1. What are the differences between prokaryotes and eukaryotes on the initiation of TRANSCRIPTION and TRANSLATION?

2. Why is gene expression tightly regulated?
For prokaryotes, it is the way that organisms adapt to the environment.
For eukaryotes
Gene expression differs among cell types: cell differentiation
Is involved in development
Is associated with physiology and pathology
Genotype+expression level (affected by environment)=phenotype

3. Gene expression regulation is different between prokaryotes and eukaryotes due to the differences in
Cellular structure
Existing form of genomic DNA
Complexity in gene expression

4. A10 Regulation of gene expression in prokaryotes

5. Regulation of gene expression
Organization of bacterial genes
The lac operon
Catabolite repression
The trp operon
Attenuation
Regulation by alternative sigma factors

6. 1. Regulation of gene expression
Regulation of gene expression allows bacteria to respond to changes in their environment, typically to the presence or absence of nutrients.
Balance between the rate of synthesis [‘sinθisis] and the rate of degradation
[ degrə'deɪʃən]

7. Factors that alter the rate of synthesis:
Changes in the rate of gene transcription, the best understood
Changes in mRNA turnover time（更新的时间）
Changes in the rate of translation

8. 2. Organization of bacterial genes
Important feature: operon['ɔpə,rɔn], transcriptional units in which several genes, usually encoding proteins with related functions, are regulated together
操纵子：是原核生物基因表达和调控的单位，由启动子、操纵基因（调控）及其所控制的一组功能上相关的结构基因所组成。操纵基因受调节基因产物的控制。

9. Operon proposed by Jacob & Monad 1961

10. In 1961, Jacob and Monod found the difference between two types of sequences in DNA: sequences that code for trans-acting products（反式作用因子）; and cis-acting sequences（顺式作用序列） that function exclusively within the DNA. Gene activity is regulated by the specific interactions of the trans-acting products (usually proteins) with the cis-acting sequences (usually sites in DNA).

11. A gene (反式作用 products) a sequence of DNA that codes for a product
A gene (反式作用 products) a sequence of DNA that codes for a product. This product may be protein (as in the case of the majority of genes) or may be RNA (as in the case of genes that code for tRNA and rRNA etc.).
The crucial feature is that the product
diffuses away from its site of synthesis to
act elsewhere.
一种基因的蛋白质产物，能影响位于基因组另一条染色体上的（或基因组别处的）另一个基因的活性，这种作用叫做反式作用。参与这种反式作用的特定因子叫做反式作用因子，一般指的是蛋白质，它能够通过与顺式作用元件（DNA）之间的相互作用而影响基因的表达。

12. The cis-acting sequence functions exclusively as a DNA sequence, affecting only the DNA to which it is physically linked. (In some cases, a cis-acting sequence functions in an RNA rather than in a DNA molecule, such as RNA termintor)
影响自身基因表达活性的非编码DNA序列。

13. Classification of operons:
Inducible operons（可诱导操纵子）: contain genes that encode enzymes involved in metabolic pathways. e.g. lac operon
Repressible operons（可阻遏操纵子): contain genes that encode enzymes involved in biosynthetic pathways and gene expression is controlled by the end product of the pathway e.g. trp operon

14. Positive regulation（正调控）：有调节蛋白（激活蛋白）存在时基因表达开启，没有调节蛋白存在时则基因的表达关闭 ；
Negative regulation（负调控）：在调节蛋白（阻遏蛋白）存在时基因的表达关闭，无调节蛋白时基因的表达得以开启。
正、负调控中调节蛋白都是反式作用因子，通常识别基因上有的顺式作用元件

15. 3. The lac operon Three enzymes for the metabolism of lactose:
Lactose permease β半乳糖苷通透酶(Lac Y): transport lactose into the cell
β-galatosidase β半乳糖苷酶(Lac Z): hydrolyzes lactose into glucose and galactose
（把乳糖分解为葡萄糖和半乳糖）
Transacetylase β半乳糖苷转乙酰基酶(Lac A): hydrolysis [hai’drɔlisis]

16. Z编码β-半乳糖苷酶：将乳糖水解成葡萄糖和半乳糖
Y编码β-半乳糖苷透过酶：使外界的β-半乳糖苷（如乳糖）能透过大肠杆菌细胞壁和原生质膜进入细胞内。
A编码β-半乳糖苷乙酰基转移酶：乙酰辅酶A上的乙酰基转到β-半乳糖苷上，形成乙酰半乳糖。

