Supplementary Information Proteome-‐wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes
Christofer Karlsson1, #, Lars Malmström2, #, Ruedi Aebersold2, 3, Johan Malmström1,4 *
1) Department of Immunotechnology, Lund, Sweden 2) Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland 3) Faculty of Science, University of Zurich, Zurich, Switzerland 4) Biognosys AG, Zurich, Switzerland #) Equal author contribution
Supplementary Figure S1 | Outline of the GAS proteome network topology and assay score.
Prophage_encoded_Exotoxins Streptococcus_pyogenes_Virulome DNA_topoisomerases_Type_II_ATP_dependent pVir_Plasmid_of_Campylobacter DNA_repair_bacterial_MutL_MutS_system DNA_topoisomerases_Type_I_ATP_independent Resistance_to_fluoroquinolones Multidrug_Resistance_Efflux_Pumps Flavohaemoglobin Adhesion_of_Campylobacter Secreted
Coenzyme_B12_biosynthesis
CBSS_176280_1_peg_1561
Periplasmic_Stress_Response Streptococcal_Mga_Regulon Campylobacter_Iron_Metabolism Flagellum_in_Campylobacter Proteasome_bacterial Surface Listeria_surface_proteins_Internalin_like_proteins Two_component_regulatory_systems_in_Campylobacter Transport_of_Manganese ZZ_gjo_need_homes
YbbK Polysaccharide_deacetylases At1g14345 DNA_Repair_Base_Excision
Glutathione_regulated_potassium_efflux_system_and_associated_functions
DNA_repair_bacterial_RecFOR_pathway Streptococcus_pyogenes_recombinatorial_zone DNA_structural_proteins_bacterial Teichoic_and_lipoteichoic_acids_biosynthesis DNA_replication DNA_repair_bacterial Lipid_A_Ara4N_pathway_Polymyxin_resistance_ D_Alanyl_Lipoteichoic_Acid_Biosynthesis DNA_repair_bacterial_DinG_and_relatives Central_meta_cleavage_pathway_of_aromatic_compound_degradation Proteolysis_in_bacteria_ATP_dependent Lipoprotein_Biosynthesis SpeB_SpeF_extended_regulon Potassium_homeostasis Iron_acquisition_in_Streptococcus Sortase rRNA_modification_Bacteria Beta_lactamase_cluster_in_Streptococcus RuvABC_plus_a_hypothetical De_Novo_Purine_Biosynthesis Transport_of_Iron Heme_hemin_uptake_and_utilization_systems_in_GramPositives dTDP_rhamnose_synthesis Lactose_and_Galactose_Uptake_and_Utilization Single_Rhodanese_domain_proteins Capsular_heptose_biosynthesis Fructose_utilization Asp_tRNA_Asn_transamidation Alginate_metabolism Protein_degradation D_ribose_utilization Streptolysin_S_Biosynthesis_and_Transport ABC_transporter_dipeptide_TC_3_A_1_5_2_
ATP_dependent_RNA_helicases_bacterial Rhamnose_containing_glycans YaaA Bacterial_Chemotaxis L_ascorbate_utilization_and_related_gene_clusters_ Mannitol_Utilization Pentose_phosphate_pathway Lactose_utilization Stringent_Response_p_ppGpp_metabolism At3g21300
D_tyrosyl_tRNA_Tyr_deacylase Sex_pheromones_in_Enterococcus_faecalis_and_other_Firmicutes D_Tagatose_and_Galactitol_Utilization Mannose_Metabolism COG3533 Teichuronic_acid_biosynthesis Nitric_oxide_synthase Sucrose_utilization Ribitol_Xylitol_Arabitol_Mannitol_and_Sorbitol_utilization Signal_peptidase tRNA_aminoacylation_Asp_and_Asn Glutathione_Redox_cycle Galactosylceramide_and_Sulfatide_metabolism cAMP_signaling_in_bacteria ABC_transporter_oligopeptide_TC_3_A_1_5_1_
Transcription_factors_bacterial Anaerobic_respiratory_reductases Ribonucleotide_reduction Glutaredoxins Glu_tRNA_Gln_transamidation Restriction_Modification_System Oxidative_stress ABC_transporter_glutamine_TC_3_A_1_3_2_ Calvin_Benson_cycle tRNA_modification_Bacteria L_Arabinose_utilization
