DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genetic resources for advanced biofuel production described with the Gene Ontology

Abstract

Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary.The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology (http://www.mengo.biochem.vt.edu) project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline,more » diesel and jet fuels, and can be stored and distributed using existing infrastructure. We review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.« less

Authors:
 [1];  [1];  [2];  [3];  [4];  [4]
  1. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
  2. European Bioinformatics Inst., Cambridge (United Kingdom)
  3. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Universidade de Sao Paulo (Brazil)
  4. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Oregon State Univ., Corvallis, OR (United States)
Publication Date:
Research Org.:
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1221624
Grant/Contract Number:  
SC0005011
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 5; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Gene ontology; advanced biofuels; synthetic biology; cellulosome; advanced alcohols; fatty acid-derived fuel; isoprenoid-derived fuel

Citation Formats

Torto-Alalibo, Trudy, Purwantini, Endang, Lomax, Jane, Setubal, Joao C., Mukhopadhyay, Biswarup, and Tyler, Brett M. Genetic resources for advanced biofuel production described with the Gene Ontology. United States: N. p., 2014. Web. doi:10.3389/fmicb.2014.00528.
Torto-Alalibo, Trudy, Purwantini, Endang, Lomax, Jane, Setubal, Joao C., Mukhopadhyay, Biswarup, & Tyler, Brett M. Genetic resources for advanced biofuel production described with the Gene Ontology. United States. https://doi.org/10.3389/fmicb.2014.00528
Torto-Alalibo, Trudy, Purwantini, Endang, Lomax, Jane, Setubal, Joao C., Mukhopadhyay, Biswarup, and Tyler, Brett M. Fri . "Genetic resources for advanced biofuel production described with the Gene Ontology". United States. https://doi.org/10.3389/fmicb.2014.00528. https://www.osti.gov/servlets/purl/1221624.
@article{osti_1221624,
title = {Genetic resources for advanced biofuel production described with the Gene Ontology},
author = {Torto-Alalibo, Trudy and Purwantini, Endang and Lomax, Jane and Setubal, Joao C. and Mukhopadhyay, Biswarup and Tyler, Brett M.},
abstractNote = {Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary.The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology (http://www.mengo.biochem.vt.edu) project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. We review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.},
doi = {10.3389/fmicb.2014.00528},
journal = {Frontiers in Microbiology},
number = ,
volume = 5,
place = {United States},
year = {Fri Oct 10 00:00:00 EDT 2014},
month = {Fri Oct 10 00:00:00 EDT 2014}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 15 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Next generation biofuel engineering in prokaryotes
journal, June 2013

  • Gronenberg, Luisa S.; Marcheschi, Ryan J.; Liao, James C.
  • Current Opinion in Chemical Biology, Vol. 17, Issue 3
  • DOI: 10.1016/j.cbpa.2013.03.037

The Gene Ontology (GO) database and informatics resource
journal, January 2004

  • Gene Ontology Consortium,
  • Nucleic Acids Research, Vol. 32, Issue 90001
  • DOI: 10.1093/nar/gkh036

Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels
journal, January 2014

  • Janßen, Helge; Steinbüchel, Alexander
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-7

Evidence for Only Oxygenative Cleavage of Aldehydes to Alk(a/e)nes and Formate by Cyanobacterial Aldehyde Decarbonylases
journal, September 2012

  • Li, Ning; Chang, Wei-chen; Warui, Douglas M.
  • Biochemistry, Vol. 51, Issue 40
  • DOI: 10.1021/bi300912n

Production of advanced biofuels in engineered E. coli
journal, June 2013

  • Wen, Miao; Bond-Watts, Brooks B.; Chang, Michelle CY
  • Current Opinion in Chemical Biology, Vol. 17, Issue 3
  • DOI: 10.1016/j.cbpa.2013.03.034

Polyhydroxyalkanoates: an overview
journal, April 2003


Physiological adaptations of Saccharomyces cerevisiae evolved for improved butanol tolerance
journal, January 2013

  • Ghiaci, Payam; Norbeck, Joakim; Larsson, Christer
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-101

Organization and distribution of the cellulosome in Clostridium thermocellum.
journal, January 1985


Structure of the AcrAB–TolC multidrug efflux pump
journal, April 2014

  • Du, Dijun; Wang, Zhao; James, Nathan R.
  • Nature, Vol. 509, Issue 7501
  • DOI: 10.1038/nature13205

Engineering microbes for tolerance to next-generation biofuels
journal, January 2011


Initiation of endospore formation in Clostridium acetobutylicum
journal, April 2004


Mapping the active site of Escherichia coli malonyl-CoA–acyl carrier protein transacylase (FabD) by protein crystallography
journal, May 2006

  • Oefner, Christian; Schulz, Henk; D'Arcy, Allan
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 6
  • DOI: 10.1107/S0907444906009474

A novel, ultra-large xylanolytic complex (xylanosome) secreted by Streptomyces olivaceoviridis
journal, March 2004


