1. Engineering magnetosomes to express novel proteins Which ones? Must be suitable for expressing in Magnetospyrillum! Can’t rely on glycosylation, disulphide bonds, lipidation, selective proteolysis, etc for function! Best bets are bacterial proteins Alternatives are eukaryotic proteins that don’t need any of the above Short peptides Tweaking p18 Linker Deleting or replacing GFP TRZN Oxalate decarboxylases Lactate dehydrogenase or other oxalate metab enzyme

2. How to bioengineer a novel protein expression system? 1.Identify a suitable candidate host 2.DNA must function in this host 3.mRNA must function in this host 4.Protein must be functional Must be able to purify large amounts of functional protein

3. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Pro Make glycoproteins “faithfully” Can’t infect plants or animals Can use promoters of “late genes” to drive expression of heterologous proteins Insect cell cultures are easier & more forgiving than mammalian cell cultures Con Trickier Requires cell cultures: expensive!

4. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Transgenic plants Pro Make authentic plant proteins (and sometimes animal proteins) Cheap “Easy” and robust techniques

5. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Transgenic plants Pro Make authentic plant proteins (and sometimes animal proteins) Cheap “Easy” and robust techniques Con Slow May not process non-plant proteins correctly

6. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Transgenic plants Animal cell cultures Pro Make authentic animal proteins “Easy” and robust techniques

7. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Transgenic plants Animal cell cultures Pro Make authentic animal proteins “Easy” and robust techniques Con Slow Expensive! Purifying proteins can be difficult

8. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Transgenic plants Animal cell cultures Transgenic animals Pro Make authentic animal proteins

9. Hosts? E. coli Saccharomyces cerevisiae (brewer’s yeast) Pichia pastoris Baculovirus in cultured insect cells Transgenic plants Animal cell cultures Transgenic animals Pro Make authentic animal proteins Con Slow Expensive! Difficult Purifying proteins can be difficult

10. Hosts? Magnetospirillum gryphiswaldense

11. Magnetospirillum gryphiswaldense Can propagate plasmids (but pBAM requires pir gene)

12. Magnetospirillum gryphiswaldense Can propagate plasmids (but pBAM requires pir gene) Or can insert into chromosome via tnpA (Tn5)-based transposition

13. Magnetospirillum gryphiswaldense Can propagate plasmids (but pBAM requires pir gene) Can insert into genome by transposition no variation in expression due to copy # or growth stage

14. Magnetospirillum gryphiswaldense Borg optimised rbs, promoter & codon usage

15. Magnetospirillum gryphiswaldense Borg optimised rbs, promoter & codon usage Developed inducible system based on tetracycline

16. Magnetospirillum gryphiswaldense Borg optimised rbs, promoter & codon usage Developed inducible system based on tetracycline Fuse protein to C-terminus of mamC

17. Magnetospirillum gryphiswaldense Borg optimised rbs, promoter & codon usage Developed inducible system based on tetracycline Fuse protein to mamC C-terminus: exposed at surface

18. Magnetospirillum gryphiswaldense Borg optimised rbs, promoter & codon usage Developed inducible system based on tetracycline Fuse protein to mamC C-terminus: exposed at surface Purify with magnets

19. Assignment Design a mamC C-terminal protein fusion Design DNA sequence encoding a useful protein

20. Assignment Design a mamC C-terminal protein fusion Design DNA sequence encoding a useful protein Replace eGFP of pJH3 with your protein Best to use MluI and NheI sites

21. Assignment Best to use MluI and NheI sites Design oligos that add MluI in frame at 5’ end and NheI at 3’end

22. Assignment Best to use MluI and NheI sites  Design oligos that add MluI in frame at 5’ and NheI at 3’end  Digest vector & clone with MluI and NheI then ligate

23. Assignment Best to use MluI and NheI sites  Design oligos that add MluI in frame at 5’ and NheI at 3’end  Digest vector & clone with MluI and NheI then ligate  Find & analyze clones

24. Transcription Prokaryotes have one RNA polymerase makes all RNA core polymerase = complex of 5 subunits (      ’  )

25. Transcription Prokaryotes have one RNA polymerase makes all RNA core polymerase = complex of 5 subunits (      ’  )  not absolutely needed, but cells lacking  are very sick

26. Initiating transcription in Prokaryotes 1) Core RNA polymerase is promiscuous

27. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity

28. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity Bind promoters

29. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity Bind promoters Different sigmas bind different promoters

30. Initiating transcription in Prokaryotes 1)Core RNA polymerase is promiscuous 2)sigma factors provide specificity Bind promoters 3) Once bound, RNA polymerase “melts” the DNA

31. Initiating transcription in Prokaryotes 3) Once bound, RNA polymerase “melts” the DNA 4) rNTPs bind template

32. Initiating transcription in Prokaryotes 3) Once bound, RNA polymerase “melts” the DNA 4) rNTPs bind template 5) RNA polymerase catalyzes phosphodiester bonds, melts and unwinds template

33. Initiating transcription in Prokaryotes 3) Once bound, RNA polymerase “melts” the DNA 4) rNTPs bind template 5) RNA polymerase catalyzes phosphodiester bonds, melts and unwinds template 6) sigma falls off after ~10 bases are added

34. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5’ to transcription start) 5’-TATAAT-3’ determines exact start site: bound by  factor

35. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor

36. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor 3) UP element : -57: bound by  factor

37. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor 3) UP element : -57: bound by  factor

38. Structure of Prokaryotic promoters Three DNA sequences (core regions) 1) Pribnow box at -10 (10 bp 5 ’ to transcription start) 5 ’ -TATAAT-3 ’ determines exact start site: bound by  factor 2) ” -35 region ” : 5 ’ -TTGACA-3 ’ : bound by  factor 3) UP element : -57: bound by  factor Other sequences also often influence transcription! Eg Trp operator

39. Prok gene regulation 5 genes (trp operon) encode trp enzymes

40. Prok gene regulation Copy genes when no trp Repressor stops operon if [trp]

41. Prok gene regulation Repressor stops operon if [trp] trp allosterically regulates repressor can't bind operator until 2 trp bind

42. lac operon Some operons use combined “on” & “off” switches E.g. E. coli lac operon Encodes enzymes to use lactose lac Z =  -galactosidase lac Y= lactose permease lac A = transacetylase

43. lac operon Make these enzymes only if: 1) - glucose

44. lac operon Make these enzymes only if: 1) - glucose 2) + lactose

45. lac operon Regulated by 2 proteins 1) CAP protein : senses [glucose]

46. lac operon Regulated by 2 proteins 1)CAP protein : senses [glucose] 2)lac repressor: senses [lactose]

47. lac operon Regulated by 2 proteins 1)CAP protein : senses [glucose] 2)lac repressor: senses [lactose] encoded by lac i gene Always on

48. lac operon 2 proteins = 2 binding sites 1) CAP site: promoter isn’t active until CAP binds

49. lac operon 2 proteins = 2 binding sites 1)CAP site: promoter isn’t active until CAP binds 2)Operator: repressor blocks transcription

50. lac operon Regulated by 2 proteins 1) CAP only binds if no glucose -> no activation

51. lac operon Regulated by 2 proteins 1) CAP only binds if no glucose -> no activation 2) Repressor blocks transcription if no lactose

52. lac operon Regulated by 2 proteins 1) CAP only binds if no glucose 2) Repressor blocks transcription if no lactose 3) Result: only make enzymes for using lactose if lactose is present and glucose is not

54. Result [  -galactosidase] rapidly rises if no glucose & lactose is present W/in 10 minutes is 6% of total protein!

55. Structure of Prokaryotic promoters Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter.

56. Structure of Prokaryotic promoters Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter. ↵

57. Structure of Prokaryotic promoters Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter. nrsBACD encode nickel transporters

58. Structure of Prokaryotic promoters Other sequences also often influence transcription! Bio502 plasmid contains the nickel promoter. nrsBACD encode nickel transporters nrsRS encode “two component” signal transducers nrsS encodes a his kinase nrsR encodes a response regulator

59. Structure of Prokaryotic promoters nrsRS encode “two component” signal transducers nrsS encodes a his kinase nrsR encodes a response regulator When nrsS binds Ni it kinases nrsR

60. Structure of Prokaryotic promoters nrsRS encode “two component” signal transducers nrsS encodes a his kinase nrsR encodes a response regulator When nrsS binds Ni it kinases nrsR nrsR binds Ni promoter and activates transcription of both operons

61. Termination of transcription in prokaryotes 1) Sometimes go until ribosomes fall too far behind

62. Termination of transcription in prokaryotes 1) Sometimes go until ribosomes fall too far behind 2) ~50% of E.coli genes require a termination factor called “rho”

63. Termination of transcription in prokaryotes 1) Sometimes go until ribosomes fall too far behind 2) ~50% of E.coli genes require a termination factor called “rho” 3) rrnB first forms an RNA hairpin, followed by an 8 base sequence TATCTGTT that halts transcription

64. Transcription in Eukaryotes 3 RNA polymerases all are multi-subunit complexes 5 in common 3 very similar variable # unique ones Now have Pols IV & V in plants Make siRNA

65. Transcription in Eukaryotes RNA polymerase I: 13 subunits (5 + 3 + 5 unique) acts exclusively in nucleolus to make 45S-rRNA precursor

66. Transcription in Eukaryotes Pol I: acts exclusively in nucleolus to make 45S-rRNA precursor accounts for 50% of total RNA synthesis

67. Transcription in Eukaryotes Pol I: acts exclusively in nucleolus to make 45S-rRNA precursor accounts for 50% of total RNA synthesis insensitive to  -aminitin

68. Transcription in Eukaryotes Pol I: only makes 45S-rRNA precursor 50 % of total RNA synthesis insensitive to  -aminitin Mg 2+ cofactor Regulated @ initiation frequency

69. RNA polymerase I promoter is 5' to "coding sequence" 2 elements 1) essential core includes transcription start site UCE -100 core +1 coding sequence

70. RNA polymerase I promoter is 5' to "coding sequence" 2 elements 1) essential core includes transcription start site 2) UCE (Upstream Control Element) at ~ -100 stimulates transcription 10-100x UCE -100 core +1 coding sequence

71. Initiation of transcription by Pol I Order of events was determined by in vitro reconstitution 1) UBF (upstream binding factor) binds UCE and core element UBF is a transcription factor: DNA-binding proteins which recruit polymerases and tell them where to begin

72. I nitiation of transcription by Pol I 1) UBF binds UCE and core element 2) SL1 (selectivity factor 1) binds UBF (not DNA) SL1 is a coactivator proteins which bind transcription factors and stimulate transcription