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From CellBiology

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Cell Cycle - General Overview

Approximate 24 hour cell cycle of a mammalian cell.

A eukaryotic cell cannot divide unless two important processes alternate:

  • Doubling of its genome (DNA) in synthesis phase (S Phase) of the cell cycle
  • Halving of the genome during mitosis (M Phase).

The phase between M and S is called G1, and the phase between S and M is G2

And so, the 4 phases of the cell cycle are:

  • G1 => growth and preparation of the chromosomes for replication
  • S => synthesis of DNA and duplication of the centrosome
  • G2 => preparation for mitosis
  • M => division into two identical daughter nuclei


Control of the Cell Cycle - Proteins

Different phases of the cell cycle.

The passage of a cell through the cell cycle is controlled by proteins in the cytoplasm. The main proteins involved in animal cells are:

  • Cyclins
    • G1 cyclins (cyclin D)
    • S phase cyclins (cyclins E and A)
    • Mitotic cyclins (cyclin B)
  • Cyclin-dependent kinases (CDKs)
    • a G1 CDK (CDK4/6)
    • an S phase CDK (CDK2)
    • and M phase CDK (CDK1)
  • Cell cyclin inhibitors
    • cip/kip family e.g., p21, p27, p51
    • INK4a/ARF family e.g., p16INK4a

Other proteins involved in the cell cycle are:

  • Retinoblastoma protein
  • The anaphase-promoting complex (APC)


Individual Project: p53 (protein 53 or tumor protein 53)

3D model of a p53 protein (blue & purple) bound to DNA (orange).

The control of the cell cycle is achieved by many proteins present in the cytoplasm. p53, or protein 53, is a multifunctional tumour suppressor protein encoded by the TP53 gene in humans, mapped to the short arm of chromosome 17. [1] It is often described as 'the guardian of the genome' , [2][3] as it has an important role in conserving the genome by preventing mutation. The name p53 comes from the molecular mass of the protein, which was measured to be 53K Dalton when it was initially discovered. [4]


Structure

The p53 protein is a polypeptide of approximately 400 amino acids, and is 393 amino acids long for a human p53. [5]

It consists of several domains: [6]

  • N-terminal transcription activation domain (TAD), which can be further divided into two smaller sub-domains, TAD-I (residues 1-40) and TAD-II (residues 41-67)
Schematic representation of p53 major domains.
  • Proline-rich region (residues 67-98)
  • Central core domain (residues 98-303)
  • Nuclear localisation signal containing region (residues 303-323)
  • Oligomerisation domain (residues 323-363) and
  • C-terminal basic domain (residues 363-393).


Function

Pathway of the activation of p53 and its functions. Levels of p53 protein are very low in normal conditions.

Its main function is to regulate the cell cycle by preventing a cell from completing the cycle when the DNA is damaged. [7] This 'growth arrest' function of p53 is important in preventing cancer by suppressing tumours, and p53 mutations or non-functioning p53 are observable in many human cancers. [8] Generally:

  • If the damage can be repaired, p53 starts a cascade of events that induces cell cycle arrest providing more time for DNA repair.
  • If the damage cannot be repaired, it triggers cell to undergo apoptosis (cell death). [9]


p53 regulates the cell cycle by binding to the DNA to produce a protein called p21, also known as cyclin-dependent kinase inhibitor 1A (CDKN1A). [10] This protein can interact with cyclin-dependent kinases (CDKs), CDK2 and CDK4 in particular. When this is complexed with CDKs, it functions as an inhibitor to interfere with the activities of CDKs to delay the progression of each phases. [11] By doing this, p53 can prevent the replication of cells to give the cell more time to repair. It also activates the transcription of some of the proteins involved in DNA repair, such as ribonucleotide reductase which is encoded by the p53R2 gene. [12] If this repair effort fails, more p53 accumulates and this increase in p53 protein will guide the cell to cell apoptosis. [13]


Abnormalities

p53 tightly controls the expression of the gene which encodes for p21 in response to a variety of stimuli. If p53 is damaged or mutated, it can no longer bind to the DNA to operate as the ‘stop signal’ for cell division. This results in the formation of tumours as cells divide uncontrollably. [14] Genetic alterations found in the central core domain of p53, which results in the loss of sequence-specific DNA binding activity, are the most commonly observed mutations in human cancer. [15]


Simian Virus 40 (SV40).

