Emeryville, CA, United States
Emeryville, CA, United States

The Joint BioEnergy Institute is a research institute funded by the Department of Energy of the United States. It is led by the Lawrence Berkeley National Laboratory, and includes participation from the Sandia National Laboratory, Lawrence Livermore National Laboratory, as well as UC Berkeley, UC Davis and the Carnegie Institute. It is located in Emeryville, California.The goal of the Institute is to develop biofuels, bio-synthesized from cellulosic materials as an alternative to fossil fuels. Wikipedia.


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News Article | May 5, 2017
Site: www.rdmag.com

A recent discovery by Sandia National Laboratories researchers may unlock the potential of biofuel waste -- and ultimately make biofuels competitive with petroleum. Fuel made from plants is much more expensive than petroleum, but one way to decrease the cost would be to sell products made from lignin, the plant waste left over from biofuel production. Lignin typically is either burned to produce electricity or left unused in piles because no one has yet determined how to convert it into useful products, such as renewable plastics, fabrics, nylon and adhesives. The electricity isn't even available to the general public; it's only used by companies that create large amounts of lignin, like pulp and paper manufacturers. Now Sandia scientists, working with researchers from Lawrence Berkeley National Laboratory at the Joint BioEnergy Institute, have decoded the structure and behavior of LigM, an enzyme that breaks down molecules derived from lignin. The group's work on LigM appears in the latest issue of the Proceedings of the National Academy of Sciences. The enzyme has little in common with other, better understood proteins, which previously made it impossible for scientists to guess how it functions. This paper marks the first time anyone has solved the structure of LigM, opening a path toward new molecules and new, marketable products. For decades, scientists have wrestled with the problem of breaking down lignin, the part of plant cell walls that provides structure and protection from bacterial and insect attacks. This strength also makes lignin difficult to deconstruct, though there have been recent breakthroughs. The plant matter used to produce ethanol can be chemically or physically pre-treated so that the lignin is deconstructed in the process. However, these methods can be expensive and reduce the amount of biofuel that can be harvested. They could also interfere with later-stage lignin harvesting. That's why some researchers are focused on finding enzymes that convert lignin naturally and gently. Sandia scientist and lead author Amanda Kohler said her team knew enzymes could metabolize lignin and its derivatives because there are decades-old records of bacteria using enzymes for this purpose. Sphingonomas bacteria was discovered living in the waste water of a pulp mill more than 30 years ago. Once researchers realized the bacterium's unique enzymatic pathways enabled it to live on lignin, their challenge was then to understand the enzymes in these pathways so they could mimic what nature had already done, and use that understanding productively. Kohler and her team focused on LigM, an enzyme used by Sphingomonas, because it performs a key step in the conversion of lignin derivatives and it is the simplest of the known enzyme systems that perform this function. "When trying to mimic natural systems in a laboratory setting, the simplest, most direct systems are the best," Kohler explained. The team found that half of LigM's structure is composed of a common protein architecture found in all forms of life, from bacteria to humans. The rest of the enzyme -- the active portion -- is not found in any other known protein structure. This unique structure gives LigM the ability to bind specifically to molecules derived from lignin. "Solving the structure allows us to understand how the organism may have evolved its unique function, which I think is scientifically one of the most interesting findings," said paper co-author and Sandia scientist Ken Sale. The team used the Advanced Light Source Synchrotron at Lawrence Berkeley National Laboratories, along with high-performance computing and fundamental biochemistry to gain their insights into LigM. LigM is designed to break down lignin derivatives, not lignin itself. It is important to understand that LigM's function is only one key step in a longer pathway of reactions needed to fully deconstruct lignin. One active area of research involves finding other organisms, possibly fungi, that can execute the first step of breaking down large lignin mass into smaller fragments. Some of the Sandia scientists who solved LigM's structure, Sale and Matthew Mills, have recently learned more about another enzyme that helps drive the breakdown of lignin into smaller fragments. LigM works on a later stage in the process, when smaller lignin fragments already have been converted into a molecule called vanillic acid. "There is still work to be done to figure out the whole reaction pathway," Kohler says. "But now we have a much-needed understanding of a key step in this process, and are developing enzymes to fit our end goals of lowering the cost of biofuels by making products from lignin."


