2019
DOI: 10.1101/706598
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PacBio amplicon sequencing method to measure pilin antigenic variation frequencies ofNeisseria gonorrhoeae

Abstract: WORD LIMIT 200 words)Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the non-expressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences amplicon sequencing and custom software to determ… Show more

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Cited by 2 publications
(8 citation statements)
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“…), it was possible that changes in R‐loop levels or R‐loop stability might still alter pilin Av frequencies. A PacBio sequencing assay was used to determine the pilin Av frequency of various strains (Ozer et al , ). Deep sequencing is the best method for determining Av frequency when the strains tested have different growth rates, a factor relevant to this work, as the rnhA + nicsP lac ::rnhA strain exhibits a slower growth in the absence of IPTG.…”
Section: Resultsmentioning
confidence: 99%
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“…), it was possible that changes in R‐loop levels or R‐loop stability might still alter pilin Av frequencies. A PacBio sequencing assay was used to determine the pilin Av frequency of various strains (Ozer et al , ). Deep sequencing is the best method for determining Av frequency when the strains tested have different growth rates, a factor relevant to this work, as the rnhA + nicsP lac ::rnhA strain exhibits a slower growth in the absence of IPTG.…”
Section: Resultsmentioning
confidence: 99%
“…The garP −35 mutation was previously reported to lower pilin Av rates using the pilus-dependent colony morphology change (PDCMC) assay in an inducible recA background (recA6) . Pilin Av frequencies of garP −10 and garP −35 mutants without a regulatable recA (parental strain, FA1090) were determined by a novel method using PacBio sequencing (Ozer et al, 2019). All starting strains were confirmed to have the same, predominate 1-81-S2 pilE sequence by Sanger sequencing of each progenitor colony used to generate the progeny used for PacBio sequencing; however, since pilin Av was unregulated each founder colony would start with different amounts of variant pilE subpopulations that were below the level of detection.…”
Section: Altering the Frequency Of G4 Srna Transcription Initiation Amentioning
confidence: 99%
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