Lec4 CpDNA2 Rev

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    Sizes of (plastid) cpDNA

    Range is 70,000 bp (70 kb) to~2,000,000 bp (2,000 kb), but most areless than 250,000 bp (250 kb)

    Land plants typically 120170 kb

    (70 kbEpifagus; ~2,000 kbAcetabularia)

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    Sizes of

    cpDNAs from

    diverse plants

    From Kloppstech, Westhof et al.

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    Epifagus virginiana -beechdrops

    From U. Wisconsin-Madison

    Botany Dept.

    Parasitic plant, no photosyn.

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    Organization of typical(angiosperm)

    chloroplast chromosome inverted repeats (IRa and IRb) separate circle

    into large and small single-copy regions (LSCand SSC, respectively)

    IRs always contain the rRNA (rrn) genes, butalso contain other genes

    ~125 genes are found, encoded on bothstrands, without much overlap

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    cpDNA Gene Content

    Most cp genes fall into 2 functional groups:

    1. genes involved in the genetic apparatus

    (replication, transcription,translation)

    2. genes involved in photosynthesis

    Also genes for protein degradation, fatty acid

    synthesis, and respiration(chlororespiration?).

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    Gene identification, or "Sorting out

    Gene-Protein Relationships"

    Two basic approaches:

    protein --> DNA

    DNAprotein

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    Gene nomenclature

    Based on bacterial naming system, which uses lower case letters, and adescriptive 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.)

    psbfor 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 rbcLand rbcS; rbcLis in cpDNA, rbcSis encoded

    in the nucleus

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    accD

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    Cp Genome in non-green algae

    In evolutionarily ancient (or distant) algae, suchas 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

    Dinoflagellateshave very weird Cp genome

    made up of many small gene-sized plasmids.

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    Porphyra

    A Rhodophyte

    Ceratium

    Dinophysis

    Dinos

    Chrysophytes - type of Chromophyte

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    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. tufAgene (chloroplast translation elongation factor Tu)is in cpDNA of most green algae, but in the nucleus inland plants.

    2. rpl22gene (chloroplast ribosomal protein) in cpDNA in

    all plants except legumes, where its (only) in thenucleus. Analysis of this gene suggests it was in thenucleus a long time before the chloroplast gene waslost.

    phylogenetic analysis shows that rpl22was transferred to the nucleus ina common ancestor of all flowering plants, >100 million years before itwas lost from the legume chloroplast lineage

    Conclusion: Gene transfer to nucleus still going on, andsome 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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    Euglenoidshave 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.

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    Chloroplast ER (CER) with

    2 membranes, making 4

    around this organelle in thechromophyte, Olisthodiscus

    S. Gibbs

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    In cryptomonads andchlorarachniophytes,

    there is even a remnant of the

    endosymbionts nucleus, called the

    Nucleomorph.

    Incryptomonas, itis made up of 3 small

    chromosomes (~600 kb) with 510 genes,

    ~30 for plastid proteins. Also has genesfor gene expression.

    Ref: Douglas et al. (2001) Nature 410:1091

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    http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html

    Cryptomonadcellw/host (blue) & endosymbiont parts (red)

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    Keeling, 2004, Am. J. Bot. 9:1481

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    Primary Endosymbiosis

    Seconda

    ry

    Endosym

    biosis

    Tertiary or Serial Endosymbiosis

    Keeling, 2004, Am. J. Bot. 9:1481

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    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.

    1. 331 genes on 3 chromosomes ( ~373,000 bp)

    2. 17 genes for plastid proteins

    3. tiny introns (20 nt) (GT.AG)

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    Elysia chlorotica

    Sea slug with active

    chloroplasts from a

    heterokontalga

    (Vaucheria).

    Chloroplasts stayactive 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.

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    Vaucheria

    Heterokontophyta

    (Xanthophyceae)

    A few nuclei (rounder) and many chloroplasts in these giant cells.

    Plastids acquired secondarily, are of red algal origin.

    Isolation of Functional Chloroplasts from the

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    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)

    Codiumgreen & marine

    How do chloroplasts

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    How do chloroplasts

    remain active for several

    months?2 possibilities:

    1. They are unusual and

    encode many genesthat are found in the

    nucleus in other plants.

    - No, but did lackpsbO

    gene

    2. The slug (Elysia) hasacquired genes for

    plastid proteins in its

    nucleus and provides

    the proteins to the

    stolen chloroplasts.

    - Found psbO in the

    nucleus of Elsyiaand

    Vaucheria.

    If 2 is correct, then there

    should be many others!!

    Rumpho et al. (2008)

    Proc Nat l Acad Sci105, 17867

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    Endosymbiosishas played a majorrole 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)?