History

  • - 1979: p53 first discovered independently by David Lane and Arnold Levine as a cellular protein in complex with the T-antigen of SV40 [16][17]
  • - 1983-1984: p53 was isolated and cloned, [18] and was found to cooperate with other oncogene in vitro transformation assays. [19][20][21]
  • - 1980s: Several observations that p53 was a oncogene. [22][23]
  • - 1984: Warren Maltzman first recognised that DNA damage in the form of ultraviolet (UV) radiation increased levels of p53 in cells. [24]
  • - 1989: Bert Vogelstein and colleagues reported there was frequent 'loss-of-heterozygosity' at the p53 locus (TP53) in a series of human colorectal cancers [25] and suggested p53 was not an oncogene, but a tumour suppressor gene (TSG). [26][27][28]
  • - Early 1990s: More confirming observations that TP53 is a TSG from analysis of many tumours of many different types:- in 1990, inherited cancer pre-disposing syndrome in humans, Li-Fraumeni (LFS) was due to germline mutation in TP53; [29] in 1992, Mice genetically deficient in TRP53 (the mouse p53 gene) were extremely tumour prone. [30]


p53 meeting 2008: Shanghai, China

Current and Future Research

Since this paradigm shift, a lot of study has been focused on the investigation of the p53 signalling pathways, mechanisms of action and how p53 functions as a tumour suppressor protein. It was also voted molecule of the year by Science magazine. [31] A diverse range of information has been collected to present and currently, there are more than 49,000 papers on p53 available. However, the complete understanding of how p53 functions is not yet fully known, and only general patterns have emerged over the years.

There are ‘International p53 Workshops’ held every two years, in different cities around the world. The last workshop was held in 2008 at Fudan University, Shanghai City, China. The next meeting in 2010 will be held in Philadelphia, Pennsylvania. These workshops provide a forum for researchers to discuss and share their latest findings relevant to p53, and provide new information for students and general public.

At present, p53 has been recognised as a key tumor suppressor and important target for novel cancer therapy. Future research will continue to focus on the role of p53 in cancer therapeutics, identifying drug targets applicable to p53, and influencing the p53 activation cascade. In the near future, we may see the use of p53 in the diagnosis and treatment of cancer.