IbrA_and_IbrB_co_activators_of_prophage_gene_expression
Copper_homeostasis tRNA_aminoacylation_Glu_and_Gln Glycogen_metabolism Fructooligosaccharides_FOS_and_Raffinose_Utilization Sucrose_Metabolism Glycolysis_and_Gluconeogenesis tRNA_aminoacylation
Cobalt_zinc_cadmium_resistance Entner_Doudoroff_Pathway Maltose_and_Maltodextrin_Utilization YcfH CBSS_342610_3_peg_1536 Pyridoxin_Vitamin_B6_Biosynthesis Conserved_gene_cluster_possibly_involved_in_RNA_metabolism Beta_Glucoside_Metabolism RNA_polymerase_bacterial
NAD_and_NADP_cofactor_biosynthesis_global Riboflavin_FMN_and_FAD_metabolism Heme_and_Siroheme_Biosynthesis Pyruvate_metabolism_I_anaplerotic_reactions_PEP N_Acetyl_Galactosamine_and_Galactosamine_Utilization COG2509 Threonine_and_Homoserine_Biosynthesis Nudix_proteins_nucleoside_triphosphate_hydrolases_ PnuC_like_transporters GroEL_GroES Hexitol_degradation Methionine_Degradation Cysteine_Biosynthesis
Methionine_Salvage
Methylglyoxal_Metabolism Niacin_Choline_transport_and_metabolism NAD_regulation D_gluconate_and_ketogluconates_metabolism Glycolysis_and_Gluconeogenesis_including_Archaeal_enzymes
Chitin_and_N_acetylglucosamine_utilization Glutathione_Non_redox_reactions Staphylococcal_pathogenicity_islands_SaPI
Biogenesis_of_c_type_cytochromes Programmed_frameshift Phenylalanine_and_Tyrosine_Branches_from_Chorismate Thiamin_biosynthesis Deoxyribose_and_Deoxynucleoside_Catabolism Sialic_Acid_Metabolism Phenylalanine_synthesis Adenosyl_nucleosidases Polyamine_Metabolism Autoinducer_2_AI_2_transport_and_processing_lsrACDBFGE_operon_ Glutamine_Glutamate_Aspartate_and_Asparagine_Biosynthesis Coenzyme_A_Biosynthesis ECF_class_transporters Redox_dependent_regulation_of_nucleus_processes
Aminotransferases_Aromatic_Pathway_and_More_A_work_in_progress Fermentations_Mixed_acid Periplasmic_disulfide_interchange Type_IV_pilus Chorismate_Synthesis Purine_conversions UDP_N_acetylmuramate_from_Fructose_6_phosphate_Biosynthesis At5g11840_At5g67370 Methionine_Biosynthesis D_Galacturonate_and_D_Glucuronate_Utilization Peptide_methionine_sulfoxide_reductase At5g04520_AT1G06240 Purine_Utilization Arginine_Deiminase_Pathway Proline_Synthesis Na_translocating_decarboxylases_and_related Conserved_gene_cluster_associated_with_Met_tRNA_formyltransferase Putative_sugar_ABC_transporter_ytf_cluster_ Ammonia_assimilation Xanthine_Metabolism_in_Bacteria _biotin_dependent_enzymes Arginine_and_Ornithine_Degradation Soluble_cytochromes_and_functionally_related_electron_carriers At4g10620_At3g57180_At3g47450 Ribosome_LSU_bacterial Poly_gamma_glutamate_biosynthesis Protein_chaperones Quinate_degradation Glycerol_and_Glycerol_3_phosphate_Uptake_and_Utilization Arginine_Biosynthesis_extended Bacteriocin_like_peptides_Blp Unknown_carbohydrate_utilization_cluster_Ydj_ CBSS_262719_3_peg_410
Trehalose_Uptake_and_Utilization
Heat_shock_dnaK_gene_cluster_extended Respiratory_dehydrogenases_1 Glycerol_fermenation_to_1_3_propanediol Glutamine_synthetases Peptidoglycan_Biosynthesis Ioja p Arginine_Biosynthesis Inorganic_Sulfur_Assimilation Intracellular Benzoate_transport_and_degradation_cluster Fatty_Acid_Biosynthesis_FASII High_affinity_phosphate_transporter_and_control_of_PHO_regulon F0F1_type_ATP_synthase Ribosomal_protein_S12p_Asp_methylthiotransferase Biotin_biosynthesis Yfa_cluster V_Type_ATP_synthase 16S_rRNA_modification_within_P_site_of_ribosome Glycerolipid_and_Glycerophospholipid_Metabolism_in_Bacteria Ribosome_biogenesis_bacterial Cell_envelope_associated_LytR_CpsA_Psr_transcriptional_attenuators Cinnamic_Acid_Degradation LMPTP_YfkJ_cluster Ribosomal_protein_S5p_acylation MLST Acetyl_CoA_fermentation_to_Butyrate Translation_factors_bacterial Ribosome_SSU_bacterial Control_of_cell_elongation_division_cycle_in_Bacilli
