This page has been archived and is no longer updated
Genomics of cellulosic biofuels.
Author: E. M. Rubin
Keywords
Keywords for this Article
Add keywords to your Content
Save
|
Cancel
Share
|
Cancel
Revoke
|
Cancel
Rate & Certify
Rate Me...
Rate Me
!
Comment
Save
|
Cancel
Flag Inappropriate
The Content is
Objectionable
Explicit
Offensive
Inaccurate
Comment
Flag Content
|
Cancel
Delete Content
Reason
Delete
|
Cancel
Close
Full Screen
"REVIEWS Genomics of cellulosic biofuels Edward M. Rubin 1,2 The development of alternatives to fossil fuels as an energy source is an urgent global priority. Cellulosic biomass has the potentialtocontributetomeetingthedemandforliquidfuel,butland-userequirementsandprocessinefficienciesrepresent hurdles for large-scale deployment of biomass-to-biofuel technologies. Genomic information gathered from across the biosphere, including potential energy crops and microorganisms able to break down biomass, will be vital for improving the prospects of significant cellulosic biofuel production. T he capture of solar energy through photosynthesis is a pro- cessthatenablesthestorageofenergyintheformofcellwall polymers (that is, cellulose, hemicellulose and lignin). The energy stored in these polymers can be accessed in a variety of ways, ranging from simple burning to complex bioconversion processes. The high energy content and portability of biologically derived fuels, and their significant compatibility with existing pet- roleum-based transportation infrastructure, helps to explain their attractiveness as a fuel source. Despite the increasing use of biofuels such as biodiesel and sugar- or starch-based ethanol, evidence sug- gests that transportation fuels based on lignocellulosic biomass rep- resent the most scalable alternative fuel source 1 . Lignocellulosic biomass in the form of plant materials (for example, grasses, wood and crop residues) offers the possibility of a renewable, geograph- ically distributed and relatively greenhouse-gas-favourable source of sugars that can be converted to ethanol and other liquid fuels. Calculations of the productivity of lignocellulosic feedstocks, in part basedontheirabilitytogrowonmarginalagriculturalland,indicates that they can probably have a large impact on transportation needs without significantly compromising the land needed for food crop production 2 . Lignocellulosic biofuel production involves collection of biomass, deconstruction of cell wall polymers into component sugars (pre- treatment and saccharification), and conversion of the sugars to biofuels (fermentation) (Fig. 1). Partially because of the historically low demand for biologically based transportation fuels, each step in this process is in the early stages of optimization for efficiency and throughput. Thecrops from which biomassiscurrently derived have not been domesticated for this particular purpose and the present methods for saccharification and fermentation are inefficient and expensive. However, the recent and pressing desire to develop alter- natives to fossil fuels has made the rapid improvement of biofuel production a high priority, in which biologically derived energy (?bioenergy?)-relevant genomic insights and resources will have an important role (Table 1). Biomass From the perspective of transportation fuels, plants can be viewed as solarenergycollectorsandthermochemicalenergystoragesystems.It is the storage of energy in a form that can later be accessed via thermochemical or enzymatic conversion that distinguishes biomass from other renewable energy sources. Cellulosic biomass, sometimes referred to as lignocellulosic biomass, is an abundant renewable resource that can be used for the production of alternative trans- portation fuels 3 . The three main components of lignocellulose are cellulose, hemicellulose and lignin (Fig. 2), with the relative propor- tions of the three dependent on the material source 4 . Cellulose, the main structural component of plant cell walls, is a long chain of glucose molecules, linked to one another primarily by glycosidic bonds 5 . Hemicellulose, the second most abundant constituent of lignocellulosic biomass, is not a chemically well defined compound but rather a family of polysaccharides, composed of different 5- and 6-carbon monosaccharide units, that links cellulose fibres into microfibrils and cross-links with lignin, creating a complex network of bonds that provide structural strength 5 . Finally lignin, a three- dimensional polymer of phenylpropanoid units, can be considered asthecellularglueprovidingtheplanttissueandtheindividualfibres withcompressivestrengthandthecellwallwithstiffness 6 ,inaddition to providing resistance to insects and pathogens. 