Table 1.

Predicted sizes of B. burgdorferi B31bdr paralog PCR amplicons and Southern blot restriction fragments

ParalogLocusLocus presence in B31 cloneaPCR primerbPCR amplicon size (bp)XbaI restriction fragment size (bp)
bdrK cp32-6+AF5718,650
bdrC/Mc cp32-2/7+++AF4753,048
bdrQ cp32-9++AF4429,368
bdrG cp32-4+++AF2893,074
bdrA cp32-1+++AG5195,788
bdrE cp32-3++AG4778,499
bdrO cp32-8+AG4655,946
bdrV lp56AG4237,927
bdrW lp56BH5819,869
bdrF cp32-3++BH4945,257
bdrD/Nc cp32-2/7+++BH4734,762
bdrP cp32-8+BH4404,743
bdrR cp32-9++BH4404,717
bdrH cp32-4+++BH3864,659
bdrT lp28-2+BI6654,165
bdrU lp28-3++BI5348,841
bdrSd lp28-1++BId 450d 1,422
bdrIe cp32-5NDf +NDNDNDND
bdrJe cp32-5ND+NDNDNDND
  • a +, presence; −, absence. For B31-ATCC and B313, plasmid profiles were determined independently in a previous study using plasmid-specific probes and PCR primers (40). The plasmid profile of B31-5A3 was deduced from the observedbdr PCR amplicon sizes.

  • b As described in the legend to Fig. 1A.

  • c B31-ATCC and B313 carry cp32-2 and not cp32-7 (40). bdrC and bdrD sequences are not in the database, since cp32-2 has not been sequenced in its entirety. The available sequences, however, indicate that cp32-2 and cp32-7 are almost identical (and in fact may be incompatible [28]). We therefore assume that their bdrparalogs are very similar if not identical.

  • d bdrS is considered a nonfunctional pseudogene, since it does not possess a consensus Shine-Dalgarno ribosomal binding site upstream of the start codon (9, 13,40). bdrS and bdrY, a pseudogene on lp38, were not considered at the point of primer design. Although primer B-fwd is complementary to the bdrS locus, I-rev is complementary for only 7 bases at the 3′ end, making PCR amplification unlikely under the conditions used. bdrS is, however, detected by Southern hybridization (Fig. 2). bdrY and a distant relative of the bdr family, bdrX on lp36, are neither amplified by PCR nor detected by Southern hybridizations.

  • e bdrM and bdrN sequences are not in the database, since cp32-5 was not sequenced in its entirety. Amplicon and fragment sizes can therefore not be predicted. However, PCR amplicons and RFLP fragments likely corresponding to the cp32-5 paralogs can be seen in B31-ATCC (see the text and Fig. 1B and2).

  • f ND, not done.