How microbes tolerate ethanol and butanol
journal, October 2009


Use of branched-chain esters to reduce the crystallization temperature of biodiesel
journal, October 1995

  • Lee, Inmok; Johnson, Lawrence A.; Hammond, Earl G.
  • Journal of the American Oil Chemists' Society, Vol. 72, Issue 10
  • DOI: 10.1007/BF02540982

Molecular characterization of the CER1 gene of arabidopsis involved in epicuticular wax biosynthesis and pollen fertility.
journal, December 1995

  • Aarts, M. G.; Keijzer, C. J.; Stiekema, W. J.
  • The Plant Cell, Vol. 7, Issue 12
  • DOI: 10.1105/tpc.7.12.2115

Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance
journal, January 2013


Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex
journal, October 2013


Microbial Biosynthesis of Alkanes
journal, July 2010


The effect of high concentration isopropanol on the growth of a solvent-tolerant strain of Chlorella vulgaris
journal, August 2004


Deconstruction of Lignocellulosic Biomass to Fuels and Chemicals
journal, July 2011


Enzymes of the mevalonate pathway of isoprenoid biosynthesis
journal, January 2011


Cellulases of Mesophilic Microorganisms: Cellulosome and Noncellulosome Producers
journal, March 2008


Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803
journal, January 2013

  • Zhu, Hongji; Ren, Xiaoyue; Wang, Jiangxin
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-106

Prospective and development of butanol as an advanced biofuel
journal, December 2013


Subunit composition of a large xylanolytic complex (xylanosome) from Streptomyces olivaceoviridis E-86
journal, November 2006


Polyhydroxyalkanoates as a source of chemicals, polymers, and biofuels
journal, December 2011


Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels
journal, June 2010

  • Weber, Christian; Farwick, Alexander; Benisch, Feline
  • Applied Microbiology and Biotechnology, Vol. 87, Issue 4
  • DOI: 10.1007/s00253-010-2707-z

Microbial production of fatty acid-derived fuels and chemicals
journal, December 2013


Unique Biosynthesis of Sesquarterpenes (C 35 Terpenes)
journal, June 2013

  • Sato, Tsutomu
  • Bioscience, Biotechnology, and Biochemistry, Vol. 77, Issue 6
  • DOI: 10.1271/bbb.130180

The chemomechanical properties of microbial polyhydroxyalkanoates
journal, February 2014


Structural Basis of Functional Group Activation by Sulfotransferases in Complex Metabolic Pathways
journal, September 2012

  • McCarthy, Jennifer Gehret; Eisman, Eli B.; Kulkarni, Sarang
  • ACS Chemical Biology, Vol. 7, Issue 12
  • DOI: 10.1021/cb300385m

Tailored fatty acid synthesis via dynamic control of fatty acid elongation
journal, June 2013

  • Torella, J. P.; Ford, T. J.; Kim, S. N.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 28
  • DOI: 10.1073/pnas.1307129110

Tailored fatty acid synthesis via dynamic control of fatty acid elongation
journal, June 2013

  • Torella, J. P.; Ford, T. J.; Kim, S. N.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 28
  • DOI: 10.1073/pnas.1307129110

Identification and Molecular Characterization of an Efflux Pump Involved in Pseudomonas putida S12 Solvent Tolerance
journal, January 1998

  • Kieboom, Jasper; Dennis, Jonathan J.; de Bont, Jan A. M.
  • Journal of Biological Chemistry, Vol. 273, Issue 1
  • DOI: 10.1074/jbc.273.1.85

Modular Synthase-Encoding Gene Involved in α-Olefin Biosynthesis in Synechococcus sp. Strain PCC 7002
journal, April 2011

  • Mendez-Perez, Daniel; Begemann, Matthew B.; Pfleger, Brian F.
  • Applied and Environmental Microbiology, Vol. 77, Issue 12, p. 4264-4267
  • DOI: 10.1128/AEM.00467-11

Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments
journal, September 2013

  • Plewniak, Frédéric; Koechler, Sandrine; Navet, Benjamin
  • Molecular Ecology, Vol. 22, Issue 19
  • DOI: 10.1111/mec.12432

Biosynthesis of glyoxylate from glycine in
journal, May 2005


Cellulase-Xylanase Synergy in Designer Cellulosomes for Enhanced Degradation of a Complex Cellulosic Substrate
journal, December 2010


Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways
journal, January 2014


Biochemistry of Polyisoprenoid Biosynthesis
journal, June 1976


Transcriptional Analysis of spo0A Overexpression in Clostridium acetobutylicum and Its Effect on the Cell's Response to Butanol Stress
journal, March 2004


Active Efflux of Organic Solvents byPseudomonas putida S12 Is Induced by Solvents
journal, December 1998


Advanced biofuel production in microbes
journal, January 2010

  • Peralta-Yahya, Pamela P.; Keasling, Jay D.
  • Biotechnology Journal, Vol. 5, Issue 2, p. 147-162
  • DOI: 10.1002/biot.200900220

