25.3: Evolutionary Profile - Photosynthetic Groups - Biology

25.3: Evolutionary Profile - Photosynthetic Groups - Biology

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25.3: Evolutionary Profile - Photosynthetic Groups



Cyanobacteria are Gram-negative bacteria. Five types of cyanobacteria have been identified as toxin producers, including two strains of Anabaena flosaquae, Aphanizomenon flosaquae, Microcystis aeruginosa and Nodularia species. Cyanobacterial toxins are of three main types: hepatotoxins, neurotoxins and lipopolysaccharide (LPS) endotoxins. Acute illness following consumption of drinking water contaminated by cyanobacteria is more commonly gastroenteritis. Cyanobacteria are not dependent on a fixed source of carbon and, as such, are widely distributed throughout aquatic environments. These include freshwater and marine environments and in some soils. Direct microscopic examination of bloom material will allow identification of the cyanobacterial species present. Preventing the formation of blooms in the source water is the best way to assure cyanobacteria-free drinking water and membrane filtration technology has the potential to remove virtually any cyanobacteria or their toxins from drinking water. Cyanobacteria have the ability to grow as biofilms.

This chapter discusses Cyanobacteria, including aspects of its basic microbiology, natural history, metabolism and physiology, clinical features, pathogenicity and virulence, survival in the environment, survival in water and epidemiology, evidence for growth in a biofilm, methods of detection, and finally, risk assessment.


An incredible variety of seedless plants populates the terrestrial landscape. Mosses may grow on a tree trunk, and horsetails may display their jointed stems and spindly leaves across the forest floor. Today, seedless plants represent only a small fraction of the plants in our environment yet, 300 million years ago, seedless plants dominated the landscape and grew in the enormous swampy forests of the Carboniferous period. Their decomposition created large deposits of coal that we mine today.

Current evolutionary thought holds that all plants—some green algae as well as land plants—are monophyletic that is, they are descendants of a single common ancestor. The evolutionary transition from water to land imposed severe constraints on plants. They had to develop strategies to avoid drying out, to disperse reproductive cells in air, for structural support, and for capturing and filtering sunlight. While seed plants have developed adaptations that allow them to populate even the most arid habitats on Earth, full independence from water did not happen in all plants. Most seedless plants still require a moist environment for reproduction.

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    8.1 Overview of Photosynthesis

    Photosynthesis is essential to all life on earth both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago.

    Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis (Figure 8.2). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds hence, they are referred to as chemoautotrophs .

    The importance of photosynthesis is not just that it can capture sunlight’s energy. A lizard sunning itself on a cold day can use the sun’s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer (Figure 8.3), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf.

    Main Structures and Summary of Photosynthesis

    Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure 8.4). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.

    The following is the chemical equation for photosynthesis (Figure 8.5):

    Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved.

    In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll . The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.

    In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast . For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). Within the chloroplast are stacked, disc-shaped structures called thylakoids . Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen . As shown in Figure 8.6, a stack of thylakoids is called a granum , and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis).

    Visual Connection

    On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

    The Two Parts of Photosynthesis

    Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light independent-reactions. In the light-dependent reactions , energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions , the chemical energy harvested during the light-dependent reactions drive the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. Figure 8.7 illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.

    Link to Learning

    Click the link to learn more about photosynthesis.

    Everyday Connection

    Photosynthesis at the Grocery Store

    Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle (Figure 8.8) contains hundreds, if not thousands, of different products for customers to buy and consume.

    Although there is a large variety, each item links back to photosynthesis. Meats and dairy link, because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from starchy grains, which are the seeds of photosynthesis-dependent plants. What about desserts and drinks? All of these products contain sugar—sucrose is a plant product, a disaccharide, a carbohydrate molecule, which is built directly from photosynthesis. Moreover, many items are less obviously derived from plants: For instance, paper goods are generally plant products, and many plastics (abundant as products and packaging) are derived from algae. Virtually every spice and flavoring in the spice aisle was produced by a plant as a leaf, root, bark, flower, fruit, or stem. Ultimately, photosynthesis connects to every meal and every food a person consumes.

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      The Process of Photosynthesis in Plants (With Diagram)

      Life on earth ultimately depends on energy derived from sun. Photosynthesis is the only process of biological importance that can harvest this energy.

      Literally photosynthesis means ‘synthesis using light’. Photosynthetic organisms use solar energy to synthesize carbon compound that cannot be formed without the input of the energy.

      Photosynthesis (Photon = Light, Synthesis = Putting together) is an anabolic, endergonic process by which green plant synthesize carbohydrates (initially glucose) requiring carbon dioxide, water, pigments and sunlight. In other words, we can say that photosynthesis is transformation of solar energy/radiant energy/light energy (ultimate source of energy for all living organisms) into chemical energy.

      Simple general equation of photo synthesis is as follows:

      According to Van Neil and Robert Hill, oxygen liberated during photosynthesis comes from water and not from carbon dioxide.

      Thus, the overall correct biochemical reaction for photosynthesis can be written as:

      Some photosynthetic bacteria use hydrogen donor other than water. Therefore, photosynthesis is also defined as the anabolic process of manufacture of organic compounds inside the chlorophyll containing cells from carbon dioxide and hydrogen donor with the help of radiant energy.

      Significance of Photosynthesis:

      1. Photosynthesis is the most important natural process which sustains life on earth.

      2. The process of photosynthesis is unique to green and other autotrophic plants. It synthesizes organic food from inorganic raw materials.

      3. All animals and heterotrophic plants depend upon the green plants for their organic food, and therefore, the green plants are called producers, while all other organisms are known as consumers.

      4. Photosynthesis converts radiant or solar energy into chemical energy. The same gets stored in the organic food as bonds between different atoms. Photosynthetic products provide energy to all organisms to carry out their life activities (all life is bottled sunshine).

      5. Coal, petroleum and natural gas are fossil fuels which have been produced by the application of heat and compression on the past plant and animal parts (all formed by photosynthesis) in the deeper layers of the earth. These are extremely important source of energy.

      6. All useful plant products are derived from the process of photosynthesis, e.g., timber, rubber, resins, drugs, oils, fibers, etc.

      7. It is the only known method by which oxygen is added to the atmosphere to compensate for oxygen being used in the respiration of organisms and burning of organic fuels. Oxygen is important in (a) efficient utilization and complete breakdown of respiratory substrate and (b) formation of ozone in stratosphere that filters out and stops harmful UV radiations in reaching earth.

      8. Photosynthesis decreases the concentration of carbon dioxide which is being added to the atmosphere by the respiration of organisms and burning of organic fuels. Higher concentration of carbon dioxide is poisonous to living beings.

      9. Productivity of agricultural crops depends upon the rate of photosynthesis. Therefore, scientists are busy in genetically manipulating the crops.

      Magnitude of Photosynthesis:

      Only 0.2% of light energy falling on earth is utilized by photosynthetic organisms. The total carbon dioxide available to plants for photosynthesis is about 11.2 x 10 14 tonnes. Out of this only 2.2 x 10 13 tonnes are present in the atmosphere @ 0.03%. Oceans contain 11 x 10 14 (110,000 billion) tonnes of carbon dioxide.

      About 70 to 80 billion tonnes of carbon dioxide are fixed annually by terrestrial and aquatic autotrophs and it produces near about 1700 million tonnes of dry organic matter. Out of these 10% (170 million tonnes) of dry matter is produced by land plants and rest by ocean (about 90%). This is an estimate by Robinowitch (1951),According to more recent figures given by Ryther and Woodwell (1970) only 1/3 of total global photosynthesis can be attributed to marine plants.

      Historical Background:

      Functional Relationship between Light and Dark Reactions:

      During photosynthesis water is oxidized and carbon dioxide is reduced, but where in the over­all process light energy intervenes to drive the reaction. However, it is possible to show that photo­synthesis consists of a combination of light-requiring reactions (the “light reactions”) and non-light requiring reactions (the “dark reactions”).

      It is now clear that tall the reactions for the incorporation of CO2 into organic materials (i.e., carbohydrate) can occur in the dark (the “dark reactions”). The reactions dependent on light (the “light reactions”) are those in which radiant energy is converted into chemical energy.

      According to Arnon, the functional relationship between the “light” and “dark” reactions can be established by examining the requirements of the dark reactions. The “dark reactions” comprise a complex cycle of enzyme-mediated reactions (the Calvin Cycle) which catalyzes the reduction of car­bon dioxide to sugar. This cycle requires reducing power in the form of reduced nicotinamide adenine dinucleotide phosphate (NADPH) and chemical energy in the form of adenosine triphosphate (ATP).

      The reduced NADP (NADPH) and ATP are produced by the “light reactions”. It is thus possible to divide a description of photosynthesis into those reactions associated with the Calvin cycle and the fixation of carbon dioxide, and those reactions (i.e., capture of light by pigments, electron transport, photophosphorylation) which are directly driven by light.

