Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis

Rhodococcus sp. 124 is a Gram-positive soil bacterium being developed for the manufacture of (-)cis-(1S,2R)-1-aminoindan-2-ol, a key precursor in the production of the HIV-1 protease inhibitor CrixivanTM, from the aromatic hydrocarbon indene. Rhodococcus sp. 124 was grown by batch fermentation in the presence of naphthalene and indene to measure changes in gene expression and aromatic hydrocarbon metabolism with DNA microarray technology. Genes were selected for microarray analysis based on functional annotation assignments made by the Consensus Annotation by Phylogeny Anchored Sequence Alignment (CAPASA) program, a high throughput system for automated functional annotation assignment of DNA sequence similarity search results. CAPASA was validated by comparison to several methods of annotation, and the agreement to other methods ranged from 75-94%. Microarray results were analyzed by the newly described method of trigonometric deconvolution, a mathematical system for the measurement of changes in gene expression across multiple growth conditions with a minimal number of hybridizations. The combined analysis of aromatic metabolism and gene expression reveal the differential expression of multiple polycyclic aromatic hydrocarbon dioxygenases in a substrate and growth phase dependent manner.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2004

Author dc:creator

• Parker, Jefferson A. (Jefferson Alexander), 1974-

Advisor dc:contributor.advisor

• Anthony J. Sinskey.

• Biology.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

en_US

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/28309

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/28309