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Nuclear Architecture/OverviewSlide 2Nuclear architecture (cont.)Slide 4Slide 5Slide 6Slide 7Slide 8Nuclear Genome in PlantsSlide 10In Vivo StudiesSlide 12Slide 13Genomes & The Tree of LifeSlide 15What about genome complexity?Slide 17Mycoplasma : How many genes essential for growth (under lab conditions)?Features that vary & contribute to the wide range of nuclear genome sizesGenetic RedundancySlide 21Impact of Horizontal Transfer on GenomesNuclear Architecture/Overview•Double-membrane envelope•Has lumen that is continuous with ER•Outer membrane also has ribosomes like ER•Nuclear envelope has pores–large, complex structures with octahedral geometry –allow proteins and RNAs to pass–transport of large proteins and RNAs requires energy•Many nuclear proteins have nuclear localization signals (NLS)–short basic peptides, not always at N-terminusNuclear architecture (cont.)•nuclear skeleton (lamina)–intermediate filaments (lamins)–anchor DNA and proteins (i.e., chromatin) to envelope•Nucleolus–site of pre-rRNA synthesis and ribosome assemblyTobacco meristem cell : Nucleus with large Nucleolus, and Euchromatin.Stars indicate heterogeneity in the nucleolus.EuchromatinNarcissus flower cell with heterochromatin in the nucleus.Heterochromatind – partially assembled ribosomes passing through pores (side view)Freeze fracture EM view c – pores “face on” view thru tunnelModel of nuclear pore (A is top view)Fig. 1.37, Buchanan et al.Nucleolus chromatin spreadRNA Pol I making pre-rRNAs Pre-ribosomesTime-lapse photos of Nucleolus dumping something??Nuclear Genome in Plants•DNA organized in chromosomes & replicated as in other systems•Euchromatin & Heterochromatin (transcrip-tionally inactive) present•DNA packaged by histones into nucleosomes, then further coiled into 30 nm fibers •DNA also attached to the nuclear matrix:–SAR (scaffold attachment regions)- A-T rich sequences that attach DNA to matrix, can promote transcription of “transgenes”H1 histoneDNANucleosomecore27Å110Å57Å30 nM Fiber is a Solenoid with 6 nucleosomes per turnSide viewEnd viewcondensationIn Vivo Studies •Promoters of active genes are often deficient in nucleosomesSV40 virus minichromosomes with a nucleosome-free zone at its twin promoters. Fig. 13.25Can also be shown for cellular genes by DNase I digestion of chromatin – promoter regions are hypersensitive to DNase I.Packing ratio ~ 25 for this step = 1000 overallSolenoid attaches to Scaffold, generating LoopsNuclear DNA also has supercoiled regions.Fig. 13.14Genomes & The Tree of Life•Archaea - small circular genome •Prokarya - small to very small (e.g., Mycobacterium) circular genomes•Eukarya - 3 genomes–Mitochondrial – small to micro-sized, linear and circular, prokaryotic origin–Chloroplast – small, circular, prokaryotic origin –Nucleus – large, linear chromosomes; evidence of archaea, prokaryotic and “protoeukaryotic?” originsPlant nuclear genome sizes are large and widely varied.x 1000 to get bpLilium longiflorum (Easter lily) = 90,000 MbFritillaria assyriaca (butterfly) = 124,900 MbProtopterus aethiopicus (lungfish) = 139,000 MbWhat about genome complexity?How many genes do plants have?Mycoplasma prokaryote517E. coli prokaryote4300Archaeoglobus archaeon2500Cyanidioschyzon rhodophyte 4700Saccharomyces yeast 6000Drosophila insect 13,600Chlamydomonas chlorophyte (unicell)15,500Arabidopsis angiosperm, dicot 25,000Homo sapiens primate 32,000Oryza (rice) angiosperm, monocot32-39,000Organism Taxon # GenesTexas wild riceMycoplasma : How many genes essential for growth (under lab conditions)?•Using transposon mutagenesis, ~150 of the 517 genes could be knocked out; ~ 300 genes deemed essential (under lab conditions), which included:–~100 of unknown function–Genes for glycolysis & ATP synthesis–ABC transporters–Genes for DNA replication, transcription and translationScience 286, 2165 (1999)Features that vary & contribute to the wide range of nuclear genome sizes1. Amount (or fraction) that is highly repeated 2. Abundance of "Selfish DNA“ (transposons, etc.)3. Frequency and sizes of introns–Humans have large introns4. Genetic redundancyGenetic Redundancy•The sizes of many gene families have increased much more in certain organisms.•May account for much of the unexpectedly high genetic complexity of angiospermsyeast Drosophila ArabidopsisNo. of genes6200 13,600 25,000No. of gene families4380 8065 11,000No. of genes from duplication1820 5535 14,000Genetic Redundancy or DuplicationImpact of Horizontal Transfer on Genomes•~ 20% of the E. coli genome was obtained by lateral transfer.•Not clear how much of plant nuclear genomes are from horizontal transfer–Some pathogens can transfer DNA between plants–Many nuclear genes came from the prokaryotic endosymbionts that became Mito. and Chloro.–Some selfish DNAs such as mobile introns or transposons occasionally transfer


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UT BIO 350M - Nuclear Architecture Overview

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