Enzymes

The following clip looks at the two types of chemical reactions…

The following video goes over enzymes and their function…

The following clip looks at enzyme-substrate interactions…

Remember also the kinetics of a reactions (the relative energy of reactants and products and the role a catalyst plays in impacting the activation energy).

Trees Make Ants Chemically Dependent, Turn Them Into Indentured Servants

Trees Make Ants Chemically Dependent, Turn Them Into Indentured Servants

November 12, 2013 | by Lisa Winter
IFL Science

Ants on Acacia Tree

Ants on Acacia Tree (Photo credit: Ryan Somma)

There are all kinds of mutually beneficial relationships that exist in nature in which two seemingly unconnected species live in harmony and provide vital services for one another. This does not always result in both parties benefiting equally – but as long as it still works, it keeps on going. A recent study has shown that certain Central American ants live on and defend a particular tree not because they want to, but because enzymes in the tree’s nectar have made it impossible for them to get food anywhere else. The research team was led by Martin Heil of Cinvestav Unidad Irapuato in Mexico and was published in Ecology Letters.

The acacia tree is covered in pods that can be taken by insects. Colonies of Pseudomyrmex ferrugineus patrol the tree, protecting the pods. Some species of acacia tree even have thorns large enough for the ants to move into. In turn for their defense against predators like termites, the tree produces nectar for the ants. The nectar is rich in sucrose, a type of sugar. Using an enzyme called invertase, the ants break up the large sucrose molecules into smaller bits which can then be used to generate energy. About eight years ago, Heil’s previous research showed that the adult ants don’t even make invertase, but it is produced by the tree and can be found in the nectar. It is a classic textbook example of mutualism, or so we all thought. The truth, as it seems, is a bit more complicated.

Five years ago, Heil found out that young ants do produce invertase, but that ability is lost at some point during life. In recent years, he has searched for the answer which, he would find out, almost seems like one of the biggest betrayals in mutualism history: the tree stops the ants from producing their own digestive enzymes. Included in the sucrose and invertase is chitinase: an enzyme that blocks invertase production.

While it is true that the ants protect the tree in exchange for food, they do so because they have no other options. They are completely unable to eat from any other source, because they rely on the invertase from the acacia’s nectar. So, the tree gives them exactly what they need to live, but only because it made them invertase-deficient in the first place. The tree makes out like a bandit by having armies of ants to protect it, who will never be able to leave.

This methodology has vague (and highly anthropomorphized) connotations to Münchausen syndrome by proxy (MSbP) in which someone believes they are sick and have a dedicated caretaker, but it turns out that the caretaker was the one making them sick in the first place. In the case of the acacia tree, it is damning the ants to an eternity of servitude on top of blocking the invertase production to ensure it is the ants’ only food source.

On a very basic level, however, this is astoundingly impressive. Solely through genetic mutations over countless generations, the acacia tree has adapted a way to protect itself from predators and the ants won’t be able to leave, leaving the tree vulnerable. It just happened to evolve this way, which is absolutely amazing. You win this one, acacia tree.

Salt-Loving Microbe Provides New Enzymes for the Production of Next-Generation Biofuels

ScienceDaily (July 10, 2011) —
In order to realize the full potential of advanced biofuels that are derived from non-food sources of lignocellulosic biomass — e.g., agricultural, forestry, and municipal waste, and crops such as poplar, switchgrass and miscanthus — new technologies that can efficiently and cost-effectively break down this biomass into simple sugars are required. Existing biomass pretreatment technologies are typically derived from the pulp and paper industry and rely on dilute acids and bases to break down the biomass. The treated biomass product is then exposed to biological catalysts, or enzymes, to liberate the sugars.

A new class of solvents, referred to as ionic liquids, have been reported to be much more efficient in treating the biomass and enhancing the yield of sugars liberated from it. While ionic liquids are useful for breaking down biomass, they can also hinder the ability of the cellulases (usually derived from fungi) used to produce sugars after pretreatment. Ionic liquids are a liquid form of salt that will inactivate enzymes by interfering with the folding of polypeptides — the building-blocks of proteins. To help identify new enzymes that are tolerant of ionic liquids, researchers from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Joint BioEnergy Institute (JBEI) at DOE’s Lawrence Berkeley National Laboratory are turning to those found in the complete genome sequences of halophilic (salt-tolerant) organisms.

As a test of this bioenergy-related application of DNA sequencing and enzyme discovery, researchers led by the Director of the DOE JGI, Eddy Rubin, and the Vice-President of the JBEI Deconstruction Division, Blake Simmons, employed a cellulose-degrading enzyme from a salt-tolerant microbe that was isolated from the Great Salt Lake. The microbe in question, Halorhabdus utahensis, is from the branch of the tree of life known as Archaea; H. utahensis was isolated from the natural environment at the Great Salt Lake and sequenced at the DOE JGI as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project.

“This is one of the only reports of salt-tolerant cellulases, and the only one that represents a true ‘genome-to-function’ relevant to ionic liquids from a halophilic environment,” said Simmons of the study published June 30, 2011 in Green Chemistry. “This strategy enhances the possibility of identifying true obligatory halophilic enzymes.” Such salt-tolerant enzymes, particularly cellulases, offer significant advantages for industrial utility over conventional enzymes.