      Site of Photosynthesis:

      Chloroplast (Fig. 6.2) in green plants constitute the photosynthetic apparatus and act as site of photosynthesis. Chloroplasts of higher plants are discoid or ellipsoidal in shape measuring 4 —6 μ in length and 1—2 μ in thickness. It is a double membranous cytoplasmic organelle of eukaryotic green plant cells. The thickness of the two membranes including periplastidial space is approximately 300Å.

      Ground substance of chloroplast is filled with a hydrophilic matrix known as stroma. It contains cp-DNA (0.5%), RNA (2—3%), Plastoribosome (70S), enzymes for carbon dioxide assimilation, proteins (50—60%), starch grains and osmophilic droplets, vitamin E and K, Mg, Fe, Mn, P, etc. in traces. In stroma are embedded a number of flattened membranous sacs known as thylakoids. Photosynthetic pigments occur in thylakoid membranes.

      Aggregation of thylakoids to form stacks of coin like struc­tures known as granna. A grannum consists near about 20 — 30 thylakoids. Each thylakoid encloses a space known asloculus. The end of disc shape thylakoid is called as margin and the area where the thylakoids membranes are appressed together is called partition.

      Some of the granna lamella are connected with thylakoids of other granna by stroma lamella or fret membranes. Thylakoid mem­brane and stroma lamella both are composed of lipid and proteins. In photosynthetic prokaryotes (blue-green algae and Bacteria) chloroplast is absent. Chromatophore is present in photosynthetic bacteria and photosynthetic lamellae in blue-green algae.

      Mechanism of Photosynthesis:

      Photosynthesis is an oxidation reduction process in which water is oxidized and carbon dioxide is reduced to carbohydrate.

      Blackmann (1905) pointed out that the process of photosynthesis consists of two phases:

      (1) Light reaction or Light phase or Light-dependent phase or Photochemical phase

      (2) Dark reaction or Dark phase or Light independent phase or Biochemical phase.

      During light reaction, oxygen is evolved and assimilatory power (ATP and NADPH2) are formed. During dark reaction assimilatory power is utilized to synthesize glucose.

      (i) Oxygenic photosynthesis (with evolution of O2) takes place in green eukaryotes and cyanobacteria (blue-green algae).

      (ii) An oxygenic photosynthesis (without the evolution of O2) takes place in photosynthetic bacteria.

      Photosynthetic Pigments:

      Photosynthetic pigments are substances that absorb sunlight and initiate the process of photo­synthesis.

      Photosynthetic pigments are grouped into 3 categories:

      (i) Chlorophyll:

      These are green coloured most abundant photosynthetic pigments that play a major role during photosynthesis. Major types of chlorophylls are known to exist in plants and photosynthetic bacteria viz., Chlorophyll a, b, c, d and e, Bacteriochlorophyll a, b and g, and Chlorobium chlorophyll (Bacterio viridin).

      The structure of chlorophyll was first studied by Wilstatter, Stoll and Fischer in 1912. Chemically a chlorophyll molecule consists of a porphyrin head (15 x 15Å) and phytol tail (20Å). Porphyrin consists of tetrapyrrole rings and central core of Mg. Phytol tail is side chain of hydrocarbon. It is attach to one of the pyrrole ring. This chain helps the chlorophyll molecules to attach with thylakoid membrane.

      Out of various types of chlorophyll, chlorophyll a and chlorophyll b are the most important for photosynthetic process. Chlorophyll a is found in all photosynthetic plants except photosynthetic bacteria. For this reason it is designated as Universal Photosynthetic Pigment or Primary Photosynthetic Pigment.

      (ii) Carotenoids:

      These are yellow, red or orange colour pigments embedded in thylakoid membrane in association with chlorophylls but their amount is less. These are insoluble in water and precursor of Vitamin A. These are of two of types viz., Carotene and Xanthophyll (Carotenol/Xanthol).

      Carotenes are pure hydrocarbons, red or orange in colour and their chemical formula is – C40H56 Some of the common carotenes are -α, β, γ and δ carotenes, Phytotene, Neurosporene, Lycopene (Red pigment found in ripe tomato). β—carotene on hydrolysis gives Vitamin A.

      Xanthophylls are yellow coloured oxygen containing carotenoids and are most abundant in nature. The ratio of xanthophyll to carotene in nature is 2:1 in young leaves. The most common xanthophyll in green plant is Lutein (C40H56O2) and it is responsible for yellow colour in autumn foliage. Both carotene and xanthophylls are soluble in organic solvents like chloroform, ethyl ether, carbondisulphide etc.

      (iii) Phycobilins (Biliproteins):

      These are water soluble pigments and are abundantly present in algae, and also found in higher plants. There are two important types of phycobilins-Phycoerythrin (Red) and Phycocyanin (Blue). Like chlorophyll, these pigments are open tetrapyrrole but do not contain Mg and Phytol chain.

      Nature of Light (Fig. 6.3):

      The source of light for photosynthesis is sunlight. Sun Light is a form of energy (solar energy) that travels as a stream of tiny particles. Discrete particles present in light are called photons. They carry energy and the energy contained in a photon is termed as quantum. The energy content of a quantum is related to its wave length.

      Shorter the wave length, the greater is the energy present in its quantum. Depending upon the wave length electro magnetic spectrum comprises cosmic rays, gamma rays, X-rays,-UV rays, visible spectrum, infra red rays, electric rays and radio waves.

      The visible spectrum ranges from 390 nm to 760 nm (3900 – 7600A), however, the plant life is affected by wave length ranging from 300 – 780 nm. Visible spectrum can be resolved into light of different colours i.e., violet (390-430 nm), blue or indigo (430-470 nm), blue green (470-500 nm), green (500 – 580 nm), yellow (580 – 600 nm), orange (600 – 650 nm), orange red (650 – 660 nm) and red (660 – 760 nm). Red light above 700 nm is called far red. Radiation shorter than violet are UV rays (100 – 390 nm). Radiation longer than those of red are called infra red (760 – 10,000 nm).

      A ray of light falling upon a leaf behaves in 3 different ways. Part of it is reflected, a part transmitted and a part absorbed. The leaves absorb near about 83% of light, transmit 5% and reflect 12%. From the total absorption, 4% light is absorbed by the chlorophyll. Engelmann (1882) performed an experiment with the freshwater, multicellular filamentous green alga spirogyra.

      In a drop of water having numerous aerobic bacteria, the alga was exposed to a narrow beam of light passing through a prism. The bacte­ria after few minutes aggregated more in that re­gions which were exposed to blue and red wave length. It confirms that maximum oxygen evolu­tion takes place in these regions due to high photosynthetic activities.

      Absorption Spectrum:

      All photosynthetic organisms contain one or more organic pigments capable of absorbing visible radiation which will initiate the photochemical reactions of photosynthesis. When the amount of light absorbed by a pigment is plotted as a function of wave length, we obtain absorption spectrum (Fig. 6.4).

      It varies from pigment to pigment. By passing light of specific wave length through a solution of a substance and measuring the fraction absorbed, we obtain the absorption spectrum of that substance. Each type of molecules have a characteristic absorption spectrum, and measuring the absorption spectrum can be useful in identifying some unknown substance isolated from a plant or animal cell.

      Action Spectrum:

      It represents the extent of response to different wave lengths of light in photosynthesis. It can also be defined as a measure of the process of photosynthesis when a light of different wave lengths is supplied but the intensity is the same. For photochemical reactions involving single pigment, the action spectrum has same general shape as the absorption spectrum of that pigment, otherwise both are quite distinct (Fig. 6.5).

      Quantum Requirement and Quantum Yield:

      The solar light comes to earth in the form of small packets of energy known as photons. The energy associated with each photon is called Quantum. Thus, requirement of solar light by a plant is measured in terms of number of photons or quanta.

      The number of photons or quanta required by a plant or leaf to release one molecule of oxygen during photosynthesis is called quantum requirement. It has been observed that in most of the cases the quantum requirement is 8.

      It means that 8 photons or quantum’s are required to release one molecule of oxygen. The number of oxygen molecules released per photon of light during photosynthesis is called Quantum yield. If the quantum requirement is 8 then quantum yield will be 0.125 (1/8).

      Photosynthetic Unit or Quantasome:

      It is defined as the smallest group of collaborating pigment molecules necessary to affect a photochemical act i.e., absorption and migration of a light quantum to trapping centre where it promotes the release of an electron.

      Emmerson and Arnold (1932) on the basis of certain experiments assumed that about 250 chlorophyll molecules are required to fix one molecule of carbon dioxide in photosynthesis. This number of chlorophyll molecules was called the chlorophyll unit but the name was subsequently changed to photosynthetic unit and later it was designated as Quantasome by Park and Biggins (1964).

      The size of a quantasome is about 18 x 16 x l0nm and found in the membrane of thylakoids. Each quantasome consists of 200 – 240 chlorophyll (160 Chlorophyll a and 70 – 80 Chlorophyll b), 48 carotenoids, 46 quinone, 116 phospholipids, 144 diagalactosyl diglyceride, 346 monogalactosyl diglyceride, 48 sulpholipids, some sterols and special chlorophyll molecules (P680 and P700).

