Skip to main content

Table 1 List of genes prioritized for functional evaluation of their role in adherence

From: Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells

Fold increase
   TIGR4 adherent/ G54 adherent/ Conserved §(Avg. BLASTP Id.) Predicted surface exposure  
Locus Annotation control control Reason for selection
SP_0018 Conserved hypothetical protein 1.7 3.3 yes (98.4%) no Ratio index ≥ 1.5
SP_0024 Hypothetical protein 2.6 0.9 yes (98.1%) no Up-regulated in the more adherent strain
SP_0025 Hypothetical protein 2.7 1.1 yes (95.7%) yes (TmHMM) Up-regulated in the more adherent strain
SP_0026 Hypothetical protein 2.2 X yes (78.8%) yes (SP, TmHMM, AR) Up-regulated in the more adherent strain
SP_0099 Hypothetical protein 2.2 1.2 yes (98.7%) yes (TmHMM, AR) Up-regulated in the more adherent strain
SP_0100 Conserved hypothetical protein 2.2 1.4 yes (99.3%) no Up-regulated in the more adherent strain
SP_0101 Putative transporter 1.4 1.9 yes (99.1%) yes (SP, TmHMM, AR) Co-opted as part of an operon
SP_0415 Enoyl-CoA hydratase 1.5 0.4 yes (99.3%) no Co-opted as part of an operon
SP_0416 Transcriptional regulator, marR family 1.7 X yes (99.4%) no Co-opted as part of an operon
SP_0417 3-oxoacyl-(acyl-carrier-protein) synthase III 1.6 1.0 yes (99.6%) no Co-opted as part of an operon
SP_0418 Acyl carrier protein 1.8 0.9 yes (99.8%) no Ratio index ≥ 1.5
SP_0419 Enoyl-(acyl-carrier-protein) reductase 1.4 0.4 yes (99.4%) no Co-opted as part of an operon
SP_0420 Malonyl CoA-acyl carrier protein transacylase 1.9 0.6 yes (99.5%) no Co-opted as part of an operon
SP_0421 3-oxoacyl-[acyl-carrier protein] reductase 2.7 0.7 yes (99.4%) yes (SP) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0422 3-oxoacyl-(acyl-carrier-protein) synthase II 2.4 0.7 yes (99.8%) yes (SP) Up-regulated in the more adherent strain
SP_0423* Acetyl-CoA carboxylase, bitoin carboxyl carrier protein 3.6 0.9 yes (99.2%) no Up-regulated in the more adherent strain
SP_0424* Similar to hydroxymyristoyl-(acyl carrier protein) dehydratase 3.6 1.0 yes (99.3%) no Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0425* Acetyl-CoA carboxylase, biotin carboxylase 4.2 1.1 yes (99.9%) no Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0426* Acetyl-CoA carboxylase, carboxyl transferase subunit beta 5.5 1.4 yes (99.9%) no Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0427* Acetyl-CoA carboxylase, carboxyl transferase subunit alpha 2.5 1.6 yes (99.9%) no Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0462* Transcriptional regulator, putative 2.1 NA no (90.5%) yes (SP, TmHMM, BCE) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0463* Cell wall surface anchor family protein 2.6 NA no (71.3%) yes (SP, TmHMM, AR, LPxTG) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0464* Cell wall surface anchor family protein 1.9 NA no (98.3%) yes (SP, TmHMM, AR, LPxTG) Ratio index ≥ 1.5
SP_0465* Cell wall surface anchor family protein 2.1 NA no no Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0466* Sortase, putative 2.0 NA no (98.6%) yes (TmHMM) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0467* Sortase, putative 2.3 NA no (96.0%) yes (TmHMM) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0468* Sortase, putative 2.2 NA no (95.8%) yes (SP, TmHMM, AR, LAS) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0617 Conserved domain protein 1.5 3.6 yes (97.8%) yes (SP, TmHMM) Ratio index ≥ 1.5
SP_0737* Sodium-dependent transporter 2.4 X yes (96.3%) yes (SP, TmHMM) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0738* Conserved domain protein 2.0 X yes (99.2%) no Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_0783* Conserved hypothetical protein 1.5 1.6 yes (96.3%) yes (SP, TmHMM, AR) Ratio index ≥ 1.5
SP_0879 Hypothetical protein 2 3.9 yes (99.2%) yes (SP, BCE, AR) Up-regulated in both strains & Ratio index ≥ 1.5
SP_1003 Conserved domain protein 0.8 3.9 yes (73.3%) yes (SP, BCE, AR) Up-regulated in the less adherent strain and downregulated in more adherent strain
SP_1127 Hypothetical protein 1.4 1.6 yes (98.6%) no Ratio index ≥ 1.5
SP_1256 Conserved hypothetical protein X 1.9 yes (96.7%) yes (TmHMM) Ratio index ≥ 1.5
SP_1270* Alcohol dehydrogenase, zinc containing 3.1 3.6 yes (99.1%) no Up-regulated in both strains
SP_1294* Crcb protein downstream of a putative chorismate mutase 2.0 1.1 yes (98.6%) yes (SP, TmHMM) Up-regulated in the more adherent strain
SP_1295* Crcb protein downstream of a putative chorismate mutase 1.8 1.1 yes (98.1%) yes (TmHMM) Co-opted as part of an operon
SP_1600 Putative membrane protein 2.0 2.0 yes (99.2%) yes (SP, TmHMM) Up-regulated in both strains
SP_1601 Conserved hypothetical protein 2.0 2.0 yes (99.0%) yes (SP, TmHMM) Up-regulated in both strains & Ratio index ≥ 1.5
SP_1602 Required for expression of the phosphonate utilization phenotype in E. coli 2.5 2.1 yes (99.0%) no Up-regulated in both strains & Ratio index ≥ 1.5
SP_1758* Glycosyl transferases in the psrP-secY2A2 pathogenicity island 2.2 X no (86.3%) no Up-regulated in the more adherent strain
SP_1855* Dehydrogenase 6.0 1.0 yes (99.7%) no Up-regulated in the more adherent strain
SP_1856 Transcriptional regulator, merR family 7.6 1.1 yes (99.7%) no Up-regulated in the more adherent strain
SP_1857 Cation efflux system protein 14.4 X yes (98.1%) yes (SP, TmHMM) Up-regulated in the more adherent strain
SP_1922* Conserved hypothetical protein 2.3 1.0 yes (99.8%) yes (BCE) Up-regulated in the more adherent strain & Ratio index ≥ 1.5
SP_1923 Pneumolysin 3.0 0.5 yes (99.8%) no Up-regulated in the more adherent strain
SP_1924 Hypothetical protein 2.6 0.4 yes (99.0%) no Up-regulated in the more adherent strain
SP_1925 Hypothetical protein 2.3 0.4 Yes (98.2) no Up-regulated in the more adherent strain
  1. *Loci selected for knockout experiments, either individually or as an entire operon.
  2. §Conserved = present in all pneumococcal loaded in the Strepneumo Sybil system [24]; Avg. BLASTP Id. = % of the characters in the alignment that match the conserved sequence, including gaps.
  3. SP = signal peptide; TmHMM = trans-membrane spans; BCE = B-cell epitopes from BepiPred; AR = antigenic regions from EMBOSS antigenic; LPxTG = proteins covalently linked to peptidoglycan; LAS = lipoprotein attachment site.