MCB 502A-2015. Lecture #12!Genome logistics. Mutagenesis. Genome logistics (continued…)— DNA packing versus DNA condensation— Principles of bulk DNA transport— The chromosome cycle Mutagenesis — The chemical basis of misincorporation— Methyl-directed mismatch removalOne-strand DNA damage and its repair— UV-irradiation damages DNASpectacular dinoflagellate mesokayonshttp://www.sci.hokudai.ac.jp/~horig/Dinohome/dinokaryon.htmlhttp://www.ncbi.nlm.nih.gov/pubmed/10704374Райков ИБ— Check out how they segregate!DNA packing vs DNA condensation-1— … four main genome functions are information maintenance, information expression, information replication and vertical information transfer,… uniform chromosomal format of genomes (L #4). — … ~1,000-fold DNA compaction … first two functions, … . — … chromosom… decompacted … for … replication. — … vertical information transfer … additional … compression. — … additional DNA compression …: 1) DNA packing; 2) DNA condensation.An example of "packing"An example of "condensation"DNA packing vs DNA condensation-2— DNA packing … final volume … severely constrained… for … long-distance travel. — …objective…: to pack DNA as densely as physically possible in all three dimensions. — … shielding … DNA negative charge. — … phage … counterions … spermidine. — … sperm head,… highly-basic … protamines. http://www.scripps.edu/lander/images.phphttp://www.nature.com/nrurol/journal/v9/n11/full/nrurol.2012.183.htmlDNA packing vs DNA condensation-3— … DNA compression in any one dimension … ~300-fold, … equal in all three dimensions… 3D DNA compression … ~3x10e7! DNA packing = 3D DNA compressionhttp://biology.cua.edu/faculty/rao.cfmDNA packing vs DNA condensation-4— DNA condensation pursues a different objective: … to minimize length of already compacted DNA in two dimensions, for the purpose of bulk DNA movement within the cell. — …. organize DNA in loops of the longest possible size… — ... exactly … organized … as rosettes of radial loops. — … modest DNA looping … DNA compaction … DNA condensation = 2D DNA compressionCourtesy H. Potter and D. Dressler, from Brock Biology of Microorganisms, 9th editionFrom Lecture #4: DNA RosettesE. coli nucleoidCross-section of a human histone-depleted chromosomeDNA packing vs DNA condensation-5— … specialized proteins called "condensins”… bundling …— … other proposals … secure DNA loops.— Condensins hold … together, … chromosome … space in the nucleus … — … condensin… regulation… is not known.http://www.embl.de/aboutus/communication_outreach/media_relations/2011/110717_Heidelberg/http://www.the-scientist.com/?articles.view/articleNo/15778/title/Single-Molecule-Compaction-of-DNA/Condensins: head domain dimerization — a molecular toggle latch? http://www.sciencedirect.com/science/article/pii/S0962892411001164http://femsre.oxfordjournals.org/content/38/3/380Toggle latchReleasable cable tieDNA packing vs DNA condensation-6— … transcriptionally-inactive interphase heterochromatin … arranging extended chromatin loops as rosettes of radial loops in a spiral fashion along the chromosome core, … total linear DNA compression … x10,000. http://www.yourarticlelibrary.com/zoology/cell/chromosomes-morphology-structure-heteropycnosis-and-other-details/30661/http://web.stanford.edu/~ajspakow/page2/page29/page41/page41.html— Other heterochromatin models are also formulated.DNA packing vs DNA condensation-7— For … segregation … DNA condensation … extreme. — … mitosis,… yet another round of condensation … total linear DNA compression … 50,000-fold.DNA packing vs DNA condensation-8— … still … by condensins, … "supercondensins" … operating with already condensed chromatin…? . — … maximally shorten the chromosomes… mitotic spindle. http://www.daviddarling.info/encyclopedia/S/spindle.htmlhttp://www.utexas.edu/courses/zoo325/chap16.htmDNA packing vs DNA condensation-9— …(besides) condensation… sister chromatids … … cohesins, … beginning of anaphase… http://www.nature.com/scitable/content/models-of-cohesin-and-condensin-action-50351http://vulgaire.com/lecture-the-cell-cycle/http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=591The linear model The circular modelEukaryotic chromosome condensation scheme— Condensin— CohesinSister chromatidsEukaryotic DNA compression ratioshttp://www.discoveryandinnovation.com/BIOL202/notes/lecture18.html~1,000Up to 50,000Relationship between the termsDNA compression(generic reduction in 1-to-3 dimensions without specifying mechanisms)Naked DNADNA compaction(mostly 1D 100-1000x compression for the purpose of metabolism and cell maintenance)Prokaryotic nucleoids,Eukaryotic euchromatinDNA packing(maximal 3D compression for the purpose of long-range (many cell lengths) mass DNA transport)Encapsidated phage DNA,DNA in sperm cellsDNA condensation(2D compression via rosettes of radial loops for the purpose of short-range (intracellular) mass DNA transport)Eukaryotic heterochromatin, mitotic chromosomesA real life connection http://www.shmoop.com/dna/dna-packaging.htmlPrinciples of bulk DNA transport-1— … newborn cell … genome … transporting the genome-size DNA mass … — … bulk DNA transport for significant distances… : 1) pull (mitotic spindle in eukaryotes); 2) push (prokaryotic plasmids); 3) pump (naked DNA pumping, as during phage encapsidation). http://jcb.rupress.org/content/179/5/1059.figures-onlyPrinciples of bulk DNA transport-2— … segregation mechanisms in prokaryotes are still unknown… — … plasmid segregation mechanisms…— … very different from … eukaryotes… — … orientation … eukaryotic bulk DNA segregation principle. http://jcb.rupress.org/content/179/5/1059.figures-onlyPrinciples of bulk DNA transport-3— … segregate 105-fold condensed chromosomes … microtubule-organizing centers … mitotic spindle. — The main features of the "pull" segregation principle are: 1) the spindle … … a few thousands of microtubules … microtubule-organizing centers (MTOCs), … around centrioles; http://www.daviddarling.info/encyclopedia/S/spindle.htmlhttp://www.nature.com/nrn/journal/v2/n6/box/nrn0601_408a_BX1.htmlPrinciples of bulk DNA transport-42) chromosomes … kinetochores… centromere… microtubules … pole; 3)
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