Method and phage for the identification of nucleic acid sequences encoding members of a multimeric (poly) peptide complex

• US 6,667,150 B1
• Filed: 02/01/2000
• Issued: 12/23/2003
• Est. Priority Date: 08/01/1997
• Status: Expired due to Fees

• Current Assignee: Morphosys Ag
• Original Assignee: Morphosys Ag
• Inventors: Ge, Liming, Rudert, Fritz, Ilag, Vic
• Primary Examiner(s): Wang, Andrew
• Assistant Examiner(s): FRIEND, TOMAS H F
• Application Number:
  US09/495,880
• Time in Patent Office: 1,421 Days
• Field of Search: 435/5, 435/7.1, 435/6
• US Class Current: 506/14
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C12N 15/1055 Protein x Protein interaction, e.g. two hybrid selection
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/02 Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures

Abstract

The present invention relates to methods for the identification of nucleic acid sequences encoding members of a multimeric (poly)peptide complex by screening for polyphage particles. Furthermore, the invention relates to products and uses thereof for the identification of nucleic acid sequences in accordance with the present invention.

Claims

1. A method for identifying a combination of nucleic acid sequences encoding two members of a multimeric polypeptide complex with a predetermined property, said combination being (i) located on separate nucleic acid molecules and (ii) contained in a combinatorial library of phage particles displaying a multitude of multimeric polypeptide complexes, said method comprising the steps (a) screening or selecting for polyphage particles that contain said combination, wherein said two members of the multimeric polypeptide complex interact to form an immunoglobulin, and wherein said predetermined property is the ability to bind to a target;

and (b) identifying said combination of nucleic acid sequences.

2. The method of claim 1, comprising the steps of

(a) providing a first library of recombinant vector molecules containing genetically diverse nucleic acid sequences comprising a variety of nucleic acid sequences, each encoding a fusion protein of a first member of a multimeric polypeptide complex fused to at least part of a phage coat protein, said fusion protein thereby being able to be directed to, and displayed at, the phage surface, wherein said vector molecules are able to be packaged in a phage particle and carry or encode a first selectable and/or screenable property;

(b) providing a second library of recombinant vector molecules containing genetically diverse nucleic acid sequences comprising a variety of nucleic acid sequences, each encoding a second member of a multimeric polypeptide complex, wherein the vector molecules of said second library are able to be packaged in a phage particle and carry or encode a second selectable and/or screenable property different from said first property;

(c) optionally, providing nucleic acid sequences encoding further members of a multimeric polypeptide complex;

(d) expressing members of said libraries of recombinant vectors mentioned in steps (a), (b), and optionally nucleic acid sequences mentioned in step (c), in appropriate host cells under appropriate conditions, so that a combinatorial library of phage particles each displaying a multimeric polypeptide complex is produced;

(e) identifying in said library of phage particles a collection of phages displaying multimeric polypeptide complexes having said predetermined property;

(f) identifying in said collection polyphage particles simultaneously containing recombinant vector molecules encoding a first and a second member of said multimeric polypeptide complex by screening or selecting for the simultaneous presence or generation of said first and second selectable and/or screenable property;

(g) optionally, carrying out further screening and/or selection steps or repeating steps (a) to (f); and

(h) identifying said combination of nucleic acid sequences.

3. The method of claim 1, comprising the steps of

(a) expressing in appropriate host cells under appropriate conditions

(i) genetically diverse nucleic acid sequences contained in a first library of recombinant vector molecules, said nucleic acid sequences comprising a variety of nucleic acid sequences, each encoding a fusion protein of a first member of a multimeric polypeptide complex fused to at least part of a phage coat protein, said fusion protein thereby being able to be directed to and displayed at the phage surface, wherein said vector molecules are able to be packaged in a phage particle and carry or encode a first selectable and/or screenable property;

(ii) genetically diverse nucleic acid sequences contained in a second library of recombinant vector molecules, said nucleic acid sequences comprising a variety of nucleic acid sequences, each encoding a second member of a multimeric polypeptide complex, wherein the vector molecules are able to be packaged in a phage particle and carry or encode a second selectable and/or screenable property different from said first property;

(iii) optionally, nucleic acid sequences encoding further members of a multimeric polypeptide complex, so that a combinatorial library of phage particles each displaying a multimeric polypeptide complex is produced;

(b) identifying in said library of phage particles a collection of phages displaying multimeric polypeptide complexes having said predetermined property;

(c) identifying in said collection polyphage particles simultaneously containing recombinant vector molecules encoding a first and a second member of said multimeric polypeptide complex by screening or selecting for the simultaneous presence or generation of said first and second selectable and/or screenable property;

(d) optionally, carrying out further screening and/or selection steps or repeating steps (a) to (c);

(e) identifying said combination of nucleic acids.

4. The method of claim 2, wherein the vectors of said first and said second library are a combination of a phage vector and a phagemid vector, respectively.

5. The method of claim 2, wherein the vectors of said first and said second library are different phagemid vectors, said appropriate conditions comprising complementation of phage genes by a helper phage.