      ‘P’ is pigment, 680 and 700 denotes the wave length of light these molecule absorb. Peso and P700 constitute the reaction centre or photo centre. Other accessory pigments and chlorophyll molecules are light gatherers or antenna molecules. It capture solar energy and transfer it to the reaction centre by resonance transfer or inductive resonance.


      It is the phenomenon of re-radiation of absorbed energy. It is of two types:

      The normal state of the molecule is called as ground state or singlet state. When an electron of a molecule absorbs a quantum of light it is raised to a higher level of energy a state called Excited Second Singlet State. From first singlet state excited electron may return to the ground state either losing its extra energy in the form of heat or by losing energy in the form of radiant energy. The later process is called fluorescence. The substance which can emit back the absorbed radiations is called fluorescent substance. All photosynthetic pigments have the property of fluorescence.

      The excited molecule also losses its electronic excitation energy by internal conversion and comes to another excited state called triplet state. From this triplet state excited molecule may return to ground state in three ways-by losing its extra energy in the form of heat, by losing extra energy in the form of radiant energy is called phosphorescence. The electron carrying extra energy may be expelled from the molecule and is consumed in some other chemical reactions and a fresh normal electron returns to the molecule. This mechanism happens in chlorophyll a (Universal Photosynthetic Pigment).

      Emerson Red Drop Effect and Enhancement Effect:

      R. Emerson and Lewis (1943) while determining the quantum yield of photosynthesis in Chlorella by using monochromatic light of different wave lengths noticed a sharp decrease in quantum yield at wave length greater than 680 mμ.This decrease in quantum yield took place in the far red part of the spectrum i.e., the curve shows quantum yield drops dramatically in the region above 680 nm (Red region). This decline in photosynthesis is called Red drop effect (Emerson’s first experiment).

      Emerson and his co-workers (1957) found that the inefficient far red light in Chlorella beyond 680nm could be made fully efficient if supplemented with light of short wave length. The quantum yield from the two combined beams was found to be greater than the effect of both beams when used separately. This enhancement of photosynthesis is called Emerson Enhancement Effect (Emerson’s second experiment) (Fig. 6.6).

      Rate of oxygen evolution in combined beam – Rate of oxygen evolution in red beam/Rate of oxygen evolution in far red beam

      Light Trapping Centres (PSI & PSII):

      The discovery of red drop effect and the Emerson’s enhancement effect concluded in a new concept about the role played bychlorophyll-a and accessary pigments in photosynthesis that photo­synthesis involves two distinct photochemical processes. These processes are associated with two groups of photosynthetic pigments called as Pigment system I (Photoact I or Photosystem I) and Pigment system II (Photoact II or Photosystem II).

      Each pigment system consists of a central core complex and light harvesting complex (LHC). LHC comprises antenna pigments associated with proteins (viz. antenna complex). Their main function is to harvest light energy and transfer it to their respective reaction centre. The core complex consists of reaction centre associated with proteins and also electon donors and acceptors.

      Wave length of light shorter than 680 nm affect both the pigment systems while wave length longer than 680 nm affect only pigment system I. PSI is found in thylakoid membrane and stroma lamella. It contains pigments chlorophyll a 660, chlorophyll a 670, chlorophyll a 680, chlorophyll a 690, chlorophyll a 700. Chlorophyll a 700 or P700 is the reaction centre of PS I. PS II is found in thylakoid membrane and it contains pigments as chlorophyll b 650, chlorophyll a 660, chlorophyll a 670, chlorophyll a 678, chlorophyll a 680 – 690 and phycobillins.

      P680-690 is the reaction centre of PS II. Chlorophyll a content is more in PS I than PS II. Carotenoids are present both in PS II and PS I. PS I is associated with both cyclic and non-cyclic photophosphorylation, but PS II is associated with only non-cyclic photophosphorylation.

      Both the pigment systems are believed to be inter-connected by a third integral protein complex called cytochrome b – f complex. The other intermediate components of electron transport chain viz., PQ (plasto quinone) and PC (plastocyanin) act as mobile electron carriers between two pigment systems. PS I is active in both red and far red light and PS II is inactive in far red light (Fig. 6.7).

      Evidence in Support of Two Phases of Photosynthesis:

      1. Physical Separation of Chloroplast into Granna and Stroma Fraction:

      It is now possible to separate granna and stroma fraction of chloroplast. If light is given to granna fraction in the presence of suitable hydrogen acceptor and in complete absence of carbon dioxide then assimilatory power, ATP and NADPH2, are produced. If these assimilatory powers are given to stroma fraction in the presence of carbon dioxide and absence of light then carbohydrate is synthesized.

      2. Temperature Coefficient (Q10):

      Q10 is the ratio of the rate of reaction at a given temperature and a temperature 10°C lower. Q10 value of photosynthesis is found to be two or three (for dark reaction) when photosynthesis is fast, but Q10 is one (for light reaction) when photosynthesis is slow.

      3. Evidence from Intermittent Light:

      Warburg observed that when intermittent light (flashes of light) of about 1/16 seconds were given to green algae (Chlorella vulgaris and Scenedesmus obliquus), the photosynthetic yield per second was higher as compared to the continuous supply of same intensity of light. This confirms that one phase of photosynthesis is independent of light.

      4. Evidence from Carbon dioxide in Dark:

      It comes from tracer technique by the use of heavy carbon in carbon dioxide (C 14 O2). The leaves which were first exposed to light have been found to reduce carbon dioxide in the dark It indicates that carbon dioxide is reduced to carbohydrate in dark and it is purely a biochemical phase.

      I. Light Reaction (Photochemical Phase):

      Light reaction or photochemical reaction takes place in thylakoid membrane or granum and it is completely dependent upon the light. The raw materials for this reactions are pigments, water and sunlight.

      It can be discussed in the following three steps:

      1. Excitation of chlorophyll

      1. Excitation of Chlorophyll:

      It is the first step of light reaction. When P680 or P700 (special type of chlorophyll a) of two pigment systems receives quantum of light then it becomes excited and releases electrons.

      2. Photolysis of Water and Oxygen Evolution (Hill Reaction):

      Before 1930 it was thought that the oxygen released during photosynthesis comes from carbon dioxide. But for the first time Van Neil discovered that the source of oxygen evolution is not carbon dioxide but H2O. In his experiment Neil used green sulphur bacteria which do not release oxygen during photosynthesis. They release sulphur. These bacteria require H2S in place of H2O.

      The idea of Van Neil was supported by R. Hill. Hill observed that the chloroplasts extracted from leaves of Stellaria media and Lamium album when suspended in a test tube containing suitable electron acceptors (Potassium feroxalate or Potassium fericyanide), Oxygen evolution took place due to photochemical splitting of water.

      The splitting of water during photosynthesis is called Photolysis of water. Mn, Ca, and CI ions play prominent role in the photolysis of water. This reaction is also known as Hill reaction. To release one molecule of oxygen, two molecules of water are required.

      The evolution of oxygen from water was also confirmed by Ruben, Randall, Hassid and Kamen (1941) using heavy isotope (O18) in green alga Chlorella. When the photosynthesis is allowed to proceed with H2O 18 and normal CO2, the evolved oxygen contains heavy isotope. If photosynthesis is allowed to proceed in presence of CO2 18 and normal water then heavy oxygen is not evolved.

      Thus the fate of different molecules can be summarized as follows:

      3. Photophosphorylation:

      Synthesis of ATP from ADP and inorganic phosphate (pi) in presence of light in chloroplast is known as photophosphorylation. It was discovered by Arnon et al (1954).

      Photophosphorylation is of two types.

      (a) Cyclic photophosphorylation

      (b) Non-cyclic photophosphorylation.

      (a) Cyclic Photophosphorylation (Fig. 6.8):

      It is a process of photophosphorylation in which an electron expelled by the excited photo Centre (PSI) is returned to it after passing through a series of electron carriers. It occurs under conditions of low light intensity, wavelength longer than 680 nm and when CO2 fixation is inhibited. Absence of CO2 fixation results in non requirement of electrons as NADPH2 is not being oxidized to NADP + . Cyclic photophosphorylation is performed by photosystem I only. Its photo Centre P700 extrudes an electron with a gain of 23 kcal/mole of energy after absorbing a photon of light (hv).

      After losing the electron the photo Centre becomes oxidized. The expelled electron passes through a series of carriers including X (a special chlorophyll molecule), FeS, ferredoxin, plastoquinone, cytochrome b- f complex and plastocyanin before returning to photo Centre. While passing between ferredoxin and plastoquinone and/or over the cytochrome complex, the electron loses sufficient energy to form ATP from ADP and inorganic phosphate.

      Halobacteria or halophile bacteria also perform photophosphorylation but ATP thus produced is not used in synthesis of food. These bacteria possess purple pigment bacteriorhodopsin attached to plasma membrane. As light falls on the pigment, it creates a proton pump which is used in ATP synthesis.

