1. Next Presentation 1.Alternative splicing 2.Alternative polyadenylation 3.Transcriptional pausing 4.Translation enhancement by RNA looping 5.ncRNA transcriptional enhancers 6.exosomes 7.RNA transport 8.Regulation of translation

2. mRNA PROCESSING Primary transcript is hnRNA undergoes 3 processing reactions before export to cytosol All three are coordinated with transcription & affect gene expression: enzymes piggy-back on POLII

3. mRNA PROCESSING 1) Capping 2) Splicing: removal of introns Evidence: electron microscopy sequence alignment

4. Splicing:The spliceosome cycle

5. Splicing: Some RNAs can self-splice! role of snRNPs is to increase rate! Why splice?

6. Splicing: Why splice? 1) Generate diversity exons often encode protein domains

7. Splicing: Why splice? 1) Generate diversity exons often encode protein domains Introns = larger target for insertions, recombination

8. Why splice? 1) Generate diversity >94% of human genes show alternate splicing

9. Why splice? 1) Generate diversity >94% of human genes show alternate splicing same gene encodes different protein in different tissues

10. Why splice? 1) Generate diversity >94% of human genes show alternate splicing same gene encodes different protein in different tissues Stressed plants use AS to make variant stress-response proteins

11. Why splice? 1) Generate diversity >94% of human genes show alternate splicing same gene encodes different protein in different tissues Stressed plants use AS to make variant Stress-response proteins Splice-regulator proteins control AS: regulated by cell-specific expression and phosphorylation

12. Why splice? 1)Generate diversity Trabzuni D, et al (2013)Nat Commun. 22:2771. Found 448 genes that were expressed differently by gender in human brains (2.6% of all genes expressed in the CNS). All major brain regions showed some gender variation, and 85% of these variations were due to RNA splicing differences

13. Why splice? 1)Generate diversity Wilson LOW, Spriggs A, Taylor JM, Fahrer AM. (2014). A novel splicing outcome reveals more than 2000 new mammalian protein isoforms. Bioinformatics 30: 151-156 Splicing created a frameshift, so was annotated as “nonsense-mediated decay” an alternate start codon rescued the protein, which was expressed

14. Why splice? Splicing created a frameshift, so was annotated as “nonsense-mediated decay” an alternate start codon rescued the protein, which was expressed Found 1849 human & 733 mouse mRNA that could encode alternate protein isoforms the same way So far 64 have been validated by mass spec

15. Splicing: Why splice? 1) Generate diversity 2) Modulate gene expression introns increase amount of mRNA produced Especially introns near the 5’ end of coding sequence

16. Splicing: Why splice? 1) Generate diversity 2) Modulate gene expression introns increase amount of mRNA produced Especially introns near the 5’ end of coding sequence Also increase export from nucleus, translation efficiency & half-life

17. Coordination of mRNA processing Splicing and polyadenylation factors bind CTD of RNA Pol II-> mechanism to coordinate the three processes Capping, Splicing and Polyadenylation all start before transcription is done!

18. Export from Nucleus Occurs through nuclear pores anything > 40 kDa needs exportin protein bound to 5’ cap

19. Export from Nucleus In cytoplasm nuclear proteins fall off, new proteins bind eIF4E/eIF-4F bind cap also new proteins bind polyA tail mRNA is ready to be translated!

20. Cytoplasmic regulation lifetime localization initiation

21. Post-transcriptional regulation Nearly ½ of human genome is transcribed, only 1% is CDS 98% of RNA made is non-coding

22. Post-transcriptional regulation Nearly ½ of human genome is transcribed, only 1% is CDS 98% of RNA made is non-coding ~1/3 intron

23. Post-transcriptional regulation Nearly ½ of human genome is transcribed, only 1% is CDS 98% of RNA made is non-coding ~1/3 intron ~2/3 “independently transcribed”

24. Post-transcriptional regulation Nearly ½ of human genome is transcribed, only 1% is CDS 98% of RNA made is non-coding ~1/3 intron ~2/3 “independently transcribed” Polymerases II & III (+ IV & V in plants) all help

25. Post-transcriptional regulation Nearly ½ of human genome is transcribed, only 1% is CDS 98% of RNA made is non-coding ~1/3 intron ~2/3 “independently transcribed” Polymerases II & III (+ IV & V in plants) all help many are from transposons or gene fragments made by transposons (pack-MULES)

