Lec4 CpDNA2 Rev

8/13/2019 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)?

Lec4 CpDNA2 Rev

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