      (b) Noncyclic Photophosphorylation (Z-Scheme) (Fig. 6.9):

      It is the normal process of photophosphorylation in which the electron expelled by the excited photo Centre (reaction centre) does not return to it. Non-cyclic photophosphorylation is carried out in collaboration of both photo system I and II. (Fig. 6.9). Electron released during photolysis of water is picked up by reaction centre of PS-II, called P680. The same is extruded out when the reaction centre absorbs light energy (hv). The extruded electron has an energy equivalent to 23 kcal/mole.

      It passes through a series of electron carriers— Phaeophytin, PQ, cytochrome b- f complex and plastocyanin. While passing over cytochrome complex, the electron loses sufficient energy for the synthesis of ATP. The electron is handed over to reaction centre P700 of PS-I by plastocyanin. P700 extrudes the electron after absorbing light energy.

      The extruded electron passes through FRS ferredoxin, and NADP -reductase which combines it with NADP + for becoming reduced through H+ releasing during photolysis to form NADPH2. ATP synthesis is not direct. The energy released by electron is actually used for pumping H + ions across the thylakoid membrane. It creates a proton gradient. This gradient triggers the coupling factor to synthesize ATP from ADP and inorganic phosphate (Pi).

      Chemiosmotic Hypothesis:

      How actually ATP is synthesized in the chloroplast?

      The chemiosmotic hypothesis has been put forward by Peter Mitchell (1961) to explain the mechanism. Like in respiration, in photosynthesis too, ATP synthesis is linked to development of a proton gradient across a membrane. This time these are membranes of the thylakoid. There is one difference though, here the proton accumulation is towards the inside of the membrane, i.e., in the lumen. In respiration, protons accumulate in the inter-membrane space of the mitochondria when electrons move through the ETS.

      Let us understand what causes the proton gradient across the membrane. We need to consider again the processes that take place during the activation of electrons and their transport to determine the steps that cause a proton gradient to develop (Figure 6.9).

      (a) Since splitting of the water molecule takes place on the inner side of the membrane, the protons or hydrogen ions that are produced by the splitting of water accumulate within the lumen of the thylakoids.

      (b) As electrons move through the photosystems, protons are transported across the membrane. This happens because the primary accepter of electron which is located towards the outer side of the membrane transfers its electron not to an electron carrier but to an H carrier. Hence, this molecule removes a proton from the stroma while transporting an electron. When this molecule passes on its electron to the electron carrier on the inner side of the membrane, the proton is released into the inner side or the lumen side of the membrane.

      (c) The NADP reductase enzyme is located on the stroma side of the membrane. Along with electrons that come from the acceptor of electrons of PS I, protons are necessary for the reduction of NADP + to NADPH+ H + .These protons are also removed from the stroma.

      Hence, within the chloroplast, protons in the stroma decrease in number, while in the lumen there is accumulation of protons. This creates a proton gradient across the thylakoid membrane as well as a measurable decrease in pH in the lumen.

      Why are we so interested in the proton gradient?

      This gradient is important because it is the breakdown of this gradient that leads to release of energy. The gradient is broken down due to the movement of protons across the membrane to the stroma through the trans membrane channel of the F0 of the ATPase. The ATPase enzyme consists of two parts: one called the F0 is embedded in the membrane and forms a trans-membrane channel that carries out facilitated diffusion of protons across the membrane. The other portion is called F1 and protrudes on the outer surface of the thylakoid membrane on the side that faces the stroma.

      The break down of the gradient provides enough energy to cause a conformational change in the F1 particle of the ATPase, which makes the enzyme synthesis several molecules of energy-packed ATP. Chemiosmosis requires a membrane, a proton pump, a proton gradient and ATPase. Energy is used to pump protons across a membrane, to create a gradient or a high concentration of protons within the thylakoid lumen.

      ATPase has a channel that allows diffusion of protons back across the membrane this releases enough energy to activate ATPase enzyme that catalyzes the formation of ATP. Along with the NADPH produced by the movement of electrons, the ATP will be used immediately in the biosynthetic reaction taking place in the stroma, responsible for fixing CO2, and synthesis of sugars.

      Where are the ATP and NADPH Used?

      We have seen that the products of light reaction are ATP, NADPH and O2. Of these O2 diffuses out of the chloroplast while ATP and NADPH are used to drive the processes leading to the synthesis of food, more accurately, sugars. This is the biosynthetic phase of photosynthesis.

      This process does not directly depend on the presence of light but is dependent on the products of the light reaction, i.e., ATP and NADPH, besides CO2 and H2O. You may wonder how this could be verified it is simple: immediately after light becomes unavailable the biosynthetic process continues for some time, and then stops. If then, light is made available, the synthesis starts again.

      Can we, hence, say that calling the biosynthetic phase as the dark reaction is a misnomer?

      II. Dark Reaction (Biosynthetic Phase)-The Second Phase of Photosynthesis:

      The pathway by which all photosynthetic eukaryotic organisms ultimately incorporate CO2 into carbohydrate is known as carbon fixation or photosynthetic carbon reduction (PCR.) cycle or dark reactions. The dark reactions are sensitive to temperature changes, but are independent of light hence it is called dark reaction, however it depends upon the products of light reaction of photosynthesis, i.e., NADPH2 and ATP.

      The carbon dioxide fixation takes place in the stroma of chloroplasts because it has enzymes essential for fixation of CO2 and synthesis of sugar. Dark reaction is the pathway by which CO2 is reduced to sugar. Since CO2 is an energy poor compound its conversion to an energy-rich carbohydrate involves a sizable jump up the energy ladder. This is accomplished through a series of complex steps involving small bits of energy.

      The CO2 assimilation takes place both in light and darkness when the substrates NADPH2 and ATP are available. Because of the need for NADPH2 as a reductant and ATP as energy equivalent, CO2 fixation is closely linked to the light reactions. During evolution three different ecological variants have evolved with different CO2 incorporation mechanism: C3, C4 and CAM plants.

      Calvin or C3 Cycle or PCR (Photosynthetic Carbon Reduction Cycle):

      It is the basic mechanism by which CO2 is fixed (reduced) to form carbohydrates. It was proposed by Melvin Calvin. Calvin along with A.A. Benson, J. Bassham used radioactive isotope of carbon (C 14 ) in Chlorella pyrenoidosa and Scenedesmus oblique’s to determine the sequences of dark reaction. For this work Calvin was awarded Nobel prize in 1961. To synthesize one glucose molecule Calvin cycle requires 6CO2, 18 ATP and 12 NADPH2.

      Calvin cycle completes in 4 major phases:

      3. Glycolytic reversal phase (sugar formation phase)

      1. Carboxylation phase:

      CO2 enters the leaf through stomata. In mesophyll cells, CO2 combines with a phosphorylated 5-carbon sugar, called Ribulose bisphosphate (or RuBP). This reaction is catalyzed by an enzyme, called RUBISCO. The reaction results in the formation of a temporary 6 carbon compound (2-carboxy 3-keto 1,5-biphosphorbitol) Which breaks down into two molecules of 3-phosphoglyceric acid (PGA) and it is the first stable product of dark reaction (C3 Cycle).

      The PGA molecules are now phosphorylated by ATP molecule and reduced by NADPH2 (product of light reaction known as assimilatory power) to form 3-phospho-glyceraldehyde (PGAL).

      3. Glycolytic Reversal (Formation of sugar) Phase:

      Out of two mols of 3-phosphoglyceraldehyde one mol is converted to its isomer 3-dihydroxyacetone phosphate.

      Regeneration of Ribulose-5-phosphate (Also known as Reductive Pentose Phosphate Pathway) takes place through number of biochemical steps.

      Summary of Photosynthesis:

      (A) Light Reaction takes place in thylakoid membrane or granum

      (B) Dark Reaction (C3 cycle) takes place in stroma of chloroplast.

      C4 Cycle (HSK Pathway or Hatch Slack and Kortschak Cycle):

      C4 cycle may also be referred as the di-carboxylic acid cycle or the β-carboxylation pathway or Hatch and Slack cycle or cooperative photosynthesis (Karpilov, 1970). For a long time, C3 cycle was considered to be the only photosynthetic pathway for reduction of CO2 into carbohydrates. Kortschak, Hartt and Burr (1965) reported that rapidly photosynthesizing sugarcane leaves produced a 4-C compound like aspartic acid and malic acid as a result of CO2 – fixation.

      It was later supported by M. D. Hatch and C. R. Slack (1966) and they reported that a 4-C compound oxaloacetic acid (OAA) is the first stable product in CO2 reduction process. This pathway was first reported in members of family Poaceae like sugarcane, maize, sorghum, etc. (tropical grasses), but later on the other subtropical plant like Atriplex spongiosa (Salt bush), Dititaria samguinolis, Cyperus rotundus, Amaranthus etc. So, the cycle has been reported not only in the members of Graminae but also among certain members of Cyperaceae and certain dicots.

      Structural Peculiarities of C4 Plants (Kranz Anatomy):

      C4 plants have a characteristic leaf anatomy called Kranz anatomy (Wreath anatomy – German meaning ring or Helo anatomy). The vascular bundles in C4 plant leaves are surrounded by a layer of bundle sheath cells that contain large number of chloroplast. Dimorphic (two morphologically distinct type) chloroplasts occur in C4 plants (Fig. 6.13).