26. Post-transcriptional regulation Nearly ½ of human genome is transcribed, only 1% is CDS 98% of RNA made is non-coding ~1/3 intron ~2/3 “independently transcribed” Polymerases II & III (+ IV & V in plants) all help many are from transposons or gene fragments made by transposons (pack-MULES) ~ 10-25% is anti-sense: same region is transcribed off both strands

27. Thousands of antisense transcripts in plants 1.Overlapping genes

28. Thousands of antisense transcripts in plants 1.Overlapping genes 2.Non-coding RNAs

29. Thousands of antisense transcripts in plants 1.Overlapping genes 2.Non-coding RNAs 3.cDNA pairs

30. Thousands of antisense transcripts in plants 1.Overlapping genes 2.Non-coding RNAs 3.cDNA pairs 4.MPSS

31. Thousands of antisense transcripts in plants 1.Overlapping genes 2.Non-coding RNAs 3.cDNA pairs 4.MPSS 5.TARs

32. Thousands of antisense transcripts in plants Hypotheses 1.Accident: transcription unveils “cryptic promoters” on opposite strand (Zilberman et al)

33. Hypotheses 1. Accident: transcription unveils “cryptic promoters” on opposite strand (Zilberman et al) 2. Functional a.siRNA b.miRNA c.Silencing

34. Hypotheses 1. Accident: transcription unveils “cryptic promoters” on opposite strand (Zilberman et al) 2. Functional a.siRNA b.miRNA c.Silencing d.Priming: chromatin remodeling requires transcription!

35. Post-transcriptional regulation RNA degradation is crucial with so much “extra” RNA

36. Post-transcriptional regulation RNA degradation is crucial with so much “extra” RNA mRNA lifespan varies 100x Highly regulated! > 30 RNAses in Arabidopsis!

37. Post-transcriptional regulation mRNA degradation lifespan varies 100x Sometimes due to AU-rich 3' UTR sequences (DST)

38. mRNA degradation lifespan varies 100x Sometimes due to AU-rich 3' UTR sequences (DST) Endonuclease cuts DST, then exosome digests 3’->5’ & XRN1 digests 5’->3’

39. mRNA degradation Most are degraded by de-Adenylation pathway Deadenylase removes tail

40. mRNA degradation Most are degraded by de-Adenylation pathway Deadenylase removes tail Exosome digests 3’ -> 5’

41. mRNA degradation Most are degraded by de-Adenylation pathway Deadenylase removes tail Exosome digests 3’ -> 5’ Or, decapping enz removes cap & XRN1 digests 5’ ->3’

42. Post-transcriptional regulation mRNA degradation: mRNA is checked & defective transcripts are degraded = mRNA surveillance 1.Nonsense-mediated decay:EJC @ each splice junction that is displaced by ribosome

43. Post-transcriptional regulation mRNA degradation: mRNA is checked & defective transcripts are degraded = mRNA surveillance 1.Nonsense-mediated decay:EJC @ each splice junction that is displaced by ribosome 2.If not-displaced, is cut by endonuclease & RNA is degraded

44. Post-transcriptional regulation mRNA degradation: mRNA is checked & defective transcripts are degraded = mRNA surveillance Non-stop decay: Ribosome goes to end & cleans off PABP

45. Post-transcriptional regulation mRNA degradation: mRNA is checked & defective transcripts are degraded = mRNA surveillance Non-stop decay: Ribosome goes to end & cleans off PABP w/o PABP exosome eats mRNA

46. Post-transcriptional regulation mRNA degradation: mRNA is checked & defective transcripts are degraded = mRNA surveillance No-go decay: cut RNA 3’ of stalled ribosomes

47. Post-transcriptional regulation mRNA degradation lifespan varies 100x Sometimes due to AU-rich 3' UTR sequences Defective mRNA may be targeted by NMD, NSD, NGD Other RNA are targeted by small interfering RNA

48. Post-transcriptional regulation Other mRNA are targeted by small interfering RNA defense against RNA viruses DICERs cut dsRNA into 21-28 bp

49. Post-transcriptional regulation Other mRNA are targeted by small interfering RNA defense against RNA viruses DICERs cut dsRNA into 21-28 bp helicase melts dsRNA

50. Post-transcriptional regulation Other mRNA are targeted by small interfering RNA defense against RNA viruses DICERs cut dsRNA into 21-28 bp helicase melts dsRNA - RNA binds RISC

