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Topic Name: Purdue University Researchers has Identified New Signaling Pathway That Moves Materials to Determine Cell Shape and Size, Will Better Biofuel Sources

Category: Biomedical

Research persons: Purdue Research Team

Location: Purdue University, United States

Details

A newly defined biochemical pathway in plants may provide the scientific tools to design plants that will yield larger quantities of alternative transportation fuels than currently can be produced, according to Purdue University researchers.
The pathway moves materials that determine cell shape and size through a system of signaling proteins, said Dan Szymanski, a plant geneticist and cellular biologist. By learning more about the growth and development process, it may be possible to engineer plants with improved properties such as cell walls that are more massive or are more easily fermented in the biofuel process.

"We expect that cell wall material will be a major source of biomass from plants designated for biofuel production," Szymanski said. "We need to learn more about how plant cells control the quality and amount of cell wall material."

He and his research team investigated plant growth and cell wall development from several scientific approaches in determining the cascade of events that leads to changes in the cell wall. They discovered that a protein called "SPIKE1" directs the protein signaling pathway. They report their findings in "Early Edition," the online publication of the journal Proceedings of the National Academy of Sciences. The study also will be published in the journal's March 11 print issue.

"Plant cells grow by expansion, which is cell wall synthesis coupled with an increase in cell size," Szymanski said. "The key questions we need to answer in trying to create plants more valuable for biofuel production center on understanding how plants integrate metabolism, cell growth and biomass production."

To answer those questions and be able to engineer plants for improved growth of biomass for alternative fuels, Szymanski and other scientists must investigate molecular function.

"Our research is focused on understanding signaling mechanisms," he said. "How does a cell interpret multiple types of information and then translate that information to a signal that says, 'Grow here, or modify or reinforce the cell wall here.' Or how does a cell know to make new cytoskeleton filaments at a certain time and place to define regions of growth that determine the cell's shape and size?"

Actin filaments comprise the cytoskeleton, which is the roadway for delivery and recycling of materials that drive plant growth and determine the cell shape and size. Actin is an abundant protein in organisms that have multiple cells with nuclei.

SPIKE1 is a master regulator of many growth control pathways, including the protein signaling pathway that produces the cytoskeleton. Szymanski and his colleagues were able to demonstrate that one of SPIKE1's functions is to control production of actin filament, which defines localized cell regions for delivery and recycling of growth materials.

"Wall construction in plants, just as in a road project, is a coordinated effort," Szymanski said. "The supply and demand of the materials needed for growth must be coordinated. The question is, how do cells regulate this?"

The signaling pathway, headed by SPIKE1, is responsible for organizing activities during construction - delivering materials and recycling materials that are used during growth, he said. After SPIKE1 initiates communication among proteins along the pathway, actin filaments are produced and changes in cell shape and size occur.

Cells also must coordinate with the activities of surrounding cells that have different shapes and functions.

"Cell expansion occurs in a crowded, but accommodating environment," Szymanski said. "As neighboring cells expand, this growth intrudes upon a neighbor. SPIKE1 generates signals so that cells can coordinate with neighboring cells' activities to promote organized cell expansion and proper cell-to-cell adhesion."

Szymanski and his colleagues used an altered version of the mustard family laboratory plant Arabidopsis to study SPIKE1's function and find the proteins that it activates and to which it binds.

They found that when they created mutant plants by switching off the SPIKE1 gene so that the function is lost, one result was improper growth that manifested as holes in the leaf epidermis.

By studying the results of turning off various other protein complexes in the pathway, Szymanski's team was able to follow the sequence of events that occur during signaling.

They also found that plants in which the function of one of the pathway's signaling proteins was altered resulted in mutants that all looked alike, Szymanski said. This suggested that the three major protein complexes the scientists investigated all function in a common pathway. The Purdue research team confirmed this by making double mutants - plants in which two of the proteins had been switched off. One of the pathway's protein complexes, called "WAVE," functions the same way in both humans and Arabidopsis, and the SPIKE1 signaling pathway is likely to function in other plants including rice and corn.

However, in other organisms with SPIKE1-like genes, switching off the gene kills the organism. This lethality has made it difficult for scientists to understand the function of SPIKE1 and comparable genes in other organisms, including humans. Since Arabidopsis survives when SPIKE1 is disrupted, the Purdue team was able to determine the signaling pathway.

The scientists hypothesize that SPIKE1 may both generate and organize protein complex signaling, Szymanski said. They also need to discover what activates SPIKE1. When the researchers understand enough about the processes involved in plant cell growth and development, then they may be able to design plants that are bigger with more cell wall that can be processed into biofuel.