1 DOEJointGenomeInstitute,2800MitchellDrive,WalnutCreek,California94598,USA. 2 LawrenceBerkeleyNationalLaboratory,1CyclotronRoad,Berkeley,California94720,USA. Solar energy Feedstock Sugars Biofuels Fuel-producing microorganisms Physical pre-treatment, chemicals and enzymes Figure 1 | Biology of bioconversion of solar energy into biofuels. Solar energy is collected by plants via photosynthesis and stored as lignocellulose. Decomposition of thecellulosicmaterialintosimple5- and 6-carbon sugars is achieved by physical and chemical pre- treatment, followed by exposure to enzymes from biomass-degrading organisms. The simple sugars can be subsequently converted into fuels by microorganisms. Vol 454j14 August 2008jdoi:10.1038/nature07190 841 �2008 Macmillan Publishers Limited. All rights reserved As we can retrospectively view the features that made certain wild plants desirable for domestication thousands of years ago to become today?s food crops, we are now prospectively defining criteria to choose plants with potential to serve as dedicated bioenergy crops in the future. These include cell wall composition, growth rate, suit- ability forgrowthindifferent geographicalregions, andresource-use efficiencies. With these features in mind, a list of potential bioenergy crops is being developed and targeted for different growing condi- tions 7 . Most plants assimilate their CO 2 first into a C 3 compound, whereas a smaller subset use a C 4 compound. Plants using C 4 pho- tosynthesis tend to be among the most productive, having higher maximum efficienciesoflight,nitrogenandwateruseinassimilating carbon. The C 4 group of potential energy crops includes various perennial grasses such as switchgrass and Miscanthus. These grasses havetheadvantagesofnotrequiringreplanting afterayearlyharvest, rapid growth, high biomass density per unit area, and low nutrient and water needs, enabling growth on marginal agricultural land. Disadvantages are that C 4 plants are rare in cold climates and unable to grow at temperatures below 10uC. In these environments, trees, which exclusively depend on C 3 photosynthesis, provide the only candidate species. The C 3 group of potential energy crops includes trees, such as poplar and eucalyptus, which have relatively rapid growth potential in difficult-to-plough environments. It is highly likely that multiple different energy feedstocks will be deployed depending on latitude, geography, water availability and landowner acceptance. Until recently, minimal effort has been directed towards optim- izing potential energy crops for the generation of transportation fuels. This is in stark contrast to the agronomic development of food crops, which have been domesticated for thousands of years to max- imize productivity. Teosinte, the wild precursor to modern maize, was first recognized by Native Americans more than 5,000years ago as a potential food crop. The domestication of teosinte resulted in its conversion from a wild plant, the characteristics of which had been orchestrated by natural selection maximizing survival and reproduc- tion,intoaplantwhose morphology andphysiology hadbeenexten- sivelyalteredbyartificialselectiontoincreaseitsnutritionalyieldand ease of harvest 8 . More recently, selective breeding as well as agro- nomic advances have resulted in improvement over several orders of magnitude in the nutritional value per acre of modern maize Table 1 | Bioenergy genomes Organism Genome size (megabases) Status Reference Feedstocks and feedstock models Populus trichocarpa (poplar) 480 Complete Ref. 9 Chlamydomonas reinhardtii 120 Complete Ref. 34 Glycine max (soya bean) 1,200 Draft ? Manihot esculenta (cassava) 770 In progress ? Sorghum bicolor 760 In progress ? Eucalyptus globulus 