Strategies for Global RNA Sequencing of the Human Pathogen Neisseria gonorrhoeae

2019 ◽  
pp. 163-183 ◽  
Author(s):  
Ryan McClure ◽  
Caroline A. Genco
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Rna Sequencing ◽  
Human Pathogen

scholarly journals Refining the Pneumococcal Competence Regulon by RNA Sequencing

2019 ◽  
Vol 201 (13) ◽  
Author(s):  
Jelle Slager ◽  
Rieza Aprianto ◽  
Jan-Willem Veening
Keyword(s):  
Antibiotic Resistance ◽  
Streptococcus Pneumoniae ◽  
Rna Sequencing ◽  
Genome Annotation ◽  
Stress Factors ◽  
Microarray Technology ◽  
Human Pathogen ◽  
Exogenous Dna ◽  
Content Type ◽  
Opportunistic Human Pathogen

ABSTRACTCompetence for genetic transformation allows the opportunistic human pathogenStreptococcus pneumoniaeto take up exogenous DNA for incorporation into its own genome. This ability may account for the extraordinary genomic plasticity of this bacterium, leading to antigenic variation, vaccine escape, and the spread of antibiotic resistance. The competence system has been thoroughly studied, and its regulation is well understood. Additionally, over the last decade, several stress factors have been shown to trigger the competent state, leading to the activation of several stress response regulons. The arrival of next-generation sequencing techniques allowed us to update the competence regulon, the latest report on which still depended on DNA microarray technology. Enabled by the availability of an up-to-date genome annotation, including transcript boundaries, we assayed time-dependent expression of all annotated features in response to competence induction, were able to identify the affected promoters, and produced a more complete overview of the various regulons activated during the competence state. We show that 4% of all annotated genes are under direct control of competence regulators ComE and ComX, while the expression of a total of up to 17% of all genes is affected, either directly or indirectly. Among the affected genes are various small RNAs with an as-yet-unknown function. Besides the ComE and ComX regulons, we were also able to refine the CiaR, VraR (LiaR), and BlpR regulons, underlining the strength of combining transcriptome sequencing (RNA-seq) with a well-annotated genome.IMPORTANCEStreptococcus pneumoniaeis an opportunistic human pathogen responsible for over a million deaths every year. Although both vaccination programs and antibiotic therapies have been effective in prevention and treatment of pneumococcal infections, respectively, the sustainability of these solutions is uncertain. The pneumococcal genome is highly flexible, leading to vaccine escape and antibiotic resistance. This flexibility is predominantly facilitated by competence, a state allowing the cell to take up and integrate exogenous DNA. Thus, it is essential to obtain a detailed overview of gene expression during competence. This is stressed by the fact that administration of several classes of antibiotics can lead to competence. Previous studies on the competence regulon were performed with microarray technology and were limited to an incomplete set of known genes. Using RNA sequencing combined with an up-to-date genome annotation, we provide an updated overview of competence-regulated genes.

Different responses to nitrate and nitrite by the model organism Escherichia coli and the human pathogen Neisseria gonorrhoeae

2006 ◽  
Vol 34 (1) ◽  
pp. 111-114 ◽  
Author(s):  
R.N. Whitehead ◽  
J.A. Cole
Keyword(s):  
Escherichia Coli ◽  
Neisseria Gonorrhoeae ◽  
Model Organism ◽  
Anaerobic Growth ◽  
Human Pathogen ◽  
Regulate Gene Expression ◽  
E Coli ◽  
Regulatory Systems ◽  
Two Component ◽  
Nitrate And Nitrite

The ability of Escherichia coli to use both nitrate and nitrite as terminal electron acceptors during anaerobic growth is mediated by the dual-acting two-component regulatory systems NarX-NarL and NarQ-NarP. In contrast, Neisseria gonorrhoeae responds only to nitrite: it expresses only NarQ-NarP. We have shown that although N. gonorrhoeae NarQ can phosphorylate E. coli NarL and NarP, the N. gonorrhoeae NarP is unable to regulate gene expression in E. coli. Mutagenesis experiments have revealed residues in E. coli NarQ that are essential for nitrate and nitrite sensing. Chimaeric proteins revealed domains of NarQ that are important for ligand sensing.

