title: Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.
abstract: DNA methylation is an important epigenetic mechanism for phenotypic diversification in all forms of life. We previously described remarkable cell-to-cell heterogeneity in epigenetic pattern within a clonal population of Streptococcus pneumoniae, a leading human pathogen. We here report that the epigenetic diversity is caused by extensive DNA inversions among hsdSA, hsdSB, and hsdSC, three methyltransferase hsdS genes in the Spn556II type-I restriction modification (R-M) locus. Because hsdSA encodes the sequence recognition subunit of this type-I R-M DNA methyltransferase, these site-specific recombinations generate pneumococcal cells with variable HsdSA alleles and thereby diverse genome methylation patterns. Most importantly, the DNA methylation pattern specified by the HsdSA1 allele leads to the formation of opaque colonies, whereas the pneumococci lacking HsdSA1 produce transparent colonies. Furthermore, this HsdSA1-dependent phase variation requires intact DNA methylase activity encoded by hsdM in the Spn556II (renamed colony opacity determinant or cod) locus. Thus, the DNA inversion-driven ON/OFF switch of the hsdSA1 allele in the cod locus and resulting epigenetic switch dictate the phase variation between the opaque and transparent phenotypes. Phase variation has been well documented for its importance in pneumococcal carriage and invasive infection, but its molecular basis remains unclear. Our work has discovered a novel epigenetic cause for this significant pathobiology phenomenon in S. pneumoniae. Lastly, our findings broadly represents a significant advancement in our understanding of bacterial R-M systems and their potential in shaping epigenetic and phenotypic diversity of the prokaryotic organisms because similar site-specific recombination systems widely exist in many archaeal and bacterial species.
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Jing-Wen
authors.initials: JW
authors.lastname: Li
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Zhixing
authors.identifier: 0000-0003-0308-8549
authors.initials: Z
authors.lastname: Feng
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Juanjuan
authors.initials: J
authors.lastname: Wang
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Haoran
authors.initials: H
authors.lastname: An
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Yanni
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Yang
authors.identifier: 0000-0002-5117-7055
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.
authors.forename: Kailing
authors.initials: K
authors.lastname: Wang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China.
authors.forename: Xuegong
authors.identifier: 0000-0002-9684-5643
authors.initials: X
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China.
authors.forename: Zhun
authors.initials: Z
authors.lastname: Miao
authors.affiliation: College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China.
authors.forename: Wenbo
authors.initials: W
authors.lastname: Liang
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Sebra
authors.affiliation: W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, United States of America.
authors.forename: Guilin
authors.initials: G
authors.lastname: Wang
authors.affiliation: Biomedical Science and Engineering Center, Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.
authors.forename: Wen-Ching
authors.initials: WC
authors.lastname: Wang
authors.affiliation: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China.|Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.
authors.forename: Jing-Ren
authors.initials: JR
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D015280:DNA Restriction-Modification Enzymes / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004195:Disease Models, Animal; D044127:Epigenesis, Genetic / Q000235:genetics*; D005260:Female; D051379:Mice; D008810:Mice, Inbred C57BL; D016297:Mutagenesis, Site-Directed; D010641:Phenotype; D011008:Pneumococcal Infections / Q000382:microbiology; D016133:Polymerase Chain Reaction; D013296:Streptococcus pneumoniae / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D015280:DNA Restriction-Modification Enzymes; D004269:DNA, Bacterial; C113046:HSDS protein, Bacteria