Genome-Wide Analysis of Plastid Gene Expression in Potato Leaf Chloroplasts and Tuber Amyloplasts

VT Valkov, N Scotti, S Kahlau, D Maclean, S Grillo, JC Gray, R Bock, T Cardi, 2009. Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranslational control. Plant Physiology. 150: 2030-2044

The full sequence of the potato chloroplast genome was recently concluded and analysis of gene expression levels is now possible. Experiments using RT-PCR techniques compared the gene expression levels in the leaf chloroplasts and the tuber amyloplasts of the potatoes. Results showed that there were significantly lower levels of expression, and therefore lower levels of resultant transcripts in the tubers than in the leaves. Explanations as to why this occurs include fewer connections between ribosomes and the tuber transcripts, overall promoter usage,  and incomplete splicing of introns in these transcripts. RNA samples of the chloroplast and amyloplast organelles were obtained in order to do a northern-blot test, and the results were consistent with the data. The test confirmed fewer transcripts in the tubers, especially those encoding photosynthetic genes. Many transcripts showed only little discrepancy in splicing of introns in leaves vs. tubers. However, one transcript in particular, atpF, showed wide discrepancy between these two regions. In the tubers, 50% were left unspliced, whereas essentially all were spliced in the leaves. The atpF transcript is one of two transcripts which actually contained less splicing in the tubers than in the leaves. Furthermore, the two genes which are involved in the actual splicing of introns in the atpF transcript, crs1 and Why1, also had lower levels of expression in the tubers.

RT-PCR Results

PCR atpF

1% agarose gel with DNAs 3-3, 3-7, 300 and 364

PCR amplification of chloroplast region atpF for four different orchid species was obtained on September 30 by Alivia McMahan and James Murphy. Agarose gel electrophoresis was then performed to reveal qualitative knowledge of the results. This method revealed a variety of success rates concerning the yields of the extracted DNA from the four orchid species.

Quantification of orchid 3-7 (lanes 5&6) showed the highest success rate, attributable to the presence of a single band of sufficient size and a yield of 91.7 ng/ul. Orchids 3-3 (shown in lanes 3&4) and 300 (lanes 7&8) were termed mildly successful due to the presence of faint banding patterns. DNA extracted from orchid 3-3 achieved a yield of 7.3 ng/ul where as orchid 300 had a yield of 5.1 ng/ul. Lastly, orchid 364 (lanes 9&10) was termed unsuccessful.

Lane	DNA Code	Species or Marker	Success?
1	N/A	Molecular mass ruler	N/A
2	N/A	Negative control	N/A
3	3-3	Cleisostoma linearilabatum	+
4	3-3	Cleisostoma linearilabatum	+
5	3-7	Holcoglossum wangii	++
6	3-7	Holcoglossum wangii	++
7	300	Cleisostoma teres	+
8	300	Cleisostoma teres	+
9	364	Papilionanthe vandarum	–
10	364	Papilionanthe vandarum	–

Papilionanthe vandarum (Rchb.f.) Garay

Kingdom: Plantae
Class: Liliopsida
Order: Asparagales
Family: Orchidaceae
Subfamily: Epidendroideae
Tribe: Vandeae
Subtribe: Aeridinae
Genus: Papilionanthe

Papilionanthe vandarum are a very rare and unique members of the subtribe Aeridinae. They are native to Assam, eastern Himalayas, India, Nepal, Bhutan, Sikkim, Myanamar and southern China at elevations of 1200 to 1750 meters.

P. vandarum grow best in cool to warm temperatures in areas with high humidity and lots of sunlight. These plants are large in size, forming masses of branched, hanging, flexous stems. The leaves are long-pointed with longitudinaly grooved leaf bases.  One to four flowers bloom in the spring from the axils of these leaves, often in pairs. They are naturally white in color with a purple base. Flower sizes range between 3.8 to 5 cm. The flower stalks are pink. One to four flowers bloom in the spring, often in pairs.

Papilionanthe vandarum translation: Vanda-Like Papilionanthe, Aerides vandarum

http://www.theorchidologist.com/blog/archives/99

P. vandarum lab specimen

http://orchids.wikia.com/wiki/Papilionanthe_vandarum
http://www.efloras.org/florataxon.aspx?flora_id=2&taxon_id=242413940
http://www.flowersofindia.in/catalog/slides/Vanda-Like%20Papilionanthe.html