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Nuclear Architecture/Overview

Nuclear 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

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Nuclear Architecture/Overview

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  1. Nuclear 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-terminus

  2. Nuclear 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 assembly

  3. Tobacco meristem cell : Nucleus with large Nucleolus, and Euchromatin. Stars indicate heterogeneity in the nucleolus. Euchromatin

  4. Narcissus flower cell with heterochromatin in the nucleus. Heterochromatin

  5. Freeze fracture EM view  c – pores “face on” view thru tunnel d – partially assembled ribosomes passing through pores (side view)

  6. Model of nuclear pore (A is top view) Fig. 1.37, Buchanan et al.

  7. Time-lapse photos of Nucleolus dumping something?? Pre-ribosomes Nucleolus chromatin spread RNA Pol I making pre-rRNAs

  8. 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”

  9. 30 nM Fiber is a Solenoid with 6 nucleosomes per turn condensation Side view End view

  10. In Vivo Studies • Promoters of active genes are often deficient in nucleosomes SV40 virus minichromosomes with a nucleosome-free zone at its twin promoters. Can also be shown for cellular genes by DNase I digestion of chromatin – promoter regions are hypersensitive to DNase I. Fig. 13.25

  11. Solenoid attaches to Scaffold, generating Loops Packing ratio ~ 25 for this step = 1000 overall

  12. Nuclear DNA also has supercoiled regions. Fig. 13.14

  13. Genomes & 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?” origins

  14. Plant nuclear genome sizes are large and widely varied. x 1000 to get bp Lilium longiflorum (Easter lily) = 90,000 Mb Fritillaria assyriaca (butterfly) = 124,900 Mb Protopterus aethiopicus (lungfish) = 139,000 Mb

  15. What about genome complexity? How many genes do plants have?

  16. Organism Taxon # Genes Texas wild rice

  17. Mycoplasma : 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 translation Science 286, 2165 (1999)

  18. Features that vary & contribute to the wide range of nuclear genome sizes • Amount (or fraction) that is highly repeated • Abundance of "Selfish DNA“ (transposons, etc.) • Frequency and sizes of introns • Humans have large introns • Genetic redundancy

  19. Genetic 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 angiosperms

  20. Genetic Redundancy or Duplication yeast Drosophila Arabidopsis

  21. Impact 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 horizontally

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