600 In progress ? Brachypodium distachyon 355 In progress ? Zea mays (maize) 2,500 In progress ? Elaeis guineensis (oil palm) ,3,400 In progress http://www.checkbiotech.org/green_News_Biofuels.aspx?infoId515100 Panicum virgatum (switchgrass) ,5,600 In progress ? Setaria italica (foxtail millet) ,515 In progress ? Biomass degraders Acidothermus cellulolyticus 11B 2.4 Complete ? Bacillus pumilis SAFR-032 3.7 Complete Ref. 35 Caldicellulosiruptor saccharolyticus DSM 8903 3.0 Complete ? Clostridium phytofermentans ISDg 4.8 Complete ? Clostridium thermocellum ATCC 27405 3.8 Complete ? Cytophaga hutchinsonii ATCC 33406 4.4 Complete ? Flavobacterium johnsoniae UW101 6.1 Complete ? Rubrobacter xylanophilus DSM9941 3.2 Complete ? Saccharophagus degradans 5.1 Complete Ref. 36 Thermobifida fusca strain YX 3.6 Complete Ref. 37 Clostridium cellulolyticum H10 4.0 Draft ? Elusimicrobium minutum Pei191 1.6 Draft ? Nectria haematococca/Fusarium solani 51 Draft ? Phanerochaete chrysosporium 35.1 Draft ? Postia placenta 33 Draft ? Sagittula stellata E-37 5.3 Draft ? Trichoderma reesei/Hypocrea jecorina 33 Draft ? Cellulomonas flavigena DSM 20109 ,4.0 In progress ? Cellvibrio japonicus Ueda107 ,6.0 In progress ? Fibrobacter succinogenes subsp. succinogenes S85 ,3.8 In progress ? Ruminococcus albus 4.0 In progress ? Teredinibacter turnerae T7902 ,2 In progress ? Termite hindgut community NA Complete Ref. 23 Poplar biomass degrading community NA In progress http://www.jgi.doe.gov/sequencing/lspssseqplans2007.html Asian longhorned beetle (Anoplophora glabripennis) gut community NA In progress http://www.jgi.doe.gov/sequencing/DOEmicrobes2007.html Bovine rumen community transcriptome NA In progress http://www.energybiosciencesinstitute.org/ index.php?option5com_content&task5view&id5159&Itemid520 Fuel producers Clostridium acetobutylicum ATCC 824 4.0 Complete Ref. 38 Clostridium beijerinckii NCIMB 8052 6.0 Complete ? Pichia stipitis 15.4 Complete Ref. 27 Thermoanaerobacter tengcongensis MB42.7 Complete Ref. 39 Zymomonas mobilis subsp. mobilis ZM .1 Complete Ref. 40 Bacillus coagulans 36D12.9 Draft ? Thermoanaerobacter pseudethanolicus 39E 2.4 Draft ? Clostridium ljungdahlii ,4.0 In progress ? Bioenergy-relevantorganismsforwhichlarge-scalegenomeprojectshavebeencompletedorareunderwayarelisted.Informationongenomeprojectswithoutreferencescanbefoundathttp:// www.ncbi.nlm.nih.gov/sites/entrez?db5genomeprj. REVIEWS NATUREjVol 454j14 August 2008 842 �2008 Macmillan Publishers Limited. All rights reserved compared to that of teosinte. Some of the most rapid increases have occurred in the past 40years, both from advances in agronomic practices and, importantly, from the application of modern genetics. The optimization ofbioenergy crops as feedstocks for transportation fuelsisinitsinfancy, butalreadygenomicinformation andresources are being developed that will be essential for accelerating their domestication.Manyofthetraitstargetedforoptimizationinpoten- tial cellulosic energy crops are those that would improve growth on poor agricultural lands, to minimize competition with food crops over land use. Populus trichocarpa (poplar), the first tree and potential bioenergy crop to have its genome sequenced (Table 1) 9 , illustrates some of the issues and potential of applying genomics to the challenge of optim- izing energy crops. The traits for which the genetic underpinnings will be sought in the genomes of bioenergy-relevant plants, such as poplar,includethoseaffectinggrowthrates,response tocompetition for light, branching habit, stem thickness and cell wall chemistry. Significant effortwill gointomaximizing biomassyieldperunitland area, because this more than any other factor will minimize the impact on overall land use. One can imagine trees optimized to have short stature to increase light access and enable dense growth, large stem diameter, and reduced branch count to maximize energy den- sityfortransportandprocessing.Treeshaveevolvedwithhighlyrigid andstablecellwallsduetoheavyselectivepressureforlonglifeandan upright habit. Plants domesticated for energy production, with a crop cycle time of only a few years, would have less need for a rigid cell wall than wild plants with lifetimes of a