51. Post-transcriptional regulation Other mRNA are targeted by small interfering RNA defense against RNA viruses DICERs cut dsRNA into 21-28 bp helicase melts dsRNA - RNA binds RISC complex binds target

52. Post-transcriptional regulation Other mRNA are targeted by small interfering RNA defense against RNA viruses DICERs cut dsRNA into 21-28 bp helicase melts dsRNA - RNA binds RISC complex binds target target is cut

53. Cytoplasmic regulation Small RNA regulation siRNA: target RNA viruses (& transgenes) miRNA: arrest translation of targets created by digestion of foldback Pol II RNA with mismatch loop

54. Cytoplasmic regulation Small RNA regulation siRNA: target RNA viruses (& transgenes) miRNA: arrest translation of targets created by digestion of foldback Pol II RNA with mismatch loop Mismatch is key difference: generated by different Dicer

55. Cytoplasmic regulation Small RNA regulation siRNA: target RNA viruses (& transgenes) miRNA: arrest translation of targets created by digestion of foldback Pol II RNA with mismatch loop Mismatch is key difference: generated by different Dicer Arrest translation in animals, target degradation in plants

56. small interfering RNA mark specific targets once cut they are removed by endonuclease-mediated decay

58. Most RNA degradation occurs in P bodies recently identified cytoplasmic sites where exosomes & XRN1 accumulate when cells are stressed

59. Most RNA degradation occurs in P bodies recently identified cytoplasmic sites where exosomes & XRN1 accumulate when cells are stressed Also where AGO & miRNAs accumulate

60. Most RNA degradation occurs in P bodies recently identified cytoplasmic sites where exosomes & XRN1 accumulate when cells are stressed Also where AGO & miRNAs accumulate w/o miRNA P bodies dissolve!

61. Post-transcriptional regulation 1) mRNA processing 2) export from nucleus 3) mRNA degradation 4) mRNA localization RNA-binding proteins link it to cytoskeleton: bring it to correct site or store it

62. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA (eg Knotted) are transported into neighboring cells

63. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1)

64. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1) Also some siRNA & miRNA!

65. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1) Also some siRNA & miRNA! siRNA mediate silencing Especially of viruses & TE

66. 4) mRNA localization RNA-binding proteins link it to cytoskeleton:bring it to correct site or store it Some RNA are transported into neighboring cells Others are transported t/o the plant in the phloem (SUT1, KN1) Also some siRNA & miRNA! siRNA mediate silencing MiR399 moves to roots to destroy PHO2 mRNA upon Pi stress PHO2 negatively regulates Pi uptake

67. Post-transcriptional regulation RNA in pollen controls first division after fertilization!

68. Post-transcriptional regulation RNA in pollen controls first division after fertilization! Delivery by pollen ensures correct development doesn’t happen unless egg is fertilized by pollen

69. Post-transcriptional regulation 4) mRNA localization RNA-binding proteins link it to cytoskeleton: bring it to correct site or store it many are stored in P-bodies! More than just an RNA- destruction site

70. Post-transcriptional regulation 4) mRNA localization RNA-binding proteins link it to cytoskeleton: bring it to correct site or store it many are stored in P-bodies! More than just an RNA- destruction site Link with initiation of translation

71. Initiation in Prokaryotes 1) IF1 & IF3 bind 30S subunit, complex binds 5' mRNA

72. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D

73. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D Next AUG is Start codon, must be w/in 7-13 bases

74. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D 3)IF2-GTP binds tRNA i fMet complex binds start codon

75. Initiation in Prokaryotes 1)IF1 & IF3 bind 30S subunit, complex binds 5' mRNA 2)Complex scans down until finds Shine-Dalgarno sequence, 16S rRNA binds S-D 3)IF2-GTP binds tRNA i fMet complex binds start codon 4)Large subunit binds IF2-GTP -> IF2-GDP tRNA i fMet is in P site IFs fall off

76. Elongation 1) EF-Tu brings charged tRNA into A site

77. Elongation 1) EF-Tu brings charged tRNA into A site anticodon binds mRNA codon, EF-Tu-GTP - > EF-Tu-GDP

78. Elongation 1) EF-Tu brings charged tRNA into A site anticodon binds codon, EF-Tu-GTP -> EF-Tu-GDP 2) ribosome bonds growing peptide on tRNA at P site to a.a. on tRNA at A site

79. Elongation 1) EF-Tu brings charged tRNA into A site anticodon binds codon, EF-Tu-GTP -> EF-Tu-GDP 2) ribosome bonds growing peptide on tRNA at P site to a.a. on tRNA at A site peptidyl transferase is 23S rRNA!

