Methods for generating a glucose permease library and uses thereof
The present disclosure describes methods for generating microbial strains expressing a heterologous bacterial glucose permease gene that produce biomolecules of interest. In aspects, the disclosure provides novel bacterial strains, which express a heterologous bacterial glucose permease gene whose expression is controlled by a native Corynebacterium glutamicum promoter or a mutant promoter derived therefrom. Also provided herein are methods for producing a library of bacterial glucose permease genes using a promoter ladder comprising a plurality of promoters derived from Corynebacterium glutamicum.
1. A host cell comprising a heterologous glucose permease gene functionally linked to a first promoter polynucleotide, wherein the first promoter polynucleotide comprises a nucleotide sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.
2. The host cell of claim 1 , wherein the glucose permease gene is a gene that encodes a polypeptide with an amino acid sequence selected from SEQ ID NO: 13, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 9and SEQ ID NO: 14.
3. The host cell of claim 1 , wherein the glucose permease gene is a gene with a nucleotide sequence selected from SEQ ID NO: 23, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 19 and SEQ ID NO: 24.
4. The host cell of claim 1 , further comprising a hexokinase gene functionally linked to a second promoter polynucleotide, wherein the second promoter polynucleotide comprises a nucleotide sequence selected from SEQ ID NO: 2, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.
5. The host cell of claim 4 , wherein the hexokinase gene is a gene that encodes a polypeptide sequence selected from SEQ ID NO: 15 and SEQ ID NO: 16.
6. The host cell of claim 4 , wherein the hexokinase gene is a gene with a nucleotide sequence selected from SEQ ID NO: 25 and SEQ ID NO: 26.
7. A method for generating a microorganism capable of increased production of a biomolecule from glucose, the method comprising:
a) genetically modifying a host microorganism, wherein the modifying comprises introducing a glucose permease gene from a library of glucose permease genes into the genome of the host microorganism, wherein each glucose permease gene from the library of glucose permease genes is functionally linked to a promoter comprising a nucleotide sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8 and wherein the modification generates a strain of the host microorganism expressing the glucose permease gene;
b) repeating step a) for a plurality of rounds until a plurality of strains of the host microorganism are generated, wherein each strain of the plurality of strains of the host microorganism expresses a separate glucose permease gene from the library of glucose permease genes;
c) contacting each strain of the plurality of strains of the host microorganism with a carbon source comprising glucose under fermentative conditions; and
d) selecting each strain of the host microorganism that produces an increased amount of a biomolecule from glucose as compared to the amount of the biomolecule produce from glucose from a control microorganism, wherein the control microorganism does not express a glucose permease gene from the library of glucose permease genes.
8. The method of claim 7 , wherein the library of glucose permease genes comprises genes that encode polypeptide sequences of SEQ ID NO: 13, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 9, SEQ ID NO: 14 or a combination thereof.
9. The method of claim 7 , wherein the library of glucose permease genes comprises genes with a nucleotide sequence of SEQ ID NO: 23, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 19, SEQ ID NO: 24 or a combination thereof.
10. The method of claim 7 , further comprising introducing a hexokinase gene from a library of hexokinase genes, wherein each hexokinase gene from the library of hexokinase genes is functionally linked to a promoter polynucleotide, wherein the promoter polynucleotide comprises a sequence selected from SEQ ID NO: 2, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.
11. The method of claim 10 , wherein the library of hexokinase genes comprises genes that encode polypeptide sequences of SEQ ID NO: 15 and/or SEQ ID NO: 16.
12. The method of claim 10 , wherein the library of hexokinase genes comprises genes with nucleotide sequences of SEQ ID NO: 25 and/or SEQ ID NO: 26.
13. A library of glucose permease genes, wherein each glucose permease gene in the library of glucose permease genes is functionally linked to a promoter comprising a nucleotide sequence selected from SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.
14. The library of claim 13 , wherein the library of glucose permease genes comprises genes that encode polypeptide sequences of SEQ ID NO: 13, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 9, SEQ ID NO: 14 or a combination thereof.
15. The library of claim 13 , wherein the library of glucose permease genes comprises genes with nucleotide sequences of SEQ ID NO: 23, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 19, SEQ ID NO: 24 or a combination thereof.
16. The library of claim 13 , wherein each glucose permease gene in the library of glucose permease genes is a first portion of a chimeric construct, wherein the chimeric construct comprises a second portion, wherein the second portion is a hexokinase gene.
17. The library of claim 16 , wherein the hexokinase gene is functionally linked to a promoter polynucleotide, wherein the promoter polynucleotide comprises a sequence selected from SEQ ID NO: 2, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, and SEQ ID NO: 8.
18. The library of claim 17 , wherein the library of hexokinase genes comprises genes that encode polypeptide sequences of SEQ ID NO: 15 and or SEQ ID NO: 16.
19. The library of claim 17 , wherein the library of hexokinase genes comprises genes with nucleotide sequences of SEQ ID NO: 25 and/or SEQ ID NO: 26.
20. A method of producing a biomolecule comprising introducing a glucose permease gene from the library of claim 13 , into a host cell and culturing the host cell under conditions suitable for producing the biomolecule.