Links


References

  1. Kern SE, Kinzler KW, Bruskin A, Jarosz D, Friedman P, Prives C, Vogelstein B. Identification of p53 as a sequence-specific DNA-binding protein. Science. 1991 Jun 21;252(5013):1708-11. PMID 2047879
  2. Joerger AC, Fersht AR. Structural biology of the tumor suppressor p53. Annu Rev Biochem. 2008;77:557-82. PMID 18410249
  3. Okorokov AL, Orlova EV. Structural biology of the p53 tumour suppressor. Curr Opin Struct Biol. 2009 Apr;19(2):197-202. PMID 19286366
  4. Linzer DI, Levine AJ. Characterization of a 54K dalton cellular SV40 tumor antigen present in SV40-transformed cells and uninfected embryonal carcinoma cells. Cell. 1979 May;17(1):43-52. PMID 222475
  5. Joerger AC, Fersht AR. Structural biology of the tumor suppressor p53. Annu Rev Biochem. 2008;77:557-82. PMID 18410249
  6. Okorokov AL, Orlova EV. Structural biology of the p53 tumour suppressor. Curr Opin Struct Biol. 2009 Apr;19(2):197-202. PMID 19286366
  7. Taylor WR, Stark GR. Regulation of the G2/M transition by p53. Oncogene. 2001 Apr 5;20(15):1803-15. PMID 11313928
  8. Diller L, Kassel J, Nelson CE, Gryka MA, Litwak G, Gebhardt M, Bressac B, Ozturk M, Baker SJ, Vogelstein B, et al. p53 functions as a cell cycle control protein in osteosarcomas. Mol Cell Biol. 1990 Nov;10(11):5772-81. PMID 2233717
  9. Kastan MB, Canman CE, Leonard CJ. P53, cell cycle control and apoptosis: implications for cancer. Cancer Metastasis Rev. 1995 Mar;14(1):3-15. PMID 7606818
  10. Santos AM, Sousa H, Portela C, Pereira D, Pinto D, Catarino R, Rodrigues C, Araújo AP, Lopes C, Medeiros R. TP53 and P21 polymorphisms: response to cisplatinum/paclitaxel-based chemotherapy in ovarian cancer. Biochem Biophys Res Commun. 2006 Feb 3;340(1):256-62. Epub 2005 Dec 9. PMID 16364249
  11. Funk JO, Waga S, Harry JB, Espling E, Stillman B, Galloway DA. Inhibition of CDK activity and PCNA-dependent DNA replication by p21 is blocked by interaction with the HPV-16 E7 oncoprotein. Genes Dev. 1997 Aug 15;11(16):2090-100. PMID 9284048
  12. Yamaguchi T, Matsuda K, Sagiya Y, Iwadate M, Fujino MA, Nakamura Y, Arakawa H. p53R2-dependent pathway for DNA synthesis in a p53-regulated cell cycle checkpoint. Cancer Res. 2001 Nov 15;61(22):8256-62. PMID 11719458
  13. Fridman JS, Lowe SW. Control of apoptosis by p53. Oncogene. 2003 Dec 8;22(56):9030-40. PMID 14663481
  14. Levine AJ, Finlay CA, Hinds PW. P53 is a tumor suppressor gene. Cell. 2004 Jan 23;116(2 Suppl):S67-9. PMID 15055586
  15. Cho Y, Gorina S, Jeffrey PD, Pavletich NP. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science. 1994 Jul 15;265(5170):346-55. PMID 8023157
  16. Lane DP, Crawford LV. T antigen is bound to a host protein in SV40-transformed cells. Nature. 1979 Mar 15;278(5701):261-3. PMID 218111
  17. Linzer DI, Levine AJ. Characterization of a 54K dalton cellular SV40 tumor antigen present in SV40-transformed cells and uninfected embryonal carcinoma cells. Cell. 1979 May;17(1):43-52. PMID 222475
  18. Oren M, Levine AJ. Molecular cloning of a cDNA specific for the murine p53 cellular tumor antigen. Proc Natl Acad Sci U S A. 1983 Jan;80(1):56-9. PMID 6296874
  19. Jenkins JR, Rudge K, Currie GA. Cellular immortalization by a cDNA clone encoding the transformation-associated phosphoprotein p53. Nature. 1984 Dec 13-19;312(5995):651-4. PMID 6095117
  20. Parada LF, Land H, Weinberg RA, Wolf D, Rotter V. Cooperation between gene encoding p53 tumour antigen and ras in cellular transformation. Nature. 1984 Dec 13-19;312(5995):649-51. PMID 6390217
  21. Wolf D, Harris N, Rotter V. Reconstitution of p53 expression in a nonproducer Ab-MuLV-transformed cell line by transfection of a functional p53 gene. Cell. 1984 Aug;38(1):119-26. PMID 6088057
  22. Crawford LV, Pim DC, Gurney EG, Goodfellow P, Taylor-Papadimitriou J. Detection of a common feature in several human tumor cell lines--a 53,000-dalton protein. Proc Natl Acad Sci U S A. 1981 Jan;78(1):41-5. PMID 6264441
  23. Mercer WE, Nelson D, DeLeo AB, Old LJ, Baserga R. Microinjection of monoclonal antibody to protein p53 inhibits serum-induced DNA synthesis in 3T3 cells. Proc Natl Acad Sci U S A. 1982 Oct;79(20):6309-12. PMID 6292898
  24. Maltzman W, Czyzyk L. UV irradiation stimulates levels of p53 cellular tumor antigen in nontransformed mouse cells. Mol Cell Biol. 1984 Sep;4(9):1689-94. PMID 6092932
  25. Vogelstein B, Fearon ER, Kern SE, Hamilton SR, Preisinger AC, Nakamura Y, White R. Vogelstein B, Fearon ER, Kern SE, Hamilton SR, Preisinger AC, Nakamura Y, White R. Allelotype of colorectal carcinomas. Science. 1989 Apr 14;244(4901):207-11. PMID 2565047
  26. Vogelstein B, Fearon ER, Kern SE, Hamilton SR, Preisinger AC, Nakamura Y, White R. Vogelstein B, Fearon ER, Kern SE, Hamilton SR, Preisinger AC, Nakamura Y, White R. Allelotype of colorectal carcinomas. Science. 1989 Apr 14;244(4901):207-11. PMID 2565047
  27. Baker SJ, Fearon ER, Nigro JM, Hamilton SR, Preisinger AC, Jessup JM, vanTuinen P, Ledbetter DH, Barker DF, Nakamura Y, White R, Vogelstein B. Chromosome 17 deletions and p53 gene mutations in colorectal carcinomas. Science. 1989 Apr 14;244(4901):217-21. PMID 2649981
  28. Lane DP, Benchimol S. p53: oncogene or anti-oncogene? Genes Dev. 1990 Jan;4(1):1-8. PMID 2137806
  29. Malkin D, Li FP, Strong LC, Fraumeni JF Jr, Nelson CE, Kim DH, Kassel J, Gryka MA, Bischoff FZ, Tainsky MA, et al. Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science. 1990 Nov 30;250(4985):1233-8. PMID 1978757
  30. Donehower LA, Harvey M, Slagle BL, McArthur MJ, Montgomery CA Jr, Butel JS, Bradley A. Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumours. Nature. 1992 Mar 19;356(6366):215-21. PMID 1552940
  31. Koshland DE Jr. Molecule of the year. Science. 1993 Dec 24;262(5142):1953. PMID 8266084


Homework Exercises

Lecture 4: Cell Nucleus

- ONE concept that I found interesting

It was intersting to know how chromosomes occupied different areas within the nucleus, and how these territories interact. I was also fascinated about how such a large amount of information (DNA) could be packed and stored within the nucleus of a cell. The orders of packing, i.e. histones, nucleosomes, second order folding, etc., play a significant role in reducing and condensing DNA.


