Sandbox Reserved 973: Difference between revisions

Line 4:

== Function and overall structure ==

The pacemaker of the circadian system is the suprachiamastic nucleus (SNC) located in the hypothalamus. This center controls the circadian rhythm through the coordination of peripheric oscillators all over the organism. The mechanisms that occur in the peripheric system are, at a molecular level, very similar to those in the SNC; that is to say a network of transcriptional and translational regulations, creating different loops that take about 24 hours to complete. This circadian cycle regulates many physiologic parameters and coordonates several phenomenon such as sleep period or hormon levels. One of the most important proteins in this rhythm is the heterodimeric complex CLOCK:BMAL1, which is a transcriptionnal factor responsible for the activation of 2 type of genes; Period(Per1,Per2) and Cryptochrome(Cry1,Cry2), by interacting with the E-box DNA. Indeed mutants mice devoid of CLOCK or <scene name='60/604492/Bmal1/1'>BMAL1</scene> proteins have seriously disrupted rhythm, at a molecular level as well as on their behavior.

The pacemaker of the circadian system is the suprachiamastic nucleus (SNC) located in the hypothalamus. This center controls the circadian rhythm through the coordination of peripheric oscillators all over the organism. The mechanisms that occur in the peripheric system are, at a molecular level, very similar to those in the SNC; that is to say a network of transcriptional and translational regulations, creating different loops that take about 24 hours to complete. This circadian cycle regulates many physiologic parameters and coordonates several phenomenon such as sleep period or hormon levels. One of the most important proteins in this rhythm is the heterodimeric complex CLOCK:BMAL1, which is a transcriptionnal factor responsible for the activation of 2 type of genes; Period(Per1,Per2) and Cryptochrome(Cry1,Cry2), by interacting with the E-box DNA. Indeed mutants mice devoid of <scene name='60/604492/Clock/1'>CLOCK</scene> or <scene name='60/604492/Bmal1/1'>BMAL1</scene> proteins have seriously disrupted rhythm, at a molecular level as well as on their behavior.

The two polypeptides involved in the dimere have very similar sequences. The structure of CLOCK and <scene name='60/604492/Bmal1/1'>BMAL1</scene> have mostly been studied in ''mus musculus''. Both of these subunits are basic helix-loop-helix-PAS proteins (bHLH-PAS) which contain the same 3 particular domains: a bHLH domain, a PAS-A domain and a PAS-B domain, plus a transactivator domain in the C-terminal region. They are involved in DNA binding and dimerization abilities. Mutations that affects the heterodimer interfaces can then disturb the activity of the complex and therefore the persistence and periodicity of the circadian cycle. Indeed the two subunits are tightly intertwined as each domain of CLOCK interact with the corresponding one of <scene name='60/604492/Bmal1/1'>BMAL1</scene>.

The two polypeptides involved in the dimere have very similar sequences. The structure of <scene name='60/604492/Clock/1'>CLOCK</scene> and <scene name='60/604492/Bmal1/1'>BMAL1</scene> have mostly been studied in ''mus musculus''. Both of these subunits are basic helix-loop-helix-PAS proteins (bHLH-PAS) which contain the same 3 particular domains: a bHLH domain, a PAS-A domain and a PAS-B domain, plus a transactivator domain in the C-terminal region. They are involved in DNA binding and dimerization abilities. Mutations that affects the heterodimer interfaces can then disturb the activity of the complex and therefore the persistence and periodicity of the circadian cycle. Indeed the two subunits are tightly intertwined as each domain of <scene name='60/604492/Clock/1'>CLOCK</scene> interact with the corresponding one of <scene name='60/604492/Bmal1/1'>BMAL1</scene>.

