PCB6528 Spring 2010 Chase exam page 1
Name _Key__________________________
This exam is worth 100 points. Please limit your answers to the space provided.
1a (6 pt) Briefly describe what is meant by sub-stoichiometric shifting (SSS) with respect to
plant mitochondrial genomes.
A change in the relative abundance of subgenomic DNA configurations
1b (6 pt) List two different DNA-based processes that could potentially contribute to SSS.
replication, recombination, degradation
1c (10 pt) Describe briefly one line of evidence that the nucleus controls or strongly influences
whether SSS takes place in the plant mitochondrial genome.
any of these:
1-The msh1 nuclear mutation in Arabidopsis results in mitochondrial SSS associated with leaf variegation
and abnormal growth phenotypes
2-The down regulation of msh1 orthologs in tomato and tobacco by RNAi results in mitochondrial SSS
associated with cytoplasmic male sterility (CMS)
3-The nuclear Fr gene restores fertility to CMS phaseolus vulgaris through an SSS event that reduces the
copy number of the mitochondrial CMS gene
PCB6528 Spring 2010 Chase exam page 2
Name _Key__________________________
2a (6 pt) Assume that the cartoon below represents a chloroplast genome. Assume NotI and
AscI are rare-cutting restriction enzymes that cleave the genome only at the indicated
positions. On the cartoon, label the large single copy (LSC). short single copy (SSC) and the
inverted repeat (IR) regions.
2b (10 pt) Next to the cartoon, draw the genome that would result from a recombination
between the inverted repeat regions.
2c (10 pt) Beneath the diagrams, explain how the two versions of the genome differ and how
you can take advantage of that difference to observe whether such recombination events do
actually take place in the plastid genome.
a)
b)
c) Note that the relative positions of the NotI and AscI restriction sites have changed so these
sites are now flanking one of the two IR copies. If recombination occurs there will be four
differently sized AscI-NotI restriction fragments and/or, four different sequence assemblies
with respect to the IR region: one flanked by AscI, one flanked by NotI, one flanked by both,
and one flanked by neither restriction site.
PCB6528 Spring 2010 Chase exam page 3
Name _Key__________________________
3a (9 pt) 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
tobacco psbL unedited RNA
5' ACG
tobacco psbL edited RNA
5' AUG
tobacco psbL edited cDNA
5' ATG
3b (6 pt) Would you expect the psbL initiation codon to be created by RNA editing in every
plant species? Explain your answer.
No, because the organelle gene codons that require correction by RNA editing are not conserved from
species to species
PCB6528 Spring 2010 Chase exam page 4
Name _Key__________________________
4a (16 pt) The scheme for chloroplast photosynthetic electron transfer is shown in the diagram
below. For each of the conditions listed in the table below, indicate whether plastoquinone
(PQ) and thioredoxin (TRX) will become more oxidized or more reduced. Based on our class
discussions of plastid gene expression processes, indicate whether the rate of psbA gene
transcription and translation is predicted to increase or decrease in each case. (Recall that
psbA encodes the D1 subunit of photosystem II (PSII); light I is optimal for photosystem I (PSI)
and light II is optimal for PSII.)
Experimental
condition
PQ
(oxidized or
reduced)
psbA
transcription
rate (increase or
decrease)
TRX
(oxidized or
reduced)
PSBA translation
rate (increase or
decrease)
Switch from light
II to light I
oxidized
increased
reduced
increased
PCB6528 Spring 2010 Chase exam page 5
Name _Key__________________________
5) Maize crp1/crp1 mutants have a complex molecular phenotype with respect to expression of
plastid electron transfer complex (PET) subunits. Some of these phenotypes are summarized in
the table below. Recall that petB and petD are part of the plastid psbB operon, petA is part of a
different plastid operon. Note that petC is a nuclear gene! + = wild-type;  = mutant
crp1/crp1 mutant phenotypes
Gene
Transcript accumulation
Protein translation
Protein accumulation
petA
+
 (no translation)
 (no accumulation)
petB
 (petB-D di-cistronic; no
monocistronic)
+
 (no accumulation)
petC
+
+
 (no accumulation)
petD
 (pet B-D di-cistronic ;
no monocistronic)
 (no translation)
 (no accumulation)
5a (5 pt) What is the whole plant phenotype of the crp1/crp1 mutants with respect to growth
and development?
Seedling lethal with pale-green, yellow or bleached leaves
5b (8 pt) Based on the table above and our class discussions, what is a likely explanation for
failure to accumulate the PETC protein in crp1/crp1 mutants?
Since the nuclear petC gene is transcribed and translated, the protein product must be degraded, likely due
to lack of assembly partners
5c) ( 8 pt) Based on the table above and our discussions of the paper by Schmitz-Linneweber et
al. what is a likely explanation for the failure to translate the PETA protein in the crp1/crp1
mutants?
The favored model is that crp1 is directly required for translation of the petA mRNA.
This is because RIP-CHIP experiments demonstrate an association between the CRP1 protein and the
petA mRNA.