Updated model of group A Streptococcus M proteins based on a comprehensive worldwide study

Abstract

Group A Streptococcus (GAS) M protein is an important virulence factor and potential vaccine antigen, and constitutes the basis for strain typing (emm-typing). Although >200 emm-types are characterized, structural data were obtained from only a limited number of emm-types. We aim to evaluate the sequence diversity of near-full-length M proteins from worldwide sources and analyse their structure, sequence conservation and classification. GAS isolates recovered from throughout the world during the last two decades underwent emm-typing and complete emm gene sequencing. Predicted amino acid sequence analyses, secondary structure predictions and vaccine epitope mapping were performed using MUSCLE and Geneious software. A total of 1086 isolates from 31 countries were analysed, representing 175 emm-types. emm-type is predictive of the whole protein structure, independent of geographical origin or clinical association. Findings of an emm-type paired with multiple, highly divergent central regions were not observed. M protein sequence length, the presence or absence of sequence repeats and predicted secondary structure were assessed in the context of the latest vaccine developments. Based on these global data, the M6 protein model is updated to a three representative M protein (M5, M80 and M77) model, to aid in epidemiological analysis, vaccine development and M protein-related pathogenesis studies.

Figure 1. Study profile

* List of countries with respective number of isolates in brackets: Argentina (5), Australia (137), Belgium (46), Brazil (105), Canada (69), Chile (5), Czech Republic (17), Germany (50), Egypt (39), Ethiopia (4), Fiji (55), India (51), Israel (67), Japan (12), Kenya (1), Malaysia (1), Mali (58), Mexico (7), New Zealand (1), Norway (19), Papua New Guinea (2), Portugal (21), Romania (22), Russia (15), South Africa (22), Sweden (45), Taiwan (37), The Gambia (1), United Kingdom (22), USA (138, including 83 in mainland and 55 in Hawaii), Venezuela (1). Geographical origin is unknown for 3 isolates. SDSE, Streptococcus dysgalactiae subspecies equisimilus. The eight emm-types recovered prior to 1987 are as follows: emm-types 17, 34, 37, 38, 46, 47, 51 and 72.

Figure 2. Three representative M proteins model

Three representative M proteins (M5, M80 and M77) were selected as prototypes for the structural characteristics within each emm pattern group. M protein length and the size of the repeat and non-repeat regions are drawn to scale. Pattern A-C emm-types represent the longest M proteins, with a (hyper)variable portion of about 230 residues. In comparison, pattern D and E proteins possess a (hyper)variable portion of ~ 150 and 100 residues, respectively. The ‘A’ repeats are absent from the vast majority of M proteins belonging to the pattern D and E groups. The ‘B’ repeats are present in most of the pattern A-C and D emm-types, but absent from most of the pattern E emm-types. Thirty-five conserved residues constitute the ‘C’ repeat unit. Consecutive ‘C’ repeat units are sometimes separated by a seven residue unit called ‘C’ repeat linker (See supplementary data S2). Twenty percent of the M proteins (such as M80) do not possess non-helicoidal amino terminus. This proportion is 10%, 19% and 25% amongst the pattern A-C, D and E emm-types respectively. The portion of the protein considered by the emm-typing method is represented.

Figure 3. Insertion-deletion (indel) characteristics of M proteins belonging to the same emm-type

Intra-emm-type alignments that include 900 M protein sequences of 80 emm-types reveal 408 indels. More than half of the indels (n=224; 55%) are located in the CRR (C Repeat Region). The remaining indels are equally distributed between regions corresponding to the 50 amino-terminus proximal residues (n=85; 21%; emm-type determinant) and from residue 51 to the beginning of the CRR (n=99; 24%; sub-N-terminal, central region). The number of indels having a heptad periodicity increases from the amino-terminal (36% of indels) to the carboxy-terminal (CRR; 99% of indels) regions of M proteins, whereas half (50%) of the indels from the central region of M protein involve multiples of seven residues.