Shortcuts to Custom Bio Production of Fuels and Chemicals

A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression.

Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism. _NatureCommunications

Nature Communications 3, Article number: 929 doi:10.1038/ncomms1928

UCSD researchers have taken an important step toward the ability to custom design the genome of organisms in order to produce synthetic fuels, chemicals, pharmaceuticals, and more, on a commercial scale.

"What you could hypothetically do with our model is simulate the total cost of producing a value-added product, such as a biofuel. That includes all the operating and maintenance costs," said Daniel Hyduke, a project scientist in Palsson's lab. Hyduke said the method has the potential to help streamline industrial metabolic engineering efforts by providing a near complete accounting of the minimal material and energy costs associated with novel strain designs for biofuel, commodity chemicals, and recombinant protein production.

Hyduke and Lerman prototyped the method on the minimal, yet metabolically versatile, hyperthermophile Thermotoga maritima. Because T. maritima is not currently ready for use in industrial applications, Hyduke and Lerman are working as part of a larger team to produce similar models for industrially relevant microorganisms, such as E. coli.

"We've built a virtual reality simulator of metabolism and gene expression for Thermotoga maritima, and shown that it much better approximates phenotypes of cells than modeling metabolism in isolation," said Lerman.

...Their method accounts, in molecular detail, for the material and energy required to keep a cell growing, the research team reported in the journal Nature Communications.

"This is a major advance in genome-scale analysis that accounts for the fundamental biological process of gene expression and notably expands the number of cellular phenotypes that we can compute," said Bernhard Palsson, Galetti Professor of Bioengineering, at the UC San Diego Jacobs School of Engineering.

"With this new method, it is now possible to perform computer simulations of systems-level molecular biology to formulate questions about fundamental life processes, the cellular impacts of genetic manipulation or to quantitatively analyze gene expression data," said Joshua Lerman, a Ph.D. candidate in Palsson's Systems Biology Research Group. _SD

This approach provides more useful information in advance, to researchers considering various approaches to the design of custom chemicals-producing organisms -- particularly microbes, but eventually plants and animals as well.

In summary, the development of this tool should streamline the design and development of organisms capable of producing commercially valuable chemicals and fuels in an economical manner. It should also prevent much wasted energy on the part of researchers, by pointing out dead-end research approaches in advance.

Synthetic Fuels from CO by Tweaking Molybdenum Nitrogenase

Nitrogenase enzymes allow living organisms to convert atmospheric N2 to organic nitrogen, for growth, development, and metabolism. But Utah State University researchers have discovered that by tweaking molybdenum nitrogenease -- substituting an alanine or glycine in place of the normal valine in a particular position -- the resulting enzyme can do a lot more than convert N2.

...when the nitrogenase MoFe protein α-70Val residue is substituted by alanine or glycine, the resulting variant proteins will catalyze the reduction and coupling of CO to form methane (CH4), ethane (C2H6), ethylene (C2H4), propene (C3H6), and propane (C3H8).

The rates and ratios of hydrocarbon production from CO can be adjusted by changing the flux of electrons through nitrogenase, by substitution of other amino acids located near FeMo-cofactor, or by changing the partial pressure of CO. Increasing the partial pressure of CO shifted the product ratio in favor of the longer chain alkanes and alkenes. _Journal of Biological Chemistry _ via _USU PDF

It is unlikely that the yields are particularly high at this point -- and organic enzymes may well prove too delicate for high volume industrial synthesis of fuels from syngas-derived CO. In that case, biomimetic nano-catalysts are likely to be crafted which can take over for the nitrogenase enzyme.

More from USU:

While studying bacterial enzymes, known as nitrogenases, used in nitrogen reduction, Utah State University biochemists Zhi-Yong Yang and Lance Seefeldt, along with colleague Dennis Dean of Virginia Tech, discovered a molybdenum nitrogenase capable of converting carbon monoxide into usable hydrocarbons. The reaction is similar, they say, to FT synthesis.