Production of butanol (a biofuel) from agricultural residues: Part I – Use of barley straw hydrolysate☆
journal, April 2010


Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
journal, January 2013


Processive and nonprocessive cellulases for biofuel production—lessons from bacterial genomes and structural analysis
journal, November 2011


A 5-hydroxymethyl furfural reducing enzyme encoded by theSaccharomyces cerevisiae ADH6 gene conveys HMF tolerance
journal, January 2006

  • Petersson, Anneli; Almeida, João R. M.; Modig, Tobias
  • Yeast, Vol. 23, Issue 6, p. 455-464
  • DOI: 10.1002/yea.1370

Solvent-tolerant bacteria for biotransformations in two-phase fermentation systems
journal, April 2007

  • Heipieper, Hermann J.; Neumann, Grit; Cornelissen, Sjef
  • Applied Microbiology and Biotechnology, Vol. 74, Issue 5
  • DOI: 10.1007/s00253-006-0833-4

The Gene Ontology (GO) database and informatics resource
journal, January 2004

  • Gene Ontology Consortium,
  • Nucleic Acids Research, Vol. 32, Issue 90001
  • DOI: 10.1093/nar/gkh036

Microdiesel: Escherichia coli engineered for fuel production
journal, September 2006

  • Kalscheuer, Rainer; Stölting, Torsten; Steinbüchel, Alexander
  • Microbiology, Vol. 152, Issue 9, p. 2529-2536
  • DOI: 10.1099/mic.0.29028-0

Conversion of Fatty Aldehydes to Alka(e)nes and Formate by a Cyanobacterial Aldehyde Decarbonylase: Cryptic Redox by an Unusual Dimetal Oxygenase
journal, April 2011

  • Li, Ning; Nørgaard, Hanne; Warui, Douglas M.
  • Journal of the American Chemical Society, Vol. 133, Issue 16
  • DOI: 10.1021/ja2013517

Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex
journal, October 2013


Cellulases of Mesophilic Microorganisms: Cellulosome and Noncellulosome Producers
journal, March 2008


Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803
journal, January 2013

  • Zhu, Hongji; Ren, Xiaoyue; Wang, Jiangxin
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-106

Three Efflux Pumps Are Required To Provide Efficient Tolerance to Toluene in Pseudomonas putida DOT-T1E
journal, July 2001


Molecular Characterization of the CER1 Gene of Arabidopsis Involved in Epicuticular Wax Biosynthesis and Pollen Fertility
journal, December 1995

  • Aarts, Mark G. M.; Keijzer, Christian J.; Stiekema, Willem J.
  • The Plant Cell, Vol. 7, Issue 12
  • DOI: 10.2307/3870155

Engineering Escherichia coli for Biodiesel Production Utilizing a Bacterial Fatty Acid Methyltransferase
journal, September 2011

  • Nawabi, Parwez; Bauer, Stefan; Kyrpides, Nikos
  • Applied and Environmental Microbiology, Vol. 77, Issue 22
  • DOI: 10.1128/AEM.05046-11

Efflux Pumps Involved in Toluene Tolerance in Pseudomonas putida DOT-T1E
journal, July 1998


The gene encoding the biotin carboxylase subunit of Escherichia coli acetyl-CoA carboxylase.
journal, January 1992


Biomass deconstruction to sugars
journal, August 2011

  • Blanch, Harvey W.; Simmons, Blake A.; Klein-Marcuschamer, Daniel
  • Biotechnology Journal, Vol. 6, Issue 9
  • DOI: 10.1002/biot.201000180

Insight into microbial hemicellulases other than xylanases: a review: Microbial hemicellulases other than xylanases
journal, November 2012

  • Juturu, Veeresh; Wu, Jin Chuan
  • Journal of Chemical Technology & Biotechnology, Vol. 88, Issue 3
  • DOI: 10.1002/jctb.3969

β-Ketoacyl-Acyl Carrier Protein Synthase III (FabH) Is Essential for Bacterial Fatty Acid Synthesis
journal, September 2003

  • Lai, Chiou-Yan; Cronan, John E.
  • Journal of Biological Chemistry, Vol. 278, Issue 51
  • DOI: 10.1074/jbc.M308638200

Metabolic engineering for advanced biofuels production from Escherichia coli
journal, October 2008


Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways
journal, February 2011

  • Bond-Watts, Brooks B.; Bellerose, Robert J.; Chang, Michelle C. Y.
  • Nature Chemical Biology, Vol. 7, Issue 4
  • DOI: 10.1038/nchembio.537

A novel pathway to produce butanol and isobutanol in Saccharomyces cerevisiae
journal, January 2013

  • Branduardi, Paola; Longo, Valeria; Berterame, Nadia Maria
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-68

Gene Ontology: tool for the unification of biology
journal, May 2000

  • Ashburner, Michael; Ball, Catherine A.; Blake, Judith A.
  • Nature Genetics, Vol. 25, Issue 1
  • DOI: 10.1038/75556

Microbial engineering for the production of advanced biofuels
journal, August 2012

