KAIST announced a novel technology to produce gasoline by a metabolically-engineered microorganism

Metabolic Engineering of Escherichia coli for the Production of Short-chain Alkanes (gasoline) from Renewable Biomass

A major scientific breakthrough in the development of renewable energy sources and other important chemicals

The research team succeeded in producing 580 mg of gasoline per liter of cultured broth by converting in vivo generated fatty acids

For many decades, we have been relying on fossil resources to produce liquid fuels such as gasoline, diesel, and many industrial and consumer chemicals for daily use. However, increasing strains on natural resources as well as environmental issues including global warming have triggered a strong interest in developing sustainable ways to obtain fuels and chemicals.

Gasoline, the petroleum-derived product that is most widely used as a fuel for transportation, is a mixture of hydrocarbons, additives, and blending agents. The hydrocarbons, called alkanes, consist only of carbon and hydrogen atoms. Gasoline has a combination of straight-chain and branched-chain alkanes (hydrocarbons) consisted of 4-12 carbon atoms linked by direct carbon-carbon bonds.

Previously, through metabolic engineering of Escherichia coli (E. coli), there have been a few research results on the production of long-chain alkanes, which consist of 13-17 carbon atoms, suitable for replacing diesel. However, there has been no report on the microbial production of short-chain alkanes, a possible substitute for gasoline.

In the paper (entitled “Microbial Production of Short-chain Alkanes”) published online in Nature on September 29, a Korean research team led by Distinguished Professor Sang Yup Lee of the Department of Chemical and Biomolecular Engineering at the Korea Advanced Institute of Science and Technology (KAIST) reported, for the first time, the development of a novel strategy for microbial gasoline production through metabolic engineering of E. coli.

The research team engineered the fatty acid metabolism to provide the fatty acid derivatives that are shorter than normal intracellular fatty acid metabolites, and introduced a novel synthetic pathway for the biosynthesis of short-chain alkanes. This allowed the development of platform E. coli strain capable of producing gasoline for the first time. Furthermore, this platform strain, if desired, can be modified to produce other products such as short-chain fatty esters and short-chain fatty alcohols.

In this paper, the Korean researchers described detailed strategies for 

1. screening of enzymes associated with the production of fatty acids, 
2. engineering of enzymes and fatty acid biosynthetic pathways to concentrate carbon flux towards the short-chain fatty acid production, and 
3. converting short-chain fatty acids to their corresponding alkanes (gasoline) by introducing a novel synthetic pathway and optimization of culture conditions. Furthermore, the research team showed the possibility of producing fatty esters and alcohols by introducing responsible enzymes into the same platform strain.

Professor Sang Yup Lee said, “It is only the beginning of the work towards sustainable production of gasoline. The titer is rather low due to the low metabolic flux towards the formation of short-chain fatty acids and their derivatives. We are currently working on increasing the titer, yield and productivity of bio-gasoline. Nonetheless, we are pleased to report, for the first time, the production of gasoline through the metabolic engineering of E. coli, which we hope will serve as a basis for the metabolic engineering of microorganisms to produce fuels and chemicals from renewable resources.”

This research was supported by the Advanced Biomass Research and Development Center of Korea through the Global Frontier Research Program of the Ministry of Science, ICT and Future Planning (MSIP) through the National Research Foundation (NRF), Republic of Korea. Systems metabolic engineering work was supported by the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries by MSIP through NRF.


ORIGINAL: KAIST

Writer Admin.

2013-09-3

Enzymes, ants and bio fuel - Audio Transcription

ORIGINAL: Univeristy of Wisconsin - Madison
Frank Aylward:, Research Fellow
Department of Bacteriology
UW-Madison College of Agricultural and Life Sciences
faylward@wisc.edu
Phone: (608) 265-0689

August 2nd, 2013

2:59 - Total Time
0:17 - New enzymes discovered
0:49 - What is and enzyme
1:01 - What makes this discovery different
1:27 - A set of entirely new enzymes
2:05 - Much like brewing beer
2:32 - A few years to go
2:49 - Lead out

Frank Aylward. Dept. of Bacteriology UW-Madison, 6145 Microbial Sciences 1550 Linden Dr., Madison, WI 53706. faylward (at) wisc.edu

TRANSCRIPT
Sevie Kenyon: Frank, can you introduce us to this new enzyme you found?

Frank Aylward: These enzymes are produced by a fungus cultivated by leafcutter ants. So the name of the fungus is Leucoagaricus gongylophorus, but it is cultivated by leafcutter ants in Central and South America. It’s essentially a mushroom, and it produces a lot of these enzymes, a lot of these proteins that are very useful for taking plant biomass and converting it into simple sugars. And we’re very interested in finding novel enzymes that can be used to degrade plant biomass and convert it into sugars.