hundred years or more. Alterations in the ratios and structures of the various macromole- cules forming the cell wall are a major target in energy crop domest- ication to facilitate post-harvest deconstruction at the cost of a less rigid plant. Already, by comparing several of the presently available plant gen- omes(poplar 9 ,rice 10,11 ,Arabidopsis 12 ;seeTable1)coupledwithlarge- scale plant gene function and expression studies, a number of can- didate genes for domestication traits have been identified 13,14 . These includemany genes involvedincelluloseandhemicellulose synthesis as well as those believed to influence various morphological growth characteristics such as height, branch number and stem thickness 15 . In addition to homology-based strategies, other genome-enabled strategies for identifying domestication candidate genes are being used. These include quantitative trait analysis of natural variation and genome-wide mutagenesis coupled with phenotypic screens for traits such as recalcitrance to sugar release, acid digestibility and general cell wall composition. The availability of high-through- put transgenesis in several plant systems 16 will facilitate functional studies to determine the in vivo activities of the large number of domesticationcandidategenes.Usingthesestrategies,genesaffecting features such as plant height, stem elongation and trunk radial growth, drought tolerance, and cell wall stability are but a few of thefeaturesthatarelikelytobeidentifiedastargetsfordomestication OH Macrofibril Plant cell Plant Cell wall Lignin Lignin Hemicellulose Pentose Crystalline cellulose Hydrogen bondCellodextrin n-3 n-3 n-3 n-3 n-3 Glucose Hexose 10?20 nm Macrofibril OH OH OH OH p-Coumaryl alcohol Coniferyl alcohol Sinapyl alcohol OH O HGS OO Figure 2 | Structure of lignocellulose. The main component of lignocellulose is cellulose, a b(1?4)-linked chain of glucose molecules. Hydrogen bonds between different layers of the polysaccharides contribute to the resistance of crystalline cellulose to degradation. Hemicellulose, the second most abundant component of lignocellulose, is composed of various 5- and 6-carbon sugars such as arabinose, galactose, glucose, mannose and xylose. Lignin is composed of three major phenolic components, namely p-coumarylalcohol(H),coniferylalcohol(G)andsinapylalcohol(S).Lignin is synthesized by polymerization of these componentsand their ratio within thepolymervariesbetweendifferentplants,woodtissuesandcellwalllayers. Cellulose, hemicellulose and lignin form structures called microfibrils, which are organizedinto macrofibrils that mediate structural stability in the plant cell wall. NATUREjVol 454j14 August 2008 REVIEWS 843 �2008 Macmillan Publishers Limited. All rights reserved in a fraction of the time required to carry out similar studies unaided by the plant genomes and genomic approaches 17 . Biomass degradation The breakdown of biomass involves the release of long-chain poly- saccharides, specifically cellulose and hemicellulose, and the sub- sequent hydrolysis of these polysaccharides into their component 5- and 6-carbon chain sugars. Early chemical processes for cellulose degradation depended heavily on acid treatments 5,18 , and even today industrial processes for biomass degradation involve heat and acidic conditions and tend to be expensive, slow and relatively inefficient 19 . Furthermore, some of these pre-treatments produce inhibitors (that is, furfural and 5-hydroxymethylfurfural) that decrease the overall yield of the fermentation process. The human need for efficient breakdown of lignocellulosic bio- mass for biofuel production is relatively new; however, a variety of organisms have evolved to take advantage of this nutrient source, including the free-living organisms and symbiotic animal?microbe consortia invariably present in biomass-rich environments. Increasing our knowledge of the biochemical machinery used by these organisms for the breakdown of biomass offers new avenues forthedevelopmentofbiologicallybasedprocessesthatcouldpoten- tially accomplish biomass conversion at an industrial scale. Just as plantgenomesareprovidinguswithnewapproachesforaccelerating feedstock domestication, genomics of biomass-degrading