  • Peralta-Yahya, Pamela P.; Zhang, Fuzhong; del Cardayre, Stephen B.
  • Nature, Vol. 488, Issue 7411
  • DOI: 10.1038/nature11478

Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus
journal, December 2009

  • Beller, H. R.; Goh, E.-B.; Keasling, J. D.
  • Applied and Environmental Microbiology, Vol. 76, Issue 4, p. 1212-1223
  • DOI: 10.1128/AEM.02312-09

Biobutanol: An attractive biofuel
journal, December 2007


New microbial fuels: a biotech perspective
journal, June 2009


Towards Designer Cellulosomes in Clostridia: Mannanase Enrichment of the Cellulosomes Produced by Clostridium cellulolyticum
journal, September 2004


Metabolic engineering of microbial pathways for advanced biofuels production
journal, December 2011


Microbial Biosynthesis of Alkanes
journal, July 2010


Incorporation of Fungal Cellulases in Bacterial Minicellulosomes Yields Viable, Synergistically Acting Cellulolytic Complexes
journal, April 2007

  • Mingardon, F.; Chanal, A.; Lopez-Contreras, A. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 12
  • DOI: 10.1128/AEM.00398-07

Forecasting of CO2 emissions from fuel combustion using trend analysis
journal, December 2010


Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
journal, January 2008

  • Atsumi, Shota; Hanai, Taizo; Liao, James C.
  • Nature, Vol. 451, Issue 7174, p. 86-89
  • DOI: 10.1038/nature06450

A cobalt-porphyrin enzyme converts a fatty aldehyde to a hydrocarbon and CO.
journal, June 1992

  • Dennis, M.; Kolattukudy, P. E.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 12
  • DOI: 10.1073/pnas.89.12.5306

Fossil fuel addiction and the implications for climate change policy
journal, June 2013


Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels
journal, June 2010

  • Weber, Christian; Farwick, Alexander; Benisch, Feline
  • Applied Microbiology and Biotechnology, Vol. 87, Issue 4
  • DOI: 10.1007/s00253-010-2707-z

The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms
journal, January 2012


Microbial production of fatty acid-derived fuels and chemicals
journal, December 2013


The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
journal, September 2008


Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol
journal, January 2008

  • Steen, Eric J.; Chan, Rossana; Prasad, Nilu
  • Microbial Cell Factories, Vol. 7, Issue 1, Article No. 36
  • DOI: 10.1186/1475-2859-7-36

Unconventional Mode of Attachment of the Ruminococcus flavefaciens Cellulosome to the Cell Surface
journal, November 2005


Bioinformatic analysis of proteomics data
journal, January 2014


The UniProt-GO Annotation database in 2011
journal, November 2011

  • Dimmer, E. C.; Huntley, R. P.; Alam-Faruque, Y.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1048

Prospective and development of butanol as an advanced biofuel
journal, December 2013


Continuous Butanol Production Using Suspended and Immobilized Clostridium beijerinckii NCIMB 8052 with Supplementary Butyrate
journal, September 2008

  • Lee, Sun-Mi; Cho, Min Ok; Park, Cheol Hee
  • Energy & Fuels, Vol. 22, Issue 5
  • DOI: 10.1021/ef800076j

Enzymatic deconstruction of xylan for biofuel production
journal, February 2009


Microbial production of fatty-acid-derived fuels and chemicals from plant biomass
journal, January 2010

  • Steen, Eric J.; Kang, Yisheng; Bokinsky, Gregory
  • Nature, Vol. 463, Issue 7280, p. 559-562
  • DOI: 10.1038/nature08721

Impact of carbon source and variable nitrogen conditions on bacterial biosynthesis of polyhydroxyalkanoates: Evidence of an atypical metabolism in Bacillus megaterium DSM 509
journal, September 2013

  • Shahid, Salma; Mosrati, Ridha; Ledauphin, Jérôme
  • Journal of Bioscience and Bioengineering, Vol. 116, Issue 3
  • DOI: 10.1016/j.jbiosc.2013.02.017

Dietary palmitic acid promotes a prometastatic memory via Schwann cells
journal, November 2021


Isolation of Butanol- and Isobutanol-Tolerant Bacteria and Physiological Characterization of Their Butanol Tolerance
journal, September 2013

  • Kanno, Manabu; Katayama, Taiki; Tamaki, Hideyuki
  • Applied and Environmental Microbiology, Vol. 79, Issue 22
  • DOI: 10.1128/aem.02900-13

Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation
journal, January 2013

  • González-Ramos, Daniel; van den Broek, Marcel; van Maris, Antonius JA
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-48

Molecular cloning of fungal xylanases: an overview
journal, July 2009

  • Ahmed, Sibtain; Riaz, Saba; Jamil, Amer
  • Applied Microbiology and Biotechnology, Vol. 84, Issue 1
  • DOI: 10.1007/s00253-009-2079-4

Identification of an NADH-dependent 5-hydroxymethylfurfural-reducing alcohol dehydrogenase inSaccharomyces cerevisiae
journal, January 2008

