Bacterial cocultures expressing a bacteriocin system
The present disclosure concerns a co-culture of bacterial cells for making a fermented product from a biomass. The co-culture comprising a first recombinant lactic acid bacteria (LAB) cell expressing at least one bacteriocin and a second recombinant lactic acid bacteria (LAB) cell capable of converting, at least in part, the biomass into the fermented product. The second recombinant LAB cell is immune to the bacteriocin produced by the first recombinant LAB cell. The co-culture can be used, optionally in combination with a yeast host cell, to make a fermented product. The present disclosure also provides processes for making the fermented product by using the co-culture as wells kits and media comprising the co-culture.
1. A co-culture of lactic acid bacterial cells for making ethanol from a biomass, the co-culture comprising:
a first recombinant lactic acid bacteria (LAB) cell:
expressing at least one bacteriocin; and
comprising heterologous nucleic acid molecules encoding polypeptides for converting the biomass into ethanol;
and
a second recombinant LAB cell:
capable of converting the biomass into ethanol; comprising heterologous nucleic acid molecules encoding polypeptides for converting the biomass into ethanol;
and comprising one or more heterologous nucleic acid molecules encoding one or more polypeptides for conferring immunity against the at least one bacteriocin expressed by the first recombinant LAB cell
wherein the polypeptides for converting the biomass into ethanol comprise at least:
a pyruvate decarboxylase; and
an alcohol dehydrogenase,
wherein the at least one bacteriocin comprises a lantibiotic, a cyclic bacteriocin, a Class IIA bacteriocin, a Class IIB bacteriocin, or a combination thereof.
2. The co-culture of claim 1 , wherein the Lantibiotic is nisin and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes NisI; the cyclic bacteriocin is gassericin and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes GaaI; the cyclic bacteriocin is plantaricyclin A and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes PlcD and/or PlcI; the Class IIA bacteriocin is plantaricin 423 and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes PlaB; the Class IIA bacteriocin is pediocin and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes PedB; the Class IIA bacteriocin is lactoccin A and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes LciA; the Class IIA bacteriocin is horediocin A and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes HdrI; or the Class IIB bacteriocin is brochocin and the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin encodes BrcI.
3. The co-culture of claim 2 , wherein nisin has the amino acid sequence of any one of SEQ ID NOS: 7 to 10, is a variant of the amino acid sequence of any one of SEQ ID NOS: 7 to 10 having nisin bacteriocin activity or is a fragment of the amino acid sequence of any one of SEQ ID NOS: 7 to 10 having nisin bacteriocin activity.
4. The co-culture of claim 2 , wherein NisI has the amino acid sequence of SEQ ID NO: 11, is a variant of the amino acid sequence of SEQ ID NO: 11 conferring immunity against nisin or is a fragment of the amino acid sequence of SEQ ID NO: 11 conferring immunity against nisin.
5. The co-culture of claim 2 , wherein the heterologous nucleic acid molecule encoding one or more polypeptides for conferring immunity against the at least one bacteriocin further encodes NisE, NisF and/or NisG.
6. The co-culture of claim 5 , wherein NisE has the amino acid sequence of SEQ ID NO: 13, is a variant of the amino acid sequence of SEQ ID NO: 13 having nisin transporter activity or is a fragment of the amino acid sequence of SEQ ID NO: 13 having nisin transporter activity.
7. The co-culture of claim 5 , wherein NisF has the amino acid sequence of SEQ ID NO: 12, is a variant of the amino acid sequence of SEQ ID NO: 12 having nisin transporter activity or is a fragment of the amino acid sequence of SEQ ID NO: 12 having nisin transporter activity.
8. The co-culture of claim 5 , wherein NisG has the amino acid sequence of SEQ ID NO: 14, is a variant of the amino acid sequence of SEQ ID NO: 14 having nisin permease activity or is a fragment of the amino acid sequence of SEQ ID NO: 14 having nisin permease activity.
9. The co-culture of claim 1 , wherein the first recombinant LAB cell expresses a plurality of bacteriocins.
10. The co-culture of claim 1 , wherein the pyruvate decarboxylase has the amino acid sequence of SEQ ID NO: 1, is a variant of the amino acid sequence of SEQ ID NO: 1 having pyruvate decarboxylase activity or is a fragment of the amino acid sequence of SEQ ID NO: 1 having pyruvate decarboxylase activity.
11. The co-culture of claim 1 , wherein the alcohol dehydrogenase has the amino acid sequence of SEQ ID NO: 3, is a variant of the amino acid sequence of SEQ ID NO: 3 having alcohol dehydrogenase activity or is a fragment of the amino acid sequence of SEQ ID NO: 3 having alcohol dehydrogenase activity.
12. The co-culture of claim 1 , wherein the first recombinant LAB cell and/or the second recombinant LAB cell comprises:
at least one inactivated or deleted native gene coding for a lactate dehydrogenase;
inactivated or deleted native ldh1, ldh2, ldh3, ldh4 and dhic genes;
at least one inactivated or deleted native gene coding for a mannitol-1-phosphate 5-dehydrogenase; and/or
inactivated or deleted native mltD1 and mltD2 genes.
13. The co-culture of claim 1 , wherein the first recombinant LAB cell is from the genus Lactococcus or from the species Lactococcus lactis.
14. The co-culture of claim 1 , wherein the second recombinant LAB cell is from the genus Lactobacillus or from the species Lactobacillus paracasei.
15. A combination comprising the co-culture of claim 1 and a yeast cell.
16. A process for converting a biomass into a fermentation product, wherein the process comprises contacting the biomass with the co-culture of claim 1 under conditions to allow the conversion of the biomass into said fermentation product of claim 1 .
17. The process of claim 16 , wherein the biomass comprises corn.
18. The process of claim 16 , wherein said fermentation product is ethanol.
19. The co-culture of claim 1 , wherein the at least one bacteriocin is native to the first recombinant LAB cell.
20. The co-culture of claim 1 , wherein the first recombinant LAB cell further comprises a heterologous nucleic acid molecule encoding the at least one bacteriocin and one or more polypeptides for conferring immunity against the at least one bacteriocin.
21. The combination of claim 15 wherein the yeast cell is from the genus Saccharomyces sp.
22. The combination of claim 15 wherein the yeast cell is from the species Saccharomyces cerevisiae.