of necrotizing fasciitis. We also observed significantly reduced survival of the isogenic carrier mutant compared to that of the parental invasive strain after exposure to human neutrophils. Elimination of pilus in the isogenic carrier mutant increased the level of survival after exposure to human neutrophils to that for the parental invasive strain. Together, our data demonstrate that the carrier mutation (liaS R135G ) affects pilus expression. Our data suggest new mechanisms of pilus gene regulation in GAS and that the invasiveness associated with pilus gene regulation in GAS differs from the enhanced invasiveness associated with increased pilus production in other bacterial pathogens.

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Section: Resultsmentioning

confidence: 99%

Increased Pilus Production Conferred by a Naturally Occurring Mutation Alters Host-Pathogen Interaction in Favor of Carriage in Streptococcus pyogenes

et al. 2017

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“…The multiple alignments were performed by means of CLUSTAL OMEGA (52) at the EMBL online server (53). The operon prediction was run in different online servers: the ProOpDB online server (54), the DOOR 2 online server (55), and the MicrobesOnline server tools (56). Analysis of these results in comparison to the transcription start site map of B. diazoefficiens (34) was carried out using the Integrated Genome Browser (57).…”

Section: Methodsmentioning

confidence: 99%

Transcriptional Control of the Lateral-Flagellar Genes of Bradyrhizobium diazoefficiens

et al. 2017

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Bradyrhizobium diazoefficiens, a soybean N 2 -fixing symbiont, possesses a dual flagellar system comprising a constitutive subpolar flagellum and inducible lateral flagella. Here, we analyzed the genomic organization and biosynthetic regulation of the lateral-flagellar genes. We found that these genes are located in a single genomic cluster, organized in two monocistronic transcriptional units and three operons, one possibly containing an internal transcription start site. Among the monocistronic units is blr6846, homologous to the class IB master regulators of flagellum synthesis in Brucella melitensis and Ensifer meliloti and required for the expression of all the lateral-flagellar genes except lafA2, whose locus encodes a single lateral flagellin. We therefore named blr6846 lafR (lateral-flagellar regulator). Despite its similarity to two-component response regulators and its possession of a phosphorylatable Asp residue, lafR behaved as an orphan response regulator by not requiring phosphorylation at this site. Among the genes induced by lafR is flbT L , a class III regulator. We observed different requirements for FlbT L in the synthesis of each flagellin subunit. Although the accumulation of lafA1, but not lafA2, transcripts required FlbT L , the production of both flagellin polypeptides required FlbT L . Moreover, the regulation cascade of this lateral-flagellar regulon appeared to be not as strictly ordered as those found in other bacterial species.IMPORTANCE Bacterial motility seems essential for the free-living style in the environment, and therefore these microorganisms allocate a great deal of their energetic resources to the biosynthesis and functioning of flagella. Despite energetic costs, some bacterial species possess dual flagellar systems, one of which is a primary system normally polar or subpolar, and the other is a secondary, lateral system that is produced only under special circumstances. Bradyrhizobium diazoefficiens, an N 2 -fixing symbiont of soybean plants, possesses dual flagellar systems, including the lateral system that contributes to swimming in wet soil and competition for nodulation and is expressed under high energy availability, as well as under requirement for high torque by the flagella. The structural organization and transcriptional regulation of the 41 genes that comprise this secondary flagellar system seem adapted to adjust bacterial energy expenditures for motility to the soil's environmental dynamics.KEYWORDS Bradyrhizobium, flagella, expression, lafR, flbT, FlbT, LafR F lagellum-driven swimming motility-a characteristic trait of many bacterial species-is essential for the colonization of diverse niches in environments such as seas, freshwaters, sediments, soils, and the organs of plant or animal hosts. This form of bacterial locomotion requires the propulsion provided by flagella, as well as a guidance system mediated by chemotaxis (1).Flagella are complex organelles formed by three main structures: a basal body that anchors the flagellum to the cell envelope...

