Method of inactivation of an end product of energy metabolism in

1. A method of site specific insertion or deletion in Zymomonas comprising:

(a) providing a Zymornonas DNA fragment;

(b) interrupting a sequence in the Zymomonas DNA fragment to provide an interrupted sequence formed of a first component part and a second component part of the Zymomonas DNA fragment;

(c) recombining the interrupted sequence with a desired sequence to form a recombinant gene fragment

wherein the first component part and the second component part of the Zyrnornonas DNA fragment respectively flank the desired sequence to facilitate site specific insertion or deletion, the first component part and the second component part targeting a by-product of a Zymomonas metabolic pathway; and

(d) transforming the Zymomonas to induce site specific insertion or deletion by homologous recombination with the interrupted sequence to provide a recombinant Zymomonas , wherein said recombinant gene fragment provides for elimination of a by-product of a metabolic pathway in the recombinant Zymomon as; and further comprising

(e) ligating the interrupted sequence with a plasmid vector; wherein the step (d) of the transforming the Z. mobilis organism occurs through homologous recombination with the interrupted sequence of the plasmid vector; wherein the plasmid is selected from the group consisting of pZB 101, pZB 102, and pZB 121.

2. The method of claim 1 wherein the DNA fragment used in the providing step (a) encodes a structural protein in a metabolic pathway of the by-product to be eliminated.

3. The method of claim 1 wherein the recombining step (c) comprises inserting a DNA sequence inside the DNA fragment.

4. The method of claim 1 wherein the interrupting step (b) and the recombining step (c) result in site-specific deletion in the transforming step (d).

5. The method of claim 2 wherein the by-product to be eliminated is lactic acid.

6. The method of claim 3 wherein the desired sequence used in the recombining step (c) comprises a selection marker.

7. The method of claim 3 wherein the desired sequence used in the recombining step (c) comprises an operon encoding at least one protein selected from the group consisting of xylose isomerase, L-ribuloltinase, L-ribulose-5-phosphate 4-epimerase, transaldolase or transketolase, and a promoter for expression of the structural gene in Zymomonas.

8. The method of claim 1 further comprising a step of curing the Zymomonas of the plasmid.

9. A method of site specific insertion or deletion in Zymomonas mobilis comprising:

(a) providing a Zymomonas mobilis DNA fragment;

(b) interrupting a sequence in the Zymomonas mobilis DNA fragment to provide an interrupted sequence formed of a first component part and a second component part of the Zymomonas mobilis DNA fragment;

(c) recombining the interrupted sequence with a desired sequence to form a recombinant gene fragment

wherein the first component part and the second component part of the Zymomonas mobilis DNA fragment respectively flank the desired sequence to facilitate site specific insertion or deletion, the first component part and the second component part targeting a by-product of a Zymomonas mobilis metabolic pathway;

(d) transforming the Zymonomas mobilis to induce site specific insertion or deletion by homologous recombination with the interrupted sequence to provide a recombinant Zymomonas mobilis , wherein said recombinant gene fragment provides for elimination of a by-product of a metabolic pathway in the recombinant Zymomonas mobilis and;

(e) ligating the interrupted sequence with a plasmid vector; wherein the step (d) of the transforming Z. mobilis organism occurs through homologous recombination with the interrupted sequence of the plasmid vector; wherein the plasmid is the integrative plasmid pZB1862-ldhL-ara that effects site-specific homologous recombination into said Z. mobilis organism at the ldhL gene to introduce components of the arabinose operon.