Compositions and methods for nucleic acid expression and protein secretion in Bacteroides
Provided are nucleic acids that include a promoter, where the promoter is operable in a Bacteroides cell and is operably linked to a heterologous nucleotide sequence of interest. Also provided are nucleic acids that include a promoter (operable in a prokaryotic cell such as a Bacteroides cell) operably linked to a sequence encoding a synthetic ribosomal binding site (RBS). Also provided are fusion proteins (and nucleic acids encoding them) in which a secreted Bacteroides polypeptide is fused to a heterologous polypeptide of interest. Also provided are prokaryotic cells (e.g., E. coli , a Bacteroides cell, and the like) that include one more nucleic acids such as those described above. Also provided are methods of expression in a prokaryotic cell, methods of detectably labeling a Bacteroides cell in an animal's gut, and methods of delivering a protein to an individual's gut.
1. A nucleic acid, comprising:
(a) a promoter operable in a prokaryotic cell, wherein the promoter comprises a nucleotide sequence
having 80% or more sequence identity with the nucleotide sequence: GTTAA (n) 3-7 GTTAA (n) 36-38 TA (n) 2 TTTG (SEQ ID NO: 400);
wherein each n is independently selected from A, C, G, and T;
and
(b) a nucleotide sequence of interest that is operably linked to the promoter, wherein the nucleotide sequence of interest and the promoter are not found operably linked in nature.
2. The nucleic acid of claim 1 , wherein the prokaryotic cell is a Bacteroides cell.
3. A nucleic acid, comprising:
(a) a promoter operable in a prokaryotic cell, wherein the promoter is a ϕB124-14 phage promoter or a functional fragment thereof and comprises a nucleotide sequence comprising one or more of the following:
(i) 80% or more sequence identity of defined nucleotides of the nucleotide sequence: GTTAA (n) 4-7 GTTAA (n) 34-38 TA (n) 2 TTTG,
(ii) 80% or more sequence identity with a sequence set forth in any of SEQ ID NOs: 388 and 407,
(iii) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA,
(iv) a nucleotide sequence comprising GTTAA (n) 44-50 TA,
(v) a nucleotide sequence comprising GTTAA (n) 48-54 TTTG,
(vi) a nucleotide sequence comprising GTTAA (n) 36-38 TA,
(vii) a nucleotide sequence comprising GTTAA (n) 40-42 TTTG,
(viii) a nucleotide sequence comprising GTTAA (n) 3-7 GTTAA (n) 36-38 TA,
(ix) a nucleotide sequence comprising GTTAA (n) 3-7 GTTAA (n) 40-42 TTTG,
(x) a nucleotide sequence comprising GTTAA (n) 44-50 TA (n) 2 TTTG,
(xi) a nucleotide sequence comprising GTTAA (n) 36-38 TA (n) 2 TTTG,
(xii) a nucleotide sequence comprising GTTAA (n) 0-20 GTTAA (n) 10-60 TA (n) 0-10 TTTG,
(xiii) a nucleotide sequence comprising TTAA (n) 0-10 TTAA (n) 30-50 TA (n) 2 TTTG,
(xiv) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA (n) 36-39 TA (n) 2 TTTGC,
(xv) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA (n) 36-39 TA (n) 2 TTTG,
(xvi) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA (n) 34-38 TA (n) 2 TTTG,
(xvii) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA (n) 36-38 TA (n) 2 TTTG,
(xviii) a nucleotide sequence comprising GTTAA (n) 3-7 GTTAA (n) 36-38 TA (n) 2 TTTG,
(xix) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA (n) 12-16 TTG (n) 18-22 TA (n) 2 TTTGC,
(xx) a nucleotide sequence comprising GTTAA (n) 3-7 GTTAA (n) 12-16 TTG (n) 18-22 TA (n) 2 TTTG,
(xxi) a nucleotide sequence comprising GTTAA (n) 4-8 GTTAA (n) 12-16 TTG (n) 18-22 TA (n) 2 TTTG, and
(xxii) a nucleotide sequence comprising GTTAA (n) 4-7 GTTAA (n) 12-16 TTG (n) 18-22 TA (n) 2 TTTG,
wherein each n is independently selected from A, C, G, and T; and
(b) a nucleotide sequence of interest that is operably linked to the promoter, wherein the nucleotide sequence of interest and the promoter are not found operably linked in nature.
4. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 388.
5. The nucleic acid of claim 1 , wherein the nucleotide sequence of interest comprises a transgene sequence that encodes a protein.
6. A prokaryotic cell comprising the nucleic acid of claim 1 .
7. The prokaryotic cell of claim 6 , wherein the nucleic acid is integrated into a chromosome of the prokaryotic cell.
8. The prokaryotic cell of claim 6 , wherein the prokaryotic cell is a Bacteroides cell.
9. The prokaryotic cell of claim 6 , wherein the prokaryotic cell is an E. coli cell.
10. A method of expressing a nucleic acid in a prokaryotic cell, the method comprising: introducing the nucleic acid of claim 1 into the prokaryotic cell.
11. A method of delivering a protein to an individual's gut, the method comprising: introducing, into an individual's gut, a Bacteroides cell comprising the nucleic acid of claim 1 .
12. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 3.
13. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 4.
14. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 5.
15. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 6.
16. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 7.
17. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 8.
18. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 383.
19. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 384.
20. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 385.
21. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 386.
22. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 387.
23. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 393.
24. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 394.
25. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 397.
26. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 406.
27. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in SEQ ID NO: 407.
28. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence set forth in any one of SEQ ID NOs: 150-364.
29. The nucleic acid of claim 1 , wherein the first n of SEQ ID NO: 400 is 3 nucleotides.
30. The nucleic acid of claim 1 , wherein the first n of SEQ ID NO: 400 is 4 nucleotides.
31. The nucleic acid of claim 1 , wherein the first n of SEQ ID NO: 400 is 5 nucleotides.
32. The nucleic acid of claim 1 , wherein the first n of SEQ ID NO: 400 is 6 nucleotides.
33. The nucleic acid of claim 1 , wherein the first n of SEQ ID NO: 400 is 7 nucleotides.
34. The nucleic acid of claim 1 , wherein the second n of SEQ ID NO: 400 is 36 nucleotides.
35. The nucleic acid of claim 1 , wherein the second n of SEQ ID NO: 400 is 37 nucleotides.
36. The nucleic acid of claim 1 , wherein the second n of SEQ ID NO: 400 is 38 nucleotides.
37. The nucleic acid of claim 1 , wherein the first n of SEQ ID NO: 400 is 4-6 nucleotides and the second n is 37 nucleotides.
38. The nucleic acid of claim 1 , wherein the promoter comprises a nucleotide sequence having 85% or more sequence identity with the nucleotide sequence:
GTTAA (n) 3-7 GTTAA (n) 36-38 TA (n) 2 TTTG (SEQ ID NO: 400).
39. The nucleic acid of claim 38 , wherein the first n of SEQ ID NO: 400 is 3 nucleotides.
40. The nucleic acid of claim 38 , wherein the first n of SEQ ID NO: 400 is 4 nucleotides.
41. The nucleic acid of claim 38 , wherein the first n of SEQ ID NO: 400 is 5 nucleotides.
42. The nucleic acid of claim 38 , wherein the first n of SEQ ID NO: 400 is 6 nucleotides.
43. The nucleic acid of claim 38 , wherein the first n of SEQ ID NO: 400 is 7 nucleotides.
44. The nucleic acid of claim 38 , wherein the second n of SEQ ID NO: 400 is 36 nucleotides.
45. The nucleic acid of claim 38 , wherein the second n of SEQ ID NO: 400 is 37 nucleotides.
46. The nucleic acid of claim 38 , wherein the second n of SEQ ID NO: 400 is 38 nucleotides.
47. The nucleic acid of claim 38 , wherein the first n of SEQ ID NO: 400 is 4-6 nucleotides and the second n is 37 nucleotides.
