scholarly journals Streptococcus suis Encodes Multiple Allelic Variants of a Phase-Variable Type III DNA Methyltransferase, ModS, That Control Distinct Phasevarions

mSphere ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Greg Tram ◽  
Freda E.-C. Jen ◽  
Zachary N. Phillips ◽  
Jamie Timms ◽  
Asma-Ul Husna ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Antibiotic Resistance ◽  
Dna Methyltransferase ◽  
Streptococcus Suis ◽  
Phase Variable ◽  
Allelic Variants ◽  
Content Type ◽  
Type Iii ◽  
Variable Type ◽  
Epigenetic Gene Regulation

ABSTRACT Streptococcus suis is a significant cause of bacterial meningitis in humans, particularly in Southeast Asia, and is a leading cause of respiratory and invasive disease in pigs. Phase-variable DNA methyltransferases, associated with restriction-modification (R-M) systems, are a source of epigenetic gene regulation, controlling the expression of multiple genes. These systems are known as phasevarions (phase-variable regulons) and have been characterized in many host-adapted bacterial pathogens. We recently described the presence of a Type III DNA methyltransferase in S. suis, ModS, which contains a simple sequence repeat (SSR) tract within the open reading frame of the modS gene and which differed in length between individual strains. We also observed that multiple allelic variants of the modS gene were present in a population of S. suis isolates. Here, we demonstrate that a biphasic ON-OFF switching of expression occurs in the two most common ModS alleles, ModS1 and ModS2, and that switching is dependent on SSR tract length. Furthermore, we show using single-molecule real-time (SMRT) sequencing that ModS1 and ModS2 are active methyltransferases in S. suis. ON-OFF switching of each ModS allele results in the regulation of distinct phasevarions, with the ModS2 phasevarion impacting growth patterns and antibiotic resistance. This is the first demonstration of a phase-variable Type III DNA methyltransferase in a Gram-positive organism that controls a phasevarion. Characterizing the phenotypic effects of phasevarions in S. suis is key to understanding pathogenesis and the development of future vaccines. IMPORTANCE Streptococcus suis is a causative agent of meningitis, polyarthritis, and polyserositis in swine, and it is a major cause of zoonotic meningitis in humans. Here, we investigate epigenetic gene regulation in S. suis by multiple phasevarions controlled by the phase-variable Type III DNA methyltransferase ModS. This is the first characterized example of a Type III R-M system regulating a phasevarion in a Gram-positive organism. We demonstrate that biphasic ON-OFF switching of ModS expression results in differences in bacterial growth and antibiotic resistance. Understanding the effects of ModS phase variation is required to determine the stably expressed antigenic repertoire of S. suis, which will direct and inform the development of antimicrobial treatments and vaccines against this important pathogen.

scholarly journals Streptococcus suis encodes multiple allelic variants of a phase-variable Type III DNA methyltransferase, ModS, that control distinct phasevarions

2021 ◽  
Author(s):  
Greg Tram ◽  
Freda E.-C. Jen ◽  
Zachary N. Phillips ◽  
Jamie Timms ◽  
Asma-Ul Husna ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Antibiotic Resistance ◽  
Dna Methyltransferase ◽  
Streptococcus Suis ◽  
Phase Variable ◽  
Gram Positive ◽  
Allelic Variants ◽  
Type Iii ◽  
Variable Type ◽  
Epigenetic Gene Regulation

