A model system of gene-enzyme nomenclature in the genome era applied to aromatic biosynthesis

Background: The accurate annotation of functional roles for newly sequenced genes of genomes is not a simple matter. Function is, of course, related to amino-acid sequence and to domain structure but not always in straightforward ways. Even where given functional roles have been identified experimentally, the application of an uneven and erratic nomenclature has generated confusion on the part of annotators and has produced errors that tend to become progressively compounded in database repositories. Results: The pathway that is deployed in nature for aromatic biosynthesis exemplifies an accumulation of chaotic nomenclature and a variety of annotation dilemmas. We view this pathway as one that is sufficiently complex to pose most of the common problems, and yet is one that at the same time is of a manageable size. A set of guidelines has been developed for naming genes of aromatic-pathway biosynthesis and the corresponding gene products, and we suggest that these can be generalized for application to other metabolic pathways. Conclusion: A system of nomenclature for aromatic biosynthesis is presented that is logical, consistent, and evolutionarily informative.

A model system of gene-enzyme nomenclature in the genome era applied to aromatic biosynthesis

Background: The accurate annotation of functional roles for newly sequenced genes of genomes is not a simple matter. Function is, of course, related to amino-acid sequence and to domain structure but not always in straightforward ways. Even where given functional roles have been identified experimentally, the application of an uneven and erratic nomenclature has generated confusion on the part of annotators and has produced errors that tend to become progressively compounded in database repositories. Results: The pathway that is deployed in nature for aromatic biosynthesis exemplifies an accumulation of chaotic nomenclature and a variety of annotation dilemmas. We view this pathway as one that is sufficiently complex to pose most of the common problems, and yet is one that at the same time is of a manageable size. A set of guidelines has been developed for naming genes of aromatic-pathway biosynthesis and the corresponding gene products, and we suggest that these can be generalized for application to other metabolic pathways. Conclusion: A system of nomenclature for aromatic biosynthesis is presented that is logical, consistent, and evolutionarily informative.

Frank William Ernest Gibson. 22 July 1923 — 11 July 2008

Frank Gibson rose from humble beginnings to become one of the most respected bacterial physiologists of his era. His identification of the elusive branch-point compound in the pathway of aromatic biosynthesis served as an initiation point for a sustained period of investigation in which the genes, enzymes and intermediates in the various pathways to phenylalanine and tyrosine, the quinones, enterochelin and 4-aminobenzoate were identified and examined in detail. studies on the function of ubiquinone led to an examination of oxidative phosphorylation and to the F 1 F 0 -ATPase of the bacterium Escherichia coli . With Graeme Cox he established a group of researchers who in the 1980s applied the various techniques of microbial genetics to construct a molecular profile of the proteins, which constituted the F 0 membrane- embedded part of the F 1 F 0 -ATPase. This work resulted in the formulation in 1986 of a rotational model and the identification of several residues that could comprise a pore through which the protons, which drove the rotation, could pass. He trained many research students during his lifetime and was an exemplary role model. Outside the laboratory he lived a full life, being an ardent skier, scuba diver and tennis player to name but a few of his pursuits. He is survived by his wife Robin and their son, Mark; by Frances, the daughter from his first marriage; and by grandchildren Teresa, Luke and Simon. His first wife, Margaret, and their second daughter, Ruth (mother of Teresa, Luke and Simon), are both deceased.

Hyperproduction of Tryptophan byCorynebacterium glutamicum with the Modified Pentose Phosphate Pathway

ABSTRACT A classically derived tryptophan-producing Corynebacterium glutamicum strain was recently significantly improved both by plasmid-mediated amplification of the genes for the rate-limiting enzymes in the terminal pathways and by construction of a plasmid stabilization system so that it produced more tryptophan. This engineered strain, KY9218 carrying pKW9901, produced 50 g of tryptophan per liter from sucrose after 80 h in fed-batch cultivation without antibiotic pressure. Analysis of carbon balances showed that at the late stage of the fermentation, tryptophan yield decreased with a concomitant increase in CO2 yield, suggesting a transition in the distribution of carbon flow from aromatic biosynthesis toward the tricarboxylic acid cycle via glycolysis. To circumvent this transition by increasing the supply of erythrose 4-phosphate, a direct precursor of aromatic biosynthesis, the transketolase gene of C. glutamicum was coamplified in the engineered strain by using low- and high-copy-number plasmids which were compatible with the resident plasmid pKW9901. The presence of the gene in low copy numbers contributed to improvement of tryptophan yield, especially at the late stage, and led to accumulation of more tryptophan (57 g/liter) than did its absence, while high-copy-number amplification of the gene resulted in a tryptophan production level even lower than that resulting from the absence of the gene due to reduced growth and sugar consumption. In order to assemble all the cloned genes onto a low-copy-number plasmid, the high-copy-number origin of pKW9901 was replaced with the low-copy-number one, generating low-copy-number plasmid pSW9911, and the transketolase gene was inserted to yield pIK9960. The pSW9911-carrying producer showed almost the same fermentation profiles as the pKW9901 carrier in fed-batch cultivation without antibiotic pressure. Under the same culture conditions, however, the pIK9960 carrier achieved a final tryptophan titer of 58 g/liter, which represented a 15% enhancement over the titers achieved by the pKW9901 and pSW9911 carriers.