# A brief history of the green lineage: the chloroplast standing center stage

Robert Blanvillain

► To cite this version:

Robert Blanvillain. A brief history of the green lineage: the chloroplast standing center stage. Licence. Génétique du développement des plantes - “ Characterization of mutants affected in plant development ”, en distanciel, visio-conférence, Spain. 2024. http://hal-04968694

HAL Id: hal-04968694

https://hal.science/hal-04968694v1

Submitted on 26 Feb 2025

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_2.png" /></figure>

A brief history of the green lineage: the chloroplast standing
center stage

Robert Blanvillain

Université Grenoble-Alpes

Elche, 2024
The green lineage &
Oxygen content of Earth's Atmosphere

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /></figure>

<figure><img src="image_9.png" /></figure>

<figure><img src="image_10.png" /></figure>
<figure><img src="image_11.png" /></figure>

Shh! Let's talk about plants, it is still a mystery

<figure><img src="image_12.png" /></figure>

Descent with modification
Natural selection
Darwin's Abominable Mystery

In a letter to his closest friend, botanist and explorer Dr Joseph Hooker, Darwin wrote: 'The rapid development as far as we can judge of all the higher plants within recent geological times is an abominable mystery.'

<figure><img src="image_13.png" /></figure>

© lyellcollection.org
# Terrestrialization of the green lineage

<figure><img src="image_14.png" /></figure>

Interaction with
substrate microbiota?
Terrestrialization of the green lineage (2)

<figure><img src="image_15.png" /></figure>
Chloroplasts are only ONE type of plastids in
multicellular organisms

<figure><img src="image_16.png" /></figure>
The structure of a plant cell

<figure><img src="image_17.png" /></figure>
The structure of a plant cell

<figure><img src="image_18.png" /></figure>
The structure of a plant cell

<figure><img src="image_19.png" /></figure>
# The photosynthetic factory of Plants: The Chloroplast

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

Cells containing chloroplasts

<figure><img src="image_22.png" /></figure>

Chloroplast
Chloroplast ultrastructure

<figure><img src="image_23.png" /></figure>

* lens-shaped organelles

* (5-8 µM long, 2-4 µM thick)

* double membrane: envelope

* thylakoid membrane system

* (grana stacks, stroma lamellae)

* stroma, lumen

* own genome

* (ca. 100-120 genes), up to 100 copies

* own gene expression system
The photosynthetic apparatus within thylakoides

<figure><img src="image_24.png" /></figure>
Types of photosynthesis

<figure><img src="image_25.png" /></figure>
Photosynthetic taxa

Bacteria

Eukarya

<figure><img src="image_26.png" /></figure>
Photosynthesis on earth

<figure><img src="image_27.png" /></figure>
Functions of chloroplasts

- Photosynthesis

- Nitrogen reduction

- sulfur reduction

• compartmentalization of biosynthetic pathways:
  amino acids / purines pyrimidines / fatty acids

* storage of energy:
  starch
From seed to plant: germination of a bean

<figure><img src="image_28.png" /></figure>

Growth in the dark

Light induces the formation of chloroplasts
Skotomorphogenesis vs Photomorphogenesis

<figure><img src="image_29.png" /></figure>
Chloroplasts are only ONE type of plastids

<figure><img src="image_30.png" /></figure>
What was the origin of plastids?

* **Autogenesis:**

Sub-compartimentation of cellular components in
eukaryotic cells (including DNA)

* **Endosymbiosis:**

Symbiotic association of a proto-eukaryote with a
photosynthetically active bacterium
Observations supporting endosymbiosis

First postulated by Constantin Mereschkowsky (1905), generally accepted (1970s), promoted by Lynn Margulis:

* circular genome

* bacteria-like 70S ribosomes

* sensitivity against bacterial translation inhibitors

* no polyadenylation of mRNAs

* bacteria-like promoters (-10 - -35 elements)

* bacteria-like ribosome binding sites

* bacteria-like operon structures
The Plastome
structure

<figure><img src="image_31.png" /></figure>
Plastid genes contain prokaryotic and
eukaryotic elements

<figure><img src="image_32.png" /></figure>
Most promoters are prokaryotic – but not all

