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.
6
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 --gt 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
(No Transcript)
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 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.

12
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.

14
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 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.

15
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.
16
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 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.
24
Vaucheria Heterokontophyta (Xanthophyceae)
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)
26
Endosymbiosis has played a major role in the
evolution of life on earth, and will likely
continue to do so.