Lecture 4: The Nucleus 2024-2025 - PDF

# Lecture 4: The Nucleus ## Prof. Mamoun Ahram ## School of Medicine ## Second year, First Semester, 2024-2025 # Structure and Function of a Nucleus - A repository of genetic information. - The nuclear membrane, known as the nuclear envelope, adds another level of gene regulation transcriptiona...

# Lecture 4: The Nucleus ## Prof. Mamoun Ahram ## School of Medicine ## Second year, First Semester, 2024-2025 # Structure and Function of a Nucleus - A repository of genetic information. - The nuclear membrane, known as the nuclear envelope, adds another level of gene regulation transcriptionally and post-transcriptionally. ## The Nuclear Envelope - A two-membrane system. - The outer membrane is continuous with the ER and is functionally similar to it with ribosomes on the outside surface, but it has different protein composition. - The inner membrane is unique having proteins that bind the lamina. - The perinuclear space resembles the ER lumen. - The nuclear envelope is underlined by a matrix of proteins known as the nuclear lamina. ## The Nuclear Lamina - The nucleoskeleton: the skeletal structure of the nucleus. - The nuclear lamina is made of a fibrous meshwork of intermediate filament proteins called *lamins* that provide structural support to the nucleus. - There are two lamin proteins: lamin A and lamin B. - The lamin polypeptides form dimers with the central α-helical regions of two chains wound around each other. Dimers form tetramers, which associate end-to-end to form filaments. - Intermediate filaments (orange) are one type of three that make up the internal skeleton of cells. The other two are actin microfilaments (green) and microtubules (red). ## Nuclear Envelope-Lamina Interaction - The lamins associate with the inner nuclear membrane via: 1. Prenylation (addition of a lipid chain to attach a protein to the membrane) 2. Proteins (emerin & lamin-binding receptor (LBR)) - The lamins and lamin-associated proteins interact with the chromatin localizing the heterochromatin (the condensed part of DNA that contains inactive genes) in the periphery of the nucleus. - The LINC complex also connects the nuclear lamina with the cytoskeleton. ## Nuclear Lamina Diseases - The same disease, Emery-Dreifuss muscular dystrophy, can be caused by mutations in two genes: 1. The emerin gene (X-linked disease) 2. The lamin A gene (autosomal dominant disease) - Mutations in A-type lamins can also cause other inherited *laminopathies* such as: - Marie-Charcot-Tooth disease type 2B1 (muscle wasting) - Hutchinson-Gilford progeria (premature aging) - Dunnigan-type partial lipodystrophy - **Mechanotransduction** hypothesis: proposes the vulnerability of the nuclear envelope to stress on muscle cells due to the connection of lamina to the cytoskeleton. - **Gene expression** hypothesis: proposes tissue-specific changes of gene expression due to connection of lamina to DNA. ## The Nuclear Pore Complex - It is composed of nucleoporins (NUPs). - It allows for nucleocytoplasmic transport. - NUPs form a barrier to the permeability of the pore and facilitate regulated transport between the nucleus and the cytoplasm. - Defective nucleocytoplasmic transport has been reported in neurodegenerative diseases. - Small molecules can pass freely through the nuclear pore complex by passive diffusion. - Macromolecules (proteins and RNAs) are recognized by specific signals and are selectively transported in/out. ## Nuclear Localization Sequence - They are recognized and targeted by nuclear transport receptors. - **Features:** Bipartite basic amino acids. - It was first identified in the simian virus 40 (SV40) T antigen, which initiated viral DNA replication in infected cells. ## Protein Import Across the Nuclear Pore: The Role of Ran - The protein, importin, recognizes and binds to the nuclear localization sequence (NLS) of the cargo proteins in the cytosol. - The complex is transported through the pore into the nucleus. - Ran/GTP binds importin releasing it from the cargo protein leaving the cargo inside the nucleus and exporting importin to the cytosol. - GTP is hydrolyzed to GDP, releasing Ran/GDP from importin, and is transported back to the nucleus where GDP is exchanged for GTP. - Importin binds to another protein cargo and Ran is transported back to the nucleus. ## Remember: Regulation of Small GTP-Binding Proteins - Ras, Ran, Rab, Rac, Rho, etc. - **ON:** Active GTPase - **OFF:** Inactive GTPase ## Nuclear Export - Ran/GTP also exports proteins from the nucleus. - Proteins with nuclear export signals (NES) bind to proteins known as exportins. - Following transport through the nuclear pore complex, GTP is hydrolyzed leading to the release of the target protein and exportin in the cytoplasm. - Exportins and Ran/GDP are then transported back to the nucleus. - Importin and exportin proteins that can transport nuclear molecules are known as Karyopherins. ## RNA Transport - Ribosomal RNAs transported as complexes associated with ribosomal proteins, which are found in the nucleolus, and possess nuclear export signals, dependent on a specialized exportin protein. - Following processing, mRNAs export: - does not involve karyopherins. - is independent of Ran mRNAs. - are transported through the nuclear pore complex by an exporter complex. - are released by a helicase in the cytoplasm. - The nucleolus is a structure found in the cell's nucleus whose primary function is to produce and assemble the cell's ribosomes and where ribosomal RNA genes are transcribed. ## Organization of Chromosomes - Chromosomes are structured as chromatins (complexes of DNA and histone proteins). - Chromatins are of 2 types of looped domains (regions): - **Heterochromatin** (condensed DNA containing transcriptionally inactive genes) - **Euchromatins** (loose DNA containing transcriptionally active genes). ## Organization of Chromatin in the Nucleus - Euchromatins are localized to the interior of the nucleus. - Heterochromatin is localized in the exterior of the nucleus as lamin-associated domains (LADs) or surrounding the nucleolus as nucleolus-associated domains (NADs). ## Nuclear Factories - DNA replication (synthesis) occurs within discrete clustered regions called replication factories. - Transcription (RNA synthesis) also occurs at clustered sites (transcription factories). - Coregulated genes from different genes (for example: immunoglobulin genes) coexist in the same factory (regions). ## Internal Organization of the Nucleus: Nuclear Bodies - Nuclear bodies: non-membranous, discrete regions with specific functions. | Nuclear Body | Number Per Nucleus | Function | |:---------------|:--------------------|:-----------------------------------------------------------------------------------| | Nucleolus | 1-4 | rRNA transcription, processing and ribosome assembly | | Cajal body | 0-10 | snRNP assembly | | Clastosome | 0-3 | Proteasomal proteolysis | | Histone locus body | 2-4 | Transcription and processing of histone pre-mRNAs | | Speckle | 20-50 | Storage of pre-mRNA splicing factors | | PML body | 10-30 | Transcriptional regulation, DNA repair | | Polycomb body | 10-20 | Gene silencing |