80. Elongation 3) ribosome translocates one codon old tRNA moves to E site & exits new tRNA moves to P site A site is free for next tRNA energy comes from EF-G-GTP -> EF-G-GDP+ Pi

81. Wobbling 1 st base of anticodon can form unusual pairs with 3 rd base of codon

82. Wobbling 1 st base of anticodon can form unusual pairs with 3 rd base of codon

83. Wobbling 1 st base of anticodon can form unusual pairs with 3 rd base of codon Reduces # tRNAs needed: bacteria have 40 or less (bare minimum is 31 + initiator tRNA) Eukaryotes have ~ 50

84. Termination 1) Process repeats until a stop codon is exposed 2) release factor binds nonsense codon 3 stop codons = 3 RF in prokaryotes (1 RF binds all 3 stop codons in euk)

85. Termination 1) Process repeats until a stop codon is exposed 2) release factor binds nonsense codon 3 stop codons = 3 RF in prokaryotes (1 RF binds all 3 stop codons in euk) 3) Releases peptide from tRNA at P site 4) Ribosome falls apart

86. Poisons Initiation: streptomycin, kanamycin Elongation: peptidyl transferase: chloramphenicol (prok) cycloheximide (euk) translocation erythromycin (prok) diptheria toxin (euk) Puromycin causes premature termination

87. Initiation in Eukaryotes 1)eIF4E binds mRNA cap Won’t bind unless 5’cap is methylated

88. Initiation in Eukaryotes 1)eIF4E binds mRNA cap Won’t bind unless 5’cap is methylated eIF4E & PABP protect RNA from degradation

89. Initiation in Eukaryotes 1)eIF4E binds mRNA cap Won’t bind unless 5’cap is methylated eIF4E & PABP protect RNA from degradation eIF4E must be kinased to be active

90. Initiation in Eukaryotes 1)eIF4E binds mRNA cap Won’t bind unless 5’cap is methylated eIF4E & PABP protect RNA from degradation eIF4E must be kinased to be active XS = cancer

91. Initiation in Eukaryotes 1)eIF4E binds mRNA cap 2)eIF4G binds eIF4E, eIF4A & PAB: complex = eIF4F

92. Initiation in Eukaryotes 1)eIF4E binds mRNA cap 2)eIF4G binds eIF4E, eIF4A & PAB: complex = eIF4F 3) i tRNA :met & eIF1, eIF2 & eIF3 bind 40S subunit

93. Initiation in Eukaryotes 3) i tRNA :met & eIF1, eIF2 & eIF3 bind 40S subunit 4)43S complex binds eIF4F 5)eIF4A & eIF4B scan down & melt mRNA (using ATP)

94. Initiation in Eukaryotes 3) i tRNA :met & eIF1, eIF2 & eIF3 bind 40S subunit 4)43S complex binds eIF4F 5)eIF4A & eIF4B scan down & melt mRNA (using ATP) 6)43S follows until finds Kozak sequence 5’-ACCAUG

95. Initiation in Eukaryotes 7) initiator tRNA:met binds start codon (AUG), eIF2 hydrolyzes GTP

96. Initiation in Eukaryotes 8) 60S subunit binds i tRNA :met is at P site ribosome thinks it is a protein! why 60S subunit doesn’t bind until i tRNA :met binds AUG why have i tRNA :met

97. Regulation 1)Key step = eIF4E binds mRNA cap Won’t bind unless 5’cap is methylated eIF4E must be kinased to be active 4E-BP1 binds eIF4E & keeps it inactive until kinased

98. Regulating Translation 1)eIF4F is also regulated many other ways!

99. Post-transcriptional regulation 2) Other key step = eIF2

100. Post-transcriptional regulation 2) Other key step = eIF2 controls assembly of 43S

101. Post-transcriptional regulation 2) Other key step = eIF2 controls assembly of 43S Highly regulated!

102. Post-transcriptional regulation 2) Other key step = eIF2 controls assembly of 43S Highly regulated! Inactive if kinased = virus defence

103. Post-transcriptional regulation initiation of translation varies >10x 5' UTR sequences also affect rate

104. Post-transcriptional regulation initiation of translation varies >10x 5' UTR sequences also affect rate some adopt 2˚ structures hard to melt