“This is pretty profound,” says Seefeldt, professor in USU’s Department of Chemistry and Biochemistry. “Understanding this process paves the way for developing better ways of converting carbon monoxide, a toxic waste product of combustion, into transportation fuel and precursors for plastics — without the time and energy required for conventional extraction of fossil fuels.”

The scientists’ findings appear in the article “Molybdenum Nitrogenase Catalyzes the Reduction and Coupling of CO to Form Hydrocarbons,” in the June 3, 2011 issue (and May 27 online issue) of Journal of Biological Chemistry. The paper was selected as “Paper of the Week” by the journal’s editorial board, an honor bestowed on the top one percent of more than 6,600 manuscripts reviewed annually by the publication’s editors. In the “Paper of the Week” feature, Yang, a doctoral candidate mentored by Seefeldt, is highlighted as an up-and-coming researcher. _USU

Of course if the researchers focused on creating better nitrogenases for converting atmospheric N2 to organic nitrogen, the revolutionary impact on human society would be just as great as discovering a breakthrough in synthetic fuels production.

It is likely that both breakthroughs will be made in time, built upon the crucial work being done at USU and other labs around the world. If so, better nitrogenases will contribute to abundant food AND abundant fuel.

H/T GreenCarCongress

Chromatin Demonstrates "Mini-Chromosome Gene Stacking" in Sugar Cane

Chromatin
Chromatin's mini-chromosome gene stacking technology promises to give bioenergy crop engineers the ability to optimise multiple desirable plant traits simultaneously.

Developers...want to insert genes that offer improvements in multiple traits – when an organism has more than one gene inserted in this process – for example, for disease resistance, insect resistance, herbicide resistance – this is called a gene stack. In 2007, for example, Monsanto and Dow introduced an eight-gene stack (SmartStax) that contained eight herbicide tolerance and insect-protection genes, including Dow’s Herculex I and Herculex RW; Monsanto’s YieldGard VT Rootworm/RR2 and YieldGard VT PRO, Roundup Ready and Liberty Link tolerance genes.

Gene stacking, thereby, is foundational in the drive for higher productivity from land crops.

You can stack in one of two ways. First, the traits are inserted, one each into one varietals. Then the varietals are cross-bred in the traditional manner so that they transfer the genes, eventually, into the target. That’s how Monsanto and Dow came up with SmartSTax.

The Chromatin process

The other way is to insert them all at one time into one varietal.
The company developed a proprietary gene stacking technology, which can be used to simultaneously, and precisely introduce multiple genes in any plant, bypassing the cross-breeding process.

... let’s say you wanted to introduce several genes, not just one – for example, insect resistance, herbicide resistance, disease resistance, higher sugar concentrations, and enzymes to enable better bagasse digestion. If you could do it at all in cane – and it would be a monumental, unprecedented achievement in cross-breeding, it would take, say 13 years or so to accomplish it. It has made changes at this level uneconomical.

So that’s what the Chromatin breakthrough is all about. Creating a method to bring the sort of possibilities that have materially advanced yields in, say, corn and soy, to a whole new array of energy and food crops. Opening up the door for more rapid improvement of the underlying per-acre yields.

...Cross breeding has been the platform technique for a 500 percent improvement in corn yields, over 100 years. That’s a long, long time, but it shows the kind of fundamental change possible. Without cross-breeding, the world would in all probability starved to death long ago – or rather, stalled in its industrial development as simply too many hands, and too much acreage, would have been needed on the farm.

Meanwhile, there are energy grasses, woods and aquatic species that have hardly been touched by cross-breeding or genetic improvement – and already in their wild state have had promising results in terms of productivity for biofuels. SG is just getting a leash on jatropha; companies like Sapphire Energy are just undertaking the first large-scale improvement programs for algae.

But doing so at the lowest possible cost, and the highest possible speed, is the surest road to the kinds of productivities that provide food, feed and fuel for all. This is an advance in science with game-changing characteristics across a host of energy crops. _BiofuelsDigest

Chromatin website

The technology as described sounds very exciting. Not having seen any of the research data, I cannot vouch for any of the claims. Genes require entire arrays of nuclear and cellular proteins for transcription and translation into structural proteins and enzymes. A highly intricate regulatory mechanism is involved in order to effectively utilise any gene -- artificial or natural. One cannot simply throw genes willy nilly into plant or animal cells and expect them to work as you wish.