microbes and microbial consortia offer a new means to enzyme discovery. Microbial strategies for degrading lignocellulose are diverse, yet ourcurrentunderstandingoftheenzymesinvolvedintheseprocesses is limited to a handful of model organisms such as the fungus Trichoderma reesei and the bacterium Clostridium thermocellum 20 . Recent genome sequencing of these two biomass degraders, as well as a host of other cellulolytic species (Table 1), has expanded our repertoireofknownorpotentialcellulolyticenzymes.Theknowledge of biomass degradation pathways is soon to be increased even more by a number of large-scale genomic surveys under way of isolated organisms and microbial communities known to degrade biomass (Table 1). Considering the current dependence on acid and heat pre-treat- ment in the deconstruction of lignocellulose, it is clear that enzymes that are stable and active at low pH values and at high temperatures areofparticularvalue.Thus,enzymesderivedfromthermophilicand acidophilic organisms known to degrade lignocellulose, such as Caldicellulosiruptor saccharolyticus and Acidothermus cellulolyticus, hold significant promise for industrial processes 21 . However, the number of sequenced thermoacidophilic organisms is low, partly because of the significant obstacles in cultivating these organisms in the laboratory. Many novel enzymes and enzyme systems that have evolved to make use of cellulosic biomass are present in difficult-to-culture microbes 22 . This is particularly the case for the communities of microbes inhabiting the guts of lignocellulose-consuming insects and ruminants. Recently, in response to the challenge of studying difficult-to-culture organisms, metagenomic approaches have been developed to access the information encoded in their genomes (Table 1). This typically involves the high-throughput sequencing of DNA extracted directly from the mixtures of organisms present in an environment. The metagenomic analysis of a wood-feeding higher termite 23 has recently revealed hundreds of genes encoding carbohydrate-active enzymes,manyofwhichweresubsequentlyshowntobebiochemically active. From the perspective of an industrial application, the termite hindgut is too complex a model to mimic because it comprises hun- dreds of microbial species and lignocellulose-degrading enzymes. However, termites tend to feed on complex diets of several plant species, which translate to more complex hindgut communities and enzyme inventories. Thus, examination of this single community revealsenzymescapableofhydrolysingabroadassortmentofchemical bonds. The saccharification of a single uniform cellulosic feedstock, particularlyoneengineeredtohaveasimplifiedcellwall, willpresum- ablyrequirefewerenzymesandlessdownstreamoptimizationofgene regulation and enzyme activity in a production host. The availability of a wide range of naturally occurring lignocellu- lose-degrading enzymes increases the chances of successful enzyme optimization for industrial processes. Optimization of the sacchar- ification processiscrucial becausethecostofcellulases remainsakey barrier to economical production of biofuels 3 . A more diverse set of candidate enzymes?identified through a combination of conven- tional cultured microbial genome studies coupled with envir- onmental prospecting methods such as metagenomics?improves the likelihood of obtaining enzymes with activities and stability sui- ted to a variety of industrial processes. Biofuel production Although the final steps of cellulosic ethanol production will require much of the same infrastructure developed for the production of sugar- and starch-based ethanol, changes will need to be made to exploit the diversity of sugars generated from the breakdown of bio- mass.Whereastheconversionofstarch-basedfeedstockresultsprim- arily in hexoses, the products from degradation of lignocellulosic biomass, composed in part of hemicellulose, include large amounts of the pentose sugars D-xylose and L-arabinose. In contrast to the hexose sugars, the pentose sugars cannot be fermented by wild-type Saccharomyces cerevisiae 24 . Another factor limiting ethanol yield is the toxicity of ethanol to the fermenting host. Most fermenting