105. Post-transcriptional regulation initiation of translation varies >10x 5' UTR sequences also affect rate some adopt 2˚ structures hard to melt

106. Post-transcriptional regulation initiation of translation varies >10x 5' UTR sequences also affect rate some adopt 2˚ structures hard to melt proteins bind others, enhance or repress translation

107. Post-transcriptional regulation initiation of translation varies >10x 5' UTR sequences also affect rate some adopt 2˚ structures hard to melt proteins bind others, enhance or repress translation microRNA bind specific mRNA & block translation

108. Post-transcriptional regulation initiation of translation varies >10x 5' UTR sequences also affect rate some adopt 2˚ structures hard to melt proteins bind others, enhance or repress translation microRNA bind specific mRNA & block translation Many bind 3’UTR!

109. Post-transcriptional regulation 1) mRNA processing 2) export from nucleus 3) mRNA degradation 4) mRNA localization 5) initiation of translation varies >10x 6) regulating enzyme activity activators Inhibitors Covalent mods

110. Post-transcriptional regulation Protein degradation rate varies 100x Some have motifs, eg Destruction box, marking them for polyubiquitination : taken to proteasome & destroyed

111. Post-transcriptional regulation Protein degradation rate varies 100x Some have motifs, eg Destruction box, marking them for polyubiquitination : taken to proteasome & destroyed N-terminal rule: Proteins with N-terminal Phe, Leu, Asp, Lys, or Arg have half lives of 3 min or less.

112. Protein degradation Some have motifs marking them for polyubiquitination : E1 enzymes activate ubiquitin E2 enzymes conjugate ubiquitin E3 ub ligases determine specificity, eg for N-terminus

113. Protein degradation E3 ub ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein

114. E3 ubiquitin ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein RBX1 (or similar) positions E2

115. E3 ubiquitin ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein RBX1 (or similar) positions E2 Linker (eg DDB1) positions substrate receptor

116. E3 ubiquitin ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein RBX1 (or similar) positions E2 Linker (eg DDB1) positions substrate receptor Substrate receptor (eg DCAF/DWD) picks substrate >100 DWD in Arabidopsis

117. E3 ubiquitin ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein RBX1 (or similar) positions E2 Linker (eg DDB1) positions substrate receptor Substrate receptor (eg DCAF/DWD) picks substrate NOT4 is an E3 ligase & a component of the CCR4–NOT de-A complex

118. E3 ubiquitin ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein RBX positions E2 DDB1 positions DCAF/DWD DCAF/DWD picks substrate: >85 DWD in rice NOT4 is an E3 ligase & a component of the CCR4–NOT de-A complex CCR4–NOT de-A Complex regulates pol II

119. E3 ubiquitin ligases determine specificity >1300 E3 ligases in Arabidopsis 4 main classes according to cullin scaffolding protein RBX positions E2 DDB1 positions DCAF/DWD DCAF/DWD picks substrate NOT4 is an E3 ligase & a component of the CCR4–NOT de-A complex CCR4–NOT de-A Complex regulates pol II Transcription, mRNA deg & prot deg are linked!

120. E3 ubiquitin ligases determine specificity Cell cycle: Anaphase Promoting Complex is an E3 ligase. MPF induces APC APC inactive until all kinetochores are bound APC then tags securin to free separase: cuts proteins linking chromatids

121. E3 ubiquitin ligases determine specificity MPF induces APC APC inactive until all kinetochores are bound APC then tags securin to free separase: cuts proteins linking chromatids APC next swaps Cdc20 for Cdh1 & tags cyclin B to enter G1

122. E3 ubiquitin ligases determine specificity APC next tags cyclin B (destruction box) to enter G1 APC also targets Sno proteins in TGF-  signaling Sno proteins prevent Smad from activating genes

123. E3 ubiquitin ligases determine specificity APC also targets Sno proteins in TGF-  signaling Sno proteins prevent Smad from activating genes APC/Smad2/Smad3 tags Sno for destruction

124. E3 ubiquitin ligases determine specificity APC also targets Sno proteins in TGF-  signaling Sno proteins prevent Smad from activating genes APC/Smad2/Smad3 tags Sno for destruction Excess Sno = cancer

125. E3 ubiquitin ligases determine specificity APC also targets Sno proteins in TGF-  signaling Sno proteins prevent Smad from activating genes APC/Smad2/Smad3 tags Sno for destruction Excess Sno = cancer Angelman syndrome = bad UBE3A Only express maternal allele because paternal allele is methylated

