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United States Department of Agriculture

Agricultural Research Service

1 - Biography
2 - Key Publications (last 5 years)
3 - Learn About Our Plant Physiology Research
Learn About Our Plant Physiology Research

Focus and Objectives of the Physiology & Biochemistry Program Area              

As a biological organism, a cotton plant is the sum total of its biochemical reactions.  Researchers in the Plant Physiology and Biochemistry Program Area investigate the various life processes (i.e., physiology) of the cotton plant and the biochemical mechanisms that underlie these processes.  We are particularly interested in processes that ultimately limit cotton yield, especially in the arid environment of the desert southwest.  Often, these processes are adversely affected by certain abiotic and biotic stresses that are regular occurrences in the environment.  The negative impact of these stresses is a major factor reducing crop yield.  Thus, a long-term objective of our research program is to enhance crop yield, particularly for cotton, by improving the tolerance of plant processes to abiotic and biotic stresses.  (see article in Agriculture Research magazine)

Photosynthesis - the ultimate sustainable process

Plants are photoautotrophic organisms, capable of using light and carbon dioxide for growth.  Photosynthesis, the conversion of light energy to chemical energy (photo) and the utilization of the chemical energy for the formation of carbohydrates from carbon dioxide (synthesis), is a central process in the life of a plant and ultimately determines the overall capacity for growth and reproduction (i.e., yield).  Photosynthesis is a highly integrated process involving complex interactions between the light (photo-) and dark (-synthesis) reactions, both of which take place in the chloroplasts of leaf cells.  In reality, each of these “reactions” represents several complex biochemical pathways, each catalyzed by numerous enzymatic proteins (enzymes).  A primary focus of research in the Plant Physiology and Biochemistry Program Area is the rate-limiting step in the overall process, the fixation of atmospheric carbon dioxide catalyzed by the enzyme Rubisco. 

Overview of photosynthesis showing integration of the light reactions (light harvesting, water splitting, electron transport and photophosphorylation) with the dark reactions (fixation of CO2 and reduction to sugar).

Rubisco - the rate-limiting enzyme in photosynthesis

Rubisco is an abbreviation for the enzyme, Ribulose-1,5-bisphosphate carboxylase/oxygenase.  The enzyme is bifunctional, catalyzing the carboxylation of the 5-carbon sugar-phosphate ribulose bisphosphate (RuBP) to form two molecules of 3-phosphoglyceric acid or the oxygenation of RuBP to form one molecule each of 3-phosphoglycerate and 2-phosphoglycolate.  The ability of Rubisco to use oxygen as an alternate substrate is costly because (1) oxygen competitively inhibits the carboxylation reaction and (2) the fixation of oxygen leads to a net loss of carbon through photorespiration.  In addition to these problems, Rubisco has a low affinity for carbon dioxide and a relatively slow rate of catalysis.  Together, these properties make  Rubisco rate-limiting for photosynthesis under conditions of adequate light. 

Research on Rubisco in the Plant Physiology & Biochemistry Program Area at the Western Cotton Research Lab centers on its regulation.  Regulation of Rubisco imposes a limit on the rate of photosynthesis by affecting the amount of Rubisco available for photosynthesis.  Rubisco regulation involves some peculiar properties of the enzyme that passively convert it from an active to an inactive form and a mechanism that actively reconverts it back to the active form.  This mechanism involves a second chloroplast enzyme called Rubisco activase.  By controlling the switching of Rubisco from an inactive to an active form (called activating the enzyme), activase ultimately determines how much of the Rubisco is in an active form.  The proportion of Rubisco in the active form is often called the “activation state” of the enzyme.  

Rubisco.  Each holoenzyme is composed of 8 large (blue & light blue) and 8 small (red & orange) subunits.  The yellow loops indicate the positions of the active-site.

