Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology

Rangel-Chávez, Cynthia Paola; Galán-Vásquez, Edgardo; Martı́nez-Antonio, Agustino

doi:10.1039/c6mb00789a

Cited by 12 publications

(13 citation statements)

References 81 publications

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“…B). The first two and last base of the −10 element are the most conserved based on the sigma70 promoter analysis of Escherichia coli , and since all the promoters conform to this consensus, we believe all will be functional to promote gar transcription (Rangel‐Chavez et al , ). Some Mc strains (class II strains) possess a different nonvariable pilE gene located in a different part of the genome, and the G4 motif and sRNA are not present in these strains (Cahoon and Seifert, ; Wormann et al , ).…”

Section: Resultsmentioning

confidence: 99%

Transcriptional initiation of a small RNA, not R‐loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae

Prister

Ozer

Cahoon

et al. 2019

Molecular Microbiology

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Summary Neisseria gonorrhoeae, the sole causative agent of gonorrhea, constitutively undergoes diversification of the Type IV pilus. Gene conversion occurs between one of the several donor silent copies located in distinct loci and the recipient pilE gene, encoding the major pilin subunit of the pilus. A guanine quadruplex (G4) DNA structure and a cis‐acting sRNA (G4‐sRNA) are located upstream of the pilE gene and both are required for pilin antigenic variation (Av). We show that the reduced sRNA transcription lowers pilin Av frequencies. Extended transcriptional elongation is not required for Av, since limiting the transcript to 32 nt allows for normal Av frequencies. Using chromatin immunoprecipitation (ChIP) assays, we show that cellular G4s are less abundant when sRNA transcription is lower. In addition, using ChIP, we demonstrate that the G4‐sRNA forms a stable RNA:DNA hybrid (R‐loop) with its template strand. However, modulating R‐loop levels by controlling RNase HI expression does not alter G4 abundance quantified through ChIP. Since pilin Av frequencies were not altered when modulating R‐loop levels by controlling RNase HI expression, we conclude that transcription of the sRNA is necessary, but stable R‐loops are not required to promote pilin Av.

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Section: Resultsmentioning

confidence: 99%

Transcriptional initiation of a small RNA, not R‐loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae

Prister

Ozer

Cahoon

et al. 2019

Molecular Microbiology

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“…MG1655 (see supplemental material) from IntergenicDB [18]. The K-12 strain choice was made considering that it is one of the considered model genomes for in silico approaches, containing well documented and experimentally verified information about its genes and their regulation [19]. From the 695 sequences available on IntergenicDB, we selected only those with a length equal or higher than 81 nucleotides for comparison and standardization purposesthe 81 nucleotides length is the standard sequence size found at RegulonDB [20].…”

Section: Data Descriptionmentioning

confidence: 99%

“…There are multiple σ factors found within bacteria. In E. coli, for instance, there are seven known σ factors: the σ 19 , σ 24 , σ 28 , σ 32 , σ 38 , σ 54 , and the σ 70 . Each σ factor interacts with specific DNA promoter sequences.…”

Section: Introductionmentioning

confidence: 99%

Untitled

2020

JBR

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Many computational methods aim to improve the prediction and recognition of transcription elements in prokaryotes. Despite this, the natural features of those elements make their prediction and recognition remain as an open field of research. In this paper, we compared the open-access tools BacPP, BPROM, bTSSfinder, CNNPromoter_b, iPro70-PseZNC, NNPP2, PePPer, and PromPredict. First, we listed the overall functionalities of each tool and the resources available on their web pages. Later, we carried out a comparison of prediction results using 206 intergenic regions. When evaluating the prediction using intergenic regions containing a single promoter within each, NNPP2 and BacPP obtained >90% correct predictions, with NNPP2 obtaining the highest values of match between predicted promoter location and location indicated by RegulonDB. Overall, many discrepancies were observed among the results. They may be explained by the differences in the methodologies that each tool applies for promoter prediction, not excluding the natural features of promoters as a factor as well. In any case, the results highlight the necessity to continue the efforts to improve promoter prediction, perhaps combining multiple approaches. Through said efforts, some of the challenges of the postgenomic era may be tackled as well.

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“…There are seven sigma factors encoded in the E. coli genome, six of them correspond to the σ 70 family (σ 70 , σ 38 , σ 32 , σ 28 , σ 24 and σ 19 ), and the remaining one corresponds to σ 54 . In a previous work we analysed around 8500 promoters annotated in the E. coli genome and proposed the architecture of transcription units and the consensus sequences of the promoters for each sigma factor [10].…”

Section: Introductionmentioning

confidence: 99%

RNA polymerases in strict endosymbiont bacteria with extreme genome reduction show distinct erosions that could result in limited and differential promoters’ recognition

Rangel-Chávez¹,

Galán-Vásquez

Pescador-Tapia³

et al. 2020

Preprint

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Strict endosymbiont bacteria with high degree of genome reduction retain smaller proteins and, in certain cases, lack complete functional domains compared to their free-living counterparts. Until now, the mechanisms underlying these genetic reductions are not well understood. However, it is thought that, in order to compensate for gene reduction, somehow hosts take over those vital functions that endosymbionts cannot perform. In the present study, the conservation of RNA polymerases, the essential machinery for gene expression, is analysed in bacteria with extreme genome reductions. For this purpose, comparative genomics, phylogenetic analysis and three-dimensional models of RNA polymerase subunits were done over four lineages of endosymbiotic proteobacteria with the smallest genomes known to date. Amino acids under positive selection in the α subunit and loss of motifs in other subunits of RNA polymerase were observed. According to three-dimensional models, sites under positive selection might compensate the loss of motifs in α subunit. In addition, variations in the σ subunit were identified, some of them already studied in E. coli as a result of random mutagenesis. Amino acid changes in RNA polymerase suggest a possible modification in the binding specificity of the canonical -10 box (TATAAT) in some of these organisms. Furthermore, the β-flap helix domain is absent in some Hodgkinia strains, as observed in RNA pol II of Archaea, thus lacking the capacity to bind to the -35 box. Here, we propose several RNA polymerases models for endosymbiont bacteria with extremely reduced genomes. Evidence suggests that RNA polymerases of each endosymbiont bacteria follow a unique evolutionary path, without necessarily following the same path as a lineage, this is probably influenced by the intimate interactions sustained with other endosymbionts and its hosts.

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Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology

Cited by 12 publications

References 81 publications

Transcriptional initiation of a small RNA, not R‐loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae

Transcriptional initiation of a small RNA, not R‐loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae

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RNA polymerases in strict endosymbiont bacteria with extreme genome reduction show distinct erosions that could result in limited and differential promoters’ recognition

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