  • Laadan, Boaz; Almeida, João R. M.; Rådström, Peter
  • Yeast, Vol. 25, Issue 3
  • DOI: 10.1002/yea.1578

Detection of Formate, Rather than Carbon Monoxide, As the Stoichiometric Coproduct in Conversion of Fatty Aldehydes to Alkanes by a Cyanobacterial Aldehyde Decarbonylase
journal, March 2011

  • Warui, Douglas M.; Li, Ning; Nørgaard, Hanne
  • Journal of the American Chemical Society, Vol. 133, Issue 10
  • DOI: 10.1021/ja111607x

Spo0A directly controls the switch from acid to solvent production in solvent-forming clostridia
journal, September 2000


Polyisoprenoid synthesis and metabolism
journal, May 1992

  • Edwards, Peter A.; Ashby, Matthew N.; Spear, David H.
  • Biochemical Society Transactions, Vol. 20, Issue 2
  • DOI: 10.1042/bst0200475

Application of ( R )-3-Hydroxyalkanoate Methyl Esters Derived from Microbial Polyhydroxyalkanoates as Novel Biofuels
journal, April 2009

  • Zhang, Xiaojun; Luo, Rongcong; Wang, Zhen
  • Biomacromolecules, Vol. 10, Issue 4
  • DOI: 10.1021/bm801424e

Widespread Head-to-Head Hydrocarbon Biosynthesis in Bacteria and Role of OleA
journal, April 2010

  • Sukovich, D. J.; Seffernick, J. L.; Richman, J. E.
  • Applied and Environmental Microbiology, Vol. 76, Issue 12
  • DOI: 10.1128/AEM.00436-10

Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production
journal, January 2013

  • Chang, Jui-Jen; Ho, Feng-Ju; Ho, Cheng-Yu
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-19

Biomass deconstruction to sugars
journal, August 2011

  • Blanch, Harvey W.; Simmons, Blake A.; Klein-Marcuschamer, Daniel
  • Biotechnology Journal, Vol. 6, Issue 9
  • DOI: 10.1002/biot.201000180

Molecular engineering of the cellulosome complex for affinity and bioenergy applications
journal, December 2008

  • Nordon, Robert E.; Craig, Scott J.; Foong, Frances C.
  • Biotechnology Letters, Vol. 31, Issue 4
  • DOI: 10.1007/s10529-008-9899-7

Bioconversion of lignocellulose: inhibitors and detoxification
journal, January 2013

  • Jönsson, Leif J.; Alriksson, Björn; Nilvebrant, Nils-Olof
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-16

Advanced bacterial polyhydroxyalkanoates: Towards a versatile and sustainable platform for unnatural tailor-made polyesters
journal, November 2012


Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass
journal, August 2004

  • Klinke, H. B.; Thomsen, A. B.; Ahring, B. K.
  • Applied Microbiology and Biotechnology, Vol. 66, Issue 1, p. 10-26
  • DOI: 10.1007/s00253-004-1642-2

Methylerythritol Phosphate Pathway of Isoprenoid Biosynthesis
journal, June 2013


A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates
journal, January 2013


The Gene Ontology ( GO ) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
journal, November 2002


Solvent tolerance in Gram-negative bacteria
journal, June 2012


Alkane biosynthesis by decarbonylation of aldehyde catalyzed by a microsomal preparation from Botryococcus braunii
journal, June 1991

  • Dennis, Michael W.; Kolattukudy, P. E.
  • Archives of Biochemistry and Biophysics, Vol. 287, Issue 2, p. 268-275
  • DOI: 10.1016/0003-9861(91)90478-2

Fossil fuel addiction and the implications for climate change policy
journal, June 2013


Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation
journal, January 2007

  • Arai, T.; Matsuoka, S.; Cho, H. -Y.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 5
  • DOI: 10.1073/pnas.0610740104

Microbial engineering for the production of advanced biofuels
journal, August 2012

  • Peralta-Yahya, Pamela P.; Zhang, Fuzhong; del Cardayre, Stephen B.
  • Nature, Vol. 488, Issue 7411
  • DOI: 10.1038/nature11478

Microdiesel: Escherichia coli engineered for fuel production
journal, September 2006

  • Kalscheuer, Rainer; Stölting, Torsten; Steinbüchel, Alexander
  • Microbiology, Vol. 152, Issue 9, p. 2529-2536
  • DOI: 10.1099/mic.0.29028-0

Moringa oleifera oil: A possible source of biodiesel
journal, November 2008


Metabolic engineering for advanced biofuels production from Escherichia coli
journal, October 2008


Metagenomic insights into microbial metabolism affecting arsenic dispersion in Mediterranean marine sediments
journal, September 2013

  • Plewniak, Frédéric; Koechler, Sandrine; Navet, Benjamin
  • Molecular Ecology, Vol. 22, Issue 19
  • DOI: 10.1111/mec.12432