Another important feature of this heterodimere is that there is an assymetric distribution of the electrostatic potential. CLOCK tends to have a global negative charge while <scene name='60/604492/Bmal1/1'>BMAL1</scene> has a positive one. The fact that the two subunits of the complex expose this charged surface in the 3D structure match with the hypothesis that CLOCK and <scene name='60/604492/Bmal1/1'>BMAL1</scene> are not involved in the same interaction with the other regulatory proteins listed before.

Another important feature of this heterodimere is that there is an assymetric distribution of the electrostatic potential. <scene name='60/604492/Clock/1'>CLOCK</scene> tends to have a global negative charge while <scene name='60/604492/Bmal1/1'>BMAL1</scene> has a positive one. The fact that the two subunits of the complex expose this charged surface in the 3D structure match with the hypothesis that <scene name='60/604492/Clock/1'>CLOCK</scene> and <scene name='60/604492/Bmal1/1'>BMAL1</scene> are not involved in the same interaction with the other regulatory proteins listed before.

== Domains of the subunits ==

This part deals with the structure of the 3 domains involved in the dimerization pattern. The transactivator domains of the two subunits, which are both transcription factors, working as positive elements in the circadian molecular clock but they will not be presented here. The data exposed below were obtained by crystallographic analysis with mouse CLOCK (residues 26–384) and <scene name='60/604492/Bmal1/1'>BMAL1</scene> (residues 62–447).

This part deals with the structure of the 3 domains involved in the dimerization pattern. The transactivator domains of the two subunits, which are both transcription factors, working as positive elements in the circadian molecular clock but they will not be presented here. The data exposed below were obtained by crystallographic analysis with mouse <scene name='60/604492/Clock/1'>CLOCK</scene> (residues 26–384) and <scene name='60/604492/Bmal1/1'>BMAL1</scene> (residues 62–447).

=== bHLH domain ===

Line 35:

On the other hand, CLOCK:BMAL 1 is also able to activate the transcription of retinoic acid-related nuclear receptors: Rev-erbα and Rorα.These proteins have the ability to regulate the transcription of Bmal1, RORα as an activator and REV-ERBα as a repressor.

But this molecular clock is also regulated by post-translational modifications of the subunits, notably phosphorylation and ubiquitination. Some modifier proteins can change the stabibility or influence the translocation of some core clock actors, including <scene name='60/604492/Bmal1/1'>BMAL1</scene> and CLOCK. That is the case of 2 types of Casein kinase 1 (CK1). Mutations in these modifiers can shorten the circadian cycle of the mammals and cause serious sleep disorders.

But this molecular clock is also regulated by post-translational modifications of the subunits, notably phosphorylation and ubiquitination. Some modifier proteins can change the stabibility or influence the translocation of some core clock actors, including <scene name='60/604492/Bmal1/1'>BMAL1</scene> and <scene name='60/604492/Clock/1'>CLOCK</scene>. That is the case of 2 types of Casein kinase 1 (CK1). Mutations in these modifiers can shorten the circadian cycle of the mammals and cause serious sleep disorders.

Mutagenesis experiments showed that <scene name='60/604492/Bmal1/1'>BMAL1</scene> is normally in excess of CLOCK, which imply that CLOCK is the limiting factor for the dimerization. Indeed, an overexpression of Clock will make the cycle shorter, whereas an overexpression of Bmal1 may have no effect on the cycle length or make it a little longer.

Mutagenesis experiments showed that <scene name='60/604492/Bmal1/1'>BMAL1</scene> is normally in excess of <scene name='60/604492/Clock/1'>CLOCK</scene>, which imply that <scene name='60/604492/Clock/1'>CLOCK</scene> is the limiting factor for the dimerization. Indeed, an overexpression of Clock will make the cycle shorter, whereas an overexpression of Bmal1 may have no effect on the cycle length or make it a little longer.