On the other hand, if a research group were able to manipulate the mechanisms of gene expression in desired ways, so as to make best use of artificial "gene stack chromosomes," the possibilities would be enormous.

GCCGenetic engineering has always held the keys to a robust bioenergy response to possible fuel shortages. One of the companies best personifying the "can do" approach to advanced biofuels, is Chromatin, Inc. Chromatin specialises in the production of artificial "mini-chromosomes", or gene stacks, that are designed to be inserted into a plant's genetic apparatus, to harness the plant's natural dynamics for the purposes of making a higher yield of fuels. Chromatin aims to use this technology with sorghum -- a hardy plant capable of producing grain, sugar, or biomass.

...sorghum holds additional advantages as a preferred biomass source for sustainable bioenergy production the company points out:

It is capable of growing across a wide geographic area within the US, offering a broad opportunity as a multi-regional, locally-available dedicated energy crop;


Sorghum thrives on marginal lands, is water and nutrient efficient and provides a low overall environmental footprint; and


Sorghum does not directly compete as a domestic food resource.


Sorghum is ideally suited as the energy crop for the future. Sorghum is adapted to 80% of the world's agricultural land, is very drought tolerant, is extremely efficient on less than optimum soils, and has a very favorable carbon footprint compared to other major grain crops. By joining forces with Chromatin, we will speed the development and distribution of advanced sorghum bioenergy feedstocks worldwide, while continuing to support our existing customers. This is truly a step forward for sorghum.

—Larry McDowell, SPI’s President, and Chromatin's Director of Seed Operations

Chromatin will be further building and commercializing its sorghum product portfolio over the near term. Using a phased approach as a platform for improving sorghum over time, the company will use technologies such as compositional screening and analysis, marker assisted breeding and gene stacking to deploy proprietary feedstocks near term and ultimately to optimize sorghum for specific bioprocessors’ needs. _GCC

Other researchers will turn their genetic expertise to transforming sugar cane, tobacco, maize, and other plants to produce higher yields of fuels. Yet other researchers are hard at work producing high yield algae, cyanobacteria, and other microbes for biofuels, chemicals, and plastics. Even more researchers will turn to the transformation of bioenergy crops and microbes for arid and saltwater environments.

Watson and Crick started an avalanche of human ingenuity, back in the early 1950s. That is as it should be.

In fact, most of humanity's resources should be devoted toward promoting greater human ingenuity in solving problems -- rather than in promoting government graft and neo-fascist corporatist greed, as we see in Obama - Pelosi and other modern national governments far too often.

Microbes and Gene Engineering at the Heart of Future Fuels Production

Scientists are slowly learning to produce in hours and days what took nature millions of years to produce. Ancient deposits of fossil fuels have been useful in jump starting the industrial age of Earth, but eventually humans will need to learn how to make their own fuels on a "pay as you go" basis.

A recent publication in Springer's Journal of Industrial Microbiology & Biotechnology provides a review of microbial approaches to the production of new fuels, by Professor Arnold Demain.

Demain reviews how microbes can help solve the energy problem, and focuses on the organisms that ferment lignocellulosic biomass to produce bioethanol, biobutanol, biodiesel and biohydrocarbons in particular. His review also highlights how the use of these biofuels would help to reduce greenhouse gas emissions. The plants that produce the biomass remove carbon dioxide from the atmosphere as part of their growth and normal metabolism.

Demain also highlights a number of important commercial developments, including the establishment of biotechnology companies in the biofuel sector since 2006, either alone or with companies of the petroleum and chemical industries. In addition, there have been a number of U.S. Government initiatives pushing for and backing the development of biofuels.

