Basics

• Plants diverged from animals around 1.5 billion years ago.

• How many genes does a plant have? : 20-25 thousand. 60% of genes are common among plants and animals.

• How to transform a plant?

  1. Stable transformation with Agrobacterium tumefaciens. Infected plants produce tumors at the infrction site.

     • Transfer-DNA (T-DNA): Genes for biosynthesis of auxin and cytokinins.
     • Dip the flower in the solution containing the agrobacteria and now 1% of the seeds will be transgenic.

  2. Stable/transient transformation with the particle gun

     • Plasmid DNA bound to small gold particles (dia 1um) are shot to the plant tissue.
     • 3-4 gold nano-particles per cell is the flux. 24 hours later, you can see the transcription of the required protein.

• How to understand a trait? (Identify genes involved in the trait)

  1. Forward genetics:

     • Screen for mutants showing altered trait behaviour.
     • Isolate gene that is defective in the mutant.
     • Study gene function.
     graph LR subgraph 2.Insertion-Mutagenesis B1(T-DNA from Agrobacterium, transposon) --> B2(Identify mutated gene by PCR of flaking DNA) end subgraph 1.Chemical-mutagenesis A1(Cause point mutations using EMS) --> A2(Identify mutated gene through genome sequencing/positional cloning) end

  2. Candidate gene approach: Reverse genetics

     • CRISPR/CAS
     • RNA interference
     • identify a T-DNA insertion mutant from available T-DNA insertion lines

  3. Use natutally occuring genetic variation within species.

     • Using QTL (qunatitatice trait locus) - mapping

• Plants survive harsh environments

  • Large environmental variations:
    1. Light conditions: shading-extreme light
    2. Temperature changes (-10° to 45°C)
    3. Water status: Drought-floods
    4. Mineral nutrients: deficiency-toxicity

• Plants do respond to high ambient temperature to optimize photosynthesis, growth and development: Thermomorphogenesis.

• Note: Hypocotyl is the stem. Specifically it is everything that grows below the germinating seed. Stuff above it is called endocotyl.

  • Steeper leaf angle is called hyponasty and is a phenotype that is amplified by rising temperature.

• Thermomorphogenesis - benefits:

  • more distance of leaves from soil: less exposure to heat reflection from soil.
  • more open rosette: better cooling due to better air circulation.
  • Cooler leaves: mean higher photosyntheti efficiency.

• Blue and red light photoreceptors that plants use to grow.

• Red light activates Phytochrome B (PHYB). PHYB is a temperature sensitive light sensor. The higher the temperature, the less active PHYB. High temperature-phenotype (29°C ) gives a low light-phenotype.

Introduction to plant responses to abiotic stress

• In plants, the development is post-embryonic. All the development in plants happen after the embroyonic stage. This is crutial for stress development.

  • For the same reason, the plant development is very plastic.
  • Developmental transitions: Light, Daylength, Temperature, $H_2O$, and Nutrients

• Plant transitions from heterotrophy (can’t produce its own food — seedling) to autotrophy.

• Seeds don’t germinate instantly to wait for seed dispersion. Enzymes that assert dormancy in seeds need to degrade for their germination.

• Number of organs — Low Nitrogen conditions would trigger more roots, whereas, the opposite will trigger inverstment in the shoot of the plant.

• Plant cells have very large vacuoles that are full of water.

  • Major driver of cell size
  • Turgor Pressure: everything that is not “woody” is supported by Turgor pressure.

• Abiotic stress: stress agents that are non-living in nature.

• Drought stress: cells increase salt concentration to hold water in the cells.

• The epidermis needs to have chloroplastics in order to have stomata. Stomata exists in all plant tissues.

• Correct Bottom part of the leaf — Daxil & top part — Basil

• Drought Response:

• Stomatal movements control water loss. And is mediated by the plant hormone ABA (Abscisic acid). Increase in ABA — closes stoma. It also controls dormency in seeds.

• Ethylene matures fruits. It is a gas and it spreads. It is also a stress hormone.

• Plants respond to cold stress by indiucing the formation of unsaturated fatty acids.

• Oxygen degradation (anerobic stress-induced proteins):

  • glycolysis and fermentation
  • ROS scavenging and signalling
  • ethylene biosynthesis

Plant membrane transporters and their role in stress response

• Siderophores chealte Iron and make them available for plants.

• Transport across cell membrane:

  • Active Transport
    • Primary Active Transport
      • Hydrolyse ATP to produce movement
    • Secondary Active Transport
      • Use another substrate for transport
  • Some famous (in)famous transporters
    • CFTR (Cystic fibrosis)
    • GLUT1 (G1D)
    • Multidrug (antibiotic) resistance: the bacteria pumps out the drugs

• Number of ion channel in plants is about half of in humans (mammals).

• ABA is a master regulator of for Growth.

• NaCl in soil. Ionic and osmotic stress together

  • $Na^+$ and $K^+$ imbalance
  • Osmotic stress
  • Increased ROS production
  • Impaired photosynthesis

• Iron deficiency: pH is a major problem that causes Iron deficiency. Plants respond by acidifying the soil around them.

Introduction to Photosynthesis/C4 and CAM Photosynthesis

• Removal of carbon requires energy equivalent to 15yrs of 2019 total energy consumption.

• Challenges to plant science: Increase net primary productivity per unit land.

• PlantACT! : aim is to fix the planet.

• Calvin-Benson Cycle: has three stages and results in photosynthesis.

• RubisCO is the most abundant protein on earth. And is important for photo-synthesis.

Assignment Discussions

1. Which genes are involved in signal transduction and response? How to find them? [Monday]

• GWAS: Genome Wide Association Study and it can be used to quantify the abundance and location of genes in comparison to using QTL (qunatitative trait locus) , which just gives you the expression of the gene (its position on the genome).
• We use EWS, a chemical mutagen to indiuce the mutations.
• Mapping by Sequencing:
• We sequence the mutated and look for particular mutated sites using GWASP.
• Allelic vs non-allelic mutations: If the mutations are allelic, the first generation cross reverts to the wild type. If not, the first generation shows mutant phenotypes.
• Rescue experiments in plants: Cross wild-type with overly expressed mutagenic specie.