ATP_dependent_Nuclease At4g38090 Biphenyl_Degradation Threonine_anaerobic_catabolism_gene_cluster tRNA_processing tRNAmodification_position_34 Flavodoxin Phosphate_metabolism Cyanate_hydrolysis Pyruvate_metabolism_II_acetyl_CoA_acetogenesis_from_pyruvate Trans_translation_by_stalled_ribosomes Transport_of_Zinc Acetoin_butanediol_metabolism COG2302 Bacterial_Cell_Division Universal_GTPases Translation_elongation_factor_G_family Allantoin_degradation Propanediol_utilization At1g26220_At1g32070 At1g69340_At2g40600 Node Color Ethanolamine_utilization
Di_Inositol_Phosphate_biosynthesis Inositol_catabolism Murein_hydrolase_regulation_and_cell_death COG0523 Lipoic_acid_metabolism D_galactarate_D_glucarate_and_D_glycerate_catabolism Fermentations_Lactate General_secretory_pathway_Sec_SRP_complex_TC_3_A_5_1_1_ Glycine_and_Serine_Utilization COG1399 19.5
1 Allantoin_Utilization Bacterial_Cytoskeleton Bacterial_signal_recognition_particle_SRP_ YjeE Hfl_operon Polyhydroxybutyrate_metabolism
Two_cell_division_clusters_relating YgjD_and_YeaZ Folate_Biosynthesis Photorespiration_oxidative_C2_cycle_ _to_chromosome_partitioning
Chorismate_Intermediate_for_synthesis_of_PAPA_antibiotics_
score
PABA_anthranilate_3_hydroxyanthranilate_and_more_ Cold_shock_CspA_family_of_proteins Ribonuclease_H Alkylphosphonate_utilization Ribosome_activity_modulation n_Phenylalkanoic_acid_degradation EcsAB_transporter_affecting_expression_and_secretion_of_secretory_preproteins Chorismate_Intermediate_for_synthesis_of_Tryptophan_PAPA_antibiotics_PABA_3_hydroxyanthranilate_and_more_ Unspecified_monosaccharide_transport_cluster Queuosine_Archaeosine_Biosynthesis Serine_Biosynthesis RNA_processing_and_degradation_bacterial Glycine_Biosynthesis Assay Macromolecular_synthesis_operon CRISPRs Butanol_Biosynthesis
At5g48545_and_At3g56490_At1g31160 Copper_homeostasis_copper_tolerance Molybdenum_cofactor_biosynthesis vg. Flagellum Tryptophan_synthesis Leucine_Biosynthesis Isoprenoid_Biosynthesis Coenzyme_F420_synthesis A Phage_capsid_proteins Experimental_Histidine_Degradation Serine_glyoxylate_cycle Experimental_Ubiquinone_BiosynthesisVDC Pyruvate_Alanine_Serine_Interconversions One_carbon_metabolism_by_tetrahydropterines Plasmid_replication Iron_sulfur_cluster_assembly Transcription_initiation_bacterial_sigma_factors Histidine_Degradation Ketoisovalerate_oxidoreductase
Glycine_cleavage_system Polyprenyl_Diphosphate_Biosynthesis 10
0 Staphylococcal_phi_Mu50B_like_prophages Thioredoxin_disulfide_reductase Leucine_Degradation_and_HMG_CoA_Metabolism Carotenoids De_Novo_Pyrimidine_Synthesis Alanine_biosynthesis Citrate_Metabolism_Transport_and_Regulation Glycine_reductase_sarcosine_reductase_and_betaine_reductase Branched_Chain_Amino_Acid_Biosynthesis
Polyadenylation_bacterial Fe_S_cluster_assembly Node Shape: tRNA_nucleotidyltransferase Choline_and_Betaine_Uptake_and_Betaine_Biosynthesis Valine_degradation Isoleucine_degradation Intra./Sur./Sec. Pyrimidine_utilization
Predicted loc.