EMERYVILLE, Calif. -- A recent discovery by Sandia National Laboratories researchers may unlock the potential of biofuel waste -- and ultimately make biofuels competitive with petroleum. Fuel made from plants is much more expensive than petroleum, but one way to decrease the cost would be to sell products made from lignin, the plant waste left over from biofuel production. Lignin typically is either burned to produce electricity or left unused in piles because no one has yet determined how to convert it into useful products, such as renewable plastics, fabrics, nylon and adhesives. The electricity isn't even available to the general public; it's only used by companies that create large amounts of lignin, like pulp and paper manufacturers. Now Sandia scientists, working with researchers from Lawrence Berkeley National Laboratory at the Joint BioEnergy Institute, have decoded the structure and behavior of LigM, an enzyme that breaks down molecules derived from lignin. The group's work on LigM appears in the latest issue of the Proceedings of the National Academy of Sciences. The enzyme has little in common with other, better understood proteins, which previously made it impossible for scientists to guess how it functions. This paper marks the first time anyone has solved the structure of LigM, opening a path toward new molecules and new, marketable products. For decades, scientists have wrestled with the problem of breaking down lignin, the part of plant cell walls that provides structure and protection from bacterial and insect attacks. This strength also makes lignin difficult to deconstruct, though there have been recent breakthroughs. The plant matter used to produce ethanol can be chemically or physically pre-treated so that the lignin is deconstructed in the process. However, these methods can be expensive and reduce the amount of biofuel that can be harvested. They could also interfere with later-stage lignin harvesting. That's why some researchers are focused on finding enzymes that convert lignin naturally and gently. Sandia scientist and lead author Amanda Kohler said her team knew enzymes could metabolize lignin and its derivatives because there are decades-old records of bacteria using enzymes for this purpose. Sphingonomas bacteria was discovered living in the waste water of a pulp mill more than 30 years ago. Once researchers realized the bacterium's unique enzymatic pathways enabled it to live on lignin, their challenge was then to understand the enzymes in these pathways so they could mimic what nature had already done, and use that understanding productively. Kohler and her team focused on LigM, an enzyme used by Sphingomonas, because it performs a key step in the conversion of lignin derivatives and it is the simplest of the known enzyme systems that perform this function. "When trying to mimic natural systems in a laboratory setting, the simplest, most direct systems are the best," Kohler explained. The team found that half of LigM's structure is composed of a common protein architecture found in all forms of life, from bacteria to humans. The rest of the enzyme -- the active portion -- is not found in any other known protein structure. This unique structure gives LigM the ability to bind specifically to molecules derived from lignin. "Solving the structure allows us to understand how the organism may have evolved its unique function, which I think is scientifically one of the most interesting findings," said paper co-author and Sandia scientist Ken Sale. The team used the Advanced Light Source Synchrotron at Lawrence Berkeley National Laboratories, along with high-performance computing and fundamental biochemistry to gain their insights into LigM. LigM is designed to break down lignin derivatives, not lignin itself. It is important to understand that LigM's function is only one key step in a longer pathway of reactions needed to fully deconstruct lignin. One active area of research involves finding other organisms, possibly fungi, that can execute the first step of breaking down large lignin mass into smaller fragments. Some of the Sandia scientists who solved LigM's structure, Sale and Matthew Mills, have recently learned more about another enzyme that helps drive the breakdown of lignin into smaller fragments. LigM works on a later stage in the process, when smaller lignin fragments already have been converted into a molecule called vanillic acid. "There is still work to be done to figure out the whole reaction pathway," Kohler says. "But now we have a much-needed understanding of a key step in this process, and are developing enzymes to fit our end goals of lowering the cost of biofuels by making products from lignin."


