(a) Explain the compartmentation of biochemical reactions in photorespiration. Comment upon the significance of the process…

(a) Compartmentation of photorespiration and its significance

Rubisco can bind either CO₂ (carboxylation) or O₂ (oxygenation) at the same active site. At today's air (about 21% O₂ and about 0.04% CO₂) and 25 °C, a C3 leaf makes roughly one oxygenation for every three to four carboxylations. Oxygenation of RuBP gives one molecule of 3-phosphoglycerate (3-PGA) and one of 2-phosphoglycolate, a two-carbon compound that is useless to the Calvin cycle and inhibits it. The photorespiratory C2 (glycolate) cycle recovers this carbon. It needs three organelles, which is why leaf cells hold chloroplasts, peroxisomes and mitochondria close together.

1. Chloroplast

• Rubisco (oxygenase): RuBP + O₂ → 3-PGA + 2-phosphoglycolate.
• Phosphoglycolate phosphatase (PGLP) → glycolate, which leaves through the glycolate/glycerate transporter PLGG1.

2. Peroxisome

• Glycolate oxidase: glycolate + O₂ → glyoxylate + H₂O₂. Catalase destroys the H₂O₂, which is why the step is kept inside the peroxisome.
• Aminotransferases: glyoxylate is aminated to glycine by glutamate:glyoxylate aminotransferase (GGAT) and serine:glyoxylate aminotransferase (SGAT).

3. Mitochondrion

• Glycine decarboxylase complex (GDC) with serine hydroxymethyltransferase (SHMT): 2 glycine + NAD⁺ → serine + CO₂ + NH₃ + NADH.
• This is where photorespiratory CO₂ is actually released. GDC is extremely abundant in leaf mitochondria.

4. Back to the peroxisome

• Serine → hydroxypyruvate (by SGAT, which makes another glycine).
• Hydroxypyruvate reductase (NADH) → glycerate.

5. Back to the chloroplast

• Glycerate kinase (ATP): glycerate → 3-PGA, which re-enters the Calvin cycle.
• The NH₃ released in the mitochondrion is re-fixed in the chloroplast by GS2 and Fd-GOGAT. The resulting glutamate returns to the peroxisome as amino donor (the photorespiratory nitrogen cycle).

Net balance: 2 phosphoglycolate (4 C) → 1 glycerate (3 C) + 1 CO₂. So 75% of the carbon diverted is recovered and 25% is lost.

Energy cost: ATP is used by glycerate kinase and by GS, and reduced ferredoxin by GOGAT. Including regeneration of RuBP, each oxygenation costs roughly 3–3.5 ATP and 2 NADPH equivalents.

Significance

• Loss of productivity: it lowers net photosynthesis of C3 crops such as wheat, rice and soybean by about 20–35%, more in hot, dry, bright conditions. In heat, Rubisco's specificity for CO₂ falls and CO₂ dissolves less readily than O₂; when stomata close, internal CO₂ falls too.
• An essential salvage and detoxification pathway: mutants lacking its enzymes (for example GOX, GDC, SHMT or Fd-GOGAT) die in normal air but grow at high CO₂. The cycle removes toxic 2-phosphoglycolate and glyoxylate and recovers 75% of the carbon.
• Photoprotection: it consumes ATP and NADPH when CO₂ is limiting (for example when stomata close under drought), acting as an energy sink that reduces photo-oxidative damage.
• Links with nitrogen and C1 metabolism: it supplies glycine and serine and interacts with nitrate assimilation.

Evolutionary and applied significance:

• The cost drove the evolution of CO₂-concentrating mechanisms. C4 plants (maize, sugarcane) confine Rubisco to bundle-sheath cells rich in CO₂, and CAM plants close stomata by day and release stored CO₂, so photorespiration is small.
• Engineering "photorespiratory bypasses" in tobacco raised biomass by about 40% in field trials (South and colleagues, 2019).
• Efforts to introduce C4 photosynthesis into rice aim at the same problem.

(b) Structure of phytochrome and its mode of action in flowering plants

Structure

• Composition: phytochrome is a soluble chromoprotein that works as a homodimer. Each monomer (about 125 kDa, about 1,100 amino acids) carries one chromophore, phytochromobilin. This is an open-chain (linear) tetrapyrrole, made in plastids from haem through biliverdin. It is attached by a thioether bond to a cysteine in the GAF domain.
• N-terminal photosensory module: NTE–PAS–GAF–PHY domains. It holds the chromophore, and its "tongue" from the PHY domain folds over the pocket.
• C-terminal regulatory module: two PAS domains and a histidine-kinase-related domain. This is needed for dimerisation, nuclear import and signalling.

Photoconversion

• Phytochrome is made as Pr, which absorbs red light (peak about 660 nm).
• Red light causes a Z→E isomerisation of the chromophore's C15=C16 double bond. This triggers a change in protein shape, forming Pfr, which absorbs far-red (about 730 nm) and is the biologically active form.
• Far-red light converts Pfr back to Pr, and Pfr also reverts slowly in darkness. Because the two absorption spectra overlap, light establishes a photoequilibrium (the Pfr/Ptotal ratio). This lets the plant sense light quality, for example shade (low red : far-red ratio under a canopy).
• Classic evidence: the lettuce-seed experiments of Borthwick and Hendricks (1952) showed red/far-red reversibility, with the last flash deciding the response.

Family: Arabidopsis has five phytochromes.

• phyA is light-labile (type I). It mediates very-low-fluence and far-red high-irradiance responses, such as de-etiolation under canopies.
• phyB–E are light-stable (type II). phyB is dominant for red-light responses and shade avoidance.

