Gershenzon J, Dudareva N. The function of terpene natural products in the natural world. Nat Chem Biol. 2007;3:408–14.
Article
CAS
PubMed
Google Scholar
Ajikumar PK, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G. Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms. Mol Pharm. 2008;5:167–90.
Article
CAS
PubMed
Google Scholar
Withers ST, Keasling JD. Biosynthesis and engineering of isoprenoid small molecules. Appl Microbiol Biotechnol. 2007;73:980–90.
Article
CAS
PubMed
Google Scholar
Cao Y, Zhang H, Liu H, Liu W, Zhang R, Xian M, Liu H. Biosynthesis and production of sabinene: current state and perspectives. Appl Microbiol Biotechnol. 2018;102:1535–44.
Article
CAS
PubMed
Google Scholar
Valente J, Zuzarte M, Gonçalves MJ, Lopes MC, Cavaleiro C, Salgueiro L, Cruz MT. Antifungal, antioxidant and anti-inflammatory activities of Oenanthe crocata L. essential oil. Food Chem Toxicol. 2013;62:349–54.
Article
CAS
PubMed
Google Scholar
Zhang H, Liu Q, Cao Y, Feng X, Zheng Y, Zou H, Liu H, Yang J, Xian M. Microbial production of sabinene—a new terpene-based precursor of advanced biofuel. Microb Cell Fact. 2014;13:20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Renninger NS, Ryder JA, Fisher KJ. Jet fuel compositions and methods of making and using same. USA. 2011; US7935156.
Rude MA, Schirmer A. New microbial fuels: a biotech perspective. Curr Opin Microbiol. 2009;12:274–81.
Article
CAS
PubMed
Google Scholar
Urabe H, Suzuki K, Sato F. Intramolecular cyclization of 2,7- or 2,8-Bis-unsaturated esters mediated by (η2-propene)Ti(O-i-Pr)2. Facile construction of mono- and bicyclic skeletons with stereoselective introduction of a side chain. A synthesis of D-sabinene. J Am Chem Soc. 1997;119:10014–27.
Article
CAS
Google Scholar
Woguem V, Maggi F, Fogang HP, Tapondjoua LA, Womeni HM, Luana Q, Bramuccic M, Vitali LA, Petrelli D, Lupidi G, et al. Antioxidant, antiproliferative and antimicrobial activities of the volatile oil from the wild pepper Piper capense used in Cameroon as a culinary spice. Nat Prod Commun. 2013;8:1791–6.
CAS
PubMed
Google Scholar
Peralta-Yahya PP, Zhang F, del Cardayre SB, Keasling JD. Microbial engineering for the production of advanced biofuels. Nature. 2012;488:320.
Article
CAS
PubMed
Google Scholar
Carothers JM, Goler JA, Keasling JD. Chemical synthesis using synthetic biology. Curr Opin Biotechnol. 2009;20:498–503.
Article
CAS
PubMed
Google Scholar
Ignea C, Pontini M, Maffei ME, Makris AM, Kampranis SC. Engineering monoterpene production in yeast using a synthetic dominant negative geranyl diphosphate synthase. ACS Synth Biol. 2014;3:298–306.
Article
CAS
PubMed
Google Scholar
Bokinsky G, Peralta-Yahya PP, George A, Holmes BM, Steen EJ, Dietrich J, Lee TS, Tullman-Ercek D, Voigt CA, Simmons BA, Keasling JD. Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. Proc Natl Acad Sci USA. 2011;108:19949–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones JA, Toparlak ÖD, Koffas MAG. Metabolic pathway balancing and its role in the production of biofuels and chemicals. Curr Opin Biotechnol. 2015;33:52–9.
Article
CAS
PubMed
Google Scholar
Pitera DJ, Paddon CJ, Newman JD, Keasling JD. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng. 2007;9:193–207.
Article
CAS
PubMed
Google Scholar
He M-X, Wu B, Shui Z-X, Hu Q-C, Wang W-G, Tan F-R, Tang X-Y, Zhu Q-L, Pan K, Li Q, Su X-H. Transcriptome profiling of Zymomonas mobilis under ethanol stress. Biotechnol Biofuels. 2012;5:75.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu C, Men X, Chen H, Li M, Ding Z, Chen G, Wang F, Liu H, Wang Q, Zhu Y, et al. A systematic optimization of styrene biosynthesis in Escherichia coli BL21(DE3). Biotechnol Biofuels. 2018;11:14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu C, Zhang K, Cao W, Zhang G, Chen G, Yang H, Wang Q, Liu H, Xian M, Zhang H. Genome mining of 2-phenylethanol biosynthetic genes from Enterobacter sp. CGMCC 5087 and heterologous overproduction in Escherichia coli. Biotechnol Biofuels. 2018;11:305.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jojima T, Inui M, Yukawa H. Production of isopropanol by metabolically engineered Escherichia coli. Appl Microbiol Biotechnol. 2008;77:1219–24.