"Learning more about SPIKE1 likely will help us gain a better understanding of the mechanics and regulation involved with the pathways that control cell architecture and development in plants, and also may be relevant to animal and human growth and development," Szymanski said.

The other researchers involved with this study were graduate student Dipanwita Basu, postdoctoral students Jie Le and Taya Zakharova, and research technician Eileen Mallery. All are in the Purdue Department of Agronomy.

Note for Biofuel
Biofuel is a basic abbreviation of biorganic fuel. This is a scientific name for any plant or animal substance that can burn (combustible (fuel) organism (organic) of two types (bi-), plant and animal). Biofuel is an alternative considered to replace petroleum gas (gasoline or petrol). Most transportation vehicles require high power density provided by internal combustion engines. These engines require clean burning fuels, which are generally in liquid form, and to a lesser extent, compressed gaseous phase. Liquids are more portable because they have high energy density, and they can be pumped, which makes handling easier. This is why most transportation fuels are liquids.
Non-transportation applications can usually tolerate the low power-density of external combustion engines, that can run directly on less-expensive solid biomass fuel, for combined heat and power. One type of biomass is wood, which has been used for millennia in varying quantities, and more recently is finding increased use. Two billion people currently cook every day, and heat their homes in the winter by burning biomass, which is a contributor to man-made climate change global warming. The black soot that is being carried from Asia to polar ice caps is causing them to melt faster in the summer. In the 19th century, wood-fired steam engines were common, contributing significantly to industrial revolution unhealthy air pollution. Coal is a form of biomass that has been compressed over millennia to produce a non-renewable, highly-polluting fossil fuel.
Wood and its byproducts can now be converted into biofuels such as woodgas, methanol or ethanol fuel.
Biofuel is considered by some as a means of reducing greenhouse gas emissions and increasing energy security by providing an alternative to fossil fuels. However, In October 2007, Nobel Laureate Paul Crutzen published findings that the release of Nitrous Oxide (N2O) from rapeseed oil, and corn (maize), contribute more to global warming than the fossil fuels they replace. However, the Crutzen paper goes on to say that crops with less nitrogen demand, such as grasses and woody coppicing will have positive but lower climate impacts. In February 2008, two articles were published in Science concluding that clearing land for biofuel production produce twice as much greenhouse gas than the U.N. IPCC had previously estimated.
Biofuels are used globally. Biofuel industries are expanding in Europe, Asia and the Americas. The most common use for biofuels is automotive transport (for example E10 fuel). Increased American and European demand has led to clearing land for Palm Oil plantations. Locations such as Indonesia are subject to deforestation and the accompanying displacement of indigenous peoples. In some areas use of pesticides for biofuel crops are disrupting clean water supplies.
Biofuel can be theoretically produced from any (biological) carbon source. The most common by far is photosynthetic plants that capture solar energy. Many different plants and plant-derived materials are used for biofuel manufacture.
The greatest technical challenge is to develop ways to convert biomass energy specifically to liquid fuels. To achieve this, the two most common strategies are:
To grow sugar crops (sugar cane, and sugar beet), or starch (corn/maize), and then use yeast fermentation to produce ethanol (ethyl alcohol).
To grow plants that (naturally) produce oils, such as algae, or jatropha. When these oils are heated, their viscosity is reduced, and they can be burned directly in a diesel engine. The oils can also be chemically processed to produce biodiesel.

Note for Biomass
Biomass refers to living and recently dead biological material that can be used as fuel or for industrial production. Most commonly, biomass refers to plant matter grown for use as biofuel, but it also includes plant or animal matter used for production of fibres, chemicals or heat. Biomass may also include biodegradable wastes that can be burnt as fuel. It excludes organic material which has been transformed by geological processes into substances such as coal or petroleum.
Biomass is grown from several plants, including miscanthus, switchgrass, hemp, corn, poplar, willow, sugarcane and oil palm (palm oil). The particular plant used is usually not very important to the end products, but it does affect the processing of the raw material. Production of biomass is a growing industry as interest in sustainable fuel sources is growing.
Although fossil fuels have their origin in ancient biomass, they are not considered biomass by the generally accepted definition because they contain carbon that has been "out" of the carbon cycle for a very long time. Their combustion therefore disturbs the carbon dioxide content in the atmosphere.
Plastics from biomass, like some recently developed to dissolve in seawater, are made the same way as petroleum-based plastics, are actually cheaper to manufacture and meet or exceed most performance standards. But they lack the same water resistance or longevity as conventional plastics.
Biomass which is not simply burned as fuel may be processed in other ways such as corn.
Low tech processes include:
composting (to make soil conditioners and fertilisers)
anaerobic digestion (decaying biomass to produce methane gas and sludge as a fertiliser)
fermentation and distillation (both produce ethyl alcohol)
More high-tech processes are:
Pyrolysis (heating organic wastes in the absence of air to produce gas and char. Both are combustable.)
Hydrogasification (produces methane and ethane)
Hydrogenation (converts biomass to oil using carbon monoxide and steam under high pressures and temperatures)
Destructive distillation (produces methyl alcohol from high cellulose organic wastes).
Acid hydrolysis (treatment of wood wastes to produce sugars, which can be distilled)
Burning biomass, or the fuel products produced from it, may be used for heat or electricity production.
Other uses of biomass, besides fuel and compost include:
Building materials
Biodegradable plastics and paper (using cellulose fibres)