      (i) Chloroplast is small in size

      (ii) Well developed grannum and less developed stroma.

      (iii) Both PS-II and PS-I are present.

      (iv) Non cyclic photophosphorylation takes place.

      (v) ATP and NADPH2 produces.

      (vi) Stroma carries PEPCO but absence of RuBisCO.

      (vii) CO2 acceptor is PEPA (3C) but absence of RUBP

      (viii) First stable product OAA (4C) produces.

      In Bundle sheath Cell:

      (i) Size of chloroplast is large

      (ii) Stroma is more developed but granna is poorly developed.

      (iii) Only PS-I present but absence of PS-II

      (iv) Non Cyclic photophosphorylation does not takes place.

      (v) Stroma carries RuBisCO but absence of PEPCO.

      (vi) CO2 acceptor RUBP (5c) is present but absence of PEPA (3C)

      (vii) C3-cycle takes place and glucose synthesies.

      (viii) To carry out C3-cycle both ATP and NADPH2 comes from mesophyll cell chloroplast.

      Carbon dioxide from atmosphere is accepted by Phosphoenol pyruvic acid (PEPA) present in stroma of mesophyll cell chloroplast and it converts to oxaloacetic acid (OAA) in the presence of enzyme PEPCO (Phosphoenolpyruvate carboxylase). This 4-C acid (OAA) enters into the chloroplast of bundle sheath cell and there it undergoes oxidative decarboxylation yielding pyruvic acid (3C) and CO2.

      The carbon dioxide released in bundle sheath cell reacts with RuBP (Ribulose 1, 5 bisphosphate) in presence of RUBISCO and carry out Calvin cycle to synthesize glucose. Pyruvic acid enters mesophyll cells and regenerates PEPA. In C4 cycle two carboxylation reactions take place.

      Reactions taking place in mesophyll cells are stated below: (1 st carboxylation)

      C4 plants are better photosynthesizes. There is no photorespiration in these plants. To synthesize one glucose molecule it requires 30 ATP and 12 NADPH2.

      Significance of C4Cycle:

      1. C4 plants have greater rate of carbon dioxide assimilation than C3 plants because PEPCO has great affinity for CO2 and it shows no photorespiration resulting in higher production of dry matter.

      2. C4 plants are better adapted to environmental stress than C3 plants.

      3. Carbon dioxide fixation by C4 plants requires more ATP than C3 plants for conversion of pyruvic acid to PEPA.

      4. Carbon dioxide acceptor in C4 plant is PEPA and key enzyme is PEPCO.

      5. They can very well grow in saline soils because of presence of C4 organic acid.

      Crassulacean Acid Metabolism (CAM Pathway):

      It is a mechanism of photosynthesis which occurs in succulents and some other plants of dry habitats where the stomata remain closed during the daytime and open only at night. The process of photosynthesis is similar to that of C4 plants but instead of spatial separation of initial PEPcase fixation and final Rubisco fixation of CO2, the two steps occur in the same cells (in the stroma of mesophyll chloroplasts) but at different times, night and day, e.g., Sedum, Kalanchoe, Opuntia, Pineapple (Fig. 6.13). (CAM was for the first time studied and reported by Ting (1971).

      Characteristics of CAM Plants:

      1. Stomatal movement is scoto-active.

      2. Presence of monomorphic chloroplast.

      3. Stroma of chloroplast carries both PEPCO and RUBISCO.

      4. Absence of Kranz anatomy.

      5. It is more similar to C4 plants than C3 plants.

      6. In these plants pH decreases during night and increases during day time.

      Mechanism of CAM Pathway:

      Stomata of Crassulacean plants remain open at night. Carbon dioxide is absorbed from outside. With the help of Phosphoenol pyruvate carboxylase (PEPCO) enzyme the CO2 is immediately fixed, and here the acceptor molecule is Phosphoenol pyruvate (PEP).

      Malic acid is the end product of dark fixation of CO2. It is stored inside cell vacuole.

      During day time the stomata in Crassulacean plants remain closed to check transpiration, but photosynthesis does take place in the presence of sun light. Malic acid moves out of the cell vacuoles. It is de-carboxylated with the help of malic enzyme. Pyruvate is produced. It is metabolized.

      The CO2 thus released is again fixed through Calvin Cycle with the help of RUBP and RUBISCO. This is a unique feature of these succulent plants where they photosynthesis without wasting much of water. They perform acidification or dark fixation of CO2 during night and de-acidification during day time to release carbon dioxide for actual photosynthesis.

      Ecological Significance of CAM Plants:

      These plants are ecologically significant because they can reduce rate of transpiration during day time, and are well adapted to dry and hot habitats.

      1. The stomata remain closed during the day and open at night when water loss is little due to prevailing low temperature.

      2. CAM plants have parenchyma cells, which are large and vacuolated. These vacuoles are used for storing malic and other acids in large amounts.

      3. CAM plants increase their water-use efficiency, and secondly through its enzyme PEP carboxylase, they are adapted to extreme hot climates.

      4. CAM plants can also obtain a CO2 compensation point of zero at night and in this way accomplish a steeper gradient for CO2 uptake compared to C3 plants.

      5. They lack a real photosynthesis during daytime and the growth rate is far lower than in all other plants (with the exception of pineapple).

      Photorespiration or C2 Cycle or Glycolate Cycle or Photosynthetic Carbon Oxidation Cycle:

      Photorespiration is the light dependent process of oxygenation of RUBP (Ribulose bi-phosphate) and release of carbon dioxide by photosynthetic organs of the plant. Otherwise, as we know, photosynthetic organs release oxygen and not CO2 under normal situation.

      Occurrence of photorespiration in a plant can be demonstrated by:

      (i) Decrease in the rate of net photosynthesis when oxygen concentration is increased from 2-3 to 21%.

      (ii) Sudden increased evolution of CO2 when an illuminated green plant is transferred to dark.

      Photorespiration is initiated under high O2 and low CO2 and intense light around the photosynthesizing plant. Photorespiration was discovered by Dicker and Tio (1959), while the term “Photorespiration” was coined by Krotkov (1963). Photorespiration should not be confused with photo- oxidation. While the former is a normal process in some green plants, the latter is an abnormal and injurious process occurring in extremely intense light resulting in destruction of cellular components, cells and tissues.

      On the basis of photorespiration, plants can be divided into two groups:

      (i) Plants with photorespiration (temperate plants) and plants without photorespiration (tropical plants).

      Site of Photorespiration:

      Photorespiration involves three cell organelles, viz., chloroplast, peroxisome and mitochondria for its completion. Peroxisome, the actual site of photorespiration, contains enzymes like glycolate oxydase, glutamate glyoxalate aminotransferase, peroxidase and catalase enzymes.

      Mechanism of Photorespiration:

      We know that the enzyme RUBISCO (Ribulose biphosphate carboxylase oxygenase) catalyzes the carboxylation reaction, where CO2 combines with RuBP for calvin cycle (dark reaction of photosynthesis) to initiate. But this enzyme RUBISCO, under intense light conditions, has the ability to catalyse the combination of O2 with RuPB, a process called oxygenation.

      In other words the enzyme RUBISCO can catalyse both carboxylation as well as oxygenation reactions in green plants under different conditions of light and O2/CO2 ratio. Respiration that is initiated in chloroplasts under light conditions is called photorespiration. This occurs essentially because of the fact that the active site of the enzyme RUBISCO is the same for both carboxylation and oxygenation (Fig. 6.16).

      The oxygenation of RuBP in the presence of O2 is the first reaction of photorespiration, which leads to the formation of one molecule of phosphoglycolate, a 2 carbon compound and one molecule of phosphoglyceric acid (PGA). While the PGA is used up in the Calvin cycle, the phosphoglycolate is dephosphorylated to form glycolate in the chloroplast (Fig. 6.16).

      From the chloroplast, the glycolate is diffused to peroxisome, where it is oxidised to glyoxylate. In the peroxisome, the glyoxylate is used to form the amino acid, glycine. Glycine enters mitochondria where two molecules of glycine (4 carbons) give rise to one molecule of serine (3 carbon) and one CO2 (one carbon).

      The serine is taken up by the peroxisome, and through a series of reactions, is converted to glycerate. The glycerate leaves the peroxisome and enters the chloroplast, where it is phosphorylated to form PGA. The PGA molecule enters the calvin cycle to make carbohydrates, but one CO2 molecule released in mitochondria during photorespiration has to be re-fixed.

      In other words, 75% of the carbon lost by oxygenation of RuBP is recovered, and 25% is lost as release of one molecule of CO2. Because of the features described above, photorespiration is also called photosynthetic carbon oxidation cycle.

      Minimization of Photorespiration (C4 and CAM Plants):

      Since photorespiration requires additional energy from the light reactions of photosynthesis, some plants have mechanisms to reduce uptake of molecular oxygen by Rubisco. They increase the concentration of CO2 in the leaves so that Rubisco is less likely to produce glycolate through reaction with O2.

