Title: Sizes of plastid cpDNA
1Sizes of (plastid) cpDNA
- Range is 70,000 bp (70 kb) to 2,000,000 bp
(2,000 kb), but most are less than 250,000 bp
(250 kb) - Land plants typically 120 170 kb
- (70 kb Epifagus 2,000 kb Acetabularia)
2Sizes of cpDNAs from diverse plants
From Kloppstech, Westhof et al.
3Parasitic plant, no photosyn.
Epifagus virginiana -beechdrops
From U. Wisconsin-Madison Botany Dept.
4 Organization of typical (angiosperm) chloroplast
chromosome
- inverted repeats (IRa and IRb) separate circle
into large and small single-copy regions (LSC and
SSC, respectively) - IRs always contain the rRNA (rrn) genes, but also
contain other genes - 125 genes are found, encoded on both strands,
without much overlap
5Tobacco cpDNA (Sugiura lab)
From Kloppstech, Westhof et al.
6cpDNA Gene Content
- Most cp genes fall into 2 functional groups
- genes involved in the genetic apparatus
(replication, transcription,translation) - genes involved in photosynthesis
- Also genes for protein degradation, fatty acid
synthesis, and respiration (chlororespiration).
7Gene identification, or "Sorting out Gene-Protein
Relationships"
- Two basic approaches
- protein ---gt DNA
- DNA --gt protein
-
8Gene nomenclature
- Based on bacterial naming system, which uses
lower case letters, and a descriptive prefix,
based on the probable function. If the gene
product is part of a multi-subunit complex, a
letter of the alphabet is used to denote
different subunits. - Examples
- psa for genes of photosystem I (psaA, psaB,
etc.) - psb for genes of photosystem II (psbA, psbB,
etc.) - A non-conforming example
- rbc for genes encoding ribulose-1,5-bisphosphate
carboxylase (RuBPCase) - - RuBPCase has two subunits, large and small
- - the genes are rbcL and rbcS rbcL is in cpDNA,
rbcS is encoded in the nucleus
9(No Transcript)
10Comparative organization of cpDNA among land
plants and green algae
- The length of the IR regions vary in different
plant families. - There is no IR in certain plants (e.g., legumes).
- Significant differences in gene order between
distantly related species, but relatively minor
differences in gene content (e.g., between land
plants and Chlamydomonas).
11Cp Genome in non-green algae
- In evolutionarily ancient algae, such as reds
(rhodophytes) or chromophytes (Chl a/c-containing
brown or golden algae) the cp genome can be quite
different - contains more genes (up to 2x more, 250), many of
which are in the nucleus in green plants - sometimes have multiple large circles
- In dinoflagellates, many cp genes on small
gene-sized plasmids.
12Chrysophytes - type of Chromophyte
Ceratium
Dinos
Dinophysis
Porphyra A Rhodophyte
13Chloroplast Origins Evolution
- The plastid genome is fairly conserved in
evolution (compared to nuclear or mito.). - It originated from the endosymbiotic
associations that formed eukaryotic cells
"Endosymbiotic Hypothesis. - The precursor endosymbiont was a
cyanobacterial-like organism. - Most of the endosymbionts genes were either
lost, or transferred to the nucleus early in
evolution.
14Can we find instances of more recent gene
transfer from plastid to nucleus?
- 1. tufA gene (chloroplast translation elongation
factor Tu) is in cpDNA of most green algae, but
in the nucleus in land plants. - 2. rpl22 gene (chloroplast ribosomal protein) in
cpDNA in all plants except legumes, where its in
the nucleus. Analysis of this gene suggests it
was in the nucleus a long time before the
chloroplast gene was lost. - 3. infA (translation initiation factor 1) has
transferred to the nucleus in a number of
different lineages of angiosperms. - Conclusion Gene transfer to nucleus still going
on, and some genes are more likely to transfer
than others.
15Phylogenetic evidence suggests a common origin
for all plastid genomes.However, some
chloroplasts were acquired secondarily.
Chromophytes, dinoflagellates and euglenoids have
3 (and sometimes 4) membranes around the
chloroplast.
16Euglenoids have 3 membranes around
chloroplast - outer inner envelope
membranes - extra membrane resembling an ER
membrane - also have many animal
characters
It is suggested that a photosynthetic eukaryote
(green alga) was the endosymbiont, and its
chloroplast was retained.
17Chloroplast ER (CER) with 2 membranes, making 4
around this organelle in the chromophyte,
Olisthodiscus
S. Gibbs
18In cryptomonads and chlorarachniophytes, there is
even a remnant of the endosymbionts nucleus,
called the Nucleomorph. In cryptomonas, it is
made up of 3 small chromosomes (600 kb) with
510 genes, 30 for plastid proteins. Also has
genes for gene expression. Ref Douglas et al.
(2001) Nature 4101091
19Cryptomonad cell w/host (blue) endosymbiont
parts (red)
http//users.rcn.com/jkimball.ma.ultranet/BiologyP
ages/E/Endosymbiosis.html
20Keeling, 2004, Am. J. Bot. 91481
21Primary Endosymbiosis
Secondary Endosymbiosis
Tertiary or Serial Endosymbiosis
Keeling, 2004, Am. J. Bot. 91481
22Nucleomorph genes (Green lineage)
- P.R. Gilson, V. Su, C. H. Slamovits, M.E. Reith,
P.J. Keeling, and G. I. McFadden (2006) Complete
nucleotide sequence of the chlorarachniophyte
nucleomorph Natures smallest nucleus. Proc.
Natl. Acad. Sci. USA 103 9566-9571. - 331 genes on 3 chromosomes ( 373,000 bp)
- 17 genes for plastid proteins
- tiny introns (20 nt) (GT.AG)
23Elysia chlorotica Sea slug with active
chloroplasts from a green heterokont alga
(Vaucheria).
Chloroplasts stay active for at least 8 months.
Rumpho, M.E., Summer, E.J. Manhart, J.R. (2000)
Solar-Powered Sea Slugs. Mollusc/Algal
Chloroplast Symbiosis. Plant Physiology, 123
29-38.
24Vaucheria Heterokontophyta (Xanthophyceae)
25Isolation of Functional Chloroplasts from the
Sacoglossan Mollusc Elysia viridis Montague M.L.
Williams A. H. Cobb. New Phytologist, Vol. 113,
pp. 153-160 (1989)
26Endosymbiosis has played a major role in the
evolution of life on earth, and will likely
continue to do so.