„-35“

rbcL TACGGTTGGG TTGCGC CATATATATGAAAGAGTA TACAAT AATGATGT

atpB AAATTTACTC TTGACA GTGGTATATGTTGTATATG TATATC CTAGATGT

psbA TAGATATTGG TTGAGA CGGGCATATAAGGCATGT TATACT GTTGAATA

psbB TCAACTCCCA TTGCGT ATTGCTACTTATCGAGTA TAGAAT AGATTTGT

„-10“

E. coli ...... TTGACA ...... 17 bp ...... TATAAT ......

psbD/C GAAAGAAGCATAAAGTAAGTAGACCTGACTCCTTGAATGATGCCTC TATCCGCTATTTCTGATATATAAA

<figure><img src="image_33.png" /></figure>
# Plastids contain two types of RNA polymerases

*Epiphagus*: early proposal of multiple RNA polymerases

<table><tr><td><strong>Nucleus</strong> coded RNA polymerase</td><td><strong>Plastid</strong> coded RNA polymerase</td></tr><tr><td>Phage type</td><td>prokaryotic type</td></tr><tr><td>one subunit</td><td>several subunits (~16 UE)</td></tr><tr><td></td><td>sigma factors</td></tr><tr><td>Expression of early genes “Housekeeping genes”</td><td>Expressions of late genes PhANGs</td></tr></table>

<figure><img src="image_34.png" /></figure>
RPO evolution from bacteria to Chloroplast:
Differences and Similarities

<figure><img src="image_35.png" /></figure>
RPO evolution from E. coli to Chloroplast:
The internal catalytic residues better conserved than the external residues

<figure><img src="image_36.png" /></figure>

<figure><img src="image_37.png" /></figure>

<figure><img src="image_38.png" /></figure>

<figure><img src="image_39.png" /></figure>

<figure><img src="image_40.png" /></figure>

<figure><img src="image_41.png" /></figure>

<figure><img src="image_42.png" /></figure>

<figure><img src="image_43.png" /></figure>

<figure><img src="image_44.png" /></figure>

Gray : conserved aa
Green : not conserved aa

<figure><img src="image_45.png" /></figure>

E. coli RPO

6KJ6

Xu et al., 2019

Ruedas et al. 2022
Subunits of the chloroplast RNA polymerase

<figure><img src="image_46.png" /></figure>

<figure><img src="image_47.png" /></figure>
Subunits of the chloroplast RNA polymerase PEP

<table><thead><tr><th>Subunit</th><th>AGI Accession No.</th><th>Mass (kD; theor. – cTP/app.)</th><th>Identity/Protein Domain</th><th>Function</th></tr></thead><tbody><tr><td>RpoC<sub>2</sub></td><td>AtCg00170</td><td>156/141</td><td>β" subunit</td><td>DNA binding</td></tr><tr><td>RpoB</td><td>AtCg00190</td><td>121/118</td><td>β subunit</td><td>RNA synthesis</td></tr><tr><td>PAP1</td><td>At3g04260</td><td>110/110</td><td>pTAC3/SAP domain</td><td>DNA/RNA binding</td></tr><tr><td>PAP2</td><td>At1g74850</td><td>89/107</td><td>pTAC2/PPR repeat, SMR domain</td><td>RNA metabolism</td></tr><tr><td>RpoC<sub>1</sub></td><td>AtCg00180</td><td>80/85</td><td>β'-l subunit</td><td>Unknown</td></tr><tr><td>PAP3</td><td>At3g48500</td><td>77/76</td><td>pTAC10/S1-like domain</td><td>RNA binding</td></tr><tr><td>PAP4</td><td>At5g23310</td><td>26/74</td><td>Iron superoxide dismutase 3</td><td>Superoxide detoxification (ex.)</td></tr><tr><td>RpoC<sub>1</sub></td><td>AtCg00180</td><td>80/72</td><td>β'-s subunit</td><td>Unknown</td></tr><tr><td>PAP5</td><td>At2g34640</td><td>57/70</td><td>pTAC12-HEMERA/RAD23 domain</td><td>Probably involved in ubiquitin-mediated proteolysis (ex.)</td></tr><tr><td>PAP6</td><td>At3g54090</td><td>49/52</td><td>FLN1/pfkB-2 fructokinase</td><td>Fru phosphorylation; substrate specificity not detectable (ex.)</td></tr><tr><td>PAP7</td><td>At4g20130</td><td>49/52</td><td>pTAC14/SET domain, Rubisco substrate binding</td><td>Lys methyltransferase, interaction with histones or Rubisco</td></tr><tr><td>RpoA</td><td>AtCg00740</td><td>38/38</td><td>α-Subunit</td><td>Complex stabilization</td></tr><tr><td>PAP8</td><td>At1g21600</td><td>31/37</td><td>pTAC6</td><td>Unknown</td></tr><tr><td>PAP9</td><td>At5g5110</td><td>29/29</td><td>Iron superoxide dismutase 2</td><td>Superoxide detoxification (ex.)</td></tr><tr><td>PAP4</td><td>At5g23310</td><td>26/26</td><td>Iron superoxide dismutase 3</td><td>Superoxide detoxification (ex.)</td></tr><tr><td>PAP10</td><td>At3g06730</td><td>12/13</td><td>TRX-z/thioredoxin WCGPC motif</td><td>Redox regulation (ex.)</td></tr></tbody></table>
<figure><img src="image_48.png" /><figcaption>PAP8/pTAC6</figcaption></figure>

