Download Nuclear genome 1

Nuclear Architecture/Overview
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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 skeleton (lamina)
– intermediate filaments (lamins)
– anchor DNA and proteins (i.e., chromatin)
to envelope
• Nucleolus
– site of pre-rRNA synthesis and ribosome
assembly
Tobacco meristem
cell : Nucleus with
large Nucleolus,
and Euchromatin.
Stars indicate
heterogeneity in the
nucleolus.
Euchromatin
Narcissus flower
cell with
heterochromatin
in the nucleus.
Heterochromatin
Freeze fracture EM view 
c – pores “face on”
view thru tunnel
d – partially assembled
ribosomes passing
through pores (side
view)
Model of nuclear pore (A is top view)
Fig. 1.37, Buchanan et al.
Time-lapse photos of
Nucleolus dumping
something??
Pre-ribosomes
Nucleolus chromatin
spread
RNA Pol I making prerRNAs
Nuclear Genome in Plants
• DNA organized in chromosomes & replicated
as in other systems
• Euchromatin & Heterochromatin (transcriptionally 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”
30 nM Fiber is a Solenoid with 6
nucleosomes per turn
DNA
27Å
H1 hist one
110Å
Nucleosome
cor e
57Å
Side view
End view
In Vivo Studies
• Promoters of active genes are often
deficient in nucleosomes
SV40 virus
minichromosomes
with a nucleosomefree 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
Solenoid attaches to Scaffold, generating Loops
Packing ratio ~ 25 for this step = 1000 overall
Nuclear DNA
also has
supercoiled
regions.
Fig. 13.14
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
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?
How many genes do plants have?
Organism
Texas wild rice
Taxon
Mycoplasma
# Genes
prokaryote
517
E. coli
prokaryote
4300
Archaeoglobus
archaeon
2500
Cyanidioschyzon rhodophyte
4700
Saccharomyces
yeast
6000
Drosophila
insect
13,600
Chlamydomonas
chlorophyte
(unicell)
15,500
Arabidopsis
angiosperm,
dicot
25,000
Homo sapiens
primate
32,000
Oryza (rice)
angiosperm,
monocot
32-39,000
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
1. Amount (or fraction) that is highly
repeated
2. Abundance of "Selfish DNA“
(transposons, etc.)
3. Frequency and sizes of introns
– Humans have large introns
4. 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
Genetic Redundancy or Duplication
yeast
Drosophila Arabidopsis
No. of
genes
6200
13,600
25,000
No. of gene
families
4380
8065
11,000
1820
5535
14,000
No. of
genes from
duplication
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