TY - GEN
T1 - A genomic level analysis of alcohol producing pathways of Zymomonas mobilis
AU - Ranjan, A. P.
AU - Prasad, C. S.
AU - Agarwal, G. P.
AU - Ramachandran, S.
PY - 2006
Y1 - 2006
N2 - The need of alternative energy source has intensified the efforts to produce bio-ethanol and study the efficiency of its industrial processes using microorganisms. Our work intends to study and analyze the alcohol producing pathways of bacteria, signifying the importance of regulatory sequence, on genomic level. Zymomonas mobilis, considered as a potent future organism for alcohol production, was chosen for this study. The pathway was analysed on the basis of promoter regulation, a key factor for synthesis of enzymes. It was found that the second TA base pair could be central to the binding of TATA box-binding protein (TBP) to TATA box. The length of the TATA box, based on analysis of bending stiffness energy ratio of left sequence to right sequence of central base pair, is proposed to be 10. A mathematical model for the prediction of promoter strength was developed based on bending stiffness energy of flanking sequence of TATA box. The relative promoter strengths of all the genes, of the enzymes that take part in alcohol production, were predicted using this model. Results were analyzed and the predictions of the model for the bacteria, Zymomonas mobilis, were supported by available experimental literature.
AB - The need of alternative energy source has intensified the efforts to produce bio-ethanol and study the efficiency of its industrial processes using microorganisms. Our work intends to study and analyze the alcohol producing pathways of bacteria, signifying the importance of regulatory sequence, on genomic level. Zymomonas mobilis, considered as a potent future organism for alcohol production, was chosen for this study. The pathway was analysed on the basis of promoter regulation, a key factor for synthesis of enzymes. It was found that the second TA base pair could be central to the binding of TATA box-binding protein (TBP) to TATA box. The length of the TATA box, based on analysis of bending stiffness energy ratio of left sequence to right sequence of central base pair, is proposed to be 10. A mathematical model for the prediction of promoter strength was developed based on bending stiffness energy of flanking sequence of TATA box. The relative promoter strengths of all the genes, of the enzymes that take part in alcohol production, were predicted using this model. Results were analyzed and the predictions of the model for the bacteria, Zymomonas mobilis, were supported by available experimental literature.
KW - Bending stiffness energy
KW - Relative strength
KW - TATA box
UR - http://www.scopus.com/inward/record.url?scp=46249108805&partnerID=8YFLogxK
U2 - 10.1109/ICBPE.2006.348638
DO - 10.1109/ICBPE.2006.348638
M3 - Conference contribution
AN - SCOPUS:46249108805
SN - 8190426249
SN - 9788190426244
T3 - ICBPE 2006 - Proceedings of the 2006 International Conference on Biomedical and Pharmaceutical Engineering
SP - 471
EP - 474
BT - ICBPE 2006 - Proceedings of the 2006 International Conference on Biomedical and Pharmaceutical Engineering
Y2 - 11 December 2006 through 14 December 2006
ER -