Table 1.
List of B. burgdorferi Genes, of Which Transcriptional Activity Was Assessed in Heart Base, Ventricular Muscle, Tibiotarsal Joint, and Quadriceps Muscle of Immunocompetent C3H and Immunodeficient C3H-scid Mice During Early (2 Weeks) and Late (2 Months) Infectiona
| Annotation | Accession number | N40 gene symbol | N40 gene location | Forward primer | Reverse primer | Probe |
|---|---|---|---|---|---|---|
| 16 ribosomal RNA (16S rRNA) | CP002228.1 | BBUN40-16SE | Ribosome | GCTTCGCTTGTAGATGAGTCTGC | TTCCAGTGTGACCGTTCACC | TACCAAGGCAATGATAAGTA |
| Acetate kinase (ackA) | CP002228.1 | BBUN40_0622 | Chromosome | GAAGCGGTGATATAGACCCATCA | AATTCCCAGTATGCCGCTTTC | TGATGAGCa |
| Alanin racemase (alr) | CP002228.1 | BBUN40_0158 | Chromosome | CCATACTTCTAATTCGGGACACATT | GCGATTGACAGTAACCGTAAAGAATA | CAATTTAATATGGTAAGACCGGG |
| Acriflavine resistance protein (acrB) | CP002228.1 | BBUN40_0140 | Chromosome | TAAGCCTTGGATTTACAAGTTCGG | CCTTCCATTAGTGGCAATGCTT | CTCCACCAa |
| Basic membrane protein A (bmpA) | CP0022281.1 | BBUN40_0383 | Chromosome | GGTAGAAGCGTTGCAACTAGAATG | ATGTAATGCCCAGAACCAAGTTC | ACATTATTCATCATGCTGCAGGCCTTGG |
| Basic membrane protein B (bmpB) | CP0022281.1 | BBUN40_0382 | Chromosome | CGGTATTTTGTTGACTTCTTGCTTTAG | TCGTCAAGAACACCATCTACCAA | AGAAATGGAATAGAATCTAG |
| Basic membrane protein C (bmpC) | CP0022281.1 | BBUN40_0384 | Chromosome | AAGGGTGGAATTATTATTGATCGG | CCTATTGTTTAAAACATCGGGATCC | GGAAGGAGa |
| Basic membrane protein D (bmpD) | CP0022281.1 | BBUN40_0385 | Chromosome | GATACTTTGCGTCGAAGGCTTC | GTTTGCATACTTAGCACCAGCTTC | TGGAGGAGa |
| Cell division protein FtsZ | CP002228.1 | BBUN40_0299 | Chromosome | GATATGGTGTTTATTACTGCTGGTATGG | CCTGCTCAGCAAGTCTCAACTTC | CAGCTCCAGTTATTGCGCAAGTTGCA |
| Colicin V production protein (colV) | DQ662922 | BBUN40_0766 | Chromosome | TAGCGGATTTGCTGAAGTTTTTG | GGTTCAACAAACCTTCTAAATTCTTCAG | TCCTGCTGa |
| Flagellin B (flaB) | CP002228.1 | BBUN40_0147 | Chromosome | TGCAGCTAATGTTGCAAATCTTTTTTC | GCAGGTGCTGGCTGTTGA | AAACTGCTCAGGCTGCACCGGTTC |
| Glyceraldehyde 3-phosphate dehydrogenase (gapDH) | CP002228.1 | BBUN40_0057 | Chromosome | GCAAAGCTTGGAATTGATGTTG | TCTCGTCTTTAGCGGGAACTGT | CTGGGGCTa |
| Glycerol-3-phosphate dehydrogenase (glpA) | CP002228.1 | BBUN40_0243 | Chromosome | GTTTGTGGAAGCACTGACATTCC | CAATCTCTTCTTCAAATCTTTTGGG | AGAAGAAGAa |