<figure><img src="image_49.png" /><figcaption>PAP1/pTAC3</figcaption></figure>

<figure><img src="image_50.png" /></figure>

<figure><img src="image_51.png" /><figcaption>PAP2/pTAC2</figcaption></figure>

<figure><img src="image_52.png" /></figure>

<figure><img src="image_53.png" /><figcaption>PAP3/pTAC10</figcaption></figure>

<figure><img src="image_54.png" /><figcaption>PAP9/FSD2</figcaption></figure>

<figure><img src="image_55.png" /></figure>

<figure><img src="image_56.png" /></figure>

<figure><img src="image_57.png" /><figcaption>PAP5/HMR/pTAC12</figcaption></figure>

<figure><img src="image_58.png" /><figcaption>PAP4/FSD3</figcaption></figure>

<figure><img src="image_59.png" /><figcaption>PAP6/FLN1</figcaption></figure>

<figure><img src="image_60.png" /></figure>

<figure><img src="image_61.png" /><figcaption>PAP7/pTAC14</figcaption></figure>

<figure><img src="image_62.png" /><figcaption>PAP10/TrxZ</figcaption></figure>

<figure><img src="image_63.png" /><figcaption>PAP12/pTAC7</figcaption></figure>

<figure><img src="image_64.png" /></figure>

<figure><img src="image_65.png" /><figcaption>PAP11/MurE-like</figcaption></figure>

<figure><img src="image_66.png" /></figure>
<figure><img src="image_67.png" /></figure>

17 567 particles
<figure><img src="image_68.png" /></figure>
The classical model

P.T.J. Hadjukiewicz, L.A. Allison & P. Maliga

<figure><img src="image_69.png" /></figure>
...Knock-outs of nuclear encoded subunits show same defects...

<table><thead><tr><th>Subunit</th><th>Size aa</th><th>Id</th><th>Protein Domain</th><th>loss of function</th></tr></thead><tbody><tr><td>PAP1</td><td>910</td><td>pTAC3</td><td>PPR</td><td>Albino/ivory</td></tr><tr><td>PAP2</td><td>862</td><td>pTAC2</td><td>PPR</td><td>Pale-green</td></tr><tr><td>PAP3</td><td>697</td><td>pTAC10</td><td>S1-like (PDE312)</td><td>Albino/ivory</td></tr><tr><td>PAP4</td><td>263</td><td>FSD3</td><td>Fe SOD 3</td><td>Pale-green</td></tr><tr><td>PAP5</td><td>527</td><td>pTAC12</td><td>HEMERA/RAD23</td><td>Albino/ivory</td></tr><tr><td>PAP6</td><td>471</td><td>FLN1</td><td>Fructokinase</td><td>Albino/ivory</td></tr><tr><td>PAP7</td><td>483</td><td>pTAC14</td><td>SET domain</td><td>Albino/ivory</td></tr><tr><td>PAP8</td><td>328</td><td>pTAC6</td><td>UNKNOWN</td><td>Albino/ivory</td></tr><tr><td>PAP9</td><td>305</td><td>FSD2</td><td>Fe SOD 2</td><td>Pale-green</td></tr><tr><td>PAP10</td><td>183</td><td>TrxZ</td><td>Thioredoxin</td><td>Albino/ivory</td></tr><tr><td>PAP11</td><td>772</td><td>MurE-like</td><td>UNKNOWN</td><td>Albino</td></tr><tr><td>PAP12</td><td>161*</td><td>pTAC7</td><td>UNKNOWN</td><td>Albino/ivory</td></tr></tbody></table>

Pfalz et al. 2006, Plant Cell
Schröter et al 2010 Proteomics
Steiner et al. 2011 Plant Phys.

