nuclear architecture/overview
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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 - PowerPoint PPT PresentationTRANSCRIPT
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 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
d – partially assembled ribosomes passing through pores (side view)
Freeze fracture EM view
c – pores “face on” view thru tunnel
Model of nuclear pore (A is top view)
Fig. 1.37, Buchanan et al.
Nucleolus chromatin spread
RNA Pol I making pre-
rRNAs
Pre-ribosomes
Time-lapse photos of Nucleolus dumping something??
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”
H1 histone
DNA
Nucleosomecore
27Å
110Å
57Å
30 nM Fiber is a Solenoid with 6 nucleosomes per turn
Side view End view
condensation
In Vivo Studies • Promoters of active genes are often
deficient in nucleosomes
SV40 virus minichromosomes with a nucleosome-free zone at its twin
promoters.
Fig. 13.25
Can also be shown for cellular genes by DNase I digestion of chromatin – promoter regions are hypersensitive to DNase I.
Packing ratio ~ 25 for this step = 1000 overall
Solenoid attaches to Scaffold, generating Loops
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?
Mycoplasma 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
Organism Taxon # Genes
Texas wild rice
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
yeast Drosophila Arabidopsis
No. of genes 6200 13,600 25,000
No. of gene families 4380 8065 11,000
No. of genes from duplication
1820 5535 14,000
Genetic Redundancy or 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