News Article | May 5, 2017
Site: www.rdmag.com

A recent discovery by Sandia National Laboratories researchers may unlock the potential of biofuel waste -- and ultimately make biofuels competitive with petroleum. Fuel made from plants is much more expensive than petroleum, but one way to decrease the cost would be to sell products made from lignin, the plant waste left over from biofuel production. Lignin typically is either burned to produce electricity or left unused in piles because no one has yet determined how to convert it into useful products, such as renewable plastics, fabrics, nylon and adhesives. The electricity isn't even available to the general public; it's only used by companies that create large amounts of lignin, like pulp and paper manufacturers. Now Sandia scientists, working with researchers from Lawrence Berkeley National Laboratory at the Joint BioEnergy Institute, have decoded the structure and behavior of LigM, an enzyme that breaks down molecules derived from lignin. The group's work on LigM appears in the latest issue of the Proceedings of the National Academy of Sciences. The enzyme has little in common with other, better understood proteins, which previously made it impossible for scientists to guess how it functions. This paper marks the first time anyone has solved the structure of LigM, opening a path toward new molecules and new, marketable products. For decades, scientists have wrestled with the problem of breaking down lignin, the part of plant cell walls that provides structure and protection from bacterial and insect attacks. This strength also makes lignin difficult to deconstruct, though there have been recent breakthroughs. The plant matter used to produce ethanol can be chemically or physically pre-treated so that the lignin is deconstructed in the process. However, these methods can be expensive and reduce the amount of biofuel that can be harvested. They could also interfere with later-stage lignin harvesting. That's why some researchers are focused on finding enzymes that convert lignin naturally and gently. Sandia scientist and lead author Amanda Kohler said her team knew enzymes could metabolize lignin and its derivatives because there are decades-old records of bacteria using enzymes for this purpose. Sphingonomas bacteria was discovered living in the waste water of a pulp mill more than 30 years ago. Once researchers realized the bacterium's unique enzymatic pathways enabled it to live on lignin, their challenge was then to understand the enzymes in these pathways so they could mimic what nature had already done, and use that understanding productively. Kohler and her team focused on LigM, an enzyme used by Sphingomonas, because it performs a key step in the conversion of lignin derivatives and it is the simplest of the known enzyme systems that perform this function. "When trying to mimic natural systems in a laboratory setting, the simplest, most direct systems are the best," Kohler explained. The team found that half of LigM's structure is composed of a common protein architecture found in all forms of life, from bacteria to humans. The rest of the enzyme -- the active portion -- is not found in any other known protein structure. This unique structure gives LigM the ability to bind specifically to molecules derived from lignin. "Solving the structure allows us to understand how the organism may have evolved its unique function, which I think is scientifically one of the most interesting findings," said paper co-author and Sandia scientist Ken Sale. The team used the Advanced Light Source Synchrotron at Lawrence Berkeley National Laboratories, along with high-performance computing and fundamental biochemistry to gain their insights into LigM. LigM is designed to break down lignin derivatives, not lignin itself. It is important to understand that LigM's function is only one key step in a longer pathway of reactions needed to fully deconstruct lignin. One active area of research involves finding other organisms, possibly fungi, that can execute the first step of breaking down large lignin mass into smaller fragments. Some of the Sandia scientists who solved LigM's structure, Sale and Matthew Mills, have recently learned more about another enzyme that helps drive the breakdown of lignin into smaller fragments. LigM works on a later stage in the process, when smaller lignin fragments already have been converted into a molecule called vanillic acid. "There is still work to be done to figure out the whole reaction pathway," Kohler says. "But now we have a much-needed understanding of a key step in this process, and are developing enzymes to fit our end goals of lowering the cost of biofuels by making products from lignin."


Ronald P.C.,University of California at Davis | Ronald P.C.,Joint BioEnergy Institute
PLoS Biology | Year: 2014

Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability. © 2014 Pamela C.


Grant
Agency: GTR | Branch: EPSRC | Program: | Phase: Research Grant | Award Amount: 2.52M | Year: 2013

We currently make more than just fuel from petroleum refining. Many of the plastics, solvents and other products that are used in everyday life are derived from these non-renewable resources. Our research programme aims to replace many of the common materials used as plastics with alternatives created from plants. This will enable us to tie together the UKs desire to move to non-petroleum fuel sources (e.g. biofuels) with our ability to produce renewable polymers and related products. Plant cell walls are made up of two main components: carbohydrate polymers (long chains of sugars) and lignin, which is the glue holding plants together. We will first develop methods of separating these two components using sustainable solvents called ionic liquids. Ionic liquids are salts which are liquids at room temperature, enabling a variety of chemical transformations to be carried out under consitions not normally available to traditional organic solvents. These ionic liquids also reduce pollution as they have no vapours and can be made from non-toxic, non-petroleum based resources. We will take the isolated carbohydrate polymers and break them down into simple sugars using enzymes and then further convert those sugars into building blocks for plastics using a variety of novel catalytic materials specifically designed for this process. The lignin stream will also be broken down and rebuilt into new plastics that can replace common materials. All of these renewable polymers will be used in a wide range of consumer products, including packaging materials, plastic containers and construction materials. The chemical feedstocks that we are creating will be flexible (used for chemical, material and fuel synthesis), safe (these feedstocks are predominantly non-toxic) and sustainable (most of the developed products are biodegradable). This will help reduce the overall environmental impact of the material economy in the UK. The chemistry that we will use focusses on creating highly energy efficient and low-cost ways of making these materials without producing large amounts of waste. We are committed to only developing future manufacturing routes that are benign to the environment in which we all live. In addition, natural material sources often have properties that are superior to those created using artificial means. We plan to exploit these advantages of natural resources in order to produce both replacements for current products and new products with improved performance. This will make our synthetic routes both environmentally responsible and economically advantageous. The UK has an opportunity to take an international lead in this area due to the accumulation of expertise within this country. The overall goal of this project is to develop sustainable manufacturing routes that will stimulate new UK businesses and environmentally responsible means of making common, high value materials. We will bring together scientific experts in designing processes, manufacturing plastics, growing raw biomass resources and developing new chemistries. The flexibility of resources is vital to the success of this endeavour, as no single plant biomass can be used for manufacturing on a year-round basis. Together with experienced leaders of responsible manufacturing industries, we will develop new ways of making everyday materials in a sustainable and economically beneficial way. The result of this research will be a fundamental philosophical shift to our material, chemical, and energy economy. The technologies proposed in this work will help break our dependence on rapidly depleting fossil resources and enable us to become both sustainable and self-sufficient. This will result in greater security, less pollution, and a much more reliable and responsible UK economy.


