1. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16

2. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16 Spend ~ 5’ setting the stage: what is the general question? Why is it important? What was previously known? What were the outstanding questions?

3. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16 Spend ~ 5’ setting the stage: what is the general question? Why is it important? What was previously known? What were the outstanding questions? Then state the specific question addressed in your paper

4. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16 State the specific question addressed in your paper Next explain how they studied it General overview of techniques first, then specifics What were they trying to do? how did they do it?

5. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16 Then state the specific question addressed in your paper Next explain how they studied it General overview of techniques first, then specifics What were they trying to do? how did they do it? Then describe their results

6. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16 First state the specific question addressed in your paper Next explain how they studied it Then describe their results General overview first

7. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Prepare a 10’-15’ journal club about it for March 16 First state the specific question addressed in your paper Next explain how they studied it Then describe their results General overview first Then specific experiments

8. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it

9. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it Conclusions they drew

10. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it Conclusions they drew Your interpretation Do you agree? How could they improve?

11. Pick one of the papers listed at http://www.nature.com/collections/vbqgtr Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it Conclusions they drew Your interpretation Do you agree? How could they improve? Translation initiation mediated by RNA looping

12. PNAS 112: 1041-1046 (Jan 27, 2015)

13. Basic question: How do euk ribosomes find start codon?

14. Current model = ribosomal scanning: euk assemble 43S complex at 5’ cap and scan down to first AUG

15. Basic question: How do euk ribosomes find start codon? Current model = ribosomal scanning: euk assemble 43S complex at 5’ cap and scan down to first AUG Why don’t 40% of mRNA start at first AUG?

16. Basic question: How do euk ribosomes find start codon? Current model = ribosomal scanning: euk assemble 43S complex at 5’ cap and scan down to first AUG Why don’t 40% of mRNA start at first AUG? How do IRES (internal ribosome entry sites) work? Found in many viral mRNAs eg polio, picornavirus

17. Basic question: How do euk ribosomes find start codon? Current model = ribosomal scanning: euk assemble 43S complex at 5’ cap and scan down to first AUG Why don’t 40% of mRNA start at first AUG? How do IRES (internal ribosome entry sites) work? Found in many viral mRNAs eg polio, picornavirus Authors propose RNA-looping finds initiator AUG

18. Basic question: How do euk ribosomes find start codon? Authors propose RNA-looping finds initiator AUG proteins which bind near initiator AUG guide initiation complex

19. Basic question: How do euk ribosomes find start codon? Authors propose RNA-looping finds initiator AUG proteins which bind near initiator AUG guide initiation complex Tested by making constructs containing internal RNA- binding protein sites and measuring effect on translation

20. Authors propose RNA-looping finds initiator AUG proteins which bind near initiator AUG guide initiation complex Tested by making constructs containing internal RNA- binding protein sites and measuring effect on translation Made a fusion between eIF4G and the MS2-RNAbp, and then added MS2 binding sites at various places

21. eIF4G was mutated so it can’t bind eIF4E & PABP, yet it still associated with eIF3 & the 40S subunit

22. Made a fusion between eIF4G and the MS2-RNAbp, and then added MS2 binding sites at various places eIF4G was mutated so it can’t bind eIF4E & PABP, yet it still associated with eIF3 & the 40S subunit Capped the mRNA with A to ensure no eIF4E binding

23. Authors propose RNA-looping finds initiator AUG Made a fusion between eIF4G and the MS2-RNAbp, and then added MS2 binding sites at various places w/in mRNA encoding luciferase Assayed by transfection into HEK293 cells, then measuring firefly luciferase/Renilla luciferase activity 4 hours later

24. Assayed by transfection into HEK293 cells, then measuring firefly luciferase/Renilla luciferase activity No activity w/o eIF4G & MS2 binding site Stem-loop (which blocks back-tracking) had no effect

25. Assayed by transfection into HEK293 cells, then measuring firefly luciferase/Renilla luciferase activity No activity w/o eIF4G & MS2 binding site Stem-loop (which blocks back-tracking) had no effect

26. Assayed by transfection into HEK293 cells, then measuring firefly luciferase/Renilla luciferase activity No activity w/o eIF4G & MS2 binding site Stem-loop (which blocks back-tracking) had no effect Concluded that eIF4G bound to the mRNA was sufficient to guide 40S to the start codon

27. Next tested effect of the eIF4G binding on a downstream ORF Put Renilla luciferase & firefly Luciferase CDS on same mRNA

28. FLuc depended on eIF4G binding G-capped RLuc did not, but A-capped RLuc did

29. Put Renilla & firefly Luciferase CDS on same mRNA Observed same effect with the encephalomyocarditis virus (EMCV) IRES

30. Put Renilla & firefly Luciferase CDS on same mRNA Observed same effect with the encephalomyocarditis virus (EMCV) IRES Overall conclusion: RNA binding proteins that can interact with the 40S complex allow it to find the start codon by looping the RNA

31. PROTEIN TARGETING All proteins are made with an “address” which determines their final cellular location Addresses are motifs within proteins

32. PROTEIN TARGETING All proteins are made with “addresses” which determine their location Addresses are motifs within proteins Remain in cytoplasm unless contain information sending it elsewhere Targeting sequences are both necessary & sufficient to send reporter proteins to new compartments.