Demain concludes that: "What remains is a major effort and challenge to biochemical engineering at the many new plants being built for biofuel production. The new processes have to be scaled up and carried out in cost-effective way. The future of biofuels looks very bright...the best is yet to come." _AtoZMaterials _ via _Biotechnology

In other publications, Demain has written:

Life on earth is not possible without microorganisms. Microbes have contributed to industrial science for over 100 years. They have given us diversity in enzymatic content and metabolic pathways. The advent of recombinant DNA brought many changes to industrial microbiology. New expression systems have been developed, biosynthetic pathways have been modified by metabolic engineering to give new metabolites, and directed evolution has provided enzymes with modified selectability, improved catalytic activity and stability. More and more genomes of industrial microorganisms are being sequenced giving valuable information about the genetic and enzymatic makeup of these valuable forms of life. _MolecularBiotechnology

and further:

In order for a natural product to become a commercial reality, laboratory improvement of its production process is a necessity since titers produced by wild strains could never compete with the power of synthetic chemistry. Strain improvement by mutagenesis has been a major success. It has mainly been carried out by ‘‘brute force’’ screening or selection, but modern genetic technologies have entered the scene in recent years. For every new strain developed genetically, there is further opportunity to raise titers by medium modifications. _JInd.MicrobiologyBiotech

Beyond using microbes such as algae, yeast, and bacteria, the possibilities of modifying the genomes of multicellular organisms such as plants and animals to produce fuels and useful chemicals / catalysts / pharmaceuticals are growing more realistic.

Despite a significant economic downturn plus a new US administration that aims to make the economy far worse than it is at present, universities continue to train new researchers who must do experiments and publish the results. The momentum of scientific discovery is immense -- despite the massive waste of resources being shunted to unscientific endeavours like catastrophic greenhouse warming.

New scientific discoveries contain the seeds of entire new industries and support structures, the building of which will pull a recalcitrant economy out of its doldrums. Obama, Pelosi, Boxer, Schumer and the other Luddites and Paleo-Socialists who currently hold unprecedented political power will try to keep the economy mired in their new Dark Ages of feudalist fascism. It is unlikely that the restless forces of human nature and evolution will allow them to take their repressive reich beyond a certain point.

Using Salt Water Irrigation to Grow Crops in Salty Soil: Expanding Cropland

Some species of Panicum grasses are quite tolerant to salt, and can be grown on salty soil to provide animal feed. Even more surprisingly, some strains of these species of Panicum can be irrigated with salt water, minimally fertilised, and grow healthy harvests!

The research team focused on a plant called Panicum turgidum that can grow in salty conditions. They measured its protein content and determined that it could be a suitable alternative to existing cattle feed.

Then they tested its growth potential when irrigated with the salty water found in the area. They showed that Panicum grew so fast it could be harvested almost monthly. Overall, with limited fertilizer, they produced 60,000 kilograms per hectare during the yearlong study. Nielsen is confident that further studies that determine the best ratios of fertilizer will boost that number over 100,000 kilograms.

The researchers also used nature to preserve a sustainable growing environment. Panicum is a "salt excluder," meaning it survives salty conditions by keeping salt out of its system, which most other plants can't do.

Although this allows Panicum to grow on salty water, the extra salt deposited by irrigation would render the soil too salty for even this hardy plant. So the researchers found that planting a companion crop that is a "salt accumulator" prevented the soil from getting too salty.

The other plant sucked up the extra salt, then was harvested and burned and the ashes turned into soap. After the yearlong study, the levels of salt in the soil were virtually unchanged. _SeedDaily

By growing large amounts of animal feed on salty soil not suitable for growing human foods, huge areas of arable cropland can be freed up for food and/or cash crops -- rather than devoting much of it to growing maize for animals.

Of course salt-tolerant plants can also be used as biomass for pyrolysis, gasification, torrefaction, etc.

The most fascinating breakthroughs will occur when the genes that allow salt tolerance, salt-rejection, and salt-concentration, can be selectively inserted (along with any necessary helper genes and epigenetic apparatus) into plants or microbes of one's choosing.

Department of Energy Maps Soybean Genome

The US DOE Joint Genome Institute has completed mapping the soybean genome. Soybeans account for 70% of Earth's edible protein, and a significant amount of biodiesel production. Soy is a nitrogen-fixing legume that grows in many different climatic regions.

