PCB6528 Spring 2012 Chase exam page 1
Name ___________________________
This exam is worth 60 points (10 short answer questions worth 6 points each). Please limit your
answers to the space provided!
1- Explain why the gene coding content of the plastid genomes (or the mitochondrial genomes)
is not identical among all plant species.
 Functional gene transfer from plastid to the nucleus has occurred in recent plant evolution.
 Different genes have undergone functional transfer in different plant lineages.
2 - Explain what is meant by chloroplast capture.
The introgression of the plastid genome of one species into another species.
3 - What is the evidence that chloroplast capture has occurred in natural populations of plants?
 Phylogenies based on plastid genome sequences do not match those based on nuclear
genome sequences or
 Phylogenies based on plastid genome sequences reflect geographic rather than taxonomic
relationships.
4 How might differences in the gene coding content of plant plastid genomes affect the
process of chloroplast capture in nature?
 These differences could limit the opportunities for capture
 Because all genes essential for plastid function must be present in at least one of the two
compartments. If the plastid genome from species A has transferred a gene to the nucleus,
but that gene remains in the plastid genome of species B, capture of species A chloroplast
by species B would not be possible an essential gene would be missing.
5 Explain how chloroplast genome transformation allowed Stegemmann et al. (Horizontal
transfer of chloroplast genomes between plant species) to investigate chloroplast capture in a
laboratory/greenhouse setting.
 The chloroplast genome of N. tabacum was transformed to confer spectinomycin resistance
and green fluorescence. (2 pt)
 Transplastomic tabacum was grafted with N. glauca or N. benthaminana carrying nuclear
kanamycin resistance and yellow fluorescence. (2 pt)
 This allowed for the selection of chloroplast capture based on combined antibiotic
resistances. (1 pt)
 The fluorescence markers confirmed the transformed plastid and nuclear genomes were in
the same cell. (1 pt)
 and/or genome sequencing confirmed capture of the full chloroplast genome (1 pt)
PCB6528 Spring 2012 Chase exam page 2
Name ___________________________
6 What is the evolutionary origin of plant mitochondrial RNA polymerase?
 This polymerase is similar to the bacteriophage T7 single subunit RNA polymerase
7 It appears that the plant mitochondrial RNA polymerase is very flexible in terms of the DNA
sequence that will function as a promoter. Why might this flexibility be especially
advantageous for plant mitochondrial genomes?
This would allow for the continued expression of essential genes despite the evolutionary
forces that tend to place novel sequences upstream of these genes:
 Plant mitochondrial genomes show extensive variation of intragenic sequences
 Plant mitochondrial genomes undergo frequent rearrangements involving
recombination events
8 The scheme for chloroplast photosynthetic electron transfer is shown in the diagram below.
If light conditions are altered from those favoring photosystem II (light II) to conditions that
favor photosystem I (light I) will plastoquinone (PQ) become more oxidized or more reduced?
Based on our class discussions of plastid gene expression processes, indicate whether the rate
of psbA gene transcription is predicted to increase or decrease in this case. (Recall that psbA
encodes the D1 subunit of photosystem II (PSII)
Experimental
condition
PQ
(oxidized or
reduced)
psbA
transcription
rate (increase or
decrease)
Switch from light
II to light I
Oxidized
(electron
deficient due to
demand pull
from PSI)
Increased (to
increase the
amount of PSII
and balance
electron flow
through the
chain)
PCB6528 Spring 2012 Chase exam page 3
Name ___________________________
9 Plant organelles have a unique RNA editing process that is essential to organelle gene
expression. In tobacco plastids, the initiation codon of the psbL gene must be created by RNA
editing. The genomic sequence at the 5' end of the tobacco gene begins with ACG. In the table
below, fill in the sequences that correspond to this codon for each different molecule.
molecule
psbL initiation codon
tobacco psbL genomic DNA
5' ACG 3'
tobacco psbL unedited RNA
ACG
tobacco psbL edited RNA
AUG
tobacco psbL edited cDNA
ATG
10 Through chloroplast transformation studies we learned that the sixteen 5' nucleotides and
ten 3' nucleotides are needed to specify an RNA editing site. Through mutant studies we also
learned that a PPR protein (CRR4) was required for an RNA editing event that creates the
initiation codon for the ndhD gene in Arabidopsis. Based upon our discussion paper on the
nature and function of another PPR protein (PPR10), propose a model for how the CRR4 protein
might act to promote RNA editing at the ndhD initiation codon.


CRR4 might bind the RNA directly in the vicinity of the RNA editing site
CCR4 binding might:
1. Re-model the RNA structure to allow access of the RNA editing machinery
2. and/or recruit the RNA editing machinery to the site