Mode of action

1. Nuclear import: Pfr moves from the cytosol into the nucleus (phyA with the help of FHY1/FHL; phyB by unmasking a nuclear localisation signal) and gathers in "photobodies".
2. PIF removal: Pfr binds PHYTOCHROME-INTERACTING FACTORS (PIFs), bHLH transcription factors that repress light responses. This causes their phosphorylation, ubiquitination and destruction by the 26S proteasome.
3. COP1–SPA inhibition: Pfr inhibits the COP1–SPA E3 ubiquitin ligase. This stabilises positive regulators such as HY5 and CONSTANS.
4. Result: thousands of genes change expression, controlling germination, de-etiolation, shade avoidance, circadian clock setting and flowering. A small cytoplasmic role, such as in chloroplast movement, also exists.

Role in flowering (photoperiodism)

Night-break experiments: these showed that night length is measured and that phytochrome is the sensor.

• A brief red flash in the middle of the long night prevents flowering in short-day plants such as Xanthium and soybean, and promotes flowering in long-day plants such as Hyoscyamus.
• Far-red immediately afterwards cancels the effect.

Modern molecular picture (external coincidence model):

• The circadian clock makes CONSTANS (CO) mRNA peak in the late afternoon.
• In long days in Arabidopsis, this peak falls in light. phyA and cryptochromes then stabilise CO protein, while phyB promotes its degradation in the morning.
• Stable CO switches on FLOWERING LOCUS T (FT) in leaf phloem. FT protein (the long-sought florigen) travels to the shoot apex, joins FD, and activates floral identity genes (SOC1, AP1, LFY).
• Short-day plants: in rice, the orthologues (Hd1, and the florigen Hd3a) work the other way, so that flowering is promoted in short days. Phytochrome signalling represses Hd3a in long days, and a night break suppresses it.
• Other effects: phyB also delays flowering under a high red : far-red ratio. Under shade (low red : far-red), inactivation of phyB accelerates flowering, as part of the shade-avoidance syndrome.

Thus phytochrome, together with the clock, allows plants to match flowering to the season.

(c) Altitudinal zonation of vegetation, with special reference to the Himalaya

Temperature falls by about 6 °C per 1,000 m of ascent (the lapse rate). Rainfall, snow cover, wind, soil depth and slope aspect also change with height. Vegetation therefore forms altitudinal belts that resemble the latitudinal zones from the tropics to the poles (Humboldt's observation). The Himalaya, rising from about 300 m to above 8,000 m over a short distance, shows this dramatically. Champion and Seth's forest types describe the belts in India.

Zones (generalised for the western and central Himalaya; limits are approximate and vary with aspect and rainfall)

• Tropical and subtropical broadleaf forests (below about 1,000 m): the Siwaliks, bhabar, tarai and doons. Sal (Shorea robusta) with Terminalia, Mallotus and Adina. Dalbergia sissoo and Acacia catechu on riverbeds. Tall grasslands occur in the tarai.
• Subtropical pine forest (about 1,000–1,800 m): chir pine (Pinus roxburghii) on dry, fire-prone south-facing slopes.

Lower temperate (montane) forests (about 1,800–2,600 m):

• banj oak (Quercus leucotrichophora) with Rhododendron arboreum (burans, the state tree of Uttarakhand);
• deodar (Cedrus deodara) and blue pine (Pinus wallichiana) on drier western slopes.
• Upper temperate forests (about 2,600–3,300 m): kharsu oak (Quercus semecarpifolia), silver fir (Abies pindrow), spruce (Picea smithiana), yew (Taxus) and maples.
• Subalpine forest (about 3,300–3,800 m): Abies spectabilis, bhojpatra (Betula utilis) and Rhododendron campanulatum. Trees become stunted and bent (krummholz) at the timberline, about 3,300–3,800 m in the west and often above 4,000 m in the wetter east.

Alpine zone (about 3,800–4,900 m):

• Alpine scrub of dwarf Rhododendron anthopogon and R. lepidotum, Juniperus and Salix.
• Above it, the rich alpine meadows ("bugyals" in Uttarakhand) with Kobresia, Danthonia, Primula, Potentilla, Aconitum, Picrorhiza, Brahma kamal (Saussurea obvallata) and the blue poppy (Meconopsis aculeata), for example in the Valley of Flowers.
• Subnival and nival zone (above about 4,900 m): scattered cushion plants such as Arenaria and Saussurea gossypiphora (a "woolly" snowball plant), lichens and mosses, up to the permanent snowline at about 5,000–5,500 m.

Regional variation

Eastern Himalaya (Sikkim, Arunachal): much wetter, so the belts are richer and higher.

• Tropical evergreen and semi-evergreen forests below about 900 m.
• Subtropical broadleaf forests of Schima, Castanopsis and Alnus.
• Wet temperate forests of Quercus lamellosa, Magnolia, Acer and Tsuga dumosa.
• Very diverse Rhododendron forests.
• Trans-Himalaya (Ladakh, Lahaul–Spiti): in the rain shadow, forests are absent. Cold-desert steppe of Artemisia, Caragana and Ephedra replaces them.
• Aspect: south-facing slopes are warmer and drier (chir, grass); north-facing slopes are moister (oak, fir).

Controlling factors: temperature (the length of the growing season decides the treeline), moisture and snow, wind and UV, soil, and human use (lopping of oaks, fire, grazing, and extraction of medicinal plants such as Picrorhiza and Aconitum).

Significance: the Himalaya is part of a global biodiversity hotspot, and its alpine plants are highly endemic. Warming, faster at high altitudes, is pushing treelines and species upslope (for example birch and rhododendron). Alpine plants risk being "squeezed" at the summits, so these zones need protection (Nanda Devi and Valley of Flowers National Parks; Khangchendzonga).