DOE JGI’s interest in sequencing the soybean centers on its use for biodiesel, a renewable, alternative fuel with the highest energy content of any alternative fuel. According to 2007 U.S. Census data, soybean is estimated to be responsible for more than 80 percent of biodiesel production.

...“The soybean genome sequence will be a valuable resource for the basic researcher and soybean breeder alike,” said Jim Collins, Assistant Director for the Biology Directorate at the NSF. _Checkbiotech

Plant breeders hope to be able to optimise soybeans to various types of soils and climates, as well as to modify its production for higher yields of desired products -- such as oils or proteins.

The genetic modification of food and energy crops is still at an early stage. The next stage would be taking specific gene sets or stacks from one plant and transferring them to another plant -- to achieve synergistic growth and yield characteristics from the combination.

Gene Stacks Instead of Smoke Stacks

Chicago based Chromatin -- an agricultural genetics company -- is raising funds to develop radical new energy crops through extreme genetic modification. Chromatin's genetic methods utilise a "mini-chromosome" technique that introduces multiple genes into a plant simultaneously. Such "gene stack" technology allows for a more radical transformation of the plant genome and characteristics.

Chromatin, which gets its name from the substance in the nucleus of a cell that condenses to form chromosomes during cell division, initially developed its “mini-chromosome” technology to enable quick improvement of crops and feedstocks for the agriculture industry. With this fresh round of funding, Chromatin said it plans to team up with companies in the biofuel industry to provide distribution channels for its genetic products, but has yet to name any potential partners for the move.

The company was founded in 2000 based on technology developed at the University of Chicago. Chromatin said its mini-chromosome technology makes it possible to introduce multiple genes, or gene stacks, simultaneously into any plant cell, with applications in crops such as corn and soybeans. The company plans to develop feedstocks with the gene stacks needed to boost yields and cut the costs of producing fermentable sugars for the burgeoning cellulosic ethanol industry.

Chromatin hasn’t said which properties it’s looking to enhance in biofuel feedstocks, but for its agricultural products the company said its technology could lead to crops with properties such as resistance to disease, greater salt and drought tolerance, and more nutritional value. The company also said its mini-chromosome process could cut the time it takes to to get those new crop traits to market by half and increase crop yields by 25 percent. _Bioenergy

Chromatin is working with Monsanto to achieve many of its biofuel crop goals.

It is easy to see that by increasing salt and drought tolerance, the amount of viable land available worldwide could easily be multiplied by an order of magnitude -- thus destroying the worth of the calculations of many biofuels naysayers.

Another genetic transformation that would have an extreme impact on the future of biofuels, is the ability to induce nitrogen fixation capability in plants -- doing away with the need to add nitrogenous fertilisers.

Biotech, Nanotech, Artificial Intelligence, Advanced Robotics, Advanced Communications and Networking . . . The convergence of these technologies will transform life as we know it, and do away with many of the limitations human societies currently chafe under.

Unfortunately, humans themselves have not changed since the days of hunter gatherer tribal warfare for resources. A psychology based upon scarcity. It is not certain that human psychology is capable of changing, on the whole.

Genetic Engineering of Oil Seed Species

The genomes of the Palm Oil and Jatropha Curcus are under intense scrutiny by researchers, who want to tweak their genomes just enough to make farm grown biofuels the next big thing.

The Asiatic Centre for Genome Technology Sdn Bhd (ACGT) and Synthetic Genomics Inc. (SGI) [ed:Craig Venter's company] have completed a first draft assembly and annotation of the oil palm genome....The organizations also announced that they have made progress in sequencing and analyzing the jatropha genome.

The oil palm and jatropha genome projects represent the first stages of research undertaken through a joint venture between SGI and ACGT which was announced in 2007 and is aimed at developing more high-yielding and disease-resistant plant feedstocks.