17. 乳糖操纵子的结构

18. Control elements repressor P Y β-Galactosidase I Operon O Z A -5 +21
Regulatory Gene P O Z Y A
DNA
m-RNA
β-Galactosidase
Permease
Transacetylase
Protein
Control elements -5
+21
repressor

19. 乳糖操纵子的结构

20. Lac Z, Y and A are transcribed as a single mRNA （多顺反子mRNA) from a single promoter. Lac I lies upstream of the operon and encodes lac repressor, which regulates the expression of Lac Z, Y and A genes.
LacI 表达阻遏物。操纵基因（O）是DNA上的一小段序列（仅为26bp），是阻遏物的结合位点。

21. P Y Control elements repressor -5 +21 I Z A β-Galactosidase Operon O
Regulatory Gene P O Z Y A
DNA
m-RNA
β-Galactosidase
Permease
Transacetylase
Protein
Control elements -5
+21
repressor

22. Lac repressor -5
+21
Plac
Lac repressor is encoded by LacI, which is active as a tetramer of identical subunits. It occupies the operator-binding site Olac (28bp, palindromic) and blocks almostly all transcription of lacZYA when lack of inducer (such as lactose).

23. Lactose metabolism in E. coli: An Inducible System

24. In the absence of lactose
Lac repressor binds to operator
Blocks the path of the RNA polymerase move through the lac promoter and operator
Prevents the transcription of lac genes

25. When lactose present
A few molecules of the lac enzymes present in the cell allow lactose to be taken up and metabolized
Lactose becomes allolactose, the latter binds to the lac repressor and changes its conformation such that it can no longer binds to the operator
The block is removed and the operon is transcribed
When the lactose is used up, lac repressor returns to its original conformation, again block transcription

27. 4. Catabolite repression
Catabolite repression: the presence of glucose in the cell switches off the lac operon
葡糖糖存在时，只利用其作为能量代谢来源物质，对乳糖的存在视而不见，因而乳糖相关的酶类也无需表达。
葡萄糖可以抑制腺苷酸环化酶的活性。
In the presence of cAMP, CAP (catabolite activator protein) binds to a DNA sequence upstream of the lac promoter and enhances binding of the RNA polymerase leading to the enhanced transcription of the operon
当细菌处于碳饥饿状态时（葡萄糖缺乏时），腺苷酸环化酶转化ATP为cAMP， cAMP 的量显著提高，可以与其激活蛋白CAP（或者叫CRP）形成二聚体，并与特定的DNA序列结合起始操作子进行转录。形成正调控体系

29. The Lac Operon: When Glucose Is Present But Not Lactose
Come on,
let me through
Repressor
mRNA
Hey man, I’m
constitutive
RNA
Pol.
Repressor
Promoter
LacY
LacA
LacZ
Operator
CAP
Binding
Repressor
No way
Jose!
Repressor
CAP

30. The Lac Operon: When Lactose Is Present But Not Glucose
Bind to me
Polymerase
Yipee…!
Repressor
mRNA
Hey man, I’m
constitutive
RNA
Pol.
RNA
Pol.
Repressor
Promoter
LacY
LacA
LacZ
Operator
CAP
Binding
CAP
cAMP X
Repressor
Repressor
CAP
cAMP
Lac
Repressor
This lactose has
bent me
out of shape
CAP
cAMP

31. The Lac Operon: When Neither Lactose Nor Glucose Is Present
Alright, I’m off to
the races . . .
Bind to me
Polymerase
Repressor
mRNA
Hey man, I’m
constitutive
Come on, let
me through!
RNA
Pol.
Repressor
Promoter
LacY
LacA
LacZ
Operator
CAP
Binding
CAP
cAMP
STOP
Right there
Polymerase
CAP
cAMP
CAP
cAMP

32. 乳糖操纵子的正调控(catabolite repression)
When glucose absent
Adenylate cyclase is active and cAMP levels are higher
CAP binds, lac operon transcription level increases

33. When glucose present
Adenylate cyclase 腺苷酸环化酶） is inhibited and cAMP levels are low。
CAP does not bind, transcription of the lac operon is very low

34. B: lac repressor C: CRP-cAMP
Summary C A B
Glucose/lactose
Repressor/operator binding
cAMP-CAP/promoter
A: RNA polymerase
B: lac repressor C: CRP-cAMP