organismssuchasS.cerevisiaecannottolerateethanolconcentrations exceeding 25% (v/v) 25 , resulting in a product that must then be con- centrated through distillation. Distillation represents an expensive and energy-intensive step in ethanol production. Theselimitationsinethanolproductionhavegeneratedsignificant interest in developing new organisms able to exploit fully the break- down products of lignocellulosic biomass as well as tolerate the pro- ducts of fermentation 26 . Pichia stipitis represents one yeast species of relevance to biofuel research based on its natural ability to ferment the pentose sugar xylose. Its recently sequenced genome revealed insights into the metabolic pathways responsible for this process 27 , and investigators are already working on the optimization of this pathway in P. stipitis as well as on the construction of systems for the heterologous expression of P. stipitis genes. Escherichia coli has already been genetically engineered for the conversion of all hexose and pentose sugars present in hemicellulose polymers 28 . The result- ing genetically engineered strain has an ethanol production rate sim- ilar to yeast 29 , and its ethanol tolerance has been increased by selection on enrichment media 30 . In the future, genomics and path- way engineering should considerably facilitate the development of a variety of organisms able to use the full repertoire of cellulosic and hemicellulosic sugars and tolerate high ethanol concentrations to optimize ethanol yields. Althoughethanolproductionfacilitiesanddistributioncentresare rapidly increasing in number, ethanol as a transportation fuel has several disadvantages that encourage the pursuit of better suited alternative biofuels in the future. Disadvantages of ethanol as a bio- fuelinclude:(1)highsolubilityofethanolinwater,whichnecessitates an energy-intensive distillation step; (2) diminished energy per gal- lon content of ethanol compared to petroleum; (3) difficulties in the distributionofethanolviatoday?spipelineinfrastructureowingtoits hygroscopic nature; and (4) incompatibilities with many current vehicles at higher blending volumes. Thus, work is under way to enable the synthesis of next-generation biofuel products, such as higher-chain alcohols, alkanes, and other molecules with structures and activities closer to that of petroleum and diesel. Butanol, for example, can be used in conventional engines either in pure form or mixed with petroleum, can be transported by existing pipelines, and has a higher energy content than petroleum 31 . A number of organisms, such as Clostridium acetobutylicum, produce butanol REVIEWS NATUREjVol 454j14 August 2008 844 �2008 Macmillan Publishers Limited. All rights reserved from sugars via the ABE (acetone, butanol, ethanol) fermentation and can be manipulated to produce mostly butanol 31 . E. coli has recently been engineered to produce isobutanol and other alcohols via a non-fermentative pathway that may be more readily adapted to large-scale production, using heterologous expression of Lactococcus lactis and Bacillus subtilis genes 32 . The genomics-enabled construc- tion of partial or fully artificial biological systems through ?synthetic biology? approaches will be key in developing efficient, inexpensive biofuel production systems 33 . Summary This perspective has focused on biofuels derived from lignocellulosic feedstocks; however, another potential source oftransportation fuels is biodiesel, derived from oil-producing plants and microbes. Predominant sources of biodiesel presently include soya bean, rape- seed and palm oils. The genomes of soya bean and oil palm are both currently being sequenced (Table1), information from which will be called on to increase oil production and facilitate plant growth in a broader range of habitats. Oil-producing algae are also under active study as an alternative source for biodiesel production. One of the major advantages ofalgaeistheir growthinliquid,negating theissue ofpotentialcompetitionbetweenfoodandenergycropsforlanduse. Chlamydomonas reinhardtii is one of a series of algal species whose genomes are becoming available for analysis 34 . Considering the mag- nitude of the transportation fuel problem, biodiesel is likely