6. The method of claim 5, wherein said two phagemid vectors are compatible.

7. The method of claim 6, wherein (i) said phagemid vectors of said first library comprise a ColE1 origin of replication and said phagemid vectors of said second library comprise a p15A plasmid origin of replication;

or (ii) said phagemid vectors of said first library comprise a p15A origin of replication and said phagemid vectors of said second library comprise a ColE1 plasmid origin of replication.

8. The method of claim 6, wherein (i) said phagemid vectors of said first library comprise a ColE1 origin of replication and said and phagemid vectors of said second library comprise a mutated ColE1 origin of replication;

or (ii) said phagemid vectors of said first library comprise a mutated ColE1 origin of replication and said phagemid vectors of said second library comprise a ColE1 plasmid origin of replication.

9. The method of claim 4 or 5, wherein said vectors and/or said helper phage comprise different phage origins of replication.

10. The method of claim 4 or 5, wherein said phage vector, said phagemid vector(s) and/or said helper phage are interference resistant.

11. The method of claim 10, wherein said phage vector, said phagemid vector(s) and/or said helper phage have mutations in the phage intergenic region(s) and/or in gene II.

12. The method of claim 10, wherein said phage vector, said phagemid vector(s) and/or said helper phage is an IR1 mutant or an IR2 mutant.

13. The method of claim 4 or 5, wherein said vectors and/or said helper phage comprise hybrid nucleic acid sequences of f1-, fd-, and/or M13-mutated sequences.

14. The method of claim 2, wherein said vector is SEQ ID NO:

31 or a mutant thereof.

15. The method of claim 14, wherein said mutant is a phagemid comprising the phage origin of replication from fpep3_—

1B-IR3seq, the gene II from fpep3_—

1B-IR3seq, or a combination of said phage origin of replication and said gene II.

16. The method of claim 14, wherein said mutant is phagemid comprising the phage origin of replication from fpep3_—

1B-IR3seq, the gene II from fpep3_—

1B-IR3seq, or a combination of said phage origin of replication and said gene II.

17. The method of claim 14, wherein said mutant is a helper phage comprising the phage origin of replication form fpep3_—

1B-IR3seq, the gene II from fpep3_—

1B-IR3seq, or a combination of said phage origin of replication and said gene II.

18. The method of any one of claims 15 to 17, wherein said mutants comprise the combined fd/f1 origin including the mutation G5737>

A (2976 in fpep3_—

1B-IR3seq), and/or the mutations G343>

A (3989) in gII, and G601>

T (4247) in gII/X.

19. The method of claim 1 or 2, wherein any of said vectors that contain the gene VII contains an amber mutation.

20. The method of claim 19, wherein said mutation is identical to those found in phage vectors R68 or R100.

21. The method of claim 1 or 2, wherein any of said vectors that contain the gene IX contains an amber mutation.

22. The method of claim 21, wherein said mutation is identical to that found in phage vector N18.

23. The method of claim 1 or 2, wherein said phage coat protein is gIIIp or gVIIIp.

24. The method of claim 1 or 2, wherein said phage particles are infectious by having a full-length copy of gIIIp.

25. The method of claim 1 or 2, wherein said phage particles are non-infectious by having no full-length copy of gIIIp, said fusion protein being formed with a truncated version of gIIIp, wherein the infectivity can be restored by interaction of the displayed multimeric polypeptide complexes with a corresponding partner coupled to an infectivity-mediating particle.

26. The method of claim 25, wherein said truncated gulp comprises the C-terminal domain of gIIIp.

27. The method of claim 26, wherein said truncated gIIIp is a mutant of phage fCA55.

28. The method of claim 1, wherein said multimeric polypeptide complex is a functional fragment of an immunoglobulin.

29. The method of claim 28, wherein said fragment is an Fv, dsFv or Fab functional fragment.

30. The method of claim 2, wherein said first and/or said second selectable and/or screenable property is the transactivation of transcription of (i) a reporter gene selected from the group consisting of beta-galactosidease and alkaline phosphatase;

or (ii) a nutritional marker selected from the group consisting of his3 and leu;

or (iii) a resistance gene giving resistance to an antibiotic selected from the group consisting of ampicillin, chloramphenicol, kanamycin, zeocin, neomycin, tetracycline and streptomcycin.

31. The method of claim 1 or 2, wherein said generation of said first and second screenable and/or selectable property is achieved after infection of appropriate host cells by said collection of phage particles.

32. The method of claim 1 or 2, wherein said identification of said nucleic acid sequences is effected by sequencing.

33. The method of claim 1 or 2, wherein said host cells are E. coli XL-1 Blue, K91 or mutants thereof, TG1, XL1kann or TOP10F.

34. The method of claim 11, wherein the mutation in the phage intergenic region corresponds to position 5986 of f1.

35. The method of claim 11, wherein the mutation in gene II corresponds to position 143 of f1.

36. The method of claim 12, wherein the IR1 mutant is selected from the group consisting of R176, R382, R383, R407, and R408.