| Glycosaminoglycan-binding protein (bgp, pfs-2) | CP002228.1 | BBUN40_0588 | Chromosome | TGTCATTAATTCTGGCGTTGCT | CACCACCACATCTCCCACTTTAATA | TGGCGTTGTTAGTGCTAA |
| Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (relA/spot) | CP002228.1 | BBUN40_0198 | Chromosome | TGGAGAGCCTTACATTATTCACCC | AAGTACGTCATGCAGTAGTCCAGC | TTCTTGCCa |
| Membrane-associated protein P66 | CP002228.1 | BBUN40_0603 | Chromosome | CTGTAATTGCAGAAACACCTTTTGA | TGATGAATTATTGAATGTCTCGTTCCC | CAGGAGCCa |
| Membrane fusion protein (mtrc) | CP002228.1 | BBUN40_0141 | Chromosome | TCTTGAAGGATCAAGAGTTGCAAC | CGCTGTGGGCAAAATAACTTC | GCTCCAAGa |
| Outer membrane efflux protein | CP002228.1 | BBUN40_0142 | Chromosome | TTGCGCTTTCATATTCCAACAT | CCTTCTGCTTTGAGTGAGCTTG | CCCAACTCCAAACCCAAAACCCCA |
| Outer membrane protein P13 | CP002228.1 | BBUN40_0034 | Chromosome | AATGGTGCGTTTGGGATGA | CAAAGGAGCCTATTCCAAACCC | TGCTGGAGa |
| Outer membrane spanning protein (oms38) | CP002228.1 | BBUN40__0418 | Chromosome | CACCATTGGCATACTTTATGAAG | GAAGGCCAAGTGTTAAAGGTTTGA | GGCAAAGAa |
| Queuine tRNA-ribosyltransferase (tgt) | EF537570 | BBUN40_0809 | Chromosome | CATTTGCAGTTCTTATGGGATTGA | GCTGCTAGCCCAATTGGTTG | GAAGCCAAa |
| Periplasmic oligopeptide-binding protein (oppA-2) | CP002228.1 | BBUN40_0329 | Chromosome | AACGAAGAATGGACAACATACTTAAACA | AATGTCAAAGGATCAGCATAATCG | ATCCATCCTGCTCTTGCTATTTCATAATTTCCATTT |
| Response regulatory protein (rrp-1) | FJ643425 | BBUN40_0419 | Chromosome | CACAGATGCTCAGCTTGAAGGA | GTAAGCCCATCAATTCTAGACAAGC | TGGTGGAGa |
| Recombinase A (recA) | NC_001318 | BBUN40_0131 | Chromosome | GGGCTCAAGCGATGATGTTATT | CCAGCTTCTCTTGAAATACCTTTCC | CTCCACCTa |
| S2 lipoprotein | CP002228.1 | BBUN40_0158 | Chromosome | CATATTAATGCTGAGTTGCGCTTT | TGGTTTGCCAGTATTGCTGTCT | AGAAACCACAATCTGTACATC |
| Exported protein A(eppA) | CP002231.1 | BBUN40_C05 | cp9 | CAAAGCGTGTTCCAGAAATTAGG | AGCAGGACCCCTAAAGCAAAC | TGATATTGTGGGTTATCTG |
| Outer surface protein C (ospC) | CP002239.1 | BBUN40_B19 | cp26 | TGTTAAAGGGCCTAATCTTACAGAAATAA | TACCAATAGCTTTGGTAGCAAGTTCAT | TACAGAATCTAACGCAGTTGTTCTGGCCGT |
| OspE related gene 23 (erp23) | CP002235.1 | BBUN40_R18 | cp32-4 | GTGGTGTTGGAGTGCAAGCTT | ACTGCCGCCATTAGAATAACTTACA | AGTGTGCCAATGAAT |