Lecture 5: Cell Export - Exocytosis

- ONE concept that I found difficult

I found it difficult to understand why there was two possible models explaining the organisation of the Golgi apparatus and the transport of proteins... Is this because the pathway is not yet fully known? Or does the two pathways exist in different organisms?

Also, you briefly mention the history and the years when it is discovered in all the lectures. Is this an important aspect of the course, and is it examinable? Or is it just to get a background idea of when and how things are found? Thnx,


Lecture 7: Cell Mitochondria

- cellular processes that requires energy from the mitochondria

  • Cellular Respiration (aerobic respiration) - most important and prominent use of energy from the mitochondria
  • Cell growth, differentiation and reproduction
  • Cell repair - constant synthesis of new molecules is required in order to maintain cellular integrity
  • Synthesis of macromolecules - including DNA, RNA and protein synthesis (transcription and translation)
  • Mitosis and Meiosis
  • Cell signaling - extracellular and intracellular signaling (including signal transduction)
  • Maintenance of the electrochemical gradient/ membrane potential - by the Na+/K+ ATPase
  • Active transport - selective transport against conc. gradient via carriers or pumps
  • Reverse osmosis - against osmotic gradient therefore requires energy
  • Contraction of muscle cells (cardiac, skeletal, and smooth m.) - ATP required for the shortening of actin and myosin filament crossbridges
  • Sperm Motility - within the tail/ flagellum (as mentioned in lect.)

How cells obtain energy explains what processes require energy, and how and where this energy comes from.


Lecture 8: Cell Junctions

- define the different "CAM" acronyms

Cell Adhesion Molecules (CAMs) are a class of membrane proteins comprising the outer surfaces of cell membranes. It is involved with the binding with other cells or with the extracellular matrix (ECM) in cell adhesion.

  • N-CAM => Neural Cell Adhesion Molecule
  • Ng-CAM => Neuron-glia Cell Adhesion Molecule
  • L-CAM => Liver Cell Adhesion Molecule
  • I-CAM => Inter-Cellular Adhesion Molecule
  • V-CAM => Vascular Cell Adhesion Molecule
  • PE-CAM => Platelet-Endothelial Cell Adhesion Molecule


Lecture 10: Cytoskeleton 1 - Intermediate Filaments

- name of the epidermal layer b/w the basal and granulosa layer and its relation to intermediate filaments

Epidermis is the outermost layer of skin, made of keratinised stratified squamous epithelium. From superficial to deep, the epidermal layers are:

  • Stratum corneum
  • Stratum lucidum
  • Stratum granulosum
  • Stratum spinosum
  • Stratum basale

Therefore, stratum spinosum is the layer between the basal and granulosa layer.

Desmosmes are structures that form the site of adhesion between two cells. They connect intermediate filaments from cell to cell and helps to resist shearing forces. It is within the stratum spinosum layer in which desmosomal structures are found.


Lab 6: Cytoskeleton Exercise

- differences in the distribution of phenotypes in Tropomyosin 4 (Tm4) over-expressing B35 cells versus control B35 cells

In both types of cells, some phenotypes were more commonly observed than other phenotypes. However, the main difference between the two types of B35 cells (Tm4 over-expressed vs. control) was that; more pronged and stringed phenotypes were observed for the Tm4 over-expressed cells compared to the control cells, which were mainly broken fan and stumped phenotypes. In other words, the majority of Tm4 over-expressed cells were visible as longer, thinner and more elongated with multiple (usually three to six) branches/ processes. However, the number of cells were significantly lower than the control cells.

- hypothesis to what changes on the molecular level have occurred, due to the over-expression of Tm4 that lead to morphological changes that were observed

From the above results, we can hypothesise; that over-expression with Tm4 causes and increase in actin filaments and stress fibres. This increase stimulates the growth of the observed branching structures such as neurites and lamella in the actin cell cortex, as well as extending the existing process (elongation). Therefore, we conclude that Tm4 plays an important role within the components of cell cytoskeleton, especially microfilaments, as it can direct the assembly of specific cellular structures to give changes in the phenotypes of neuro-epithelial cells.


Lecture 14: Extracellular Matrix 2

- the 2 main forms of generating confocal microscopy

The two main forms are: 1) laser light (laser scanning) and 2) spinning disc.


Lecture 15: Cell Cycle

- what does S stand for in S-phase?

It stands for Synthesis (DNA replication).