Sizes of (plastid) cpDNA

1
Sizes 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)

2
Sizes of cpDNAs from diverse plants
From Kloppstech, Westhof et al.
3
Parasitic 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

5
Tobacco cpDNA (Sugiura lab)
From Kloppstech, Westhof et al.
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cpDNA 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?).

7
Gene identification, or "Sorting out Gene-Protein
Relationships"

• Two basic approaches
• protein --gt DNA
• DNA ? protein

8
Gene 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
accD
10
Comparative 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).

11
Cp Genome in non-green algae

• In evolutionarily ancient (or distant) 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
• Dinoflagellates have very weird Cp genome made up
  of many small gene-sized plasmids.

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Chrysophytes - type of Chromophyte
Ceratium
Dinos
Dinophysis
Porphyra A Rhodophyte
13
Chloroplast 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.

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Can 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
  (only) in the nucleus. Analysis of this gene
  suggests it was in the nucleus a long time before
  the chloroplast gene was lost.
• phylogenetic analysis shows that rpl22 was
  transferred to the nucleus in a common ancestor
  of all flowering plants, gt100 million years
  before it was lost from the legume chloroplast
  lineage
• Conclusion Gene transfer to nucleus still going
  on, and some genes are more likely to transfer
  than others.

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Phylogenetic 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.
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Euglenoids 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.
17
Chloroplast ER (CER) with 2 membranes, making 4
around this organelle in the chromophyte,
Olisthodiscus
S. Gibbs
18
In 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
19
Cryptomonad cell w/host (blue) endosymbiont
parts (red)
http//users.rcn.com/jkimball.ma.ultranet/BiologyP
ages/E/Endosymbiosis.html
20
Keeling, 2004, Am. J. Bot. 91481
21
Primary Endosymbiosis
Secondary Endosymbiosis
Tertiary or Serial Endosymbiosis
Keeling, 2004, Am. J. Bot. 91481
22
Nucleomorph 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)

23
Elysia chlorotica Sea slug with active
chloroplasts from a heterokont alga (Vaucheria).
Chloroplasts stay active for at least 8
months. Kleptoplasty growing with stolen
plastids
Rumpho, M.E., Summer, E.J. Manhart, J.R. (2000)
Solar-Powered Sea Slugs. Mollusc/Algal
Chloroplast Symbiosis. Plant Physiology, 123
29-38.
24
Vaucheria Heterokontophyta (Xanthophyceae)
A few nuclei (rounder) and many chloroplasts in
these giant cells. Plastids acquired secondarily,
are of red algal origin.
25
Isolation of Functional Chloroplasts from the
Sacoglossan Mollusc Elysia viridis Montague M.L.
Williams A. H. Cobb. New Phytologist, Vol. 113,
pp. 153-160 (1989)
Codium green marine
26

• How do chloroplasts remain active for several
  months?
• 2 possibilities
• They are unusual and encode many genes that are
  found in the nucleus in other plants.
• - No, but did lack psbO gene
• The slug (Elysia) has acquired genes for plastid
  proteins in its nucleus and provides the proteins
  to the stolen chloroplasts.
• - Found psbO in the nucleus of Elsyia and
  Vaucheria.
• If 2 is correct, then there should be many
  others!!

Rumpho et al. (2008) Proc Nat l Acad Sci 105,
17867
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Endosymbiosis has played a major role in the
evolution of life on earth, and will likely
continue to do so. Maybe animals, or
animal-plant hybrids that photosynthesize are out
there? Or have come and gone (extinct)?