48. The nucleic acid of claim 1 , wherein the promoter comprises a nucleotide sequence having 90% or more sequence identity with the nucleotide sequence:
GTTAA (n) 3-7 GTTAA (n) 36-38 TA (n) 2 TTTG (SEQ ID NO: 400).
49. The nucleic acid of claim 48 , wherein the first n of SEQ ID NO: 400 is 3 nucleotides.
50. The nucleic acid of claim 48 , wherein the first n of SEQ ID NO: 400 is 4 nucleotides.
51. The nucleic acid of claim 48 , wherein the first n of SEQ ID NO: 400 is 5 nucleotides.
52. The nucleic acid of claim 48 , wherein the first n of SEQ ID NO: 400 is 6 nucleotides.
53. The nucleic acid of claim 48 , wherein the first n of SEQ ID NO: 400 is 7 nucleotides.
54. The nucleic acid of claim 48 , wherein the second n of SEQ ID NO: 400 is 36 nucleotides.
55. The nucleic acid of claim 48 , wherein the second n of SEQ ID NO: 400 is 37 nucleotides.
56. The nucleic acid of claim 48 , wherein the second n of SEQ ID NO: 400 is 38 nucleotides.
57. The nucleic acid of claim 48 , wherein the first n of SEQ ID NO: 400 is 4-6 nucleotides and the second n is 37 nucleotides.
58. The nucleic acid of claim 1 , wherein the promoter comprises a nucleotide sequence having 95% or more sequence identity with the nucleotide sequence:
GTTAA (n) 3-7 GTTAA (n) 36-38 TA (n) 2 TTTG (SEQ ID NO: 400).
59. The nucleic acid of claim 58 , wherein the first n of SEQ ID NO: 400 is 3 nucleotides.
60. The nucleic acid of claim 58 , wherein the first n of SEQ ID NO: 400 is 4 nucleotides.
61. The nucleic acid of claim 58 , wherein the first n of SEQ ID NO: 400 is 5 nucleotides.
62. The nucleic acid of claim 58 , wherein the first n of SEQ ID NO: 400 is 6 nucleotides.
63. The nucleic acid of claim 58 , wherein the first n of SEQ ID NO: 400 is 7 nucleotides.
64. The nucleic acid of claim 58 , wherein the second n of SEQ ID NO: 400 is 36 nucleotides.
65. The nucleic acid of claim 58 , wherein the second n of SEQ ID NO: 400 is 37 nucleotides.
66. The nucleic acid of claim 58 , wherein the second n of SEQ ID NO: 400 is 38 nucleotides.
67. The nucleic acid of claim 58 , wherein the first n of SEQ ID NO: 400 is 4-6 nucleotides and the second n is 37 nucleotides.
68. The nucleic acid of claim 1 , wherein the promoter comprises the nucleotide sequence:
GTTAA (n) 3-7 GTTAA (n) 36-38 TA (n) 2 TTTG (SEQ ID NO: 400).
69. The nucleic acid of claim 68 , wherein the first n of SEQ ID NO: 400 is 3 nucleotides.
70. The nucleic acid of claim 68 , wherein the first n of SEQ ID NO: 400 is 4 nucleotides.
71. The nucleic acid of claim 68 , wherein the first n of SEQ ID NO: 400 is 5 nucleotides.
72. The nucleic acid of claim 68 , wherein the first n of SEQ ID NO: 400 is 6 nucleotides.
73. The nucleic acid of claim 68 , wherein the first n of SEQ ID NO: 400 is 7 nucleotides.
74. The nucleic acid of claim 68 , wherein the second n of SEQ ID NO: 400 is 36 nucleotides.
75. The nucleic acid of claim 68 , wherein the second n of SEQ ID NO: 400 is 37 nucleotides.
76. The nucleic acid of claim 68 , wherein the second n of SEQ ID NO: 400 is 38 nucleotides.
77. The nucleic acid of claim 68 , wherein the first n of SEQ ID NO: 400 is 4-6 nucleotides and the second n is 37 nucleotides.
78. The nucleic acid of claim 1 , further comprising a terminator sequence upstream of the promoter.
79. The nucleic acid of claim 78 , wherein the terminator sequence comprises SEQ ID NO: 409.