DNA_repair_bacterial_UvrD_and_related_helicases DNA_repair_UvrABC_system
Hemin_transport_system
Listeria_Pathogenicity_Island_LIPI_1_extended
Heme_hemin_uptake_and_utilization_systems_in_GramNegatives
Circles represent NMPDR subsystems where all proteins predominantly have the same subcellular location, secreted, surface associated or intracellular, according to the subcellular protein profiles in Figure 4a-d. Rectangles represent NMPDR subsystems where an equal number of members have opposing subcellular location profiles. The localization of the rectangles in the network is influenced by the edges, which represent protein members that belong to more than one NMPDR subsystem. Increasing node size represents increasing number of member proteins. The color represents average SRM assay score, where red indicates NMPDR subsystems with high-average SRM assay score and black indicating NMPDR subsystems with low average SRM assays score. Supplementary Figure S2 | Phylogenetic relationships among selected species in the Firmicutes phylum Streptococcus pyogenes M1GAS Streptococcus pyogenes MGAS5005 Streptococcus pyogenes MGAS315 Streptococcus pyogenes SSI-1 Streptococcus pyogenes MGAS9429 Streptococcus pyogenes MGAS2096 Streptococcus pyogenes MGAS8232 Streptococcus pyogenes MGAS10270 Streptococcus pyogenes str.Manfredo Streptococcus pyogenes MGAS6180 Streptococcus pyogenes MGAS10394 Streptococcus pyogenes MGAS10750 Streptococcus pyogenes NZ131 Streptococcus dysgalactiae subsp. dysgalactiae ATCC2795 Streptococcus equi subsp. equi 4047 Streptococcus uberis 0140J Streptococcus pseudoporcinus LQ940-04 Streptococcus parauberis KCTC11537 Streptococcus mutans NN2025 Streptococcus macacae NCTC11558 Streptococcus urinalis 2285-97 Streptococcus agalactiae 18RS21 Streptococcus gallolyticus subsp. gallolyticus ATCC43143 Streptococcus bovis ATCC700338 Streptococcus equinus ATCC9812 Streptococcus infantarius subsp. infantarius ATCCBAA-102 Streptococcus salivarius SK126 Streptococcus vestibularis ATCC49124 Streptococcus thermophilus CNRZ1066 Streptococcus downei F0415 Streptococcus criceti HS-6 Streptococcus suis ST3 Streptococcus cristatus ATCC51100 Streptococcus mitis ATCC6249 Streptococcus oralis ATCC35037 Streptococcus sanguinis ATCC49296 Streptococcus peroris ATCC700780 Streptococcus infantis SK1302 Streptococcus parasanguinis ATCC903 Streptococcus anginosus 1 2 62CV Lactococcus garvieae UNIUD074 Lactococcus garvieae 21881 Lactococcus garvieae 8831 Lactococcus lactis subsp. cremoris SK11 Lactococcus lactis subsp.cremoris NZ9000 Lactococcus lactis subsp. cremoris MG1363 Lactococcus lactis subsp. lactis KF147 Lactococcus lactis subsp. lactis CV56 Lactococcus lactis subsp. lactis Il1403 Enterococcus faecalis TX0012 Enterococcus faecium C68 Enterococcus gallinarum EG2 Enterococcus casseliflavus EC30 Granulicatella adiacens ATCC49175 Eremococcus coleocola ACS-139-V-Col8 Aerococcus urinae ACS-120-V-Col10a Lactobacillus animalis KCTC3501 Lactobacillus delbrueckii subsp. lactis DSM20072 Lactobacillus acidophilus 30SC Bacillus megaterium DSM319 Bacillus subtilis BSn5 Bacillus thuringiensis BMB171 Bacillus anthracisstr. A1055 Listeriamono cytogenes 08-5578 Planococcus donghaensis MPA1U2 Staphylococcus aureus 04-02981 Staphylococcus epidermidis ATCC12228 Bulleidia extructa W1219 Brevibacillus brevis NBRC100599 Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM446 Megamonas hypermegale ART12/1 Abiotrophia defectiva ATCC49176 Clostridium botulinum A2 str. Kyoto Alkaliphilus metalliredigens QYMF Anaerococcus prevotii DSM20548 Finegoldia magna ATCC29328 Root
