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Table 2 SMR subclass member diversity within putative metabolite operons and their association to common metabolite ORF based on genomic loci surveys of sequenced Archaeal and Bacterial chromosomes.

From: Diversity and evolution of the small multidrug resistance protein family

    SMR association to the following operons
     Amino Acid Transport/Metabolism Multidrug Resistance Lipid Mtabolism
SMR Subclass Subclass Member Total number of Loci   Lys/Arg Trp/Tyr/Phe Other Amino Acids Polyamine (spe/cad/put) & Betaine Glyco-peptide & Poly-ketide β-lactam metabolism Sn-G3P Fatty Acid synthesis
SUG sugE           
Putative operons   118   lys trp/aro liv/ilv/pro put/spe/bet MFS/ABC/ecn/bleo tetR/pbp ugp/pls fab/acc
Frequency in operon/total surveyed loci     0.8% 4.2% 1.7%/0.8%/0.8% 0.8%/1.7%/0.8% 3.4%/2.5%/3.4%/0.8% 5.1%/0.8% 0.8%/2.5% 1.7%/0.8%
Frequency of occurrence in each locus (10 gene radius)     29.7% 20.3% 2.0% 5.1% 22.9% 23.7% 7.6% 17.8%
SMP emrE/smr           
Putative operons   92   lys tyr pro/his/met/cys put/bet/dpp ABC/bleo/hlx tetR/pbp glp fab/ech
Frequency in operon/total surveyed loci     1.1% 1.1% 1.1%/1.1%/1.1%/2.2% 1.1%/3.3%/1.1% 1.1%/1.1%/2.2% 8.7%/1.1% 3.3% 1.1%/2.2%
Frequency of occurrence in each locus (10 gene radius)     22.8% 14.1% 12.0% 14.1% 28.3% 10.9% 9.8% 22.8%
PSMR yvaE**           
Putative operons   16   --- --- pro --- MFS/ABC tetR --- acp/fab
Frequency in operon/total surveyed loci     --- --- 12.5% --- 6.3%/18.8% 1.1% --- 12.5%/6.3%
Frequency of occurrence in each locus (10 gene radius)     25.0%   18.8% --- 43.8% 12.5% 6.3% 18.8%
PSMR yvaD**           
Putative operons   7   arg --- --- --- --- tetR --- acp/fab
Frequency in operon/total surveyed loci     14.3% --- --- --- --- 14.3% --- 28.6%
Frequency of occurrence in each locus (10 gene radius)     14.3% --- --- --- --- 28.6% --- 42.9%
PSMR ydgE/ydgF           
Putative operons   22   lysR --- --- spe* --- --- --- ---
Frequency in operon/total surveyed loci     4.5% --- --- --- --- --- --- ---
Frequency of occurrence in each locus (10 gene radius)     54.5% --- --- 31.8% 22.7% --- --- 22.7%
PSMR ebrA/ebrB           
Putative operons   16   --- --- --- --- --- --- --- ---
Frequency in operon/total surveyed loci     --- --- --- --- --- --- --- ---
Frequency of occurrence in each locus (10 gene radius)     12.5% 6.3% --- 6.3% 31.3% 43.8% --- 50.0%
PSMR ykkC/ykkD           
Putative operons   9   --- aro liv spe MFS --- --- ---
Frequency in operon/total surveyed loci     --- 11.1% 11.1% 11.1% 11.1% --- --- ---
Frequency of occurrence in each locus (10 gene radius)     22.2% 55.6% 11.1% 11.1% 33.3% 33.3% 11.1% 44.4%
PSMR yvdR/yvdS 3   NA NA NA NA NA NA NA NA
Total loci   283          
    SMR association to the following operons
    Vitamin Metabolism Nucleotide Metabolism Horizontal Gene Transfer System
SMR Subclass Subclass Member Total number of Loci Vitamin (Vit.) B1, B2, & BB3 (thi, rib, nia) Vit. B7 & BB9 (bio/fol) Vit. B6 & BB12 (Pyd & Cob) Coenz. Q10 (Ubi) & F420 Pur Pyr Int/Tn/Mat Plasmid Phage genes
SUG sugE           
Putative operons   118 thi/nad fol --- ubi pur ctp tn/rve vap/kill ---
Frequency in operon/total surveyed loci    0.8/2.5% 0.8% --- 1.7% 4.2% 0.8% 2.5% 2.5% ---
Frequency of occurrence in each locus (10 gene radius)    7.6% 1.7% 2.5% 11.9% 22.0% 3.4% 21.2% 9.3% 5.9%
SMP emrE/smr           
Putative operons   92 thi/nad bio/fol cob --- pur --- tn/rve --- Pro-phage DLP12
Frequency in operon/total surveyed loci    1.1%/1.1% 1.1%/1.1% 2.2% --- 1.1% --- 3.3% --- 1.1%
