Analysis of Global Collection of Group A Streptococcus Genomes Reveals that the Majority Encode a Trio of M and M-Like Proteins

Abstract

The core Mga (multiple gene activator) regulon of group A Streptococcus (GAS) contains genes encoding proteins involved in adhesion and immune evasion. While all GAS genomes contain genes for Mga and C5a peptidase, the intervening genes encoding M and M-like proteins vary between strains. The genetic make-up of the Mga regulon of GAS was characterized by utilizing a collection of 1,688 GAS genomes that are representative of the global GAS population. Sequence variations were examined with multiple alignments, and the expression of all core Mga regulon genes was examined by quantitative reverse transcription-PCR in a representative strain collection. In 85.2% of the sampled genomes, the Mga locus contained genes encoding Mga, Mrp, M, Enn, and C5a peptidase proteins. These isolates account for 53% of global infections. Only 9.1% of genomes did not contain either an mrp or an enn gene. The pairwise identity within Enn (68.6%) and Mrp (83.2%) protein sequences was higher than within M proteins (44.7%). Gene expression varied between strains tested, but high expression was recorded for all genes in at least one strain. Previous nomenclature issues were clarified with molecular gene definitions. Our findings support a shift in focus in the GAS research field to further consider the role of Mrp and Enn in virulence and vaccine development. IMPORTANCE While the GAS M protein has been the leading vaccine target for decades, the bacteria encode many other virulence factors of interest for vaccine development. In this work, we show that emm-like genes are encoded in a remarkable majority of GAS genomes and expressed at a level similar to that for the emm gene. In collaboration with the U.S. Centers for Disease Control, we developed molecular definitions of the different emm and emm-like gene families. This clarification should abrogate mistyping of strains, especially in the area of whole-genome typing. We have also updated the emm-typing collection by removing emm-like gene sequences and provided in-depth analysis of Mrp and Enn protein sequence structure and diversity.

In silico characterisation of stand-alone response regulators of Streptococcus pyogenes

“…In a novel finding, throat-associated emm 12 ST36 isolate (SP1LAU) encoded both mga-1 and mga-2 ( Fig 4 ). In addition to an intact rofA , ralp3 , and rivR , SP1LAU also encoded mga-1 in the canonical locus, of the allele-type mga 379 [ 103 ]. The mga-2 -like gene displayed 91.1% similarity to the nucleotide sequence of mga-2 , and was encoded 8963 nucleotides downstream of the phage-related DNase ( spd1 ) between recombinase ( recT ) and a gene encoding a phage subunit.…”

“…Traditionally, GAS mga has been classified in two similar allele types mga-1 and mga-2 . Today, it seems logical and cost-effective to utilise the resolution of next-generation sequencing to define additional mga allele-types based on individual nucleotide variation [ 103 ]. However, moving forward it is important to realise the ongoing utility of the mga-1 and mga-2 variants, given their strong association with niche preference and tissue tropism.…”

Genetics, Structure, and Function of Group A Streptococcal Pili

“…Further comparative crystal structure analyses and examination of pilin regions for antigenicity may lead to refinement of protective epitopes and development of a peptide-based pilin vaccine. Theoretical findings of combinations of a multivalent vaccine with other antigens, such as a family of M-related proteins ( Frost et al, 2020 ), have demonstrated increased vaccine coverage and enhanced effectiveness ( Courtney et al, 2017 ). Such combinations with other vaccine antigens might offer potentiating effects on prophylactic efforts for combatting GAS infections.…”

“…While emm typing is based on the sequence of 5′-end of the emm gene, the 3’-ends of emm and emm -like genes encoding M-like proteins, such as Mrp and Enn ( Frost et al, 2018 ; Frost et al, 2020 ), are used for emm pattern groupings ( Bessen et al, 1996 ). A strong correspondence between three groupings (patterns A-C, D, and E) and infection site preference, i.e., throat or skin, has been shown.…”

Nonimmune antibody interactions of Group A Streptococcus M and M-like proteins

“…Namely, these are Enn proteins [ 33 , 42 ] and M-related proteins (Mrp) [ 45 ], which are encoded immediately downstream or upstream, respectively, of emm in the mga regulon [ 46 , 47 ]. A recent survey of a collection of 1,688 globally distributed Strep A isolates showed that approximately 85% encode both Enn protein and Mrp [ 48 ]. Enn proteins are sequence variable but to a lesser extent than M proteins [ 48 , 49 ], and Mrps are even less sequence variable [ 50 ].…”