AbstractStreptococcus suis is a significant cause of bacterial meningitis in humans, particularly in S.E. Asia, and is a leading cause of respiratory and invasive disease in pigs. Phase-variable DNA methyltransferases, associated with Restriction-Modification (R-M) systems, are a source of epigenetic gene regulation, controlling the expression of multiple genes. These systems are known as phasevarions (phase-variable regulons), and have been characterised in many host-adapted bacterial pathogens. We recently described the presence of a Type III DNA methyltransferase in S. suis, ModS, which contains a simple sequence repeat (SSR) tract within the open reading frame of the modS gene, and which varied in length between individual strains. We also observed multiple allelic variants of the modS gene were present in a population of S. suis isolates. Here, we demonstrate that a biphasic ON-OFF switching of expression occurs in the two most common ModS alleles, ModS1 and ModS2, and that switching is dependent on SSR tract length. Further, we show that ModS1 and ModS2 are active methyltransferases in S. suis using Single-Molecule, Real Time (SMRT) sequencing. ON-OFF switching of each ModS allele results in the regulation of distinct phasevarions, with the ModS2 phasevarion impacting growth patterns and antibiotic resistance. This is the first demonstration of a phase-variable Type III DNA methyltransferase in a Gram-positive organism that controls a phasevarion. Characterising the phenotypic effects of phasevarions in S. suis is key to understanding pathogenesis and the development of future vaccines.ImportanceStreptococcus suis is a causative agent of meningitis, polyarthritis and polyserositis in swine, and is a major cause of zoonotic meningitis in humans. Here we investigate epigenetic gene regulation in S. suis by multiple phasevarions controlled by the phase-variable Type III DNA methyltransferase ModS. This is the first characterised example of a Type III R-M system regulating a phasevarion in a Gram-positive organism. We demonstrate that biphasic ON-OFF switching of ModS expression results in differences in bacterial growth and antibiotic resistance. Understanding the effects of ModS phase variation is required to determine the stably expressed antigenic repertoire of S. suis, which will direct and inform the development of antimicrobial treatments and vaccines against this important pathogen.

scholarly journals Phasevarion-Regulated Virulence in the Emerging Pediatric Pathogen Kingella kingae

2017 ◽  
Vol 85 (12) ◽  
Author(s):  
Yogitha N. Srikhanta ◽  
Ka Yee Fung ◽  
Georgina L. Pollock ◽  
Vicki Bennett-Wood ◽  
Benjamin P. Howden ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Heat Shock ◽  
Virulence Gene ◽  
Dna Methyltransferases ◽  
Epigenetic Mechanism ◽  
Phase Variable ◽  
Kingella Kingae ◽  
Content Type ◽  
Associated Proteins ◽  
Virulence Gene Regulation

ABSTRACT Kingella kingae is a common etiological agent of pediatric osteoarticular infections. While current research has expanded our understanding of K. kingae pathogenesis, there is a paucity of knowledge about host-pathogen interactions and virulence gene regulation. Many host-adapted bacterial pathogens contain phase variable DNA methyltransferases (mod genes), which can control expression of a regulon of genes (phasevarion) through differential methylation of the genome. Here, we identify a phase variable type III mod gene in K. kingae, suggesting that phasevarions operate in this pathogen. Phylogenetic studies revealed that there are two active modK alleles in K. kingae. Proteomic analysis of secreted and surface-associated proteins, quantitative PCR, and a heat shock assay comparing the wild-type modK1 ON (i.e., in frame for expression) strain to a modK1 OFF (i.e., out of frame) strain revealed three virulence-associated genes under ModK1 control. These include the K. kingae toxin rtxA and the heat shock genes groEL and dnaK. Cytokine expression analysis showed that the interleukin-8 (IL-8), IL-1β, and tumor necrosis factor responses of THP-1 macrophages were lower in the modK1 ON strain than in the modK1::kan mutant. This suggests that the ModK1 phasevarion influences the host inflammatory response and provides the first evidence of this phase variable epigenetic mechanism of gene regulation in K. kingae.

scholarly journals The Histone Code of Toxoplasma gondii Comprises Conserved and Unique Posttranslational Modifications

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Sheila C. Nardelli ◽  
Fa-Yun Che ◽  
Natalie C. Silmon de Monerri ◽  
Hui Xiao ◽  
Edward Nieves ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Toxoplasma Gondii ◽  
Posttranslational Modifications ◽  
Epigenetic Modifications ◽  
Histone Code ◽  
Parasitic Infections ◽  
Content Type ◽  
Epigenetic Gene Regulation