| OspE related gene 24 (erp24) | CP002235.1 | BBUN40_R19 | cp32-4 | CTTCAAATGGTCCAAAAGTAGATGAAG | GACTATTATTAGGATCATCACCCTGCA | AGAAGAAGAa |
| OspE related protein 25 (erp25) | AY142085 | BBUN40_V37 | cp32-5 | GGTTTTGCGATGATAAGTTCTTGC | TCGGCTTGCATTAATTCTTCAAC | TTGGTGGTa |
| Outer surface protein E (ospE) | CP002229.1 | BBUN40_026 | cp32-7 | TGTTTATGCTGTTTTTATACTTATAGGTGC | TGACTCACCACTACTTTGCTCATCA | TGCAAGATTCATACTTCAT |
| OspE related gene 22 (erp22) | CP002242.1 | BBUN40_N45 | cp32-9 | GGAAGAAGCTAGGGCTAAAGCAG | CTTCTGCTCCTATGCTAGTTTGACC | AGAAGAAGAa |
| Protein 21 (p21) | CP002242.1 | BBUN40_N44 | cp32-9 | GGAAGACTTAGGAACTTTGGTTGTAAG | GCAGAGTATCCCTTCCCAACAT | AGATGGTATTGATACAGGGTTA |
| OspE related protein 26 (erp26) | AY142087 | BBUN40_Q42 | cp32-10 | CGCCTCAAATGGTCCAACA | CATCGCCCTGCATTAATTCTTC | AGAAGAAGAa |
| P23-T2, conserved hypothetical protein | CP002240.1 | BBUN40_Q32 | cp32-10 | AGATAAGAAATACACGCAACAAAACATAC | CTTAGTGTAGTGGGAGCTAGACCATTC | CTACTGCTTTAACGAAAAT |
| OspE related protein 27 (erp27) | AY142088 | BBUN40_X36 | cp32-12 | AAGAGCAGATTGGTAGTGCTAGTGG | ATACCAAGCCCTAATGAATTAACACA | ATTGGACTGCAGGCTT |
| Borrelia persistence in ticks (bptA) | AY894345 | BBUN40_E05 | lp25 | TTGAAGATAATGTTGTTATCGATGAAATC | CTGCACGATAACCTGTCGCTT | CAGCTTATAATTCCTGAGCTT |
| Arthritis related protein (arp) | DQ903071 | BBUN40_Y16 | lp28-5 | CTTCGCCCCATGTATTGGAT | ATCGGGAAAAGAAGTTGAAGAAAA | TCCGGGATTATTACCGCTT |
| Fibronectin-binding protein (fbp) | CP002230.1 | BBUN40_K30 | lp36 | AACAACAAGATGAATATAAAGGGATGACT | TTTGGCCTTAAATCAGAATCTATAGTAAGA | TCACCACTTTCACCGCTAAGGGAATTTAAACT |
| Outer surface protein VlsE | CP002230.1 | BBUN40_K37 | lp36 | TGATATGAAGAAGAAGGATAAGGTTGCT | TTTAGTACATCCTCCTTCTTACCAACAG | AGTAACCGAAAACTTCCCATCTTTAGCCAA |
| Complement regulator acquiring protein 1 (crasp1) | CP001651.1 | BBUN40_A68 | lp54 | CCCCGGATTGGTGATTTTT | CATGCGCACCTTTTAGCAAA | CTTAGTGTTTGCATTTGC |
| Decorin binding protein A (dbpA) | CP001651.1 | BBUN40_A24 | lp54 | GATAACAATGTAAATTTTGCTGCCTTT | GTAGCTCGCACTTTTGCTTCAAG | GTGAAACAGGTAGCAAGGTATCAGAAAATTCAT |
| Outer surface protein A (ospA) | CP001651.1 | BBUN40_A15 | lp54 | TGAAGGCGTAAAAGCTGACAAAA | TTCTGTTGATGACTTGTCTTTGGAA | CAATTTCTGACGATCTAGGTCAAACCACACTTGA |
a
Locked nucleic acid (LNA) probe (Roche, Pleasanton, CA).