Thermophilic lignocellulose deconstruction
journal, May 2014

  • Blumer-Schuette, Sara E.; Brown, Steven D.; Sander, Kyle B.
  • FEMS Microbiology Reviews, Vol. 38, Issue 3
  • DOI: 10.1111/1574-6976.12044

Metabolic engineering of microbial pathways for advanced biofuels production
journal, December 2011


Acetone, Isopropanol, and Butanol Production by Clostridium beijerinckii (syn. Clostridium butylicum) and Clostridium aurantibutyricum
journal, January 1983


Processive and nonprocessive cellulases for biofuel production—lessons from bacterial genomes and structural analysis
journal, November 2011


Lipid and fatty acid metabolism in Ralstonia eutropha: relevance for the biotechnological production of value-added products
journal, December 2013

  • Riedel, Sebastian L.; Lu, Jingnan; Stahl, Ulf
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 4
  • DOI: 10.1007/s00253-013-5430-8

Functional assembly and characterization of a modular xylanosome for hemicellulose hydrolysis in yeast
journal, August 2012

  • Srikrishnan, Sneha; Chen, Wilfred; Da Silva, Nancy A.
  • Biotechnology and Bioengineering, Vol. 110, Issue 1
  • DOI: 10.1002/bit.24609

Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology
journal, February 2010

  • Clomburg, James M.; Gonzalez, Ramon
  • Applied Microbiology and Biotechnology, Vol. 86, Issue 2
  • DOI: 10.1007/s00253-010-2446-1

The rosettazyme: A synthetic cellulosome
journal, August 2009


An Investigation of the Metabolism of Valine to Isobutyl Alcohol in Saccharomyces cerevisiae
journal, October 1998

  • Dickinson, J. Richard; Harrison, Scott J.; Hewlins, Michael J. E.
  • Journal of Biological Chemistry, Vol. 273, Issue 40, p. 25751-25756
  • DOI: 10.1074/jbc.273.40.25751

Enoyl-Acyl Carrier Protein Reductase ( fabI ) Plays a Determinant Role in Completing Cycles of Fatty Acid Elongation in Escherichia coli
journal, November 1995


Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns
journal, July 2009

  • Christie, Karen R.; Hong, Eurie L.; Cherry, J. Michael
  • Trends in Microbiology, Vol. 17, Issue 7
  • DOI: 10.1016/j.tim.2009.04.005

Terpenoid biomaterials
journal, May 2008


Evaluation of Fuel Properties of Butanol−Biodiesel−Diesel Blends and Their Impact on Engine Performance and Emissions
journal, August 2010

  • Mehta, Rakhi N.; Chakraborty, Mousumi; Mahanta, Pinakeswar
  • Industrial & Engineering Chemistry Research, Vol. 49, Issue 16
  • DOI: 10.1021/ie1006257

A Set of Genes Encoding a Second Toluene Efflux System in Pseudomonas putida DOT-T1E Is Linked to the tod Genes for Toluene Metabolism
journal, February 2000


Application of ( R )-3-Hydroxyalkanoate Methyl Esters Derived from Microbial Polyhydroxyalkanoates as Novel Biofuels
journal, April 2009

  • Zhang, Xiaojun; Luo, Rongcong; Wang, Zhen
  • Biomacromolecules, Vol. 10, Issue 4
  • DOI: 10.1021/bm801424e

Acetone-butanol-isopropanol production byClostridium beijerinckii (synonym,Clostridium butylicum)
journal, May 1986

  • Chen, Jiann-Shin; Hiu, Stephen F.
  • Biotechnology Letters, Vol. 8, Issue 5, p. 371-376
  • DOI: 10.1007/BF01040869

The cellulolytic system of Thermobifida fusca
journal, March 2013


Fermentative butanol production by clostridia
journal, October 2008

  • Lee, Sang Yup; Park, Jin Hwan; Jang, Seh Hee
  • Biotechnology and Bioengineering, Vol. 101, Issue 2, p. 209-228
  • DOI: 10.1002/bit.22003

Unique Biosynthesis of Sesquarterpenes (C 35 Terpenes)
journal, June 2013

  • Sato, Tsutomu
  • Bioscience, Biotechnology, and Biochemistry, Vol. 77, Issue 6
  • DOI: 10.1271/bbb.130180

Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli
journal, January 2008

  • Inui, Masayuki; Suda, Masako; Kimura, Sakurako
  • Applied Microbiology and Biotechnology, Vol. 77, Issue 6
  • DOI: 10.1007/s00253-007-1257-5

Biobutanol: An attractive biofuel
journal, December 2007


Subunit composition of a large xylanolytic complex (xylanosome) from Streptomyces olivaceoviridis E-86
journal, November 2006


Enzymes of the mevalonate pathway of isoprenoid biosynthesis
journal, January 2011


Soluble chromogenic substrates for the assay of endo-1,4-β-xylanases and endo-1,4-β-glucanases
journal, January 1985


A cobalt-porphyrin enzyme converts a fatty aldehyde to a hydrocarbon and CO.
journal, June 1992

