Regulated Operon: ypuE-ribDEAHT

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
ypuE
- 2430519..2430671

 
ribD ribG - 2429452..2430537 riboflavin-specific deaminase COG1985 ribD-STA ribG-BAC ribG-BAC  
ribE ribB - 2428794..2429441 riboflavin synthase (alpha subunit) COG0307  
ribA
- 2427583..2428779 GTP cyclohydrolase II and 3,4-dihydroxy-2-butanone 4-phosphate synthase COG0807 ribA-BAC ribA-STA  
ribH
- 2427086..2427550 riboflavin synthase (beta subunit) COG0054 ribH-BAC-1 ribH-BAC-2 ribH-STA  
ribT ribD - 2426599..2426973 reductase
ribD-STA ribG-BAC  

Operon evidence: Northern blotting (4.3 kb transcript); nuclease protection mapping of the 5' and 3' end
Reference: Mironov VN, et al. (1990), Azevedo V, et al. (1993), Mironov VN, et al. (1994), Perkins JB, et al., Mironov AS, et al. (2002), Genbank L09228
Comments: The 3' end of the mRNA was mapped 47 bp downstream of ribT in a T-rich region. Internal promoters in front of ribA and ribT, leading to a 2.4 kb and a 0.4 kb transcript. The original papers do not mention the existence of the ypuE gene, which partly overlaps ribD. The promoter site that was found experimentally for ribD lies upstream of ypuE. Azevedo also finds a 0.16 kb ypuE-specific transcript. Just upstream of ribD is a putative terminator/antiterminator structure. Binding of flavin mononucleotide or flavin adenine dinucleotide to the rfn (riboflavin) box favor transcriptional termination.


Promoters

Binding
factor
Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
SigA Promoter -43:+9 2430822..2430873 TATTTCATTGCGTACTTTAAAAAGGATCGCTATAATAACCAATAAGGACAAA Mironov VN, et al. (1994): NB S1
Perkins JB, et al. (1999): RG NB

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]
Downstream of
TAAAATACCTAAAGCCCCGAATTTTTTATAAATTCGGGGCTTTTTTGACGGTAAA
             >>>>>>>>>>>     <<<<<<<<<<<
2430577..2430603
-84..-58
-19.6
ypuE
ATTAAGCAGAGGCTGTGATCAGTCTCTGCTTTTTTTTCTGCGTT
     >>>>>>>>>>    <<<<<<<<<<
2426575..2426598
1..24
-17.0
ribT

Overview



Upper Region






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