Regulated Operon: ctsR-mcsAB-clpC-radA-yacK

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
ctsR yacG + 101446..101910 transcriptional regulator COG4463 ctsR-BAC ctsR-STA ctsR-STR  
mcsA yacH + 101924..102481
COG3880  
mcsB yacI + 102481..103572
COG3869  
clpC mecB + 103569..106001 class III stress response-related ATPase COG0542 clpC-BAC clpC-STA  
radA sms, yacJ + 106093..107469 DNA repair protein homolog COG1066 radA-BAC  
yacK
+ 107473..108555
COG1623  

Operon evidence: Northern blotting (7.0 kb transcript) and S1 nuclease mapping of the 3' end
Reference: Kruger E, et al. (1996)
Comments: A ctsR-mcsAB-clpC transcript and various transcripts in the radA-yacKLMN region are listed in BSORF. The 3' nuclease mapping showed two weak termination signals in the AT-rich region at the end of a proposed terminator structure eight base pairs downstream of the stop codon (i.e., in the TTAAAA region in the left arm of the indicated stem-loop). However, mfold cannot detect such a stem-loop structure. Northern blotting results in BSORF show a ctsR-mcsAB-clpC transcript.

Promoters

Binding
factor		 Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
CtsR Negative +1:+29 101406..101434 AAAGTCAAATATAGTCAAAGTCAGTAAAG Derre I, et al. (1999): GS FT
SigA Promoter -43:+9 101363..101414 CGAGAAAGTTGAAAATTCTCGAGAAACGGCTTATAGTAAGATTAAAGTCAAA Kruger E, et al. (1996): NB PE
SigB Promoter -46:+6 101311..101362 ATCAGCAATCAGGTTTTGTGGACCGGGAAAATGGAAATAATGAAGGATAGAG Kruger E, et al. (1996): NB PE

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]		 Downstream of
TAAAACCTTATGAATACGGGTATATTAATGTTGGTTTTTGTTTATTCTG
     >>>>>>>>>>>      <<<<<<<<<<<<
108568..108596
13..41
-4.4
 yacK

Overview



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