  • Dennis, M.; Kolattukudy, P. E.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 12
  • DOI: 10.1073/pnas.89.12.5306

Detection of Formate, Rather than Carbon Monoxide, As the Stoichiometric Coproduct in Conversion of Fatty Aldehydes to Alkanes by a Cyanobacterial Aldehyde Decarbonylase
journal, March 2011

  • Warui, Douglas M.; Li, Ning; Nørgaard, Hanne
  • Journal of the American Chemical Society, Vol. 133, Issue 10
  • DOI: 10.1021/ja111607x

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns
journal, July 2009

  • Christie, Karen R.; Hong, Eurie L.; Cherry, J. Michael
  • Trends in Microbiology, Vol. 17, Issue 7
  • DOI: 10.1016/j.tim.2009.04.005

The rosettazyme: A synthetic cellulosome
journal, August 2009


The genome-wide screening of yeast deletion mutants to identify the genes required for tolerance to ethanol and other alcohols
journal, August 2006


Moringa oleifera oil: A possible source of biodiesel
journal, November 2008


Enzymatic deconstruction of xylan for biofuel production
journal, February 2009


Next generation biofuel engineering in prokaryotes
journal, June 2013

  • Gronenberg, Luisa S.; Marcheschi, Ryan J.; Liao, James C.
  • Current Opinion in Chemical Biology, Vol. 17, Issue 3
  • DOI: 10.1016/j.cbpa.2013.03.037

Northern, Morphological, and Fermentation Analysis of spo0A Inactivation and Overexpression in Clostridium acetobutylicum ATCC 824
journal, July 2002


A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates
journal, January 2013


Ultrastructure of the cell surface cellulosome of Clostridium thermocellum and its interaction with cellulose.
journal, September 1986


Spo0A directly controls the switch from acid to solvent production in solvent-forming clostridia
journal, September 2000


Solvent tolerance in Gram-negative bacteria
journal, June 2012


Engineering microbes for tolerance to next-generation biofuels
journal, January 2011


Production of butanol (a biofuel) from agricultural residues: Part I – Use of barley straw hydrolysate☆
journal, April 2010


Lipid and fatty acid metabolism in Ralstonia eutropha: relevance for the biotechnological production of value-added products
journal, December 2013

  • Riedel, Sebastian L.; Lu, Jingnan; Stahl, Ulf
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 4
  • DOI: 10.1007/s00253-013-5430-8

Thermophilic lignocellulose deconstruction
journal, May 2014

  • Blumer-Schuette, Sara E.; Brown, Steven D.; Sander, Kyle B.
  • FEMS Microbiology Reviews, Vol. 38, Issue 3
  • DOI: 10.1111/1574-6976.12044

The UniProt-GO Annotation database in 2011
journal, November 2011

  • Dimmer, E. C.; Huntley, R. P.; Alam-Faruque, Y.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1048

Historical and Recent Achievements in the Field of Microbial Degradation of Natural and Synthetic Rubber
journal, April 2012

  • Yikmis, Meral; Steinbüchel, Alexander
  • Applied and Environmental Microbiology, Vol. 78, Issue 13
  • DOI: 10.1128/aem.00001-12

Initiation of endospore formation in Clostridium acetobutylicum
journal, April 2004


Impact of carbon source and variable nitrogen conditions on bacterial biosynthesis of polyhydroxyalkanoates: Evidence of an atypical metabolism in Bacillus megaterium DSM 509
journal, September 2013

  • Shahid, Salma; Mosrati, Ridha; Ledauphin, Jérôme
  • Journal of Bioscience and Bioengineering, Vol. 116, Issue 3
  • DOI: 10.1016/j.jbiosc.2013.02.017

Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids
journal, June 2014


Terminal Olefin (1-Alkene) Biosynthesis by a Novel P450 Fatty Acid Decarboxylase from Jeotgalicoccus Species
journal, January 2011

  • Rude, Mathew A.; Baron, Tarah S.; Brubaker, Shane
  • Applied and Environmental Microbiology, Vol. 77, Issue 5
  • DOI: 10.1128/AEM.02580-10

Structure of the AcrAB–TolC multidrug efflux pump
journal, April 2014

  • Du, Dijun; Wang, Zhao; James, Nathan R.
  • Nature, Vol. 509, Issue 7501
  • DOI: 10.1038/nature13205

Heterologous Production of Clostridium cellulovorans engB, Using Protease-Deficient Bacillus subtilis, and Preparation of Active Recombinant Cellulosomes
journal, January 2002


Production of advanced biofuels in engineered E. coli
journal, June 2013

  • Wen, Miao; Bond-Watts, Brooks B.; Chang, Michelle CY
  • Current Opinion in Chemical Biology, Vol. 17, Issue 3
  • DOI: 10.1016/j.cbpa.2013.03.034

SpoIIE Regulates Sporulation but Does Not Directly Affect Solventogenesis in Clostridium acetobutylicum ATCC 824
journal, March 2005