35. 5. The trp operon Structure
five genes encoding enzymes involved in biosynthesis of tryptophan
Leader
Trp operator
Trp promoter
Trp repressor lies upstream of the trp operon
当环境中存在可利用的色氨酸时，细菌会减少和停止自身的合成，通过Trp 操纵子来实现这种阻遏。

36. 3.4.1.2 Tryptophan Metabolism in E. coli: A Repressible Gene System
trpE、D、C、B和A分别编码： 邻氨基苯甲酸合成酶的ε和δ亚基、吲哚甘油磷酸合成酶、色氨酸合成酶的β和α链。它们都是合成色氨酸必需的原料。

37. When tryptophan present
Tryptophan binds to trp repressor enabling it to binds to trp operator
Obstruct binding of RNA polymerase to the trp promoter
Prevent transcription
（变构）

38. When tryptophan absent
Trp repressor is incapable of binding to trp operator, transcription proceeds

39. 6. Attenuation（衰减作用）
Expression level is finely tuned.（与翻译过程相偶联的转录调控模型）

41. Structure of attenuator（衰减子的结构）
Trp mRNA: 14 codons followed by a stop codon, two consecutive trp codons
Trp L: including four complementary sequences which can form two stem-loop structures. The small one terminates transcription （ρ-factor independent terminator）, while the large one not.

42. 抗终止信号
终止信号

43. If levels of tryptophan are adequate
Trp mRNA is translated, ribosome prevents formation of larger stem-loop, transcription ends

44. If tryptophan is lacking
The ribosome will be stalled as it translates the coding region
RNA polymerase will move ahead, form larger stem-loop, transcription can proceed

45. Low Trp
High Trp

46. Attenuation determines how efficiency it is transcribed.
Attenuation depends on the fact that transcription and translation are linked in bacteria.

47. 7. Regulation by alternative sigma factors
Sigma factor (σ) is responsible for initiating transcription by recognizing bacterial promoter DNA sequences.
By using different sigma factors, different sets of genes are transcribed to meet different environmental conditions.

48.  factors: is bifunctional protein
Bind to core RNA Pol
 factor subunit bound to RNA pol for transcription initiation
Released core enzyme 2’
RNA elongation
识别启动子共有序列并且只为转录起始所需
(-35 and –10) in DNA

49. s factor:

50. Promoter recognition 多种不同的σ factors binding to the same RNA Pol
70 factors is most common one in E. coli under the normal growth condition

51. Sporulation in Bacillus subtilis
Many bacteria produce alternative sets of σ factors to meet the regulation requirements of transcription under normal and extreme growth condition
E. coli: Heat shock
σ32 is used to transcribe 17 heat shock related genes
Sporulation in Bacillus subtilis
alternative σfactors are used when spore germinates.
bacteriophage σfactors
use σfactors to instruct host RNA polymerase to transcribe phage genes; produce a series of σfactors that allow temporal control of their own gene

52. Heat shock
Around 17 proteins are specifically expressed in E. coli when the temperature is increased above 37ºC.
These proteins are expressed through transcription by RNA polymerase using an alternative  factor 32 coded by rhoH gene. 32 has its own specific promoter consensus sequences.

53. Comparison of the heat-shock 32 and general 70 responsive promoter
Consensus promoter
–35 sequence –10 sequence
Standard 70
Heat shock 32
TTGACA ~18bp---TATAAT
T--C--C--CTTGAA--13~15bp--CCCCAT--T

54. Sporulation in Bacillus subtilis
营养生长的枯草杆菌对不良环境作出反应时形成孢子。孢子形成过程包括细胞非对称地裂解为两部分：一部分为前孢子，它最终形成孢子，另一部分为母细胞，最终被遗弃。

56. Vegetative B. subtilis cell contains a diverse set of  factors 自身含有不同的 因子
Sporulation is regulated by a further set of  factors 孢子形成前，在前孢子和母细胞中，细胞分化开始前不同的σ具有各自特殊的活性。
Cross-regulation of this compartmentalization permits the forespore and mother cell to tightly coordinate the differentiation process.

57. Bacteriophage  factors
Many bacteriophages synthesize their own  factors in order to ‘take over’ the host cell’s own transcription machinery by substituting the normal cellular  factor and altering the promoter specificity of the RNA polymerase.

58. Key points: Definition of an operon
Lac operon: P, O, lacZ, lacY and lacA.
In E coli, how lactose metabolism is carried out?
Repressor by Lac I and Activation by CRP/CAP
Trp operon: structure.
In E coli, tryptophan synthesis is regulated both in a repressible form and by attenuation.
Sigma factors (normal and alternative).