Sevie Kenyon: Can you tell us what an enzyme is?

Frank Aylward: An enzyme is a protein that is a catalyst, and in this case, it will degrade plant biomass and convert it into a simple sugar.

Sevie Kenyon: And this enzyme you discovered, what makes it different?

Frank Aylward: Well these enzymes have never been identified before. So it’s a novel genome with novel enzymes that have not been characterized before. We think that the enzymes are particularly useful for the degradation of plant biomass because ants, leafcutter ants are extremely good at taking huge volumes of plant biomass and converting it into nutrients for themselves.

Sevie Kenyon: How many different kinds of enzymes are there?

Frank Aylward: We identified over two-hundred total. So we have a lot of enzymes that are sort of working towards a common goal. It’s like a team is working towards this common goal of winning a game. So with the enzymes, it’s very difficult to evaluate a specific enzyme individually because they all work together, they’re all synergistic. So that’s why we really think it’s interesting that we found this set of about two-hundred or so enzymes, because altogether they are degrading plant biomass very efficiently, and that’s why we’re really interested in the fungus- garden ecosystem itself.

Sevie Kenyon: Do you think these enzymes will come in buckets, and they’ll be dumped on corn stover? How might that look?

Frank Aylward: The actual fermentation process is probably going to be very similar to what you might expect at a brewery. In that respect, it’s not all that different than what many of us are very familiar with. I think this is a great example of how by analyzing ants, by looking at leafcutter ants in Panama, we’re actually able to come up with some enzymes which may have a tangible impact on our lives here in Wisconsin.

Sevie Kenyon: Frank, how long do you think it will be before we’re actually using these enzymes?

Frank Aylward: Well, you know it could be very soon, it could be a few years from now; it really depends on the future directions of this research. So I think the next step is to start testing these enzymes for the degradation of plant biomass, and you know how soon we can actually start using these enzymes for the production of bio fuel.

Sevie Kenyon: We’ve been visiting with Frank Aylward. Department of bacteriology, University of Wisconsin in the College of Agricultural and Life Sciences, Madison, Wisconsin, and I am Sevie Kenyon.

Podcast: Download (Duration: 2:59 — 2.7MB)

Aylward, F.O., Burnum-Johnson, K.E., Tringe, S.G., Teiling, C., Tremmel, D.M., Moeller, J.A., Scott, J.J., Barry, K.W., Piehowski, P.D., Nicora, C.D., Malfatti, S.A., Monroe, M.E., Purvine, P.O., Goodwin, L.A., Smith, R.D., Weinstock, G.M., Gerardo, N.M., Suen, G., Lipton, M.S., and C.R. Currie . Leucoagaricus gongylophorus produces diverse enzymes for the degradation of recalcitrant plant polymers in leaf-cutter ant fungus gardens. Applied and Environmental Microbiology. 2013, 79(12):3770-3778. , DOI: 10.1128/AEM.03833-12 

Dibujan el “mapa cartográfico interactivo” de las enzimas durante las reacciones químicas

ORIGINAL: UIJ.es

Esta entrada también está disponible en: Inglés, Catalán

Conocer el funcionamiento de las enzimas resulta clave para controlar los procesos químicos en los que intervienen estas macromoléculas biológicas con infinidad de aplicaciones en campos como la medicina y la industria. La química computacional ha permitido por primera vez dibujar el “mapa cartográfico” de las enzimas durante el proceso de catálisis, incluido el momento en el que se encuentran en el punto de máxima energía en el camino desde reactivos a productos y que apenas dura un femtosegundo, la milbillonésima parte de un segundo. Un mapa que es además interactivo en el sentido de que relaciona los cambios que sufre la molécula con los movimientos de la proteína que la alberga. La relevancia del estudio desarrollado por investigadores de la Universitat Jaume I de Castellón y la Universitat de València, le ha valido la portada de la prestigiosa revista Nature Chemistry, que hasta la fecha únicamente ha publicado 27 artículos con participación de científicos españoles.