      C4 plants capture carbon dioxide in cells of their mesophyll (using an enzyme called PEP carboxylase), and they release it to the bundle sheath cells (site of carbon dioxide fixation by Rubisco) where oxygen concentration is low.

      The enzyme PEP carboxylase is also found in other plants such as cacti and succulents who use a mechanism called Crassulacean acid metabolism or CAM in which PEP carboxylase put aside carbon at night and releases it to the photosynthesizing cells during the day.

      This provides a mechanism for reducing high rates of water loss (transpiration) by stomata during the day. This ability to avoid photorespiration makes these plants more hardy than other plants in dry conditions where stomata are closed and oxygen concentration rises.

      Factors Affecting Photosynthesis:

      Photosynthesis is affected by both environmental and genetic (internal) factors. The environmental factors are light, CO2, temperature, soil, water, nutrients etc. Internal or genetic factors are all related with leaf and include protoplasmic factors, chlorophyll contents, structure of leaf, accumulation of end product etc.

      Some of the important factors are discussed below:

      1. Concept of Cardinal Values:

      The metabolic processes are influenced by a number of factors of the environment. The rate of a metabolic process is controlled by the magnitude of each factor. Sachs (1860) recognized three critical values, the cardinal values or points of the magnitude of each factor. These are minimum, optimum and maximum. The minimum cardinal value is that magnitudes of a factor below which the metabolic process cannot proceed.

      Optimum value is the one at which the metabolic process proceeds at its highest rate. Maximum is that magnitude of a factor beyond which the process stops. At magnitudes below and above the optimum, the rate of a metabolic process declines till minimum and maximum values are attained.

      2. Principle of Limiting Factors:

      Liebig (1843) proposed law of minimum which states that the rate of a process is limited by the pace (rapidity) of the slowest factor. However, it was later on modified by Blackman (1905) who formulated the “principle of limiting factors”. It states that when a metabolic process is conditioned as to its rapidity by a number of separate factors, the rate of the process is limited by the pace (rapidity) of the slowest factor. This principle is also known as “Blackman’s Law of Limiting Factors.”

      A metabolic process is conditioned by a number of factors. The slowest factor or the limiting factor is the one whose increase in magnitude is directly responsible for an increase in the rate of the metabolic process (here photosynthesis).

      To explain it further, say at a given time, only the factor that is most limiting among all will determine the rate of photosynthesis. For example, if CO2 is available in plenty but light is limiting due to cloudy weather, the rate of photosynthesis under such a situation will be controlled by the light. Furthermore, if both CO2 and light are limiting, then the factor which is the most limiting of the two, will control the rate of photosynthesis.

      Blackman (1905) studied the effect of CO2 concentration, light intensity and temperature on rate of photosynthesis. All other factors were maintained in optimum concentration. Initially the photosynthetic material was kept at 20°C in an environment having 0.01% CO2. When no light was provided to photosynthetic material, it did not perform photosynthesis. Instead, it evolved CO2 and absorbed O2 from its environment. He provided light of low intensity (say 150 foot candles) and found photosynthesis to occur.

      When light intensity was increased (say 800 foot candles), the rate of photosynthesis increased initially but soon it leveled off. The rate of photosynthesis could be further enhanced only on the increase in availability of CO2. Thus, initially light intensity was limiting the rate of photosynthesis.

      When sufficient light became available, CO2 became limiting factor (Fig. 6.17). When both are provided in sufficient quantity, the rate of photosynthesis rose initially but again reached a peak. It could not be increased further. At this time, it was found that increase in temperature could raise the rate of photosynthesis up to 35°C. Further increase was not possible. At this stage, some other factor became limiting. Therefore, at one time only one factor limits the rate of physiological process.

      Objections have been raised to the validity of Blackman’s law of limiting factors. For instance:

      (i) It has been observed that the rate of a process cannot be increased indefinitely by increasing the availability of all the known factors

      (ii) The principle of Blackman is not operative for toxic chemicals or inhibitors and

      (iii) Some workers have shown that the pace of reaction can be controlled simultaneously by two or more factors.

      3. External Factors:

      The environmental factors which can affect the rate of photosynthesis are carbon dioxide, light, temperature, water, oxygen, minerals, pollutants and inhibitors.

      1. Effect of Carbon dioxide:

      Being one of the raw materials, carbon dioxide concentration has great effect on the rate of photosynthesis. The atmosphere normally contains 0.03 to 0.04 per cent by volume of carbon dioxide. It has been experimentally proved that an increase in carbon dioxide content of the air up to about one per cent will produce a corresponding increase in photosynthesis provided the intensity of light is also increased.

      2. Effect of Light:

      The ultimate source of light for photosynthesis in green plants is solar radiation, which moves in the form of electromagnetic waves. Out of the total solar energy reaching to the earth, about 2% is used in photosynthesis and about 10% is used in other metabolic activities. Light varies in intensity, quality (wavelength) and duration.

      The effect of light on photosynthesis can be studied under following three headings:

      The total light perceived by a plant depends on its general form (viz., height of plant and size of leaves, etc.) and arrangement of leaves. Of the total light falling on a leaf, about 80% is absorbed, 10% is reflected and 10% is transmitted. Intensity of light can be measured by lux meter.

      Effect of light intensity varies from plant to plant, e.g., more in heliophytes (sun loving plants) and less in sciophytes (shade loving plants). For a complete plant, rate of photosynthesis increases with increase in light intensity, except under very high light intensity where phenomenon of Solarization’ occurs, (i.e., photo-oxidation of different cellular components including chlorophyll). It also affects the opening and closing of stomata thereby affecting the gaseous exchange. The value of light saturation at which further increase is not accompanied by an increase in CO2 uptake is called light saturation point.

      Photosynthetic pigments absorb visible part of the radiation i.e., 380 mμ, to 760 mμ. For example, chlorophyll absorbs blue and red light. Usually plants show high rate of photosynthesis in the blue and red light. Maximum photosynthesis has been observed in red light than in blue light followed by yellow light (monochromatic light). The green light has minimum effect. The rate of photosynthesis is maximum in white light or sunlight (polychromatic light). On the other hand, red algae shows maximum photosynthesis in green light and brown algae in blue light.

      (iii) Duration of Light:

      Longer duration of light period favours photosynthesis. Generally, if the plants get 10 to 12 hrs. of light per day it favours good photosynthesis. Plants can actively exhibit photosynthesis under continuous light without being damaged. Rate of photosynthesis is independent of duration of light.

      3. Effect of Temperature:

      The rate of photosynthesis markedly increases with an increase in temperature provided other factors such as CO2 and light are not limiting. The temperature affects the velocity of enzyme controlled reactions in the dark stage. When the intensity of light is low, the reaction is limited by the small quantities of reduced coenzymes available so that any increase in temperature has little effect on the overall rate of photosynthesis.

      At high light intensities, it is the enzyme-controlled dark stage which controls the rate of photosynthesis and there the Q10 = 2. If the temperature is greater than about 30°C, the rate of photosynthesis abruptly falls due to thermal inactivation of enzymes.

      4. Effect of Water:

      Although the amount of water required during photosynthesis is hardly one percent of the total amount of water absorbed by the plant, yet any change in the amount of water absorbed by a plant has significant effect on its rate of photosynthesis. Under normal conditions water rarely seems to be a controlling factor as the chloroplasts normally contain plenty of water.

      Many experimental observations indicate that in the field the plant is able to withstand a wide range of soil moisture without any significant effect on photosynthesis and it is only when wilting sets in that the photosynthesis is retarded. Some of the effect of drought may be secondary since stomata tend to close when the plant is deprived of water. A more specific effect of drought on photosynthesis results from dehydration of protoplasm.

      5. Effect of Oxygen:

      Excess of O2 may become inhibitory for the process. Enhanced supply of O2 increases the rate of respiration simultaneously decreasing the rate of photosynthesis by the common intermediate substances. The concentration for oxygen in the atmosphere is about 21% by volume and it seldom fluctuates. O2 is not a limiting factor of photosynthesis.

      An increase in oxygen concentration decreases photosynthesis and the phenomenon is called Warburg effect. [Reported by German scientist Warburg (1920) in Chlorella algae]. This is due to competitive inhibition of RuBP-carboxylase at increased O2 levels, i.e., O2 competes for active sites of RuBP-carboxylase enzyme with CO2. The explanation of this problem lies in the phenomenon of photorespiration. If the amount of oxygen in the atmosphere decreases then photosynthesis will increase in C3 cycle and no change in C4 cycle.

      6. Effect of Minerals:

      Presence of Mn ++ and CI – is essential for smooth operation of light reactions (Photolysis of water/evolution of oxygen) Mg ++ , Cu ++ and Fe ++ ions are important for synthesis of chlorophyll.

      7. Effect of Pollutants and Inhibitors:

      The oxides of nitrogen and hydrocarbons present in smoke react to form peroxyacetyl nitrate (PAN) and ozone. PAN is known to inhibit Hill’s reaction. Diquat and Paraquat (commonly called as Viologens) block the transfer of electrons between Q and PQ in PS II.

