Regulated Operon: rtpA-ycbK

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
rtpLP
+ 277098..277127 rtpA leader peptide
 
yczA rtpA + 277151..277312

 
ycbK
+ 277333..278271
COG0697  

Operon evidence: Genome analysis; primer extension of the downstream ycbK gene
Reference: Sarsero JP, et al. (2000)
Comments: Northern blotting results in BSORF show various transcripts in the rtpA-ycbK region. Sarsero et al. suggest that rtpA-ycbK may be part of a longer operon, since no clear terminator was found downstream of ycbK. Binding of uncharged tRNA-Trp (TrnD-Trp) to the T-box sequence promotes readthrough at the terminator structure upstream of rtpA. The tRNA anticodon binds to the UGG codon in the sequence GAAUGGGCU in the rtpA leader mRNA. RtpA is the anti-TRAP protein AT, which binds to and inactivates TRAP. Translation of the leader peptide rtpLP, which contains three consecutive Trp codons, regulates AT synthesis. Binding of the mtrB product (TRAP) causes translational attenuation of ycbK.

Promoters

Binding
factor		 Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
SigA Promoter -40:+5 276749..276793 AGAATTGACTTCGTTTCATGAACCGAGTATTATAAACTCTACAAA Sarsero JP, et al. (2000): PE
TrnD-Trp Positive ND 277018..277039 TAATAAAGGTGGTACCGCGAGA Sarsero JP, et al. (2000): DB SDM, RNA dot blot analysis
MtrB Negative ND 277307..277365 AAGTAAAGGAGAAAAGCTGAGCTGAGATGAGAGCAGAAGAGCAGAGTAAGATTCGTGAG Sarsero JP, et al. (2000): RG DB DP
Yakhnin H, et al. (2006): RG GS FT, toeprint

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]		 Downstream of
TTACAATAAGTGTAATTACGTGTGTGTTTTTTGATTTTGTA
     >>>>>>>    <<<<<<<<<
278304..278323
33..52
-2.7
 ycbK
TACCGCGAGACCCTCGTCCTTTGCATAGGACGGGGGTTTTTTGTGTTTCTT
          >>>>>>>>>>      <<<<<<<<<<
277040..277065
-87..-62
-19.5
 rtpLP

Overview



Upper Region
Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2006
Contact: Kenta Nakai