Nuclear ArchitectureOverview - PowerPoint PPT Presentation

Title: Nuclear ArchitectureOverview


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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
• transport of large proteins and RNAs requires
  energy
• Many nuclear proteins have nuclear localization
  signals (NLS)
• short basic peptides, not always at N-terminus

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(No Transcript)
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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

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Tobacco meristem cell Nucleus with large
Nucleolus, and Euchromatin. Stars indicate
heterogeneity in the nucleolus.
Euchromatin
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Narcissus flower cell with heterochromatin in the
nucleus.
Heterochromatin
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Freeze fracture EM view ?
c pores face on view thru tunnel
d partially assembled ribosomes passing through
pores (side view)
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Model of nuclear pore (A is top view)
Fig. 1.37, Buchanan et al.
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Time-lapse photos of Nucleolus dumping
something??
?Pre-ribosomes
?Nucleolus chromatin spread RNA Pol I making
pre-rRNAs
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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

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30 nM Fiber is a Solenoid with 6 nucleosomes per
turn
condensation
Side view
End view
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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
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Solenoid attaches to Scaffold, generating Loops
Packing ratio 25 for this step 1000 overall
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Nuclear DNA also has supercoiled regions.
Fig. 13.14
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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
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What about genome complexity?

• How many genes do plants have?

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Organism Taxon Genes
Texas wild rice
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Does Mycoplasma have the smallest genome possible
for an independently -replicating organism?

• Using transposon mutagenesis, 150 of the 517
  genes could be knocked out and Mycoplasma still
  grew (under lab conditions)
• 270-350 genes are essential (under lab
  conditions)

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What accounts for the wide differences in nuclear
genome (physical) size?

• Variation in
• Amounts of highly repeated DNA
• Amounts of "Selfish DNA
  (transposons, etc.)
• Frequency and sizes of introns
• Other intergenic DNA
• Genetic redundancy

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Genetic Redundancy

• The sizes of many gene families has increased in
  some organisms more than others.
• May account for much of the unexpectedly high
  genetic complexity of angiosperms relative to
  humans.

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Genetic Redundancy or Duplication
yeast
Drosophila
Arabidopsis
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• Only a small fraction of the nuclear genome in
  plants with large genomes is transcribed
• R. Goldberg estimated about 1-2 of the tobacco
  nuclear genome (440 MB) was transcribed and
  processed to mature mRNA (based on hybridization
  of mRNA to genomic DNA)
• Arabidopsis genome (150 MB) very streamlined
  most probably transcribed (at least).

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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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NCBI
http//www.ncbi.nlm.nih.gov/
http//genome.jgi-psf.org/
JGI