Pneumococcal Phasevarions Control Multiple Virulence Traits, Including Vaccine Candidate Expression

Phillips, Zachary N.; Trappetti, Claudia; Bergh, Annelies Van Den; Martin, Gael; Calcutt, Ainslie; Ozberk, Victoria; Guillon, Patrice; Pandey, Manisha; Itzstein, Mark von; Swords, W. Edward; Paton, James C.; Jennings, Michael P.; Atack, John M.

doi:10.1128/spectrum.00916-22

Cited by 10 publications

(14 citation statements)

References 53 publications

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“…Analysis of these TRD sequences revealed that there are four unique 5 ′ -TRD sequences, and four unique 3 ′ -TRD sequences present in these strains (Figure 3B ; full sequences and analysis in Supplementary Data 1 ), meaning a potential 16 unique HsdS proteins are possible dependent on the encoded TRDs present (four possible 5 ′ -TRD x four possible 3 ′ -TRD). This is unlike other phase-variable Type I systems, such as the SpnD39III system in S. pneumoniae ( 34 , 37 , 38 , 61 ), and the phase-variable Type I system in S. suis , ( 39 ) where all strains encode the same TRDs, and therefore shuffle between the same complement of expressed HsdS proteins. Our prototype strains of AP76 and JL03 encoded a subset of these sixteen potential TRDs: AP76 encoded a combination of 5’-TRD-1 and 3’-TRD-1 (abbreviated TRD1-1) and TRDs 1-2, 2-2 and 2-1 (comprising alleles A-D; Figure 3C ); while in strain JL03 we found TRDs 2-1, 2-3, 3-3 and 3-1 (comprising alleles D-G; Figure 3D ).…”

Section: Resultsmentioning

confidence: 90%

“…The SpnD39III system in S. pneumoniae contains multiple variable hsdS loci which contain inverted repeats, and a gene encoding a recombinase ( creX ). Homologous recombination between these multiple variable hsdS genes via these inverted repeats, and catalysed in part by the associated recombinase ( 36 ), results in the expression of six different methyltransferase variants within a population, which control six different phasevarions, resulting in six different phenotypic sub-variants within a pneumococcal population ( 34 , 37 , 38 ). A phase-variable Type I DNA methyltransferase has also been characterised in the related organism Streptococcus suis ( 39 ), with this system switching between four different HsdS variants.…”

Section: Introductionmentioning

confidence: 99%

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Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions

Nahar

Tram

Jen

et al. 2023

Nucleic Acids Research

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Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferases, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase in A. pleuropneumoniae results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.

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Section: Resultsmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions

Nahar

Tram

Jen

et al. 2023

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

show abstract

“…full sequences and analysis in Supplementary Data 1), meaning a potential 16 unique HsdS proteins were possible dependent on the encoded TRDs present (four possible 5′-TRD x four possible 3′-TRD). This is unlike other phase-variable Type I systems, such as the SpnD39III system in S. pneumoniae (34,37,38,61), and the phase-variable Type I system in S. suis, (39) where all strains encode the same TRDs, and therefore shuffle between the same complement of expressed HsdS proteins. Our prototype strains of AP76 and JL03 encoded a subset of these sixteen potential TRDs: AP76 encoded a combination of 5′-TRD-1 and 3′-TRD-1; 5′-TRD-1 and 3′-TRD-2; 5′-TRD-2 and 3′-TRD-2; 5′-TRD-2 and 3′-TRD-1, which we have named alleles A-D, respectively (Figure 3C).…”

Section: Distribution Of the Phase-variable Methyltransferases In A P...mentioning

confidence: 91%

Actinobacillus pleuropneumoniaeencodes multiple phase-variable DNA methyltransferases that comprise distinct phasevarions

Nahar

Tram

Jen

et al. 2022

Preprint

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Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferase, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase variants results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.

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“…This diversity inherently serves as a bet-hedging strategy in the face of multiple potential invading bacteriophage strains, forbidding any one bacteriophage from eliminating the entire bacterial population ( 6 , 20 ). These variants were also observed to differ in opacity ( 10 ), virulence in mice ( 10 ), as well as human cell infection efficiency and survival in human blood ( 11 ), presumably resulting from Type I RM phase variants inducing differential methylation of host DNA ( 20 ). Other interesting phase variation systems include a programmed inversion targeting the pilV gene (shufflon), leading to phase variants differing in the specificity of their conjugative pili ( 21 ), and a programmed inversion targeting phage tail genes, conferring different host specificity ( 22 ).…”

Section: Introductionmentioning

confidence: 99%

Systematic identification of gene-altering programmed inversions across the bacterial domain

Milman

Yelin

Kishony

2023

Nucleic Acids Research

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Programmed chromosomal inversions allow bacteria to generate intra-population genotypic and functional heterogeneity, a bet-hedging strategy important in changing environments. Some programmed inversions modify coding sequences, producing different alleles in several gene families, most notably in specificity-determining genes such as Type I restriction-modification systems, where systematic searches revealed cross phylum abundance. Yet, a broad, gene-independent, systematic search for gene-altering programmed inversions has been absent, and little is known about their genomic sequence attributes and prevalence across gene families. Here, identifying intra-species variation in genomes of over 35 000 species, we develop a predictive model of gene-altering inversions, revealing key attributes of their genomic sequence attributes, including gene-pseudogene size asymmetry and orientation bias. The model predicted over 11,000 gene-altering loci covering known targeted gene families, as well as novel targeted families including Type II restriction-modification systems, a protein of unknown function, and a fusion-protein containing conjugative-pilus and phage tail domains. Publicly available long-read sequencing datasets validated representatives of these newly predicted inversion-targeted gene families, confirming intra-population genetic heterogeneity. Together, these results reveal gene-altering programmed inversions as a key strategy adopted across the bacterial domain, and highlight programmed inversions that modify Type II restriction-modification systems as a possible new mechanism for maintaining intra-population heterogeneity.

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Pneumococcal Phasevarions Control Multiple Virulence Traits, Including Vaccine Candidate Expression

Cited by 10 publications

References 53 publications

Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions

Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions

Actinobacillus pleuropneumoniaeencodes multiple phase-variable DNA methyltransferases that comprise distinct phasevarions

Systematic identification of gene-altering programmed inversions across the bacterial domain

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