0.4 0.3 0.2 0.1 0.0 A maximum likelihood phylogenetic tree for selected bacterial species based on the Tamura-Nei model49 was built upon an alignment of nucleotide sequences of rpoB50 extracted from respective genome (downloaded from PATRIC Bacterial Bioinformatics Resource Center28). The tree with the highest log likelihood (-76672.8395) is shown. Initial tree(s) for the heuristic search were obtained automatically as follows. When the number of common sites was < 100 or less than one fourth of the total number of sites, the maximum parsimony method was used; otherwise BIONJ method with MCL distance matrix was used. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 76 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 2323 positions in the final dataset. Evolutionary analyses were conducted in MEGA551. Supplementary Figure S3 | Transportability of GAS SF370 SRM assays within the Firmicutes phylum.
a Genomes
GAS Streptococcus
Streptococcaceae Lactobacillales Bacilli
Firmicutes SRM assays
b Genomes
GAS Streptococcus
Streptococcaceae Lactobacillales
Ribosome_SSU_bacterial Bacilli F0F1−type_ATP_synthase Ribosome_LSU_bacterial Not annotated tRNA_aminoacylation Purine_conversions Universal_GTPases RNA_polymerase_bacterial Translation_factors_bacterial Glycolysis_and_Gluconeogenesis Resistance_to_fluoroquinolones Heat_shock_dnaK_gene_cluster_extended Rhamnose_containing_glycans Firmicutes DNA−replication tRNAmodification_position_34 Iojap Proteolysis_in_bacteria,_ATP−dependent Sialic_Acid_Metabolism De_Novo_Purine_Biosynthesis Fructose_utilization Peptidoglycan_Biosynthesis At3g21300 Fermentations:_Mixed_acid Bacterial_Cell_Division Sucrose_Metabolism Ribonucleotide_reduction DNA_repair,_UvrABC_system De_Novo_Pyrimidine_Synthesis Fe−S_cluster_assembly Folate_Biosynthesis Transcription_factors_bacterial Staphylococcal_pathogenicity_islands_SaPI Glycerolipid_and_Glycerophospholipid_Metabolism_in_Bacteria Serine−glyoxylate_cycle Arginine_Deiminase_Pathway ATP−dependent_RNA_helicases,_bacterial Acetoin,_butanediol_metabolism Macromolecular_synthesis_operon DNA_repair,_bacterial Ribosome_biogenesis_bacterial NAD_and_NADP_cofactor_biosynthesis_global Streptococcus_pyogenes_Virulome General_secretory_pathway_(Sec−SRP)_complex_(TC_3.A.5.1.1) Polyadenylation_bacterial Fatty_Acid_Biosynthesis_FASII Pyruvate_metabolism_I:_anaplerotic_reactions,_PEP Phosphate_metabolism Maltose_and_Maltodextrin_Utilization Pentose_phosphate_pathway V−Type_ATP_synthase pVir_Plasmid_of_Campylobacter Deoxyribose_and_Deoxynucleoside_Catabolism Lactose_and_Galactose_Uptake_and_Utilization Experimental_−_Histidine_Degradation Methionine_Biosynthesis Control_of_cell_elongation_−_division_cycle_in_Bacilli Thioredoxin−disulfide_reductase Polyamine_Metabolism COG1399 ABC_transporter_dipeptide_(TC_3.A.1.5.2) YbbK DNA_repair,_bacterial_MutL−MutS_system Citrate_Metabolism,_Transport,_and_Regulation Heme,_hemin_uptake_and_utilization_systems_in_GramPositives Isoprenoid_Biosynthesis ABC_transporter_oligopeptide_(TC_3.A.1.5.1) Mannitol_Utilization At1g69340_At2g40600 Chorismate_Synthesis Glutathione−regulated_potassium−efflux_system_and_associated_functions