Nevertheless, recent studies showed that each cell has its autonomy towards the circadian cycle and it is important to notice that the two genes Clock and Bmal1 are not identically expressed in every tissues, and that the two proteins don't act the same way in this different cell types. Clock mRNA follows a transcriptional cycle in the peripheric oscillators whereas it is constitutively expressed in the SCN. Futhermore the different ROR proteins which have feedback effects on Bmal1 transcription are expressed in a tissue-specific manner, so <scene name='60/604492/Bmal1/1'>BMAL1</scene> has various functions at various moments. Again, CLOCK doesn't have the same influence on downstream regulated genes, depending on the tissue. For example, CLOCK has a limited impact on the amplitudes of the Rev-erbα mRNA oscillation in the SCN. But Clock−/− mice show a important decrease of the same amplitude in the liver. Thus, it is important to keep in mind that the CLOCK:BMAL1 complex subunits are expressed in tissue-specific patterns and that the heterodimer makes a tissue-specific regulation of the circadian clock, which drive the study of the complex functions very difficult.

Nevertheless, recent studies showed that each cell has its autonomy towards the circadian cycle and it is important to notice that the two genes Clock and Bmal1 are not identically expressed in every tissues, and that the two proteins don't act the same way in this different cell types. Clock mRNA follows a transcriptional cycle in the peripheric oscillators whereas it is constitutively expressed in the SCN. Futhermore the different ROR proteins which have feedback effects on Bmal1 transcription are expressed in a tissue-specific manner, so <scene name='60/604492/Bmal1/1'>BMAL1</scene> has various functions at various moments. Again, <scene name='60/604492/Clock/1'>CLOCK</scene> doesn't have the same influence on downstream regulated genes, depending on the tissue. For example, CLOCK has a limited impact on the amplitudes of the Rev-erbα mRNA oscillation in the SCN. But Clock−/− mice show a important decrease of the same amplitude in the liver. Thus, it is important to keep in mind that the CLOCK:BMAL1 complex subunits are expressed in tissue-specific patterns and that the heterodimer makes a tissue-specific regulation of the circadian clock, which drive the study of the complex functions very difficult.