ABSTRACT Epigenetic gene regulation has emerged as a major mechanism for gene regulation in all eukaryotes. Histones are small, basic proteins that constitute the major protein component of chromatin, and posttranslational modifications (PTM) of histones are essential for epigenetic gene regulation. The different combinations of histone PTM form the histone code for an organism, marking functional units of chromatin that recruit macromolecular complexes that govern chromatin structure and regulate gene expression. To characterize the repertoire of Toxoplasma gondii histone PTM, we enriched histones using standard acid extraction protocols and analyzed them with several complementary middle-down and bottom-up proteomic approaches with the high-resolution Orbitrap mass spectrometer using collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), and/or electron transfer dissociation (ETD) fragmentation. We identified 249 peptides with unique combinations of PTM that comprise the T. gondii histone code. T. gondii histones share a high degree of sequence conservation with human histones, and many modifications are conserved between these species. In addition, T. gondii histones have unique modifications not previously identified in other species. Finally, T. gondii histones are modified by succinylation, propionylation, and formylation, recently described histone PTM that have not previously been identified in parasitic protozoa. The characterization of the T. gondii histone code will facilitate in-depth analysis of how epigenetic regulation affects gene expression in pathogenic apicomplexan parasites and identify a new model system for elucidating the biological functions of novel histone PTM. IMPORTANCE Toxoplasma gondii is among the most common parasitic infections in humans. The transition between the different stages of the T. gondii life cycle are essential for parasite virulence and survival. These differentiation events are accompanied by significant changes in gene expression, and the control mechanisms for these transitions have not been elucidated. Important mechanisms that are involved in the control of gene expression are the epigenetic modifications that have been identified in several eukaryotes. T. gondii has a full complement of histone-modifying enzymes, histones, and variants. In this paper, we identify over a hundred PTM and a full repertoire of PTM combinations for T. gondii histones, providing the first large-scale characterization of the T. gondii histone code and an essential initial step for understanding how epigenetic modifications affect gene expression and other processes in this organism.

scholarly journals Methylation Warfare: Interaction of Pneumococcal Bacteriophages with Their Host

2019 ◽  
Vol 201 (19) ◽  
Author(s):  
Leonardo Furi ◽  
Liam A. Crawford ◽  
Guillermo Rangel-Pineros ◽  
Ana S. Manso ◽  
Megan De Ste Croix ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Lytic Replication ◽  
Host Cells ◽  
Transcriptional Analysis ◽  
Type I ◽  
Phase Variable ◽  
Abortive Infection ◽  
Content Type ◽  
Variable Type ◽  
Restriction Modification

ABSTRACTVirus-host interactions are regulated by complex coevolutionary dynamics. InStreptococcus pneumoniae, phase-variable type I restriction-modification (R-M) systems are part of the core genome. We hypothesized that the ability of the R-M systems to switch between six target DNA specificities also has a key role in preventing the spread of bacteriophages. Using the streptococcal temperate bacteriophage SpSL1, we show that the variants of both the SpnIII and SpnIV R-M systems are able to restrict invading bacteriophage with an efficiency approximately proportional to the number of target sites in the bacteriophage genome. In addition to restriction of lytic replication, SpnIII also led to abortive infection in the majority of host cells. During lytic infection, transcriptional analysis found evidence of phage-host interaction through the strong upregulation of thenrdRnucleotide biosynthesis regulon. During lysogeny, the phage had less of an effect on host gene regulation. This research demonstrates a novel combined bacteriophage restriction and abortive infection mechanism, highlighting the importance that the phase-variable type I R-M systems have in the multifunctional defense against bacteriophage infection in the respiratory pathogenS. pneumoniae.IMPORTANCEWith antimicrobial drug resistance becoming an increasing burden on human health, much attention has been focused on the potential use of bacteriophages and their enzymes as therapeutics. However, the investigations into the physiology of the complex interactions of bacteriophages with their hosts have attracted far less attention, in comparison. This work describes the molecular characterization of the infectious cycle of a bacteriophage in the important human pathogenStreptococcus pneumoniaeand explores the intricate relationship between phase-variable host defense mechanisms and the virus. This is the first report showing how a phase-variable type I restriction-modification system is involved in bacteriophage restriction while it also provides an additional level of infection control through abortive infection.

scholarly journals Phase-Variable Control of Multiple Phenotypes in Acinetobacter baumannii Strain AB5075

2015 ◽  
Vol 197 (15) ◽  
pp. 2593-2599 ◽  
Author(s):  
Kyle A. Tipton ◽  
Daniela Dimitrova ◽  
Philip N. Rather
Keyword(s):  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Cell Density ◽  
Biofilm Formation ◽  
Galleria Mellonella ◽  
Phase Variation ◽  
Phase Variable ◽  
Dependent Manner ◽  
Content Type ◽  
Variable Control