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“…A table containing all operon annotations (1,526 single-gene operons and 851 operons consisting of multiple genes) was downloaded from the Database of prOkaryotic OpeRons (DOOR) 2.0 website (35) and compared to a final set of 2,441 TSS.…”

Section: Nc_0009132)mentioning

confidence: 99%

“…To assess the coverage of our TSS predictions, we compared the number of TSS classified as pTSS only or pTSS and asTSS (2,057) and the number classified as pTSS and iTSS or pTSS, iTSS, and asTSS (615) with the number of genes classified as single-standing genes (1,526) or first genes within operons (851) in the Database of prOkaryotic OpeRons (DOOR) (35). In total, after excluding all TSS assigned to genes not annotated in DOOR (see Materials and Methods in the supplemental material), we used 2,441 of our TSS classified as pTSS.…”

Section: Drna-seq Reveals the Primary Transcriptome Of E Coli Mg1655mentioning

confidence: 99%

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

et al. 2015

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cWhile the model organism Escherichia coli has been the subject of intense study for decades, the full complement of its RNAs is only now being examined. Here we describe a survey of the E. coli transcriptome carried out using a differential RNA sequencing (dRNA-seq) approach, which can distinguish between primary and processed transcripts, and an automated prediction algorithm for transcriptional start sites (TSS). With the criterion of expression under at least one of three growth conditions examined, we predicted 14,868 TSS candidates, including 5,574 internal to annotated genes (iTSS) and 5,495 TSS corresponding to potential antisense RNAs (asRNAs). We examined expression of 14 candidate asRNAs by Northern analysis using RNA from wild-type E. coli and from strains defective for RNases III and E, two RNases reported to be involved in asRNA processing. Interestingly, nine asRNAs detected as distinct bands by Northern analysis were differentially affected by the rnc and rne mutations. We also compared our asRNA candidates with previously published asRNA annotations from RNA-seq data and discuss the challenges associated with these cross-comparisons. Our global transcriptional start site map represents a valuable resource for identification of transcription start sites, promoters, and novel transcripts in E. coli and is easily accessible, together with the cDNA coverage plots, in an online genome browser.A fter many years of study, we are only now beginning to understand and appreciate the complexity of bacterial transcriptomes. With the recent advances in deep-sequencing technology, transcriptome sequencing (RNA-seq) now allows for the detection of transcripts that are present at low levels or were previously missed by other methods of detection, the generation of global transcript maps, and improved genome annotation (reviewed in references 1 and 2). While these studies provide vast amounts of information about bacterial transcriptomes and regulatory elements, they also raise challenges regarding comparisons between studies and functions of the newly identified transcripts.One group of underappreciated transcripts being uncovered by these genome-wide analyses are RNAs that map opposite annotated coding regions, termed antisense RNAs (asRNAs). The abundance of pervasive antisense transcription start sites (asTSS) was first highlighted in an RNA-seq survey of the human pathogen Helicobacter pylori, where asTSS were identified opposite ϳ46% of the genes (3). Subsequent RNA-seq studies in cyanobacteria (4) and Gram-negative (5, 6) and Gram-positive (7-9) bacteria identified asRNAs expressed opposite 2 to 30% of annotated genes. This wide range in numbers of asRNAs reported may reflect differences in bacterial lifestyle or differences in the experimental setup or analyses of the RNA-seq data sets.Even for the transcriptome analyses of the well-studied model organism Escherichia coli (10-22), the numbers of asRNAs reported range from hundreds to thousands. This significant variation is due, in part, to differences i...

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DOOR 2.0: presenting operons and their functions through dynamic and integrated views

Cited by 151 publications

References 23 publications

Increased Pilus Production Conferred by a Naturally Occurring Mutation Alters Host-Pathogen Interaction in Favor of Carriage in Streptococcus pyogenes

Increased Pilus Production Conferred by a Naturally Occurring Mutation Alters Host-Pathogen Interaction in Favor of Carriage in Streptococcus pyogenes

Transcriptional Control of the Lateral-Flagellar Genes of Bradyrhizobium diazoefficiens

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

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