Activase - a molecular chaperone that regulates Rubisco

Activase is a soluble chloroplast ATPase, a member of the AAA+ superfamily of proteins.  Like other members of this family, activase functions as a molecular chaperone, interacting with a target protein, in this case, Rubisco.  The chaperoning action of activase facilitates the unfolding of certain loop regions of Rubisco, thereby converting Rubisco from an inactive to an active form.  Environmental conditions that affect Rubisco, activase or the interaction between the two enzymes will influence the rate of photosynthesis by changing the proportion of Rubisco that is active.  For example, since activase requires ATP and is inhibited by ADP, its activity is adversely affected by a condition like high carbon dioxide that reduces the ratio of ATP to ADP in the chloroplasts.  Another condition that negatively impacts photosynthesis by inhibiting Rubisco activation via activase is high temperature or heat stress.  Heat stress is often experienced by plants in warm weather regions throughout the world, including the deserts of the US southwest.


Scheme for the conversion of Rubisco (yellow) from an inactive to an active form by activase (blue) involving the unfolding of certain loop regions of Rubisco.



Heat stress - a factor reducing photosynthetic performance

Heat stress reduces crop yield by inhibiting photosynthesis.  Yield reductions can also occur from an inhibition of pollination.  However, unlike photosynthesis, pollination, generally occurs during a relatively narrow portion of the plant’s life span.  Also, once pollinated the developing fruit is totally dependent on the supply of photosynthate.  In cotton, photosynthesis is inhibited when leaf temperature exceed about 32°C.  During the summer months, daytime temperatures in the Phoenix area can exceed 45°C (113°F) and relatively humidity can be as low as 4%.  Because of the high temperatures, cotton cultivation in this arid region is only possible if ample water is available to the crop through irrigation.  In well-watered plants, transpiration of water through open stomates evaporatively cools the leaves, reducing their temperature by about 10°C.  This cooling is sufficient to prevent inhibition of photosynthesis on all but the hottest days.  However, even well watered plants will experience some heat stress on the hottest days, and heat stress will be severe if the hottest days occur at the wrong time, for example, near the end of a watering cycle.  In cotton production areas like the mid-south, severe heat stress can occur even though air temperatures are generally lower than in the southwest.  The reason is that the higher relative humidity in these less arid regions reduces the capacity for evaporative cooling. 

An area of the Sonoran Desert near Phoenix, AZ. The plants in this picture are adapted to a high temperature environment.

A major focus of our research is the inhibition of photosynthesis by heat stress.  Recent findings have shown that the amount of inactive Rubisco increases under heat stress paralleling the loss of photosynthetic activity.  This loss of Rubisco activation in response to high temperature occurs before any other plant process is adversely affected.  Detailed biochemical studies in our laboratory (Crafts-Brandner & Salvucci, 2000 PDF version, 120KB) have shown that the loss of Rubisco activation appears to be related to both an inability of activase to keep pace with a faster rate of Rubisco deactivation and an exceptional sensitivity of activase to thermal denaturation.  Understanding and improving the thermal stability of activase may provide a means of increasing the thermal tolerance of plants.  Studies underway in our laboratory include examination of activase from high temperature-tolerant plants, particularly plant from the desert areas surrounding Phoenix. 

Inhibition of photosynthesis by high temperature.  The blue line indicates the predicted response of photosynthesis to temperature.  The red line shows the actual response measured for intact cotton leaves.


High CO2

Although not considered a stress, the effects of elevated levels of carbon dioxide on photosynthesis represent another area of interest to our group.  Fossil fuel burning is increasing the levels of carbon dioxide in the environment, with consequent effects on the global climate.  Because Rubisco has a low affinity for carbon dioxide, photosynthesis should increase as atmospheric levels of carbon dioxide rise, increasing productivity and converting some of the excess carbon dioxide into biomass.  However, the actual increase that occurs is generally lower than predicted.  Research by our group, as well as others has shown that the activation state of Rubisco decreases with carbon dioxide.  We have attributed this decrease to a reduction in the ratio of ATP/ADP, which in turn inhibits the ability of activase to keep Rubisco in an active form.  Understanding and improving the affinity of activase for ATP may provide a means of increasing photosynthesis and hence plant productivity under elevated levels of carbon dioxide. 