ABSTRACTAcinetobacter baumanniistrain AB5075 produces colonies with two opacity phenotypes, designated opaque and translucent. These phenotypes were unstable and opaque and translucent colony variants were observed to interconvert at high frequency, suggesting that a phase-variable mechanism was responsible. The frequency of phase variation both within colonies and in broth cultures increased in a cell density-dependent manner and was mediated by the accumulation of an extracellular factor. This factor was distinct from the knownA. baumanniisignaling molecule 3-OH C12-homoserine lactone. Opaque and translucent colony variants exhibited a number of phenotypic differences, including cell morphology, surface motility, biofilm formation, antibiotic resistance, and virulence in aGalleria mellonellamodel. Additional clinical isolates exhibited a similar phase-variable control of colony opacity, suggesting that this may be a common feature ofA. baumannii.IMPORTANCEA novel phase-variable mechanism has been identified inAcinetobacter baumanniithat results in an interconversion between opaque and translucent colony phenotypes. This phase variation also coordinately regulates motility, cell shape, biofilm formation, antibiotic resistance, and virulence. The frequency of phase variation is increased at high cell density via a diffusible extracellular signal. To our knowledge, this report presents the first example of phase variation inA. baumanniiand also the first example of quorum sensing-mediated control of phase variation in a bacterium. The findings are important, as this phase-variable mechanism can be identified only via changes in colony opacity using oblique light; therefore, many researchers studyingA. baumanniimay unknowingly be working with different colony variants.

scholarly journals Characterization of the NgoAXP: phase-variable type III restriction–modification system inNeisseria gonorrhoeae

2009 ◽  
Vol 300 (1) ◽  
pp. 25-35 ◽  
Author(s):  
Monika Adamczyk-Poplawska ◽  
MichaÅ‚ Lower ◽  
Andrzej Piekarowicz
Keyword(s):  
Phase Variable ◽  
Modification System ◽  
Type Iii ◽  
Variable Type

scholarly journals Expanding U.S. Laboratory Capacity for Neisseria gonorrhoeae Antimicrobial Susceptibility Testing and Whole-Genome Sequencing through the CDC's Antibiotic Resistance Laboratory Network

2020 ◽  
Vol 58 (4) ◽  
Author(s):  
Ellen N. Kersh ◽  
Cau D. Pham ◽  
John R. Papp ◽  
Robert Myers ◽  
Richard Steece ◽  
...  
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Whole Genome ◽  
Content Type ◽  
Laboratory Capacity

ABSTRACT U.S. gonorrhea rates are rising, and antibiotic-resistant Neisseria gonorrhoeae (AR-Ng) is an urgent public health threat. Since implementation of nucleic acid amplification tests for N. gonorrhoeae identification, the capacity for culturing N. gonorrhoeae in the United States has declined, along with the ability to perform culture-based antimicrobial susceptibility testing (AST). Yet AST is critical for detecting and monitoring AR-Ng. In 2016, the CDC established the Antibiotic Resistance Laboratory Network (AR Lab Network) to shore up the national capacity for detecting several resistance threats including N. gonorrhoeae. AR-Ng testing, a subactivity of the CDC’s AR Lab Network, is performed in a tiered network of approximately 35 local laboratories, four regional laboratories (state public health laboratories in Maryland, Tennessee, Texas, and Washington), and the CDC’s national reference laboratory. Local laboratories receive specimens from approximately 60 clinics associated with the Gonococcal Isolate Surveillance Project (GISP), enhanced GISP (eGISP), and the program Strengthening the U.S. Response to Resistant Gonorrhea (SURRG). They isolate and ship up to 20,000 isolates to regional laboratories for culture-based agar dilution AST with seven antibiotics and for whole-genome sequencing of up to 5,000 isolates. The CDC further examines concerning isolates and monitors genetic AR markers. During 2017 and 2018, the network tested 8,214 and 8,628 N. gonorrhoeae isolates, respectively, and the CDC received 531 and 646 concerning isolates and 605 and 3,159 sequences, respectively. In summary, the AR Lab Network supported the laboratory capacity for N. gonorrhoeae AST and associated genetic marker detection, expanding preexisting notification and analysis systems for resistance detection. Continued, robust AST and genomic capacity can help inform national public health monitoring and intervention.

Sign in / Sign up

Export Citation Format

Share Document