Sandbox Reserved 973: Difference between revisions

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@@ Line 4: / Line 4: @@
 == Function and overall structure ==
-The pacemaker of the circadian system is the suprachiamastic nucleus (SNC) located in the hypothalamus. This center controls the circadian rhythm through the coordination of peripheric oscillators all over the organism. The mechanisms that occur in the peripheric system are, at a molecular level, very similar to those in the SNC; that is to say a network of transcriptional and translational regulations, creating different loops that take about 24 hours to complete. This circadian cycle regulates many physiologic parameters and coordonates several phenomenon such as sleep period or hormon levels. One of the most important proteins in this rhythm is the heterodimeric complex CLOCK:BMAL1, which is a transcriptionnal factor responsible for the activation of 2 type of genes; Period(Per1,Per2) and Cryptochrome(Cry1,Cry2), by interacting with the E-box DNA. Indeed mutants mice devoid of CLOCK or <scene name='60/604492/Bmal1/1'>BMAL1</scene> proteins have seriously disrupted rhythm, at a molecular level as well as on their behavior.
+The pacemaker of the circadian system is the suprachiamastic nucleus (SNC) located in the hypothalamus. This center controls the circadian rhythm through the coordination of peripheric oscillators all over the organism. The mechanisms that occur in the peripheric system are, at a molecular level, very similar to those in the SNC; that is to say a network of transcriptional and translational regulations, creating different loops that take about 24 hours to complete. This circadian cycle regulates many physiologic parameters and coordonates several phenomenon such as sleep period or hormon levels. One of the most important proteins in this rhythm is the heterodimeric complex CLOCK:BMAL1, which is a transcriptionnal factor responsible for the activation of 2 type of genes; Period(Per1,Per2) and Cryptochrome(Cry1,Cry2), by interacting with the E-box DNA. Indeed mutants mice devoid of <scene name='60/604492/Clock/1'>CLOCK</scene> or <scene name='60/604492/Bmal1/1'>BMAL1</scene> proteins have seriously disrupted rhythm, at a molecular level as well as on their behavior.
-The two polypeptides involved in the dimere have very similar sequences. The structure of CLOCK and <scene name='60/604492/Bmal1/1'>BMAL1</scene> have mostly been studied in ''mus musculus''. Both of these subunits are basic helix-loop-helix-PAS proteins (bHLH-PAS) which contain the same 3 particular domains: a bHLH domain, a PAS-A domain and a PAS-B domain, plus a transactivator domain in the C-terminal region. They are involved in DNA binding and dimerization abilities. Mutations that affects the heterodimer interfaces can then disturb the activity of the complex and therefore the persistence and periodicity of the circadian cycle. Indeed the two subunits are tightly intertwined as each domain of CLOCK interact with the corresponding one of <scene name='60/604492/Bmal1/1'>BMAL1</scene>.
+The two polypeptides involved in the dimere have very similar sequences. The structure of <scene name='60/604492/Clock/1'>CLOCK</scene> and <scene name='60/604492/Bmal1/1'>BMAL1</scene> have mostly been studied in ''mus musculus''. Both of these subunits are basic helix-loop-helix-PAS proteins (bHLH-PAS) which contain the same 3 particular domains: a bHLH domain, a PAS-A domain and a PAS-B domain, plus a transactivator domain in the C-terminal region. They are involved in DNA binding and dimerization abilities. Mutations that affects the heterodimer interfaces can then disturb the activity of the complex and therefore the persistence and periodicity of the circadian cycle. Indeed the two subunits are tightly intertwined as each domain of <scene name='60/604492/Clock/1'>CLOCK</scene> interact with the corresponding one of <scene name='60/604492/Bmal1/1'>BMAL1</scene>.
-Another important feature of this heterodimere is that there is an assymetric distribution of the electrostatic potential. CLOCK tends to have a global negative charge while <scene name='60/604492/Bmal1/1'>BMAL1</scene> has a positive one. The fact that the two subunits of the complex expose this charged surface in the 3D structure match with the hypothesis that CLOCK and <scene name='60/604492/Bmal1/1'>BMAL1</scene> are not involved in the same interaction with the other regulatory proteins listed before.
+Another important feature of this heterodimere is that there is an assymetric distribution of the electrostatic potential. <scene name='60/604492/Clock/1'>CLOCK</scene> tends to have a global negative charge while <scene name='60/604492/Bmal1/1'>BMAL1</scene> has a positive one. The fact that the two subunits of the complex expose this charged surface in the 3D structure match with the hypothesis that <scene name='60/604492/Clock/1'>CLOCK</scene> and <scene name='60/604492/Bmal1/1'>BMAL1</scene> are not involved in the same interaction with the other regulatory proteins listed before.
 == Domains of the subunits ==