to con- tribute at least in part to the solution, and genomic research on oil producers will aid inmaking biodiesel production cheaper and more efficient. Placing a man on the Moon and sequencing the human genome represented large-scale technologically challenging projects. In both theseinstances,substantialresearchanddevelopmenteffortsresulted in technological advances unforeseen at the projects? initiation. The strategies that were pioneered in sequencing and interpreting the human genome for the improvement of human health are now poised to be an important contributing technology in the challenge to develop environmentally and socially acceptable alternatives to fossil fuels. 1. Hill, J., Nelson, E., Tilman, D., Polasky, S. & Tiffany, D. Environmental, economic, andenergeticcostsandbenefitsofbiodieselandethanolbiofuels.Proc. NatlAcad. Sci. USA 103, 11206?11210 (2006). 2. Tilman, D., Hill, J. & Lehman, C. Carbon-negative biofuels from low-input high- diversity grassland biomass. Science 314, 1598?1600 (2006). A demonstration of why grassland perennials, such as switchgrass, are superior for biofuel production when compared to crops that presently serve as food crops, such as soya bean or maize. 3. Himmel, M. E. et al. Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315, 804?807 (2007). 4. Reddy, N. & Yang, Y. Biofibers from agricultural byproducts for industrial applications. Trends Biotechnol. 23, 22?27 (2005). 5. van Wyk, J. P. Biotechnology and the utilization of biowaste as a resource for bioproduct development. Trends Biotechnol. 19, 172?177 (2001). A discussion of biowaste as a potential source of lignocellulose for biofuel production. 6. DelRio,J.C.,Marques,G.,Rencoret,J.,Martinez,A.T.&Gutierrez,A.Occurrence of naturally acetylated lignin units. J. Agric. Food Chem. 55, 5461?5468 (2007). 7. Sanderson, K. US biofuels: a field in ferment. Nature 444, 673?676 (2006). 8. Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309?1321 (2006). 9. Tuskan, G. A. et al. The genome ofblack cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596?1604 (2006). 10. Yu,J.etal.Adraftsequenceofthericegenome(OryzasativaL.ssp.indica).Science 296, 79?92 (2002). 11. Goff,S.A.etal.Adraftsequenceofthericegenome(OryzasativaL.ssp.japonica). Science 296, 92?100 (2002). 12. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796?815 (2000). 13. Kalluri, U. C., Difazio, S. P., Brunner, A. M. & Tuskan, G. A. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol. 7, 59 (2007). 14. Busov, V.B.,Brunner, A.M.&Strauss,S.H.Genesfor controlofplantstature and form. New Phytol. 177, 589?607 (2008). 15. Ragauskas, A. J. et al. The path forward for biofuels and biomaterials. Science 311, 484?489 (2006). 16. Filichkin, S. A. et al. Efficiency of gene silencing in Arabidopsis: direct inverted repeats vs. transitive RNAi vectors. Plant Biotechnol. J. 5, 615?626 (2007). 17. Dinus, R. J., Payne, P., Sewell, M. M., Chiang, V. L. & Tuskan, G. A. Genetic modification of short rotation poplar wood properties for energy and fiber production. Crit. Rev. Plant Sci. 20, 51?69 (2001). 18. LaForge, F. B. & Hudson, C. S. The preparation of several useful substances from corn cobs. J. Ind. Eng. Chem. 10, 925?927 (1918). 19. Mosier, N. et al. Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresour. Technol. 96, 673?686 (2005). 20. Gilbert, H. J. Cellulosomes: microbial nanomachines that display plasticity in quaternary structure. Mol. Microbiol. 63, 1568?1576 (2007). 21. Viikari, L., Alapuranen, M., Puranen, T., Vehmaanpera, J. & Siika-Aho, M. Thermostableenzymesinlignocellulosehydrolysis. Adv. Biochem. Eng. Biotechnol. 108, 121?145 (2007). 22. Hugenholtz, P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3, REVIEWS0003 (2002). 23. Warnecke, F. et al. Metagenomic andfunctional analysisofhindgutmicrobiota of a wood-feeding higher termite. Nature 450, 560?565 (2007). A metagenomic study of an invertebrate gut microbial community involved in lignocellulolytic degradation. 24. van Maris, A. J. et al. Alcoholic fermentation of carbon sources in biomass hydrolysates by Saccharomyces cerevisiae: current status. Antonie Van Leeuwenhoek 90, 391?418 (2006). 