<figure><img src="image_70.png" /></figure>

<figure><img src="image_71.png" /></figure>

Kevin Pounot
# The PAP albino syndrome

* Albino/ivory appearance; viable on sucrose only

* Arrest in plastid development

* NEP dependent genes highly expressed, PEP-dependent genes weakly expressed

<figure><img src="image_72.png" /></figure>

Liebers *et al.*, emboJ

<figure><img src="image_73.png" /></figure>

Mininno *et al.*, unpublished

<figure><img src="image_74.png" /></figure>

Arsova *et al.*, 2010
The origin of plastids

An endosymbiotic event happened only **once** in evolution and **all** existing plastids trace back to this single event.
# Primary endosymbiosis

Eukaryote

Cyanobacterium

N

<figure><img src="image_75.png" /></figure>

Endosymbiosis

2-2.1 billion YA

<figure><img src="image_76.png" /></figure>

Plastid with 2 membranes

Lateral gene transfer

<figure><img src="image_77.png" /></figure>

N

Green Lineage

N

<figure><img src="image_78.png" /></figure>

N

<figure><img src="image_79.png" /></figure>

Glaucocystophyta

<figure><img src="image_80.png" /></figure>

Chlorophyta
(Green algae)

N

<figure><img src="image_81.png" /></figure>

Rhodophyta
(Red algae)

Terrestrial Plants
(450-500 MYA)
The riddle of the envelope

Chloroplasts
with
**2**-envelope
membranes

<figure><img src="image_82.png" /></figure>

Chloroplasts
with
**3** or **4**-envelope
membranes

<figure><img src="image_83.png" /></figure>
The theory of secondary endosymbiosis

<figure><img src="image_84.png" /></figure>
# The nucleomorph
an evidence for Secondary Endosymbiosis

<figure><img src="image_85.png" /></figure>
Algae with secondary plastids

Chloroplasts with 2-envelope membranes

<figure><img src="image_86.png" /></figure>
How did evolve plastids with 3 or 4-envelope membranes?

<figure><img src="image_87.png" /></figure>
Algae with secondary plastids

Chloroplasts with 2-envelope membranes

<figure><img src="image_88.png" /></figure>
Primary and secondary endosymbiosis
is that the whole story ?

<figure><img src="image_89.png" /><figcaption>Plate III 27–29 (von Stein, 1883)</figcaption></figure>

<figure><img src="image_90.png" /></figure>

Tertiary endosymbiosis ?
Tertiary endosymbiosis in dinoflagellates

<figure><img src="image_91.png" /><figcaption>z.B. *Peridinium balticum*, *Glenodinium foliaceum*</figcaption></figure>
Summary

* Plastids evolved by **endosymbiosis**

* Plastids are of **monophyletic** origin

* **All** existing plastids trace back to this single event

* It exists **primary, secondary** and **tertiary** endosymbiosis

* This explains plastids with **2, 3, 4** and **5** membranes
<figure><img src="image_92.png" /></figure>

From Delwiche 1999
Special cases (1) Apicoplasts

* Apicomplexa (Sporozoa) contain secondary non-photosynthetic plastids, the apicoplasts

* 4 membranes, plastome highly reduced

* Apicoplasts are essential for biosynthesis of fatty acids and haem

* Plasmodium sp., Toxoplasma sp.

* Novel drug target fighting diseases like Malaria
Special cases (2) – Kleptoplastids

Kleptoplastids originate from endocytotic uptake of the cytoplasms of plastid-
containing prey.

e.g.

Heterotrophic dinoflagellates use „stolen“ chloroplasts

Sea slugs (Ophistobranchia, Ascoglossa) use chloroplasts from their algae food

> independent from algae for months

> time separation of uptake and digestion
Emerald sea slug, Elysia Chlorotica

<figure><img src="image_93.png" /><figcaption>Dorsal view</figcaption></figure>

<figure><img src="image_94.png" /><figcaption>Feeding on algae</figcaption></figure>

<figure><img src="image_95.png" /><figcaption>sunbathe</figcaption></figure>

<caption>Plant Wanabes</caption>
<figure><img src="image_96.png" /><figcaption>Costasiella-kuroshimae</figcaption></figure>