scholarly journals Complete Genome Sequence of Neisseria gonorrhoeae NCCP11945

2008 ◽  
Vol 190 (17) ◽  
pp. 6035-6036 ◽  
Author(s):  
Gyung Tae Chung ◽  
Jeong Sik Yoo ◽  
Hee Bok Oh ◽  
Yeong Seon Lee ◽  
Sun Ho Cha ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Neisseria Gonorrhoeae ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Multidrug Resistant ◽  
Human Pathogen ◽  
Korean Patient

ABSTRACT Neisseria gonorrhoeae is an obligate human pathogen that is the etiological agent of gonorrhea. We explored variations in the genes of a multidrug-resistant N. gonorrhoeae isolate from a Korean patient in an effort to understand the prevalence, antibiotic resistance, and importance of horizontal gene transfer within this important, naturally competent organism. Here, we report the complete annotated genome sequence of N. gonorrhoeae strain NCCP11945.

Crystal Structures of Two Solute Receptors for l-Cystine and l-Cysteine, Respectively, of the Human Pathogen Neisseria gonorrhoeae

2012 ◽  
Vol 415 (3) ◽  
pp. 560-572 ◽  
Author(s):  
Haydar Bulut ◽  
Sebastien Moniot ◽  
Anke Licht ◽  
Frank Scheffel ◽  
Stephanie Gathmann ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Crystal Structures ◽  
Human Pathogen

Species specificity of factor H interaction with the uniquely human pathogen, Neisseria gonorrhoeae, resides in arginine substitution at position 1203 in domain 20

2010 ◽  
Vol 47 (13) ◽  
pp. 2247-2247
Author(s):  
Jutamas Shaughnessy ◽  
Sanjay Ram ◽  
Arnab Bhattacharjee ◽  
Connie Tran ◽  
Gabor Horvath ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Factor H ◽  
Species Specificity ◽  
Human Pathogen

scholarly journals Broad spectrum O-linked protein glycosylation in the human pathogen Neisseria gonorrhoeae

2009 ◽  
Vol 106 (11) ◽  
pp. 4447-4452 ◽  
Author(s):  
A. Vik ◽  
F. E. Aas ◽  
J. H. Anonsen ◽  
S. Bilsborough ◽  
A. Schneider ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Broad Spectrum ◽  
Protein Glycosylation ◽  
Human Pathogen

scholarly journals Regulation of mtrF Expression in Neisseria gonorrhoeae and Its Role in High-Level Antimicrobial Resistance

2005 ◽  
Vol 187 (11) ◽  
pp. 3713-3720 ◽  
Author(s):  
Jason P. Folster ◽  
William M. Shafer
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Antimicrobial Agents ◽  
Efflux Pump ◽  
Sublethal Concentration ◽  
Human Pathogen ◽  
Mucosal Surfaces ◽  
Induction Process ◽  
Inner Membrane Protein ◽  
High Level ◽  
Triton X

ABSTRACT The obligate human pathogen Neisseria gonorrhoeae uses the MtrC-MtrD-MtrE efflux pump to resist structurally diverse hydrophobic antimicrobial agents (HAs), some of which bathe mucosal surfaces that become infected during transmission of gonococci. Constitutive high-level HA resistance occurs by the loss of a repressor (MtrR) that negatively controls transcription of the mtrCDE operon. This high-level HA resistance also requires the product of the mtrF gene, which is located downstream and transcriptionally divergent from mtrCDE. MtrF is a putative inner membrane protein, but its role in HA resistance mediated by the MtrC-MtrD-MtrE efflux pump remains to be determined. High-level HA resistance can also be mediated through an induction process that requires enhanced transcription of mtrCDE when gonococci are grown in the presence of a sublethal concentration of Triton X-100. We now report that inactivation of mtrF results in a significant reduction in the induction of HA resistance and that the expression of mtrF is enhanced when gonococci are grown under inducing conditions. However, no effect was observed on the induction of mtrCDE expression in an MtrF-negative strain. The expression of mtrF was repressed by MtrR, the major repressor of mtrCDE expression. In addition to MtrR, another repressor (MpeR) can downregulate the expression of mtrF. Repression of mtrF by MtrR and MpeR was additive, demonstrating that the repressive effects mediated by these regulators are independent processes.

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