Oxidative_stress Alanine_biosynthesis Trehalose_Uptake_and_Utilization At1g14345 L−ascorbate_utilization_(and_related_gene_clusters) Copper_homeostasis Choline_and_Betaine_Uptake_and_Betaine_Biosynthesis Glutathione:_Redox_cycle tRNA_processing DNA_repair,_bacterial_UvrD_and_related_helicases Polyhydroxybutyrate_metabolism COG0523 Adhesion_of_Campylobacter ZZ_gjo_need_homes Glycerol_and_Glycerol−3−phosphate_Uptake_and_Utilization Single−Rhodanese−domain_proteins Coenzyme_A_Biosynthesis Streptolysin_S_Biosynthesis_and_Transport Stringent_Response,_(p)ppGpp_metabolism At4g10620_At3g57180_At3g47450 Mannose_Metabolism Potassium_homeostasis Peptide_methionine_sulfoxide_reductase ABC_transporter_glutamine_(TC_3.A.1.3.2) At4g38090 Teichoic_and_lipoteichoic_acids_biosynthesis Conserved_gene_cluster_possibly_involved_in_RNA_metabolism Fructooligosaccharides(FOS)_and_Raffinose_Utilization Beta−Glucoside_Metabolism Polysaccharide_deacetylases RNA_processing_and_degradation,_bacterial Conserved_gene_cluster_associated_with_Met−tRNA_formyltransferase Transport_of_Zinc Glycine_and_Serine_Utilization ATP−dependent_Nuclease Two_cell_division_clusters_relating_to_chromosome_partitioning At5g48545_and_At3g56490_At1g31160 Pyruvate_metabolism_II:_acetyl−CoA,_acetogenesis_from_pyruvate ECF_class_transporters Queuosine−Archaeosine_Biosynthesis Listeria_Pathogenicity_Island_LIPI−1_extended Unspecified_monosaccharide_transport_cluster Beta−lactamase_cluster_in_Streptococcus SpeB−SpeF_extended_regulon Restriction−Modification_System CBSS−262719.3.peg.410 Cobalt−zinc−cadmium_resistance Transport_of_Manganese Streptococcal_Mga_Regulon Protein_degradation Phage_capsid_proteins CRISPRs NMPDR subsystems N−Acetyl−Galactosamine_and_Galactosamine_Utilization Streptococcus_pyogenes_recombinatorial_zone IbrA_and_IbrB:_co−activators_of_prophage_gene_expression Periplasmic_Stress_Response Sortase Cyanate_hydrolysis DNA_Repair_Base_Excision Listeria_surface_proteins:_Internalin−like_proteins Cell_envelope−associated_LytR−CpsA−Psr_transcriptional_attenuators Ribosome_activity_modulation Glutamine,_Glutamate,_Aspartate_and_Asparagine_Biosynthesis Programmed_frameshift rRNA_modification_Bacteria Alkylphosphonate_utilization Purine_Utilization Xanthine_Metabolism_in_Bacteria Proteasome_bacterial Thiamin_biosynthesis Coenzyme_B12_biosynthesis D−Galacturonate_and_D−Glucuronate_Utilization COG2509 YcfH At1g26220_At1g32070 Soluble_cytochromes_and_functionally_related_electron_carriers Multidrug_Resistance_Efflux_Pumps Glycine_cleavage_system YjeE Arginine_Biosynthesis Pyridoxin_(Vitamin_B6)_Biosynthesis Histidine_Degradation Signal_peptidase Glutaredoxins Copper_homeostasis:_copper_tolerance DNA_structural_proteins,_bacterial LMPTP_YfkJ_cluster tRNA_nucleotidyltransferase DNA_repair,_bacterial_RecFOR_pathway Anaerobic_respiratory_reductases CBSS−176280.1.peg.1561 Acetyl−CoA_fermentation_to_Butyrate tRNA_modification_Bacteria Sex_pheromones_in_Enterococcus_faecalis_and_other_Firmicutes RuvABC_plus_a_hypothetical Flavohaemoglobin Biotin_biosynthesis Methylglyoxal_Metabolism Cold_shock,_CspA_family_of_proteins DNA_repair,_bacterial_DinG_and_relatives Glycine_reductase,_sarcosine_reductase_and_betaine_reductase Bacterial_Cytoskeleton Flavodoxin Proline_Synthesis COG2302 Murein_hydrolase_regulation_and_cell_death Hemin_transport_system NusA−TFII_Cluster Nudix_proteins_(nucleoside_triphosphate_hydrolases) Iron_acquisition_in_Streptococcus Bacteriocin−like_peptides_Blp Yfa_cluster Sucrose_utilization At5g04520_AT1G06240 Entner−Doudoroff_Pathway Coenzyme_F420_synthesis Campylobacter_Iron_Metabolism Central_meta−cleavage_pathway_of_aromatic_compound_degradation Ribonuclease_H YaaA GroEL_GroES Inositol_catabolism