Keasling J.D.,University of California at Berkeley | Keasling J.D.,Lawrence Berkeley National Laboratory | Keasling J.D.,Joint BioEnergy Institute
Metabolic Engineering | Year: 2012

Synthetic biology can significantly advance metabolic engineering by contributing tools (minimal hosts, vectors, genetic controllers, characterized enzymes). The development of these tools significantly reduced the costs and time to develop the antimalarial drug artemisinin, but the availability of more tools could have reduced these costs substantially. © 2012 .


Mukhopadhyay A.,Joint BioEnergy Institute | Mukhopadhyay A.,Lawrence Berkeley National Laboratory
Trends in Microbiology | Year: 2015

During microbial production of solvent-like compounds, such as advanced biofuels and bulk chemicals, accumulation of the final product can negatively impact the cultivation of the host microbe and limit the production levels. Consequently, improving solvent tolerance is becoming an essential aspect of engineering microbial production strains. Mechanisms ranging from chaperones to transcriptional factors have been used to obtain solvent-tolerant strains. However, alleviating growth inhibition does not invariably result in increased production. Transporters specifically have emerged as a powerful category of proteins that bestow tolerance and often improve production but are difficult targets for cellular expression. Here we review strain engineering, primarily as it pertains to bacterial solvent tolerance, and the benefits and challenges associated with the expression of membrane-localized transporters in improving solvent tolerance and production. © 2015 Elsevier Ltd.


Rosengarten R.D.,Joint BioEnergy Institute | Nicotra M.L.,University of Pittsburgh
Current Biology | Year: 2011

Nearly all colonial marine invertebrates are capable of allorecognition - the ability to distinguish between self and genetically distinct members of the same species. When two or more colonies grow into contact, they either reject each other and compete for the contested space or fuse and form a single, chimeric colony. The specificity of this response is conferred by genetic systems that restrict fusion to self and close kin. Two selective pressures, intraspecific spatial competition between whole colonies and competition between stem cells for access to the germline in fused chimeras, are thought to drive the evolution of extensive polymorphism at invertebrate allorecognition loci. After decades of study, genes controlling allorecognition have been identified in two model systems, the protochordate Botryllus schlosseri and the cnidarian Hydractinia symbiolongicarpus. In both species, allorecognition specificity is determined by highly polymorphic cell-surface molecules, encoded by the fuhc and fester genes in Botryllus, and by the alr1 and alr2 genes in Hydractinia. Here we review allorecognition phenomena in both systems, summarizing recent molecular advances, comparing and contrasting the life history traits that shape the evolution of these distinct allorecognition systems, and highlighting questions that remain open in the field. © 2011 Elsevier Ltd All rights reserved.


Scheller H.V.,Joint BioEnergy Institute | Ulvskov P.,Copenhagen University
Annual Review of Plant Biology | Year: 2010

Hemicelluloses are polysaccharides in plant cell walls that have β-(1 → 4)-linked backbones with an equatorial configuration. Hemicelluloses include xyloglucans, xylans, mannans and glucomannans, and β-(1 → 3,1 → 4)-glucans. These types of hemicelluloses are present in the cell walls of all terrestrial plants, except for β-(1 → 3,1 → 4)-glucans, which are restricted to Poales and a few other groups. The detailed structure of the hemicelluloses and their abundance vary widely between different species and cell types. The most important biological role of hemicelluloses is their contribution to strengthening the cell wall by interaction with cellulose and, in some walls, with lignin. These features are discussed in relation to widely accepted models of the primary wall. Hemicelluloses are synthesized by glycosyltransferases located in the Golgi membranes. Many glycosyltransferases needed for biosynthesis of xyloglucans and mannans are known. In contrast, the biosynthesis of xylans and β-(1 → 3,1 → 4)-glucans remains very elusive, and recent studies have led to more questions than answers. Copyright © 2010 by Annual Reviews. All rights reserved.


Grant
Agency: GTR | Branch: BBSRC | Program: | Phase: Research Grant | Award Amount: 5.00K | Year: 2013

United States

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