La simulación de los procesos de catálisis a través de supercomputadores ha permitido conocer cómo evoluciona durante el proceso la enzima. “Si hacemos un símil con un mapa cartográfico, en un eje tendríamos una coordenada que representa la molécula que se está transformando y en el otro eje lo que se representa es lo que cambia la proteína que alberga y modifica esta molécula. Combinando esos datos puedes hacer una estimación cuantitativa de la flexibilidad de la proteína, cuánto se deforma, cuánta energía necesitas para deformar esa proteína para que genere la reacción que buscas, etc.”, explica Vicent Moliner, coordinador del grupo de Bioquímica Computacional de la UJI que ha desarrollado el proyecto en colaboración con el Grupo de Investigación de Efectos del Medio de la Universidad de Valencia, dirigido por Iñaki Tuñón. En la investigación también han participado José Javier Ruiz y Sergio Martí, de la UJI, y Rafael García-Meseguer, de la UV.

Hasta la fecha se podía tener información sobre la estructura inicial y final de la proteína, pero no se sabía cómo era en el estado de transición, en el denominado “punto de máxima energía”, que marca el nivel más alto de la barrera para pasar de un punto a otro. “Conocer cómo evoluciona la proteína a medida que la reacción tiene lugar es ir un paso más allá, porque la proteína o determinados aminoácidos de la proteína también están participando de forma sincrónica con la rotura y formación de enlaces durante ese proceso que está siendo catalizado”, explica Moliner. Aprovechando que en estas fechas se cumple el 60 aniversario de la primera ascensión documentada al Everest, el catedrático de Química Física de la UJI establece un símil con la montaña, donde para pasar de un valle a otro has de conocer el punto más elevado por el que has de pasar, “en los valles la situación es estable, esas moléculas son estables y se pueden estudiar con técnicas experimentales (resonancia magnética nuclear, difracción de rayos X, etc.), pero las que están en el punto de máxima energía, en el punto más alto, están durante muy poco tiempo, y hasta ahora no se habían podido estudiar. Si conoces lo alta que es la barrera y cómo es, entonces puedes controlarla, intentar bajarla o incluso buscar un camino alternativo”.

Las enzimas son catalizadores que permiten que una reacción química que transcurre a una velocidad muy baja, y que en condiciones ambientales normales sería incluso prácticamente imposible, se produzca a gran velocidad. En la industria para provocar estas reacciones se recurre a las altas temperaturas o altas presiones, lo que supone un elevado coste energético y repercusiones medioambientales. La biotecnología permite desarrollar biocatalizadores que generen estas reacciones de forma más económica, eficiente y sostenible. “Si somos capaces de sintetizar un catalizador para que las reacciones que requieren altas temperaturas o presiones tengan lugar en condiciones naturales, a temperatura ambiente, supondría un gran ahorro económico y energético”, resalta el investigador.

En los seres vivos, las enzimas posibilitan ir de un punto a otro por un camino mucho más fácil. “Reacciones que se producen en los seres vivos en minutos o segundos, sin enzimas tardarían el tiempo equivalente a la vida de la Tierra, billones de años”, señala. En el campo de la medicina, tanto el desarrollo de nuevos catalizadores como el de inhibidores que bloqueen la acción de estas enzimas resultan claves. “La quimioterapia, por ejemplo, lo que hace es bloquear las enzimas que favorecen la reproducción de células malignas, pero con unos importantes efectos secundarios. Un mayor conocimiento de las enzimas puede permitir bloquearlas de forma más selectiva y eficiente”, resalta Moliner.

El objetivo del grupo de investigación de Bioquímica Computacional de la Jaume I pasa por seguir avanzando en el mayor conocimiento de las enzimas y de los procesos de catálisis ya que, como dice Moliner, “si conoces su funcionamiento estás en una posición privilegiada para controlar la mayoría de los procesos químicos”.

Videonoticia: http://blogs.uji.es/cienciatv/?p=2163
Artículo: http://www.nature.com/nchem/journal/v5/n7/index.html

Scripps Research Institute Scientists Discover How a Protein Finds Its Way

ORIGINAL: Scripps Research Institute

Katrin Karbstein.
Photo: TSRI

JUPITER, FL, April 29, 2013 – Proteins, the workhorses of the body, can have more than one function, but they often need to be very specific in their action or they create cellular havoc, possibly leading to disease.

Scientists from the Florida campus of The Scripps Research Institute (TSRI) have uncovered how an enzyme co-factor can bestow specificity on a class of proteins with otherwise nonspecific biochemical activity.

The protein in question helps in the assembly of ribosomes, large macromolecular machines that are critical to protein production and cell growth. This new discovery expands scientists’ view of the role of co-factors and suggests such co-factors could be used to modify the activity of related proteins and their role in disease.

“In ribosome production, you need to do things very specifically,” said TSRI Associate Professor Katrin Karbstein, who led the study. “Adding a co-factor like Rrp5 forces these enzymes to be specific in their actions. The obvious possibility is that if you could manipulate the co-factor, you could alter protein activity, which could prove to be tremendously important.”