      Other inhibitors of photosynthesis are monouron or CMU (Chlorophenyl dimethyl urea), diuron or DCMU (Dichlorophenyl dimethyl urea), bromocil and atrazine etc., which have the same mechanism of action as that of violates. At low light intensities potassium cyanide appears to have no inhibiting effect on photosynthesis.

      4. Internal Factors:

      The important internal factors that regulate the rate of photosynthesis are:

      1. Protoplasmic factors:

      There is some unknown factor in protoplasm which affects the rate of photosynthesis. This factor affect the dark reactions. The decline in the rate of photosynthesis at temperature.above 30°C or at strong light intensities in many plants suggests the enzyme nature of this unknown factor.

      2. Chlorophyll content:

      Chlorophyll is an essential internal factor for photosynthesis. The amount of CO2 fixed by a gram of chlorophyll in an hour is called photosynthetic number or assimilation number. It is usually constant for a plant species but rarely it varies. The assimilation number of variegated variety of a species was found to be higher than the green leaves variety.

      3. Accumulation of end products:

      Accumulation of food in the chloroplasts reduces the rate of photosynthesis.

      4. Structure of leaves:

      The amount of CO2 that reaches the chloroplasts depends on structural features of the leaves like the size, position and behaviour of the stomata and the amount of intercellular spaces. Some other characters like thickness of cuticle, epidermis, presence of epidermal hairs, amount of mesophyll tissue, etc., influence the intensity and quality of light reaching the chloroplast.

      5. CO2 Compensation Point:

      It is that value or point in light intensity and atmospheric CO2 concentration when the rate of photosynthesis is just equivalent to the rate of respiration in the photosynthetic organs so that there is no net gaseous exchange. The value of light compensation point is 2.5 -100 ft. candles for shade plants and 100-400 ft. candles for sun plants. The value of CO2 compensation point is very low in C4 plants (0-5 ppm), where as in C3 plants it is quite high (25-100 ppm). A plant can not survive for long at compensation point because there is net lose of organic matter due to respiration of non-green organs and dark respiration.


      Evolutionary Adaptations to Poikilothermy and Its Ecological Implications

      Evolutionary adaptations of poikilotherms are dictated by the necessity to withstand a substantial variation in body temperature. Across the animal kingdom, different species of poikilotherms have evolved to operate at body temperatures from −1.86 °C (e.g., some polar fish and invertebrates) to up to 44–45 °C in certain tropical fish, desert insects, and reptiles, while dormant or quiescent life stages of some animals (such as some rotifers and tardigrades) can survive temperatures spanning from nearly −273 to over 100 °C. Within each species of poikilotherms, the range of tolerated body temperatures is smaller, but can still be very appreciable. Thus, in temperate and subpolar poikilotherms, seasonal temperature changes may lead to a gradual change in Tb by 15–30 °C. On a short-term basis, some land insects and reptiles from temperate climates and marine intertidal invertebrates may experience rapid variations of Tb in excess of 20–30 °C during diurnal or tidal cycles. Behavioral escape mechanisms (such as migration or habitat choice) may reduce thermal stress but are rarely sufficient to completely prevent a change in Tb. As a result, physiological and biochemical functions of poikilotherms have evolved to withstand a wide range of fluctuations in Tb which would be immediately lethal for most active homeotherms.

      Temperature change directly affects the rates of all biological processes as well as stability of macromolecules and membrane structures. At high temperatures, increasing molecular motion may lead to structural destabilization and eventually damage. At low temperatures, a decrease in kinetic energy of the molecules results in low rates of biochemical reactions and the loss of membrane fluidity incompatible with sustaining active life. If the temperature drops further, below the freezing point of intracellular fluids, water crystallization and resulting mechanical damage to the cells becomes a problem. Therefore, a major challenge of poikilothermy is to maintain cellular and systemic homeostasis in the face of temperature-induced functional and structural alterations in their cells. Poikilotherms have evolved multiple ways to achieve this homeostasis, which include profound alterations of intracellular milieu, membrane composition and properties, enzyme activities, and concentrations of molecular chaperones and cryoprotectants.

      Biological membranes are among the most temperature-sensitive cellular sites in poikilotherms. Changes in Tb strongly affect membrane fluidity, which in turn may affect its integrity and permeability, as well as signal transduction and function of membrane-associated proteins and cytoskeleton. A suite of biochemical mechanisms known as homeoviscous adaptation allows poikilotherms to maintain optimal levels of membrane fluidity in the face of temperature change. These mechanisms involve adaptive changes in the degree of acyl chain saturation of the membrane phospholipids, changes in the cholesterol content and ratio of different phospholipid classes (phosphatidyl choline to phosphatidyl ethanolamine) in the membrane. In different poikilotherms, homeoviscous adaptation may be brought about by the de novo synthesis of certain lipid classes, biochemical modification of existing membrane lipids, cholesterol synthesis or breakdown, as well as by seasonal changes in the diet. Some mammalian hibernators selectively feed on plants rich in polyunsaturated fatty acids before entering into hibernation. This leads to an increase of the unsaturated lipid content in their membranes and fat depots, lower temperature set points during hibernation, and improved winter survival rates. Interestingly, diet can also affect temperature preference of an organism resulting in modified behavior. For example, Australian shingleback skinks select cooler environments when fed diets artificially enriched in polyunsaturated fatty acids, and this diet-induced shift in the preferred body temperature may reach 5 °C.

      Another key aspect of the variable Tb in poikilotherms is variation in the rates of enzymatic reactions, which has profound ‘ripple’ effects on the rates of all integrative processes, from metabolism and growth to neurotransmission and behavior. Decrease in body temperature results in slowing down the rates of enzymatic reactions, which may in turn result in reduced rates of growth and reproduction, as well as impaired locomotion and ability to escape predators or to find food. On the short-term scale, homeostasis of enzymatic reaction rates may be achieved by changing concentrations of reaction substrates and products, or variation in intracellular levels of allosteric regulators of enzyme activity. During a prolonged decrease in Tb (e.g., during seasonal cold acclimatization), decreasing reaction rates can be compensated by elevated enzyme concentrations, expression of less-temperature-sensitive isoforms of enzymes, or both. However, this compensation is often incomplete, and in most poikilotherms a decrease in body temperature is associated with a decreased activity and growth rate.

      Although elevated temperatures enhance rates of enzymatic processes (and thus, ‘the rate of living’) in poikilotherms, an excessive increase in Tb is damaging and potentially lethal due to the destabilization and eventual denaturation of cellular proteins. In order to protect against such denaturation, poikilotherms may express molecular chaperones (particularly so-called heat shock proteins, or HSPs), which assist in proper folding of partially denatured proteins and stabilization of their native conformation. Expression of HSPs is almost universal response to heat stress in the animal kingdom and found in all poikilotherms, as well as most homeotherms. The only known exception is some extremely stenothermal and cold-adapted Antarctic fish species which have lost the ability to induce HSPs in response to heat stress. Increasing Tb also results in a decline in intracellular pH in poikilotherms, which helps to support normal folding and function of intracellular proteins through the maintenance of constant levels of protonation of their critical α-imidazol groups. Taken together, these changes in intracellular milieu help to maintain structural integrity and cellular homeostasis in poikilotherms facing a change in Tb.

      Preventing ice formation is a significant challenge for poikilotherms living in habitats where environmental temperatures fall below the freezing point of intracellular fluids. Many poikilothermic species such as Arctic and Antarctic fishes, terrestrial arthropods and amphibians, plants and fungi are known to seasonally synthesize and accumulate antifreeze agents such as glycerol, sorbitol (and other polyols), trimethylamine-N-oxide (TMAO), as well as specialized antifreeze proteins and glycoproteins. These compounds decrease the freezing point of intracellular fluids and some of them also provide thermal hysteresis (lowering of the temperature required for crystal growth beyond that needed for crystal melting), thus preventing formation and growth of intracellular ice crystals. Owing to these mechanisms, some glycerol-rich insects may supercool to −60 °C without freezing. Caterpillars of the butterflies Aporia crataegi can survive several months with body temperature as low as −50 °C to achieve such remarkable hardiness, 14% of their body weight is composed of cryoprotectants. In hibernating land frogs, high tissue levels of glucose serve as cryoprotectants. Synthesis of the cryoprotectants in poikilotherms is regulated by hormonal systems, which in turn are typically activated by photoperiod rather than temperature. This allows animals to accumulate sufficient levels of cryoprotectants in their tissues before the environmental temperature actually drops below freezing.


      The gymnosperms probably evolved from an extinct phylum of seedless vascular plants, the progymnosperms, that appeared about 380 million years ago. The fossils of these plants, some of which were large trees, appear to form a link between the trimerophytes (another extinct phylum of seedless vascular plants) and true gymnosperms. Progymnosperms reproduced by means of spores like the former, but their vascular tissues were very similar to those of living conifers. The oldest true gymnosperms, which produce seeds rather than spores, first appeared about 365 million years ago. The evolution of seeds, with their hard, resilient coats, was almost certainly a key factor in the success of the group. A second factor was the evolution of pollen grains to protect and transport the male gametes. As a consequence of this, gymnosperms, unlike seedless vascular plants, were no longer dependent on water for successful fertilization and could broadcast their male gametes on the wind.