To determine which of the generated SRM assays targets homologous proteins in other GAS strains or other members of the Firmicutes phylum, all SRM assays (Supplementary Dataset 2) were mapped onto 75 selected genomes (see Supplementary Figure S2). (a) Black color represents SRM assay conservation in respective taxa. (b) The identity of functional proteins categories with transferable SRM assays were addressed by determining which NMPDR subsystems contained at least 10 conserved SRM assays in respective taxa, indicated by black color. Rows and columns of the heatmaps have been re-orded according to hierarchical clustering represented by the dendrograms. Respective taxonomic rank is indicated with colors. The heatmaps were generated with R programming language (http://www.r- project.org/). Supplementary Table S1 ⏐ Genome sequenced GAS strains used in this work.
PATRIC Genome Genome Name Serotype CDS† Publication‡ 28 Info Id 52 79812 Streptococcus pyogenes M1 GAS (SF370) M1 1919 11296296 31 7871 Streptococcus pyogenes MGAS5005 M1 1931 16088826 30 120482 Streptococcus pyogenes MGAS10270 M2 2024 16636287 53 110589 Streptococcus pyogenes SSI-1 M3 2009 12799345 54 96585 Streptococcus pyogenes MGAS315 M3 2010 12122206 30 25933 Streptococcus pyogenes MGAS10750 M4 2030 16636287 55 41547 Streptococcus pyogenes str. Manfredo M5 1935 17012393 56 30273 Streptococcus pyogenes MGAS10394 M6 1960 15272401 30 37061 Streptococcus pyogenes MGAS9429 M12 1893 16636287 30 133020 Streptococcus pyogenes MGAS2096 M12 1953 16636287 57 4396 Streptococcus pyogenes MGAS8232 M18 2007 11917108 58 35950 Streptococcus pyogenes MGAS6180 M28 1956 16088825 32 129711 Streptococcus pyogenes NZ131 M49 1876 18820018
† Coding sequences from PATRIC annotation source ‡ PUBMED identifier
Supplementary References 49. Tamura, K. & Nei, M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512–526 (1993). 50. Case, R. J. et al. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73, 278–288 (2007). 51. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739 (2011). 52. Ferretti, J. J. et al. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci USA 98, 4658–4663 (2001). 53. Nakagawa, I. et al. Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res 13, 1042–1055 (2003). 54. Beres, S. B. et al. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci USA 99, 10078–10083 (2002). 55. Holden, M. T. G. et al. Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo. J Bacteriol 189, 1473– 1477 (2007). 56. Banks, D. J. et al. Progress toward characterization of the group A Streptococcus metagenome: complete genome sequence of a macrolide-resistant serotype M6 strain. J Infect Dis 190, 727–738 (2004). 57. Smoot, J. C. et al. Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc Natl Acad Sci USA 99, 4668–4673 (2002). 58. Green, N. M. et al. Genome sequence of a serotype M28 strain of group a streptococcus: potential new insights into puerperal sepsis and bacterial disease specificity. J Infect Dis 192, 760–770 (2005).