...The draft oil palm genome is already yielding important information including unique genetic variations linked to traits that differ in the two races. One example of this pertains to kernel shell thickness which differs between the two. Since fruits with thinner kernel shells yield more oil, the groups are seeking to understand the genetic basis for shell thickness. These molecular markers and others can be used in breeding and tissue-culture based approaches to address plant yield, oil quality, growth and height and other important properties, including fertilizer requirements and stress and disease tolerance.

...The Asiatic Group has 66,000 hectares of land in Malaysia and is developing 98,300 hectares in Indonesia on a joint venture basis. The Group owns 5 oil mills with a total milling capacity of 235 tonnes per hour and is reputed to be one of the lowest cost palm oil producers with fresh fruit bunches production of over one million tonnes. Asiatic is one of the early members of the Roundtable on Sustainable Palm Oil (RSPO).

Synthetic Genomics Inc. is focusing on genomic-driven solutions to address global energy and environmental challenges. The company’s main research and business programs are focused on major bioenergy areas: designing advanced biofuels with superior properties compared to ethanol and biodiesel; harnessing photosynthetic organisms to produce value added products directly from sunlight and carbon dioxide; developing new biological solutions to increase production and/or recovery rates of subsurface hydrocarbons and developing high-yielding, more disease resistant and economic feedstocks. __GCC

For now, these two species require a tropical or semi-tropical growing environment, which limits the growing regions mainly to countries of the third world. If these countries are able to develop these and similar warm weather cash crops before Venter's crew hits the jackpot, we may see some emerging billionaires from the third world.

Both the Palm Oil and the Jatropha Curcus oil seed species offer relatively high yield bio-oil production. But both suffer from significant weaknesses that limit their ability to make a more significant contribution to world biodiesel production. Genetically engineering the oil seed trees and shrubs to provide higher yield, in more locations, with less costly cultivation, would push them into the forefront of biofuels.

Reducing Petroleum Demand: Synthetic Biology and Bio-Plastics

Craig Venter claims that his synthetic biology venture may produce an artificial bio-energy factory as early as the next few years. The overall field of synthetic biology is certainly capable of attracting top talent and financing.

Researchers will gather in London this week to outline plans to promote one of the most audacious, and controversial, scientific ideas of the 21st century - synthetic biology.

The new discipline, established by scientists such as human genome pioneer Craig Venter, involves stripping microbes down to their basic genetic constituents so they can be reassembled and manipulated to create new life forms. These organisms can then be exploited to manufacture drugs and fuels or to act as bio-sensors inside the body.

...The crucial point, said Holliger, who will be speaking at this week's conference, Engineering Life, is that 'scientists are now learning how to design life down to the last letter. We don't know enough to be sophisticated as yet but our knowledge is increasing all the time.'

Most scientists working on synthetic biology projects - including Holliger - say that their research is safe and stress its potential benefits. 'Synthetic biology represents a new approach to engineering,' said Professor Richard Kitney of Imperial College London, another speaker at the meeting, which will debate the risks and ethics of synthetic biology. 'It has brought us to the cusp of a new industrial revolution in which new fuels, drugs, medical treatments and sensors can be created from biological materials.'

One idea is the creation of organisms that could soak up carbon dioxide from the atmosphere and turn it into hydrocarbon biofuels. __Source

Yep. Of course, once you tame the little beasties, you can pretty much get them to make anything you want. ;-)

The bio-plastics industry provides another way to reduce demand for petroleum--the primary feedstock for plastics.

Bioplastics are biodegradable and can be made from a wide range of different plants. In the future genetically modified plants will need less water and reduce the costs. Bioplastics has the potential to reduce the petroleum consumption for plastic by 15 to 20 percent in 2025. Improved technical properties and innovations open new markets and applications with higher profit potentials in automotive, medicine and electronics. ___Source

Biology provides many approaches to reducing demand for petroleum--thus easing some of the pressures on worldwide petroleum prices and food prices. Biomass CHP, cellulosic electricity, cellulosic alcohol fuels, biomass to liquid fuels (BTL), bio-oils, bio-diesel, and waste to energy, among many approaches currently being explored.

An enlightened society would welcome all these approaches to reducing food and fuel costs, rather than scapegoating the entire bio-energy industry.