Chloroplast Genomes Flashcards
Chloroplast genomes
- circular
- many per cell
- smaller than plant mito and bigger than animal mito
- 3 regions: large single copy, small single copy, inverted repeat
- 70 protein coding genes (more than plant mito)
- gene content mostly conserved
- short intergenic regions
- some have introns
- usually maternally inherited
- few genes have c to u RNA editing
- rate of nt substitutions: higher than plant mito, lower than animal mito
Chloroplast genomes and phylogenetics
entire genomes are sequenced
- illumina sequencing
- DNA is being tagged and sequenced simultaneously = Barcoding— cost effective
- disadvantage- only half lineage so wont represent original phylogeny
Duplicate transfer of organelle DNA among cellular components
- M–>Nucleus = most common, sometimes functional
- C–> N= common, sometimes functional
- C–>M = non-functional
- M–> rare, non-functional
- N–>M = remnants of transposons, pseudogenes, non-functional
non-functional gene transfer to nucleus
Mitochondria/chloroplast gene transfer to nucleus
- integrates but non-functional
- happens frequently
- gene fragment, single gene, multi-gene region
- many mito and chloroplast pseudogenes in the nuclear genome
functional gene transfer to nucleus
integrated and functional gene that creates product or RNA
- In plants BUT NOT animals
- transfer often occurs by RNA intermediate
- proven by no introns
- direct DNA wouldn’t have correct aa sequence due to c to u RNA editing
- needs to acquire RNA targeting sequence
- from other genes or de novo
- needs regulatory elements for nucleus expression
- Original mito or chloroplast copy is still expressed until nuclear copy becomes functional
why no functional mito-nucleus transfer in animals
- deviation from standard genetic code (lack or start/stop codon)
- genes whose products can be imported have already been transferred (ribosomal protein genes)
Why are genes transferred to the nucleus
- Muller’s ratchet: deleterious mutational buildup in asexual mitochondrial genome is relieved when transferred to nucleus
- Beneficial mutations: recombination can occur to fix beneficial mutations
- Neutral process: Probably most likely
why do mitochondria still have genomes
- Hydrophobicity: some hydrophobic proteins are difficult to import across membrane
- lots of evidence
- expression of genes who function in respiration must be quickly directed and regulated by redox state
- -some genes already in nucleus so doesn’t fit
- proteins coded by mitochondrial genes would be transported to ER if synthesized in cytosol
How to target cytosolic proteins to Mitochondria
- MTP – to target to mitochondria
- MT DNA codons need to be changed to human nuclear codons
What are the 2 competing signals for protein targeting to mitochodria
- MTP at N-terminus– post-translational signal to target to mitochondria
- Hydrophobic TMD’s would act as co-translational signal– bind to SRP and stall translation and target whole ribosomal protein complex to ER
would proteins synthesized in cytosol be targeted to mitochondria
no most targeted to ER
- except atp8 – hydrophobic TMD no SRP recognition
Hydrophobicity of Mitochondrial proteins
hypothesis: long hydrophobic proteins with hydrophobic TMDs are targets for ER
alternate hyp: hydrophobic segments of mt proteins prevent import across the mitochondrial membrane
atp8
- mitochondrial gene still encoded by mitochondria even though targeted to mitochondria when expressed in cytosol
- overlaps with atp6– not mito targeted
- alternate codons/ changes in genetic code
