TABLE 2.
Overview of putative sRNAs in B. burgdorferi identified with the different methods used
| Method and genetic materiala | Locationb | Coordinatesc | Testingd by:
|
Test result | Commentg | |
|---|---|---|---|---|---|---|
| PCRe | Oligonucleotidef | |||||
| Homology approach | ||||||
| IS063 | cp26 | 11741-12013 | T | NT | − | |
| Comparative genomics approach | ||||||
| BB0260-BB0261 | Chromosome | 273648-273853 | NT | T | − | |
| BB0564-BB0565 | Chromosome | 577188-577394 | T | NT | − | Same as region complementary to rpoS |
| BBD08-BBD09 | lp17 | 4806-5057 | T | T | − | |
| BBE02-BBE03 | lp25 | 4157-4418 | T | NT | − | |
| BBP27-BBP28 | cp32-1 | 17061-17231 | T | NT | + | Untranslated mRNA from BBP27 or BBP28 |
| BBK02.1-BBK05 | lp36 | 3771-4901 | NT | T | − | |
| BBK14-BBK15 | lp36 | 9017-9372 | T | T | + | tmRNA4 located within this region |
| BBK31-BBK32 | lp36 | 20170-20388 | T | NT | + | Large band, probably untranslated mRNA of adjacent gene |
| BBI24-BBI25 | lp28-4 | 14442-15210 | T | NT | − | |
| BBH13-BBH14 | lp28-3 | 10517-10817 | T | NT | − | |
| BBL35-BBL36 | cp32-8 | 22692-23305 | T | NT | − | rnpB1 located within this region |
| BBQ80-BBQ81 | lp56 | 48627-49046 | T | NT | − | |
| Ortholog-based search strategy | ||||||
| BB0402-BB0403 | Chromosome | 415794-415845 | T | NT | − | |
| BB0564-BB0565 | Chromosome | 577188-577394 | T | NT | − | Complementary to rpoS upstream region |
| BB0577-BB0578 | Chromosome | 590936-591187 | T | T | + | |
| BB0607-BB0608 | Chromosome | 634465-634580 | T | NT | − | |
| Annotation-based search strategy | ||||||
| srp | Chromosome | 482285-482439 | T | NT | + | Overlaps with tRNA_Ser-3 |
| rnpB1 | cp32-8 | 22959-23354 | T | NT | − | |
| rnpB2 | Chromosome | 750818-751169 | T | T | + | Previously annotated rnpB |
| rnpB3 | lp21 | 4744-5129 | NT | T | + | |
| rnpB4 | lp21 | 5431-5816 | NT | T | + | |
| rnpB5 | lp21 | 13049-13432 | NT | T | + | 376 additional homologs on lp21 |
| rnpB6 | lp21 | 14051-14436 | NT | T | + | |
| rnpB7 | lp28-3 | 26447-26836 | T | NT | − | |
| rnpB8 | lp38 | 29152-29520 | T | NT | − | |
| rnpB9 | lp28-4 | 2288-2668 | T | NT | − | |
| rnpB10 | lp28-4 | 9445-9849 | T | NT | − | |
| tmRNA1 | cp32-9 | 28239-28454 | T | T | − | |
| tmRNA2 | lp17 | 542-886 | T | T | − | Two copies inside BBQ88 and BBH02 |
| tmRNA3 | Chromosome | 46691-47049 | T | T | + | Previously annotated tmRNA |
| tmRNA4 | lp36 | 9099-9314 | T | T | + | Same as BBK14-BBK15 |
a
Homologous or annotated sRNA or intergenic region as described in the text.
b
Designations are of plasmids.
c
According to http://www.tigr.org.
d
Testing for presence of sRNA with Northern blotting experiments. T, tested; NT, not tested.
e
32P-labeled PCR fragments comprising the specific sRNA as intergenic region.
f
32P-labeled oligonucleotides showing complementarity to the specific sRNA or intergenic region.
g
Specific comments relative to extra copies, homologs, complementary regions, etc., of particular sRNAs.