Frequency of occurrence in each locus (10 gene radius)    17.4% 12.0% 3.3% 9.8% 8.7% 3.3% 14.1% 2.2% 4.3%
PSMR yvaE**           
Putative operons   16 --- --- --- --- --- --- --- --- ---
Frequency in operon/total surveyed loci    --- --- --- --- --- --- --- --- ---
Frequency of occurrence in each locus (10 gene radius)    --- 6.3% --- 25.0% --- --- 12.5% --- ---
PSMR yvaD**           
Putative operons   7 --- --- --- ubi pur --- --- --- ---
Frequency in operon/total surveyed loci    --- --- --- 28.6% 14.3% --- --- --- ---
Frequency of occurrence in each locus (10 gene radius)    --- 14.3% --- 42.9% 42.9% 28.6% 14.3% --- ---
PSMR ydgE/ydgF           
Putative operons   22 --- --- --- --- --- --- tn/rve tra/cop ---
Frequency in operon/total surveyed loci    --- --- --- --- --- --- 4.5% 9.1% ---
Frequency of occurrence in each locus (10 gene radius)    13.6% 18.2% --- --- 18.2% 4.5% 9.1% 9.1% 13.6%
PSMR ebrA/ebrB           
Putative operons   16 nad* fol --- --- pur --- --- --- ---
Frequency in operon/total surveyed loci    12.5% 6.3% --- --- 6.3% --- --- --- ---
Frequency of occurrence in each locus (10 gene radius)    18.8% 25.0% 12.5% 6.3% 25.0% --- 25.0% --- 6.3%
PSMR ykkC/ykkD           
Putative operons   9 rib bio --- --- pur pyr --- cdt ---
Frequency in operon/total surveyed loci    11.1% 11.1% --- --- 22.2% 11.1% --- 11.1% ---
Frequency of occurrence in each locus (10 gene radius)    22.2% 11.1% 11.1% --- 33.3% 11.1% 11.1% 11.1% ---
PSMR yvdR/yvdS 3 N/A N/A N/A N/A N/A N/A N/A N/A N/A
Total loci   283          
  1. * Indicates these SMR members have experimentally demonstrated transport involvement in the metabolite transport.
  2. ** Calculated value listed in table includes both isogenic gene occurances and gene pairs.
  3. Abreviations of genes listed in table: ABC ABC-type antimicrobial peptide transport system; aro aromatic amino acid biosynthesis; bet transport and biosynthesis/degradation of glycine betaines; bleo bleomycin resistance genes; bio involved in biotin (vitamin B7) metabolism; cdt plasmid encoded cytotoxin genes; cob involved in cobalamin vitamin B6 metabolism; dpp ABC-type dipeptide/oligopeptide/nickel transport system; fol involved in folate metabolism; glp utilization of glycerol and sn-glycerol 3-phosphate (sn-G3P); hlx hemolysin genes involved in host virulence; lysR lysine transcriptional regulator; liv/ile branched amino acid biosynthesis (val, ile, leu); met/pro/his/cys amino acid biosynthetic genes; MFS multidrug efflux major facillitator superfamily genes; nad involved in nicotine and nicotinamide metabolism; nag GlcNAc uptake and metabolism; nai (niacin) vitamin B3 metabolism; pbp penicillin binding proteins/cell wall biosynthesis proteins; pls involved in sn-glycerol-3-phosphate phsopholipid biosynthesis; put transport and biosynthesis/degradation of putrescine; pts phosphoenolpyruvate-dependent phosphotransferase system; pur involved in purine nucleotide biosynthesis; pyd (pyridoxine) vitamin B12 metabolism pyr involved in pyrimidine nucleotide biosynthesis; rib involved in riboflavin metabolism; spe transport and biosynthesis/degradation of spermidine; tetR tetracyclin resistance transcriptional regulator; thi (thiamin) vitamin B1 metabolism; tn/rve transposons and integron maturases; trp/tyr biosynthesis of tryptophan/tyrosine; ubi involved in ubiquinone (coenzyme Q10) biosynthesis; ugp uptake of sn-glycerol-3-phosphate and glycerophosphoryl diesters; vap/kill host plasmid virulence and toxin genes.