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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
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
nuclear architecture cont
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
slide4

Tobacco meristem cell : Nucleus with large Nucleolus, and Euchromatin.

Stars indicate heterogeneity in the nucleolus.

Euchromatin

slide6

Freeze fracture EM view 

c – pores “face on” view thru tunnel

d – partially assembled ribosomes passing through pores (side view)

slide7

Model of nuclear pore (A is top view)

Fig. 1.37, Buchanan et al.

slide8

Time-lapse photos of

Nucleolus dumping something??

Pre-ribosomes

Nucleolus chromatin spread

RNA Pol I making pre-rRNAs

nuclear genome in plants
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”
in vivo studies
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

slide12

Solenoid attaches to Scaffold, generating Loops

Packing ratio ~ 25 for this step = 1000 overall

genomes the tree of life
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
slide15

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

what about genome complexity
What about genome complexity?

How many genes do plants have?

slide17

Organism Taxon # Genes

Texas wild rice

mycoplasma how many genes essential for growth under lab conditions
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)

features that vary contribute to the wide range of nuclear genome sizes
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
genetic redundancy
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
slide21

Genetic Redundancy or Duplication

yeast

Drosophila

Arabidopsis

impact of horizontal transfer on genomes
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