126. Auxin signaling Auxin receptors eg TIR1 are E3 ubiquitin ligases Upon binding auxin they activate complexes targeting AUX/IAA proteins for degradation

127. Auxin signaling Auxin receptors eg TIR1 are E3 ubiquitin ligases! Upon binding auxin they activate complexes targeting AUX/IAA proteins for degradation AUX/IAA inhibit ARF transcription factors, so this turns on "early genes"

128. Auxin signaling Auxin receptors eg TIR1 are E3 ubiquitin ligases! Upon binding auxin they activate complexes targeting AUX/IAA proteins for degradation! AUX/IAA inhibit ARF transcription factors, so this turns on "early genes" Some early genes turn on 'late genes" needed for development

129. DWD Proteins Jae-Hoon Lee’s research putative substrate receptors for CUL4-based E3 ligases

130. DWD Proteins Jae-Hoon Lee’s research putative substrate receptors for CUL4-based E3 ligases used bioinformatics to find all Arabidopsis & rice DWDs

131. DWD Proteins used bioinformatics to find all Arabidopsis & rice DWDs Placed in subgroups based on DWD sequence

132. DWD Proteins used bioinformatics to find all Arabidopsis & rice DWDs Placed in subgroups based on DWD sequence Tested members of each subgroup for DDB1 binding

133. DWD Proteins Tested members of each subgroup for DDB1 binding co-immunoprecipitation

134. DWD Proteins Tested members of each subgroup for DDB1 binding co-immunoprecipitation Two-hybrid: identifies interacting proteins

135. DWD Proteins Tested members of each subgroup for DDB1 binding co-immunoprecipitation Two-hybrid: identifies interacting proteins Only get transcription if one hybrid supplies Act D & other supplies DNA Binding Domain

136. DWD Proteins Two-hybrid libraries are used to screen for protein-protein interactions

137. DWD Proteins Tested members of each subgroup for DDB1 binding co-immunoprecipitation Two-hybrid

138. DWD Proteins Tested members of each subgroup for DDB1 binding co-immunoprecipitation Cul4cs &PRL1 (Pleiotropic Regulatory Locus 1) had Similar phenotypes

139. DWD Proteins Cul4cs &PRL1 (PleiotropicRegulatory Locus 1) had similar phenotypes PRL1 may be receptor for AKIN10 degradation (involved in sugar sensing)

140. DWD Proteins Found T-DNA insertions 3 were sensitive to ABA

141. DWD Proteins Found T-DNA insertions 3 were sensitive to ABA ABI5 was elevated in dwa mutants

142. DWD Proteins Found T-DNA insertions 3 were sensitive to ABA ABI5 was elevated in dwa mutants ABI5 was degraded more slowly in dwa extracts

143. DWD Proteins Found T-DNA insertions 3 were sensitive to ABA ABI5 was elevated in dwa mutants ABI5 was degraded more slowly in dwa extracts DWA1 & DWA2 target ABI5 for degradation

144. Regulating E3 ligases The COP9 signalosome (CSN), a complex of 8 proteins, regulates E3 ligases by removing Nedd8 from cullin

145. Regulating E3 ligases The COP9 signalosome (CSN), a complex of 8 proteins, regulates E3 ligases by removing Nedd8 from cullin CAND1 then blocks cullin

146. Regulating E3 ligases The COP9 signalosome (CSN), a complex of 8 proteins, regulates E3 ligases by removing Nedd8 from cullin CAND1 then blocks cullin Ubc12 replaces Nedd8

147. Regulating E3 ligases The COP9 signalosome (CSN), a complex of 8 proteins, regulates E3 ligases by removing Nedd8 from cullin CAND1 then blocks cullin Ubc12 replaces Nedd8 Regulates DNA-damage response, cell-cycle & gene expression

148. Regulating E3 ligases The COP9 signalosome (CSN), a complex of 8 proteins, regulates E3 ligases by removing Nedd8 from cullin CAND1 then blocks cullin Ubc12 replaces Nedd8 Regulates DNA-damage response, cell-cycle & gene expression Not all E3 ligases associate with Cullins!