In collaboration with Jerry Eichler from Ben Gurion University of the Negev in Israel they cloned and expressed a gene from H. utahensis in another haloarchaeal microbe, and were able to identify a salt-dependent enzyme that can tolerate high temperatures and is resistant to ionic liquids. “This project has established a very important link between genomic science and the realization of enzymes that can handle very demanding chemical environments, such as those present in a biorefinery,” said Simmons.

The group plans to expand this research to develop a full complement of enzymes that is tailored for the ionic liquid process technology with the goal of demonstrating a complete biomass-to-sugar process, one they hope can enable the commercial viability of advanced biofuels.

Other contributors to the project include Tao Zhang, Natalia Ivanova, Seth Axen, Cheryl Kerfeld, Feng Chen, Nikos Kyrpides, Jan-Fang Cheng of the DOE JGI along with Philip Hugenholtz now with The University of Queensland, and Supratim Datta and Kenneth Sale of JBEI.

Engineered Plants Make Potential Precursor to Raw Material for Plastics


ScienceDaily (Nov. 8, 2010)

In theory, plants could be the ultimate “green” factories, engineered to pump out the kinds of raw materials we now obtain from petroleum-based chemicals. But in reality, getting plants to accumulate high levels of desired products has been an elusive goal. Now, in a first step toward achieving industrial-scale green production, scientists from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and collaborators at Dow AgroSciences report engineering a plant that produces industrially relevant levels of compounds that could potentially be used to make plastics.

The research is reported online in Plant Physiology, and will appear in print in the December issue.

“We’ve engineered a new metabolic pathway in plants for producing a kind of fatty acid that could be used as a source of precursors to chemical building blocks for making plastics such as polyethylene,” said Brookhaven biochemist John Shanklin, who led the research. “The raw materials for most precursors currently come from petroleum or coal-derived synthetic gas. Our new way of providing a feedstock sourced from fatty acids in plant seeds would be renewable and sustainable indefinitely. Additional technology to efficiently convert the plant fatty acids into chemical building blocks is needed, but our research shows that high levels of the appropriate feedstock can be made in plants.”

The method builds on Shanklin’s longstanding interest in fatty acids — the building blocks for plant oils — and the enzymes that control their production. Discovery of the genes that code for the enzymes responsible for so called “unusual” plant oil production encouraged many researchers to explore ways of expressing these genes and producing certain desired oils in various plants.

“There are plants that naturally produce the desired fatty acids, called ‘omega-7 fatty acids,’ in their seeds — for example, cat’s claw vine and milkweed — but their yields and growth characteristics are not suitable for commercial production,” Shanklin said. Initial attempts to express the relevant genes in more suitable plant species resulted in much lower levels of the desired oils than are produced in plants from which the genes were isolated. “This suggests that other metabolic modifications might be necessary to increase the accumulation of the desired plant seed oils,” Shanklin said.

“To overcome the problem of poor accumulation, we performed a series of systematic metabolic engineering experiments to optimize the accumulation of omega-7 fatty acids in transgenic plants,” Shanklin said. For these proof-of-principle experiments, the scientists worked with Arabidopsis, a common laboratory plant.

Enzymes that make the unusual fatty acids are variants of enzymes called “desaturases,” which remove specific hydrogen atoms from fatty acid chains to form carbon-carbon double bonds, thus desaturating the fatty acid. First the researchers identified naturally occurring variant desaturases with desired specificities, but they worked poorly when introduced into Arabidopsis. They next engineered a laboratory-derived variant of a natural plant enzyme that worked faster and with greater specificity than the natural enzymes, which increased the accumulation of the desired fatty acid from less than 2 percent to around 14 percent.

Though an improvement, that level was still insufficient for industrial-scale production. The scientists then assessed a number of additional modifications to the plant’s metabolic pathways. For example, they “down-regulated” genes that compete for the introduced enzyme’s fatty acid substrate. They also introduced desaturases capable of intercepting substrate that had escaped the first desaturase enzyme as it progressed through the oil-accumulation pathway. In many of these experiments they observed more of the desired product accumulating. Having tested various traits individually, the scientists then combined the most promising traits into a single new plant.

The result was an accumulation of the desired omega-7 fatty acid at levels of about 71 percent in the best-engineered line of Arabidopsis. This was much higher than the omega-7 fatty acid levels in milkweed, and equivalent to those seen in cat’s claw vine. Growth and development of the engineered Arabidopsis plants was unaffected by the genetic modifications and accumulation of omega-7 fatty acid.

“This proof-of-principle experiment is a successful demonstration of a general strategy for metabolically engineering the sustainable production of omega-7 fatty acids as an industrial feedstock source from plants,” Shanklin said.

This general approach — identifying and expressing natural or synthetic enzymes, quantifying incremental improvements resulting from additional genetic/metabolic modifications, and “stacking” of traits — may also be fruitful for improving production of a wide range of other unusual fatty acids in plant seeds.

This research was funded by the DOE Office Science, and by The Dow Chemical Company and Dow AgroSciences.