Screening method for micro-organisms and methods for the production of a product

Patent metadata

Field	Value
Publication number	US-9617592-B2
Application number	US-201314403537-A
Country	US
Kind code	B2
Filing date	May 24, 2013
Priority date	May 24, 2012
Publication date	Apr 11, 2017
Grant date	Apr 11, 2017

Abstract

In one aspect the disclosure relations to means and methods for identifying a protein or a DNA encoding the protein, involved in the production of a product by a micro-organism. In the methods the micro-organism is cultured under different culture conditions each of which exhibit a different level of the product that is produced by the micro-organism. The genetic expression of the genes of the micro-organism is compared with the level of the product, and groups of DNAs are identified that are involved in the production of the product by the micro-organism.

First claim

The invention claimed is:

1. A method for identifying a candidate protein, or a DNA encoding the candidate protein, said method comprising
culturing said micro-organism under at least two different culture conditions,
selecting from said different culture conditions at least two cultures in which the level of a product that is produced by said micro-organism is different than the other culture,
preparing a protein and/or RNA sample from the selected cultures of micro-organisms,
determining a sequence of at least part of the proteins and/or RNA in said samples,
selecting sequences of proteins and/or sequences of RNA of which the amount differs between the samples of the selected cultures of micro-organisms,
grouping selected sequences of proteins and/or sequences of RNA coded for by DNAs into a first group that comprises selected sequences that are separated by no more than 30 open reading frames (ORFs) on the genome of the micro-organism,
grouping remaining selected sequences of proteins and/or sequences of RNA coded for by DNAs (if any) into a second group that comprises selected sequences that are separated by no more than 30 ORFs on the genome of the micro-organism group,
identifying a group of selected sequences that contains the coding regions of at least two different RNAs or proteins of which the amount correlates with the level of the product that is produced by said micro-organism under said at least two different culture conditions, and
identifying a protein or DNA that comprises a sequence of the identified group thereby identifying a candidate protein that is likely involved in the production of the product by said micro-organism.

2. A method according to claim 1 , wherein said product is a metabolite or an enzyme.

3. A method according to claim 2 , wherein said metabolite is a secondary metabolite.

4. The method according to claim 3 , wherein said secondary metabolite is an antibiotic, an antibiotic resistance inhibitor, an anti-cancer compound, an enzyme-inhibitor, an antifungal, an antihelminthic, an immunostimulant, an immunosuppressant, an insecticide, or an herbicide.

5. The method according to claim 3 , wherein the identity of the secondary metabolite is not known prior to preparing said samples.

6. The method according to claim 5 , further comprising:
identifying the secondary metabolite.

7. The method according to claim 1 , wherein at least three cultures are selected in which the level of the product that is produced by the micro-organism is different in the different culture conditions.

8. The method according to claim 1 , wherein said micro-organism belongs to the phylum Actinobacteria.

9. The method according to claim 1 , wherein said culture conditions differ from each other in that
the culture medium has a different pH at the start of the culture,
the culture conditions differ in the presence, amount and/or type of soil in the culture,
the culture conditions differ in the presence, amount and/or type of bacterial remains at the start of the culture,
the culture conditions differ in amount or type of carbon source in the culture medium,
the culture conditions differ in the amount or type of nitrogen source in the culture medium,
the culture conditions differ in metal composition,
the culture conditions differ in the presence, amount and/or type of a further micro-organism in the culture,
the culture conditions differ in the temperature, and/or
the culture conditions differ in the presence of a signal molecule.

10. The method according to claim 1 , further comprising sequencing at least 50% of the genome of said micro-organism.

11. The method according to claim 1 , further comprising isolating the identified gene from the genome of said micro-organism.

12. The method according to claim 11 , further comprising: providing a micro-organism of a different species with said identified gene.

13. A method according to claim 12 , comprising providing said micro-organism of a different species with the genes of a gene cluster comprising said identified gene.

14. The method according to claim 1 , further comprising culturing said micro-organism or said micro-organism of a different species comprising the genes of a gene cluster comprising said identified gene.

15. A method for obtaining a product produced by a micro-organism, said method comprising:
performing the method according to claim 3 , and
producing said secondary metabolite by said micro-organism or a micro-organism of a different species comprising the genes of a gene cluster comprising said identified gene and obtaining the produced product.

16. A method for identifying a protein, or a DNA encoding said protein, the method comprising:
culturing a microorganism under at least two different culture conditions,
selecting from the different cultures at least three cultures in which the production level of a product produced by the microorganism is different than the other,
preparing a protein sample and/or RNA sample from each of the at least three selected cultures of microorganisms,
sequencing at least part of the proteins and/or RNA in the samples,
selecting sequences of proteins and/or sequences of RNA of which the amount differs between the samples of the selected cultures of microorganisms,
grouping selected sequences of proteins and/or sequences of RNA encoded by DNAs into a first group comprising selected sequences separated by no more than thirty open reading frames (ORFs) on the microorganism's genome,
grouping any remaining selected sequences of proteins and/or sequences of RNA encoded by DNAs into a second group comprising the selected sequences separated by no more than thirty ORFs on the microorganism's genome, and
identifying a group of the selected sequences that contains the coding regions of at least two different RNAs or proteins of which the amount correlates with the production level of the product.

17. The method according to claim 16 , wherein the product is a metabolite, enzyme, or secondary metabolite.

18. The method according to claim 16 , wherein the product is an antibiotic, an antibiotic resistance inhibitor, an anti-cancer compound, an enzyme-inhibitor, an antifungal, an antihelminthic, an immunostimulant, an immunosuppressant, an insecticide, or an herbicide.

19. The method according to claim 16 , wherein the microorganism belongs to the phylum Actinobacteria .

20. The method according to claim 19 , wherein the microorganism is a Streptomyces bacterium.

Assignees

• Univ Leiden

Inventors

• Van Wezel Gilles Philippus
• Gubbens Jacob
• Zhu Hua

Classifications

• G01N2333/36

  from Actinomyces; from Streptomyces (G) · CPC title

• C12Q1/02 Primary

  involving viable microorganisms · CPC title

• C12Q1/6869 Primary

  Methods for sequencing · CPC title

• G01N33/6851

  Methods of protein analysis involving laser desorption ionisation mass spectrometry · CPC title

• G01N33/6818

  Sequencing of polypeptides · CPC title