Inhibition of photosynthesis by high temperature and carbon dioxide. The blue line indicates the predicted response of photosynthesis to temperature at 5x ambient carbon dioxide. The red line shows the actual response measured for intact cotton leaves.



Temperature effects on C4 photosynthesis

Crop plants such as maize and sorghum are referred to as C4 plants because of a unique type of anatomy and photosynthetic metabolism that elevates the level of carbon dioxide around Rubisco, making it much higher than in C3 plants such as cotton and soybean. Plants with C4 anatomy and metabolism have higher rates of photosynthesis and enhanced tolerance to high temperature compared to non-C4 plants. As shown below (blue line), maize leaf photosynthesis is not inhibited until leaf temperature approaches about 40°C. The activation state of Rubisco, however, decreases progressively at temperatures above about 30°C (Crafts-Brandner and Salvucci, 2002). This inactivation of Rubisco effectively prevents photosynthesis from increasing with leaf temperature. In the figure below it can be seen that significant gains in photosynthesis would be realized if Rubisco activation could be prevented, thus allowing photosynthesis to occur at the predicted rate (red line). The loss of Rubisco activation state is due to the temperature sensitivity of Rubisco activase via the mechanism described above for cotton and other non-C4 plants.


Inhibition of C4 photosynthesis by high temperature.  The red line indicates the predicted response of photosynthesis to temperature.  The blue line shows the actual response measured for intact maize leaves.




Yield physiology

Improving the yield and quality of both upland and Pima cotton is the ultimate goal of the Western Cotton Research Laboratory.  Investigators conduct research on the genetic and environmental factors that limit the number and the growth of cotton bolls produced by a plant.  Boll growth relies on a supply of carbohydrate, which is supplied by photosynthesis.  Later in the growing season, nutrients for the growing boll, especially nitrogen, come from the breakdown and remobilization of Rubisco and other chloroplast proteins by a physiological process known as senescence.  Leaf senescence is still poorly understood at the biochemical level even though this process can limit the supply of carbon for boll growth and negatively impact yield and quality.  Understanding the senescence process, especially the loss of carbon dioxide fixation from Rubisco degradation and the effects of environmental stresses such as high temperature on senescence, are topics of interest.


A cotton field near Gila Bend, Arizona.  Notice the irrigation canal at the bottom right of the picture.  This field is irrigated with water from the Colorado River.




Plant-Insect Interactions

Because cotton is grown exclusively in warm regions of the world, it is plagued by insect pests.  In fact, insecticide use on cotton accounts for 25% of the total insecticides used on crop plants worldwide.  A major insect pest of interest to researchers at the Western Cotton Research Laboratory, including investigators in the Cotton Physiology, Genetics & Plant-Insect Interactions Research Unit, is the silverleaf whitefly.  Whiteflies are sap-sucking insects that derive their nutrition from the sugar-rich phloem tissue of leaves.  When the insect is present at high populations, its feeding can reduce yield and deposits of its excreted material known as honeydew damage the cotton fiber by producing what is known as “sticky cotton”.  Since whiteflies require plant nutrients for growth, we are investigating the physiology and biochemistry of nutrient uptake and metabolism in the whitefly.  Of specific interest are the metabolism of sugars (carbohydrates), amino acids, and proteins and the effect of plant nutrition on the availability, and acquisition of these nutrients.  We are also interested in the biochemical and molecular mechanisms that allow whiteflies to survive periods of high temperature.  The ultimate goal of this research is to develop new approaches for controlling whiteflies and other homopteran insects that target nutrient metabolism and/or thermal tolerance.

Clean and "Sticky" cotton. The boll on the left is from an uninfested plant, the one on the right is from a plant infested with whiteflies. The black material on the "sticky" boll is sooty mold, a fungus that lives on the sugars excreted by the whiteflies.
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Last Modified: 11/19/2010
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