Note for Metabolism
Metabolism is the set of chemical reactions that occur in living organisms in order to maintain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. Catabolism breaks down large molecules, for example to harvest energy in cellular respiration. Anabolism, on the other hand, uses energy to construct components of cells such as proteins and nucleic acids.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed into another by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable but thermodynamically unfavorable reactions by coupling them to favorable ones. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells.
The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the metabolic rate, also influences how much food an organism will require.
A striking feature of metabolism is the similarity of the basic metabolic pathways between even vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all organisms, being found in species as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants. These striking similarities in metabolism are most likely the result of the high efficiency of these pathways, and of their early appearance in evolutionary history.
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reaction is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously being made, consumed and then recycled.
One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between catabolism and anabolism, with catabolic reactions generating ATP and anabolic reactions consuming it. It also serves as a carrier of phosphate groups in phosphorylation reactions.
A vitamin is an organic compound needed in small quantities that cannot be made in the cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells. Nicotinamide adenine dinucleotide (NADH), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.

Note for Cytoskeleton
The cytoskeleton (also CSK) is a cellular "scaffolding" or "skeleton" contained within the cytoplasm. The cytoskeleton is present in all cells; it was once thought this structure was unique to eukaryotes, but recent research has identified the prokaryotic cytoskeleton. It is a dynamic structure that maintains cell shape, often protects the cell, enables cellular motion (using structures such as flagella, cilia and lamellipodia), and plays important roles in both intracellular transport (the movement of vesicles and organelles, for example) and cellular division.
Eukaryotic cells contain three main kinds of cytoskeletal filaments, which are microfilaments, intermediate filaments, and microtubules. The cytoskeleton provides the cell's cytoplasm with structure and shape.
These filaments, 8 to 12 nanometers in diameter, are more stable (strongly bound) than actin filaments, and heterogeneous constituents of the cytoskeleton. Like actin filaments, they function in the maintenance of cell-shape by bearing tension (microtubules, by contrast, resist compression. It may be useful to think of micro- and intermediate filaments as cables, and of microtubules as cellular support beams). Intermediate filaments organize the internal tridimensional structure of the cell, anchoring organelles and serving as structural components of the nuclear lamina and sarcomeres. They also participate in some cell-cell and cell-matrix junctions.
Different intermediate filaments are:
made of vimentins, being the common structural support of many cells.
made of keratin, found in skin cells, hair and nails.
neurofilaments of neural cells.
made of lamin, giving structural support to the nuclear envelope.
The cytoskeleton was previously thought to be a feature only of eukaryotic cells, but homologues to all the major proteins of the eukaryotic cytoskeleton have recently been found in prokaryotes. Although the evolutionary relationships are so distant that they are not obvious from protein sequence comparisons alone, the similarity of their three-dimensional structures and similar functions in maintaining cell shape and polarity provides strong evidence that the eukaryotic and prokaryotic cytoskeletons are truly homologous.

The National Science Foundation and the Purdue Agricultural Research Program funded this project.

In figure 1, A Purdue research team is studying plant growth and cell wall development. By investigating plant cells at the molecular level, they may be able to design plants that are better sources of alternative transportation fuels. In these three slides, green outlines the outer epidermal cells. The red is from chloroplasts from the underlying cell layer. The final slide shows cells of a mutant plant in which a gene called SPIKE1 has been turned off. These mutant cells form abnormally and the cell walls won't properly adhere to each, resulting in holes in the epidermis that you can see through.

In figure 2, Plant geneticist Dan Szymanski of the Purdue Department of Agronomy is leading a research team that has defined a biochemical pathway that may make it possible to engineer plants with improved properties, potentially leading to better biofuel sources. The scientists are particularly interested in the signaling that leads to cell growth and development.