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Sizes of plastid cpDNA

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Sizes of (plastid) cpDNA ... Sizes of cpDNAs from diverse plants. From ... Rumpho, M.E., Summer, E.J. & Manhart, J.R. (2000) Solar-Powered Sea Slugs. ... – PowerPoint PPT presentation

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Title: 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.
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