149. COP1 is a non-cullin-associated E3 ligase Protein degradation is important for light regulation COP1/SPA1 tags transcription factors for degradation W/O COP1 they act in dark In light COP1 is exported to cytoplasm so TF can act

150. COP1 is a non-cullin-associated E3 ligase Recent data indicates that COP1 may also associate with CUL4

151. Protein degradation rate varies 100x Most have motifs marking them for polyubiquitination : taken to proteosome & destroyed Other signals for selective degradation include PEST & KFERQ PEST : found in many rapidly degraded proteins e.g. ABCA1 (which exports cholesterol in association with apoA-I) is degraded by calpain

152. Protein degradation rate varies 100x Other signals for selective degradation include PEST & KFERQ PEST : found in many rapidly degraded proteins e.g. ABCA1 (which exports cholesterol in association with apoA-I) is degraded by calpain Deletion increases t 1/2 10x, adding PEST drops t 1/2 10x

153. Protein degradation rate varies 100x Other signals for selective degradation include PEST & KFERQ PEST : found in many rapidly degraded proteins e.g. ABCA1 (which exports cholesterol in association with apoA-I) is degraded by calpain Deletion increases t 1/2 10x, adding PEST drops t 1/2 10x Sometimes targets poly-Ub

154. Protein degradation rate varies 100x Other signals for selective degradation include PEST & KFERQ PEST : found in many rapidly degraded proteins e.g. ABCA1 (which exports cholesterol in association with apoA-I) is degraded by calpain Deletion increases t 1/2 10x, adding PEST drops t 1/2 10x Sometimes targets poly-Ub Recent yeast study doesn’t support general role

155. Protein degradation rate varies 100x Other signals for selective degradation include PEST & KFERQ PEST : found in many rapidly degraded proteins e.g. ABCA1 (which exports cholesterol in association with apoA-I) is degraded by calpain Deletion increases t 1/2 10x, adding PEST drops t 1/2 10x Sometimes targets poly-Ub Recent yeast study doesn’t support general role KFERQ: cytosolic proteins with KFERQ are selectively taken up by lysosomes in chaperone-mediated autophagy under conditions of nutritional or oxidative stress.

156. Protein degradation in bacteria Also highly regulated, involves chaperone-like proteins 1.Lon

157. Protein degradation in bacteria Also highly regulated, involves chaperone like proteins 1.Lon 2.Clp

158. Protein degradation in bacteria Also highly regulated, involves chaperone like proteins 1.Lon 2.Clp 3.FtsH in IM

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

160. 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

161. PROTEIN TARGETING Targeting sequences are both necessary & sufficient to send reporter proteins to new compartments.

162. PROTEIN TARGETING 2 Pathways in E.coli http://www.membranetransport.org/ 1.Tat: for periplasmic redox proteins & thylakoid lumen!

163. 2 Pathways in E.coli 1.Tat: for periplasmic redox proteins & thylakoid lumen! Preprotein has signal seqS/TRRXFLK

164. 2 Pathways in E.coli 1.Tat: for periplasmic redox proteins & thylakoid lumen! Preprotein has signal seqS/TRRXFLK Make preprotein, folds & binds cofactor in cytosol

165. 2 Pathways in E.coli 1.Tat: for periplasmic redox proteins & thylakoid lumen! Preprotein has signal seqS/TRRXFLK Make preprotein, folds & binds cofactor in cytosol Binds Tat in IM & is sent to periplasm

166. 2 Pathways in E.coli 1.Tat: for periplasmic redox proteins & thylakoid lumen! Preprotein has signal seqS/TRRXFLK Make preprotein, folds & binds cofactor in cytosol Binds Tat in IM & is sent to periplasm Signal seq is removed in periplasm

167. 2 Pathways in E.coli http://www.membranetransport.org/ 1.Tat: for periplasmic redox proteins & thylakoid lumen! 2.Sec pathway SecB binds preprotein as it emerges from rib

168. Sec pathway SecB binds preprotein as it emerges from rib & prevents folding

169. Sec pathway SecB binds preprotein as it emerges from rib & prevents folding Guides it to SecA, which drives it through SecYEG into periplasm using ATP

170. Sec pathway SecB binds preprotein as it emerges from rib & prevents folding Guides it to SecA, which drives it through SecYEG into periplasm using ATP In periplasm signal peptide is removed and protein folds

171. 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

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

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

174. 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

175. 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

176. 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

177. 2 Protein Targeting pathways 1) Post -translational 2) Co-translational: Endomembrane system proteins are imported co-translationally inserted in RER as they are made

178. 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

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

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

181. 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

182. 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