Nuclear ArchitectureOverview

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
(No Transcript)
3
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

4
Tobacco meristem cell Nucleus with large
Nucleolus, and Euchromatin. Stars indicate
heterogeneity in the nucleolus.
Euchromatin
5
Narcissus flower cell with heterochromatin in the
nucleus.
Heterochromatin
6
Freeze fracture EM view ?
c pores face on view thru tunnel
d partially assembled ribosomes passing through
pores (side view)
7
Model of nuclear pore (A is top view)
Fig. 1.37, Buchanan et al.
8
Time-lapse photos of Nucleolus dumping
something??
?Pre-ribosomes
?Nucleolus chromatin spread RNA Pol I making
pre-rRNAs
9
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

10
30 nM Fiber is a Solenoid with 6 nucleosomes per
turn
condensation
Side view
End view
11
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
12
Solenoid attaches to Scaffold, generating Loops
Packing ratio 25 for this step 1000 overall
13
Nuclear DNA also has supercoiled regions.
Fig. 13.14
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
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)

18
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

19
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.

20
Genetic Redundancy or Duplication
yeast
Drosophila
Arabidopsis
21

• 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).

22
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

23
NCBI
http//www.ncbi.nlm.nih.gov/
http//genome.jgi-psf.org/
JGI