The new study, which is being published the week of April 29, 2013, in the online Early Edition of the Proceedings of the National Academy of Science, sheds light on proteins called DEAD-box proteins, a provocative title actually derived from their amino acid sequence. These proteins regulate all aspects of gene expression and RNA metabolism, particularly in the production of ribosomes, and are involved in cell metabolism. The link between defects in ribosome assembly and cancer and between DEAD-box proteins and cancer is well documented.

The findings show that the DEAD-box protein Rok1, needed in the production of a small ribosomal subunit, recognizes the RNA backbone, the basic structural framework of nucleic acids. The co-factor Rrp5 then gives Rok1 the ability to target a specific RNA sequence by modulating the structure of Rok1.

“Despite extensive efforts, the roles of these DEAD-box proteins in the assembly of the two ribosomal subunits remain largely unknown,” Karbstein said. “Our study suggests that the solution may be to identify their cofactors first.”

The first author of the study, “Cofactor-Dependent Specificity of a DEAD-box Protein,” is Crystal L. Young. Also a co-author of the paper is Sohail Khoshnevis.

The study was supported by National Institutes of Health Grant R01-GM086451 and the American Heart Association.

About The Scripps Research Institute

The Scripps Research Institute (TSRI) is one of the world's largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs about 3,000 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including three Nobel laureates—work toward their next discoveries. The institute's graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. For more information, see www.scripps.edu.

# # #

For information:

Office of Communications 

Tel: 858-784-2666

Fax: 858-784-8136

press@scripps.edu

Controlled Evolution In A Test Tube Produces Artificial Enzymes

ORIGINAL: PopSci

By Clay Dillow

01.31.2013

Artificial Enzymes From Evolution This visual explainer should clarify the process. University of Minnesota / Peggy Rinard

Researchers at the University of Minnesota have just created an artificial enzyme in a test tube by following the rules of natural selection.

This artificial enzyme likely resembles what enzymes looked like billions of years ago, when life began evolving.

Enzymes created in laboratories typically follow principles of rational enzyme design, in which researchers develop a preconceived idea of what an enzyme should be, model it on a computer, and then influence its development to produce the molecule that they want.

By contrast, this new enzyme, developed by Burckhard Seelig’s lab at UM’s College of Biological Sciences, was developed in the same way enzymes evolve in nature. A large quantity of candidate proteins were placed together in culture and screened with every successive generation for their ability to perform a desired function (in this case, joining two pieces of RNA together). Unlike rational enzyme design, this approach isn’t limited by what the researchers know about enzyme structure. All the researchers really need to know is what they want from the enzyme. Evolution finds the best way to get there.

Enzymes are manipulated for use in all kinds of things, from manufacturing processes to fuel refinement to the development of new food products. Industry uses both natural and artificial enzymes for specific purposes, as they catalyze the chemical reactions that generate desired processes and products. Now, the ability to generate enzymes by evolutionary means could lead to whole new applications for tailored enzymes that aren’t achievable with rational enzyme design.

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[PhysOrg]

Genetically engineered bacterial enzyme to produce alternative fuel from CO2

ORIGINAL: EcoChunk

By Anupam Jolly

Converting ambient and environmentally destructive carbon dioxide into usable alternative fuels has often been referred to as the “holy grail” of energy. Researchers over the globe have been working on a possible way by which carbon dioxide can be captured from the atmosphere and somehow converted into alternative fuel such as methane and the most recent advancement has surfaced courtesy of biochemists at the Utah State University.

The biochemists here knew that molybdenum nitrogenases, bacterial enzymes used in nitrogen reduction, can effectively convert carbon monoxide into hydrocarbons, but cannot do the same stuff in converting carbon dioxide. Using this knowledge the team of biochemists genetically engineered molybdenum nitrogenase so that it can convert carbon dioxide into methane.

Though the research looks promising, the team humbly states that their process isn’t quite efficient in the conversion process. Till now they’ve only managed to convert a tiny amount of CO2 into methane and the process is very slow for commercial use. However, it definitely is a step in the right direction. The team is now being challenged to find out how the process actually works and then transferring the knowledge to create robust catalysts that can escalate the process and finally manage to produce something useful from carbon dioxide in the atmosphere.

Written by Anupam Jolly

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With a bachelor’s degree in Information Technology and over five years of experience in online content generation and distribution, Anupam Jolly has been creating and editing content spanning across a variety of domains. An avid environmentalist, Anupam Jolly believes that if humans can degrade the environment, they can save it from disaster too.