      Several early gymnosperm groups are now extinct, but there are four phyla with living representatives: the cycads, the gnetophytes, the conifers, and one phylum (Ginkgophyta) that has only a single living species, the ginkgo tree (Ginkgo biloba ). Of these, the conifers are by far the most abundant and diverse, and many species are of considerable ecological and economic importance. Most conifers are well adapted to dry environments, particularly in their leaf morphology , and some can withstand severe cold. These features may have enabled them to thrive in the Permian, when Earth became much drier and colder than it had been in the Carboniferous.

      Author information

      Ray Ming, Robert VanBuren, Ching Man Wai and Haibao Tang: These authors contributed equally to this work.


      Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign–School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China

      Ray Ming, Robert VanBuren, Ching Man Wai, Haibao Tang, Jisen Zhang, Lixian Huang, Lingmao Zhang, Wenjing Miao, Jian Zhang, Zhangyao Ye, Chenyong Miao, Zhicong Lin, Zhenyang Liao, Jingping Fang, Juan Liu, Xiaodan Zhang, Qing Zhang, Weichang Hu, Yuan Qin, Kai Wang & Li-Yu Chen

      Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, China

      Ray Ming, Robert VanBuren, Ching Man Wai, Haibao Tang, Jisen Zhang, Lixian Huang, Lingmao Zhang, Wenjing Miao, Jian Zhang, Zhangyao Ye, Chenyong Miao, Zhicong Lin, Zhenyang Liao, Jingping Fang, Juan Liu, Xiaodan Zhang, Qing Zhang, Weichang Hu, Yuan Qin, Kai Wang & Li-Yu Chen

      Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

      Ray Ming, Robert VanBuren, Ching Man Wai & Katy Heath

      Donald Danforth Plant Science Center, St. Louis, Missouri, USA

      Robert VanBuren, Henry D Priest, Michael R McKain & Todd Mockler

      iPlant Collaborative/University of Arizona, Tucson, Arizona, USA

      Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

      Michael C Schatz, Eric Biggers, Hayan Lee, James Gurtowski & Fritz J Sedlazeck

      Department of Plant Biology, University of Georgia, Athens, Georgia, USA

      John E Bowers, Hao Wang, Hongye Zhou, Alex Harkess, James H Leebens-Mack & Jeffrey L Bennetzen

      Hawaii Agriculture Research Center, Kunia, Hawaii, USA

      Ming-Li Wang & Paul H Moore

      Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, Hawaii, USA

      Jung Chen & Robert E Paull

      Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Nevada, USA

      Won C Yim & John C Cushman

      Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada

      Chunfang Zheng & David Sankoff

      Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA

      Margaret Woodhouse, Patrick P Edger & Michael Freeling

      Institut de Recherche pour le Développement, Diversité Adaptation et Développement des Plantes, Montpellier, France

      Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA

      Key Laboratory of Computational Biology, Chinese Academy of Sciences–Max Planck Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China

      Guangyong Zheng & Xinguang Zhu

      Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research, Texas A&M University System, Dallas, Texas, USA

      Ratnesh Singh, Anupma Sharma & Qingyi Yu

      Department of Biological Sciences, Youngstown State University, Youngstown, Ohio, USA

      Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China

      Australian Research Council (ARC) Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, Adelaide, South Australia, Australia

      Neil Shirley & Vincent Bulone

      Department of Agronomy, National Taiwan University, Taipei, Taiwan

      W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

      Alvaro G Hernandez & Chris L Wright

      Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

      Gerald A Tuskan & Xiaohan Yang

      US Department of Agriculture–Agricultural Research Service (USDA-ARS), Pacific Basin Agricultural Research Center, Hilo, Hawaii, USA

      Department of Biochemistry and Molecular Biology, Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA

      Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA

      Department of Plant Sciences, University of Oxford, Oxford, UK

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      R.M., Q.Y., R.E.P., P.H.M., R.V. and C.M.W. conceived the experiments. L.H., L.Z., W.M., A.G.H. and C.L.W. sequenced the genomes. M.C.S., E.B., H.L., J.G. and F.J.S. assembled the genome. H.T., C.M. and Z.Y. annotated the genome. R.M., R.V., C.M.W., J.E.B., E.L., M.-L.W., J.C., Jisen Zhang, Z. Lin, Jian Zhang, H.W., H.Z., W.C.Y., H.D.P., C.Z., M.W., P.P.E., R.G., H.-B.G., H.G., G.Z., R. Singh, A.S., X.M., Y.Z., A.H., M.R.M., Z. Liao, J.F., J.L., X. Zhang, Q.Z., W.H., Y.Q., K.W., L.-Y.C., N.S., Y.-R.L., L.-Y.L., V.B., G.A.T., K.H., F.Z., R. Sunkar, J.H.L.-M., T.M., J.L.B., M.F., D.S., A.H.P., X. Zhu, X.Y., J.A.C.S., J.C.C., R.E.P. and Q.Y. analyzed the genomes. R.M., R.V., C.M.W., H.T., M.C.S., D.S., M.W., M.F., X. Zhu, X.Y., J.A.C.S. and J.C.C. wrote the manuscript.

      Corresponding authors


      In summary, we have revisited the quantum aspects of photosynthetic light harvesting. It has become clear from basic considerations that there is no equivalence between quantumness of the processes and coherences observed in femtosecond spectroscopy experiments. Even the very fundamental question if nonstationary coherences in photosynthetic systems can be excited by sunlight still awaits full clarification (6264, 103). Whatever the state preparation is, the dynamics will be governed by the associated couplings of the system and its interaction with the bath. Furthermore, the claims of the persistence of these coherences in femtosecond experiments have been critically reevaluated. In particular, detailed analysis of the exemplar system in quantum biology—the FMO complex—shows unambiguously the absence of long-lived interexciton coherence on relevant time scales in this system, both at cryogenic and physiological temperatures. Instead, it has become clear that the long-lived oscillating signals originate from vibrational modes predominantly on the electronic ground state. More advanced data analysis and theoretical treatments using realistic parametrization of the bath are needed for clear identification of coherence signals. The extensive discussion of earlier assignment of these spectral signatures, propagating in the community for a decade, underlines this need.

      The major positive outcome is the improvement of theoretical and experimental methods that have led to a deeper understanding of the system-bath interactions responsible for decoherence and dissipation in biological systems. Nature does not engineer the bath to avoid decoherence to direct functional processes such an approach almost certainly would not be robust. Nature, rather than trying to avoid dissipation, specifically exploits it together with the engineering of site energies and excitonic coupling to direct energy transport. The role of thermodynamic parameters in driving biological functions is well appreciated on other levels. Here, we see that this principle applies even to the energy transfer processes involved in photosynthesis that occur on the fastest possible time scales. The basic physics behind thermalization is used to impose direction. This simple concept, mastered by nature over all relevant time and spatial dimensions, is truly a marvel of biology.

      Repressed Gene Expression of Photosynthetic Antenna Proteins Associated with Yellow Leaf Variation as Revealed by Bulked Segregant RNA-seq in Tea Plant Camellia sinensis

      The young leaves and shoots of albino tea cultivars are usually characterized as having a yellow or pale color, high amino acid, and low catechin. Increasing attention has been paid to albino tea cultivars in recent years because their tea generally shows high umami and reduced astringency. However, the genetic mechanism of yellow-leaf variation in albino tea cultivar has not been elucidated clearly. In this study, bulked segregant RNA-seq (BSR-seq) was performed on bulked yellow- and green-leaf hybrid progenies from a leaf color variation population. A total of 359 and 1134 differentially expressed genes (DEGs) were identified in the yellow and green hybrid bulked groups (Yf vs Gf) and parent plants (Yp vs Gp), respectively. The significantly smaller number of DEGs in Yf versus Gf than in Yp versus Gp indicated that individual differences could be reduced within the same hybrid progeny. Analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed that the photosynthetic antenna protein was most significantly enriched in either the bulked groups or their parents. Interaction was found among light-harvesting chlorophyll a/b -binding proteins (LHC), heat shock proteins (HSPs), and enzymes involved in cuticle formation. Combined with the transcriptomic expression profile, results showed that the repressed genes encoding LHC were closely linked to aberrant chloroplast development in yellow-leaf tea plants. Furthermore, the photoprotection and light stress response possessed by genes involved in HSP protein interaction and cuticle formation were discussed. The expression profile of DEGs was verified via quantitative real-time PCR analysis of the bulked samples and other F1 individuals. In summary, using BSR-seq on a hybrid population eliminated certain disturbing effects of genetic background and individual discrepancy, thereby helping this study to intensively focus on the key genes controlling leaf color variation in yellow-leaf tea plants.

      Keywords: Camellia sinensis bulked segregant RNA-seq chloroplast leaf color.

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