33. 2 Pathways in E.coli http://www.membranetransport.org/ 1.Tat: for periplasmic redox proteins & thylakoid lumen! Post-translational 2.Sec pathway Co-translational

34. Sec pathway part deux SRP binds preprotein as it emerges from rib & stops translation Guides rib to FtsY FtsY & SecA guide it to SecYEG, where it resumes translation & inserts protein into membrane as it is made

35. Periplasmic proteins with the correct signals (exposed after cleaving signal peptide) are exported by XcpQ system

36. PROTEIN TARGETING Protein synthesis always begins on free ribosomes in cytoplasm

37. 2 Protein Targeting pathways Protein synthesis always begins on free ribosomes in cytoplasm 1) proteins of plastids, mitochondria, peroxisomes and nuclei are imported post-translationally

38. 2 Protein Targeting pathways Protein synthesis always begins on free ribosomes in cytoplasm 1) proteins of plastids, mitochondria, peroxisomes and nuclei are imported post-translationally made in cytoplasm, then imported when complete

39. 2 Protein Targeting pathways Protein synthesis always begins on free ribosomes in cytoplasm 1) Post -translational: proteins of plastids, mitochondria, peroxisomes and nuclei 2) Endomembrane system proteins are imported co-translationally

40. 2 Protein Targeting pathways 1) Post -translational 2) Co-translational: Endomembrane system proteins are imported co-translationally inserted in RER as they are made

41. 2 pathways for Protein Targeting 1) Post -translational 2) Co-translational: Endomembrane system proteins are imported co-translationally inserted in RER as they are made transported to final destination in vesicles

42. SIGNAL HYPOTHESIS Protein synthesis always begins on free ribosomes in cytoplasm in vivo always see mix of free and attached ribosomes

43. SIGNAL HYPOTHESIS Protein synthesis begins on free ribosomes in cytoplasm endomembrane proteins have "signal sequence"that directs them to RER Signal sequence

44. SIGNAL HYPOTHESIS Protein synthesis begins on free ribosomes in cytoplasm endomembrane proteins have "signal sequence"that directs them to RER “attached” ribosomes are tethered to RER by the signal sequence

45. SIGNAL HYPOTHESIS Protein synthesis begins on free ribosomes in cytoplasm Endomembrane proteins have "signal sequence"that directs them to RER SRP (Signal Recognition Peptide) binds signal sequence when it pops out of ribosome & swaps GDP for GTP

46. SIGNAL HYPOTHESIS SRP (Signal Recognition Peptide) binds signal sequence when it pops out of ribosome & swaps GDP for GTP 1 RNA & 7 proteins

47. SIGNAL HYPOTHESIS SRP binds signal sequence when it pops out of ribosome SRP stops protein synthesis until it binds “docking protein”(SRP receptor) in RER

48. SIGNAL HYPOTHESIS SRP stops protein synthesis until it binds “docking protein”(SRP receptor) in RER Ribosome binds Translocon & secretes protein through it as it is made

49. SIGNAL HYPOTHESIS SRP stops protein synthesis until it binds “docking protein”(SRP receptor) in RER Ribosome binds Translocon & secretes protein through it as it is made BiP (a chaperone) helps the protein fold in the lumen

50. SIGNAL HYPOTHESIS Ribosome binds Translocon & secretes protein through it as it is made secretion must be cotranslational

51. Subsequent events Simplest case: 1) signal is cleaved within lumen by signal peptidase 2) BiP helps protein fold correctly 3) protein is soluble inside lumen

52. Subsequent events Complications: proteins embedded in membranes

53. proteins embedded in membranes protein has a stop-transfer sequence too hydrophobic to enter aqueous lumen

54. proteins embedded in membranes protein has a stop-transfer sequence too hydrophobic to enter aqueous lumen therefore gets stuck in membrane ribosome releases translocon, finishes job in cytoplasm

55. More Complications Some proteins have multiple trans-membrane domains (e.g. G-protein-linked receptors)

56. More Complications Explanation: combinations of stop-transfer and internal signals -> results in weaving the protein into the membrane

57. Sorting proteins made on RER Simplest case: no sorting proteins in RER lumen are secreted

58. Sorting proteins made on RER Simplest case: no sorting proteins in RER lumen are secreted embedded proteins go to plasma membrane

59. Sorting proteins made on RER Redirection requires extra information:

60. Sorting proteins made on RER Redirection requires extra information: 1) specific motif 2) receptors

61. Sorting proteins made on RER ER lumen proteins have KDEL (Lys-Asp-Glu-Leu) motif Receptor in Golgi binds & returns these proteins ER membrane proteins have KKXX motif

62. Sorting proteins made on RER Golgi membrane proteins cis- or medial- golgi proteins are marked by sequences in the membrane-spanning domain trans-golgi proteins have a tyrosine-rich sequence in their cytoplasmic C-terminus

63. Sorting proteins made on RER Plant vacuolar proteins are zymogens (proenzymes) signal VTS Barley aleurain Barley lectin mature protein

64. Sorting proteins made on RER Plant vacuolar proteins are zymogens (proenzymes), cleaved to mature form on arrival targeting motif may be at either end of protein signal VTS Barley aleurain Barley lectin mature protein

65. Sorting proteins made on RER lysosomal proteins are targeted by mannose 6-phosphate M 6-P receptors in trans-Golgi direct protein to lysosomes (via endosomes) M 6-P is added in Golgi by enzyme that recognizes lysosomal motif