The chemomechanical properties of microbial polyhydroxyalkanoates
journal, February 2014


Enoyl-Acyl Carrier Protein Reductase ( fabI ) Plays a Determinant Role in Completing Cycles of Fatty Acid Elongation in Escherichia coli
journal, November 1995


A 5-hydroxymethyl furfural reducing enzyme encoded by theSaccharomyces cerevisiae ADH6 gene conveys HMF tolerance
journal, January 2006

  • Petersson, Anneli; Almeida, João R. M.; Modig, Tobias
  • Yeast, Vol. 23, Issue 6, p. 455-464
  • DOI: 10.1002/yea.1370

Microbial diversity of cellulose hydrolysis
journal, June 2011


The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons
journal, January 2014

  • Hong, Wei; Zhang, Jie; Feng, Yingang
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-80

Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum.
journal, November 1984

  • Cheesbrough, T. M.; Kolattukudy, P. E.
  • Proceedings of the National Academy of Sciences, Vol. 81, Issue 21, p. 6613-6617
  • DOI: 10.1073/pnas.81.21.6613

Forecasting of CO2 emissions from fuel combustion using trend analysis
journal, December 2010


Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology
journal, January 2013


Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
journal, January 2008

  • Atsumi, Shota; Hanai, Taizo; Liao, James C.
  • Nature, Vol. 451, Issue 7174, p. 86-89
  • DOI: 10.1038/nature06450

Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways
journal, January 2014


The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms
journal, January 2012


Engineering Escherichia coli to synthesize free fatty acids
journal, December 2012


Bacterial Fatty Acid Biosynthesis: Targets for Antibacterial Drug Discovery
journal, October 2001


Functional assembly and characterization of a modular xylanosome for hemicellulose hydrolysis in yeast
journal, August 2012

  • Srikrishnan, Sneha; Chen, Wilfred; Da Silva, Nancy A.
  • Biotechnology and Bioengineering, Vol. 110, Issue 1
  • DOI: 10.1002/bit.24609

Structural and functional characterization of a novel type-III dockerin from Ruminococcus flavefaciens
journal, November 2012


A novel pathway to produce butanol and isobutanol in Saccharomyces cerevisiae
journal, January 2013

  • Branduardi, Paola; Longo, Valeria; Berterame, Nadia Maria
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-68

Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology
journal, February 2010

  • Clomburg, James M.; Gonzalez, Ramon
  • Applied Microbiology and Biotechnology, Vol. 86, Issue 2
  • DOI: 10.1007/s00253-010-2446-1

Alkane biosynthesis by decarbonylation of aldehyde catalyzed by a microsomal preparation from Botryococcus braunii
journal, June 1991

  • Dennis, Michael W.; Kolattukudy, P. E.
  • Archives of Biochemistry and Biophysics, Vol. 287, Issue 2, p. 268-275
  • DOI: 10.1016/0003-9861(91)90478-2

Structural Basis of Functional Group Activation by Sulfotransferases in Complex Metabolic Pathways
journal, September 2012

  • McCarthy, Jennifer Gehret; Eisman, Eli B.; Kulkarni, Sarang
  • ACS Chemical Biology, Vol. 7, Issue 12
  • DOI: 10.1021/cb300385m

Insight into microbial hemicellulases other than xylanases: a review: Microbial hemicellulases other than xylanases
journal, November 2012

  • Juturu, Veeresh; Wu, Jin Chuan
  • Journal of Chemical Technology & Biotechnology, Vol. 88, Issue 3
  • DOI: 10.1002/jctb.3969

Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli
journal, January 2008

  • Inui, Masayuki; Suda, Masako; Kimura, Sakurako
  • Applied Microbiology and Biotechnology, Vol. 77, Issue 6
  • DOI: 10.1007/s00253-007-1257-5

Synthesis of Clostridium cellulovorans minicellulosomes by intercellular complementation
journal, January 2007

  • Arai, T.; Matsuoka, S.; Cho, H. -Y.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 5
  • DOI: 10.1073/pnas.0610740104

Fermentative butanol production by clostridia
journal, October 2008

  • Lee, Sang Yup; Park, Jin Hwan; Jang, Seh Hee
  • Biotechnology and Bioengineering, Vol. 101, Issue 2, p. 209-228
  • DOI: 10.1002/bit.22003

Works referencing / citing this record:

Identification of Common Genes Refers to Colorectal Carcinogenesis with Paired Cancer and Noncancer Samples
journal, January 2018


Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis
journal, March 2017


Identification of key genes involved in the metastasis of clear cell renal cell carcinoma
journal, March 2019


Identification of Common Genes Refers to Colorectal Carcinogenesis with Paired Cancer and Noncancer Samples
journal, January 2018


Biochemical functional predictions for protein structures of unknown or uncertain function
journal, January 2015

  • Mills, Caitlyn L.; Beuning, Penny J.; Ondrechen, Mary Jo
  • Computational and Structural Biotechnology Journal, Vol. 13
  • DOI: 10.1016/j.csbj.2015.02.003