25. Wang, M., Zhao, J., Yang, Z. & Du, Z. Electrochemical insights into the ethanol tolerance of Saccharomyces cerevisiae. Bioelectrochemistry 71, 107?112 (2007). 26. Georgieva, T. I., Mikkelsen, M. J. & Ahring, B. K. High ethanol tolerance of the thermophilic anaerobic ethanol producer Thermoanaerobacter BG1L1. Central Eur. J. Biol. 2, 364?377 (2007). 27. Jeffries, T. W. et al. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nature Biotechnol. 25, 319?326 (2007). 28. Ohta, K., Beall, D. S., Mejia, J. P., Shanmugam, K. T. & Ingram, L. O. Genetic improvement of Escherichia coli for ethanol production: chromosomal integration of Zymomonas mobilis genes encoding pyruvate decarboxylase and alcohol dehydrogenase II. Appl. Environ. Microbiol. 57, 893?900 (1991). A description of the genetic modification of E. coli, yielding a strain capable of fermenting pentose and hexose sugars?which are present in lignocellulose? into ethanol. 29. Jarboe, L. R., Grabar, T. B., Yomano, L. P., Shanmugan, K. T. & Ingram, L. O. Development of ethanologenic bacteria. Adv. Biochem. Eng. Biotechnol. 108, 237?261 (2007). 30. Yomano, L. P., York, S. W. & Ingram, L. O. Isolation and characterization of ethanol-tolerantmutantsofEscherichiacoliKO11forfuelethanolproduction.J.Ind. Microbiol. Biotechnol. 20, 132?138 (1998). 31. Durre, P. Biobutanol: an attractive biofuel. Biotechnol. J. 2, 1525?1534 (2007). 32. Atsumi, S., Hanai, T. & Liao, J. C. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86?89 (2008). 33. Lartigue, C. et al. Genome transplantation in bacteria: changing one species to another. Science 317, 632?638 (2007). 34. Merchant, S. S. et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245?250 (2007). 35. Gioia, J. et al. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS ONE 2, e928 (2007). 36. Taylor, L. E. et al. Complete cellulase system in the marine bacterium Saccharophagus degradans strain 2-40T. J. Bacteriol. 188, 3849?3861 (2006). 37. Lykidis, A. et al. Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. J. Bacteriol. 189, 2477?2486 (2007). 38. Nolling, J. et al. Genome sequence and comparative analysis of the solvent- producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183, 4823?4838 (2001). 39. Bao,Q.etal.AcompletesequenceoftheT.tengcongensisgenome.GenomeRes12, 689?700 (2002). 40. Seo,J.S. et al. The genomesequence ofthe ethanologenic bacterium Zymomonas mobilis ZM4. Nature Biotechnol. 23, 63?68 (2005). Acknowledgements I would like to thank S. Tringe, M. Hess, J. Tuskan, P. Hugenholtz, J. Bristow, B. Simmons, S. Long, J. Fruchart-Najib and H. Blanch for their input to the manuscript. This work was performed under the auspices of the US Department of Energy?s Office of Science, Biological and Environmental ResearchProgram,andbytheUniversityofCalifornia,LawrenceBerkeleyNational Laboratory under contract number DE-AC02-05CH11231, Lawrence Livermore National Laboratory under contract number DE-AC52-07NA27344, and Los Alamos National Laboratory under contract number DE-AC02-06NA25396. Author Information Reprints and permissions information is available at www.nature.com/reprints. Correspondence should be addressed to E.M.R. (emrubin@lbl.gov). NATUREjVol 454j14 August 2008 REVIEWS 845 �2008 Macmillan Publishers Limited. All rights reserved "
Add Content to Group
|
Bookmark
|
Keywords
|
Flag Inappropriate
share
Close
Digg
Facebook
MySpace
Google+
Comments
Close
Please Post Your Comment
*
The Comment you have entered exceeds the maximum length.
Submit
|
Cancel
*
Required
Comments
Please Post Your Comment
No comments yet.
Save Note
Note
View
Public
Private
Friends & Groups
Friends
Groups
Save
|
Cancel
|
Delete
Please provide your notes.
Next
|
Prev
|
Close
|
Edit
|
Delete
Genetics
Gene Inheritance and Transmission
Gene Expression and Regulation
Nucleic Acid Structure and Function
Chromosomes and Cytogenetics
Evolutionary Genetics
Population and Quantitative Genetics
Genomics
Genes and Disease
Genetics and Society
Cell Biology
Cell Origins and Metabolism
Proteins and Gene Expression
Subcellular Compartments
Cell Communication
Cell Cycle and Cell Division
Scientific Communication
Career Planning
Loading ...
Scitable Chat
Register
|
Sign In
Visual Browse
Close
Comments
CloseComments
Please Post Your Comment