-This part deals with the structure of the 3 domains involved in the dimerization pattern. The transactivator domains of the two subunits, which are both transcription factors, working as positive elements in the circadian molecular clock but they will not be presented here. The data exposed below were obtained by crystallographic analysis with mouse CLOCK (residues 26–384) and <scene name='60/604492/Bmal1/1'>BMAL1</scene> (residues 62–447).
+This part deals with the structure of the 3 domains involved in the dimerization pattern. The transactivator domains of the two subunits, which are both transcription factors, working as positive elements in the circadian molecular clock but they will not be presented here. The data exposed below were obtained by crystallographic analysis with mouse <scene name='60/604492/Clock/1'>CLOCK</scene> (residues 26–384) and <scene name='60/604492/Bmal1/1'>BMAL1</scene> (residues 62–447).
 === bHLH domain ===
@@ Line 35: / Line 35: @@
 On the other hand, CLOCK:BMAL 1 is also able to activate the transcription of retinoic acid-related nuclear receptors: Rev-erbα and Rorα.These proteins have the ability to regulate the transcription of Bmal1, RORα as an activator and REV-ERBα as a repressor.
-But this molecular clock is also regulated by post-translational modifications of the subunits, notably phosphorylation and ubiquitination. Some modifier proteins can change the stabibility or influence the translocation of some core clock actors, including <scene name='60/604492/Bmal1/1'>BMAL1</scene> and CLOCK. That is the case of 2 types of Casein kinase 1 (CK1). Mutations in these modifiers can shorten the circadian cycle of the mammals and cause serious sleep disorders.
+But this molecular clock is also regulated by post-translational modifications of the subunits, notably phosphorylation and ubiquitination. Some modifier proteins can change the stabibility or influence the translocation of some core clock actors, including <scene name='60/604492/Bmal1/1'>BMAL1</scene> and <scene name='60/604492/Clock/1'>CLOCK</scene>. That is the case of 2 types of Casein kinase 1 (CK1). Mutations in these modifiers can shorten the circadian cycle of the mammals and cause serious sleep disorders.
-Mutagenesis experiments showed that <scene name='60/604492/Bmal1/1'>BMAL1</scene> is normally in excess of CLOCK, which imply that CLOCK is the limiting factor for the dimerization. Indeed, an overexpression of Clock will make the cycle shorter, whereas an overexpression of Bmal1 may have no effect on the cycle length or make it a little longer.
+Mutagenesis experiments showed that <scene name='60/604492/Bmal1/1'>BMAL1</scene> is normally in excess of <scene name='60/604492/Clock/1'>CLOCK</scene>, which imply that <scene name='60/604492/Clock/1'>CLOCK</scene> is the limiting factor for the dimerization. Indeed, an overexpression of Clock will make the cycle shorter, whereas an overexpression of Bmal1 may have no effect on the cycle length or make it a little longer.
-Nevertheless, recent studies showed that each cell has its autonomy towards the circadian cycle and it is important to notice that the two genes Clock and Bmal1 are not identically expressed in every tissues, and that the two proteins don't act the same way in this different cell types. Clock mRNA follows a transcriptional cycle in the peripheric oscillators whereas it is constitutively expressed in the SCN. Futhermore the different ROR proteins which have feedback effects on Bmal1 transcription are expressed in a tissue-specific manner, so <scene name='60/604492/Bmal1/1'>BMAL1</scene> has various functions at various moments. Again, CLOCK doesn't have the same influence on downstream regulated genes, depending on the tissue. For example, CLOCK has a limited impact on the amplitudes of the Rev-erbα mRNA oscillation in the SCN. But Clock−/− mice show a important decrease of the same amplitude in the liver. Thus, it is important to keep in mind that the CLOCK:BMAL1 complex subunits are expressed in tissue-specific patterns and that the heterodimer makes a tissue-specific regulation of the circadian clock, which drive the study of the complex functions very difficult.
+Nevertheless, recent studies showed that each cell has its autonomy towards the circadian cycle and it is important to notice that the two genes Clock and Bmal1 are not identically expressed in every tissues, and that the two proteins don't act the same way in this different cell types. Clock mRNA follows a transcriptional cycle in the peripheric oscillators whereas it is constitutively expressed in the SCN. Futhermore the different ROR proteins which have feedback effects on Bmal1 transcription are expressed in a tissue-specific manner, so <scene name='60/604492/Bmal1/1'>BMAL1</scene> has various functions at various moments. Again, <scene name='60/604492/Clock/1'>CLOCK</scene> doesn't have the same influence on downstream regulated genes, depending on the tissue. For example, CLOCK has a limited impact on the amplitudes of the Rev-erbα mRNA oscillation in the SCN. But Clock−/− mice show a important decrease of the same amplitude in the liver. Thus, it is important to keep in mind that the CLOCK:BMAL1 complex subunits are expressed in tissue-specific patterns and that the heterodimer makes a tissue-specific regulation of the circadian clock, which drive the study of the complex functions very difficult.