Article
CAS
PubMed
Google Scholar
Griffin SG, Wyllie SG, Markham JL. Antimicrobially active terpenes cause K + leakage in E-coli cells. J Essent Oil Res. 2005;17:686–90.
Article
CAS
Google Scholar
Yang J, Nie Q, Ren M, Feng H, Jiang X, Zheng Y, Liu M, Zhang H, Xian M. Metabolic engineering of Escherichia coli for the biosynthesis of alpha-pinene. Biotechnol Biofuels. 2013;6:60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dragosits M, Mattanovich D. Adaptive laboratory evolution—principles and applications for biotechnology. Microb Cell Fact. 2013;12:64.
Article
PubMed
PubMed Central
Google Scholar
Portnoy VA, Bezdan D, Zengler K. Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering. Curr Opin Biotechnol. 2011;22:590–4.
Article
CAS
PubMed
Google Scholar
Horinouchi T, Sakai A, Kotani H, Tanabe K, Furusawa C. Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies. J Biotechnol. 2017;255:47–56.
Article
CAS
PubMed
Google Scholar
Brennan TCR, Williams TC, Schulz BL, Palfreyman RW, Krömer JO, Nielsen LK. Evolutionary engineering improves tolerance for replacement jet fuels in Saccharomyces cerevisiae. Appl Environ Microbiol. 2015;81:3316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weaver RF. Molecular biology. 4th ed. New York: McGraw-Hill Higher Education; 2008.
Google Scholar
Battesti A, Majdalani N, Gottesman S. The RpoS-mediated general stress response in Escherichia coli. Annu Rev Microbiol. 2011;65:189.
Article
CAS
PubMed
PubMed Central
Google Scholar
Takada A, Umitsuki G, Nagai K. Rnase e is required for induction of the glutamate-dependent acid resistance system in Escherichia coli. J Agric Chem Soc Japan. 2007;71:158–64.
CAS
Google Scholar
Battistoni A, Pacello F, Folcarelli S, Ajello M, Donnarumma G, Greco R, Ammendolia MG, Touati D, Rotilio G, Valenti P. Increased expression of periplasmic Cu, Zn superoxide dismutase enhances survival of Escherichia coli invasive strains within nonphagocytic cells. Infect Immun. 2000;68:30–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yoon JW, Youn LJ, Park YH, Hovde CJ. Involvement of the Escherichia coli O157:H7(pO157) ecf operon and lipid a myristoyl transferase activity in bacterial survival in the bovine gastrointestinal tract and bacterial persistence in farm water troughs. Infect Immun. 2005;73:2367–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sandoval NR, Papoutsakis ET. Engineering membrane and cell-wall programs for tolerance to toxic chemicals: beyond solo genes. Curr Opin Microbiol. 2016;33:56–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Olaya R, Laetitia T, Patricia LL, Thierry F, Julie M, Erick D, Jean-Marc G. Screening of Escherichia coli species biodiversity reveals new biofilm-associated antiadhesion polysaccharides. MBio. 2011;2:00043-11.
Google Scholar
Yong-Mei Z, Rock CO. Membrane lipid homeostasis in bacteria. Nat Rev Microbiol. 2008;6:222.
Article
CAS
Google Scholar
Oh HY, Lee JO, Kim OB. Increase of organic solvent tolerance of Escherichia coli by the deletion of two regulator genes, fadR and marR. Appl Microbiol Biotechnol. 2012;96:1619–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yunck R, Cho H, Bernhardt TG. Identification of MltG as a potential terminase for peptidoglycan polymerization in bacteria. Mol Microbiol. 2016;99:700–18.
Article
CAS
PubMed
Google Scholar
Mueller EA, Egan AJF, Breukink E, Vollmer W, Levin PA. Plasticity in Escherichia coli cell wall metabolism promotes fitness and mediates intrinsic antibiotic resistance across environmental conditions. Micr Infec Dis. 2018;8:e40754.
Google Scholar
McPhee JB, Lewenza S, Hancock RE. Cationic antimicrobial peptides activate a two-component regulatory system, PmrA–PmrB, that regulates resistance to polymyxin B and cationic antimicrobial peptides in Pseudomonas aeruginosa. Mol Microbiol. 2003;50:205–17.
Article
CAS
PubMed
Google Scholar
Perez JC, Groisman EA. Acid pH activation of the PmrA/PmrB two-component regulatory system of Salmonella enterica. Mol Microbiol. 2007;63:283–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jung K, Fried L, Behr S, Heermann R. Histidine kinases and response regulators in networks. Curr Opin Microbiol. 2012;15:118–24.
Article
CAS
PubMed
Google Scholar
Kang A, Tan MH, Ling H, Chang MW. Systems-level characterization and engineering of oxidative stress tolerance in Escherichia coli under anaerobic conditions. Mol BioSyst. 2013;9:285–95.
Article
CAS
PubMed
Google Scholar
Schneider BL, James VH, Larry R. Putrescine catabolism is a metabolic response to several stresses in Escherichia coli. Mol Microbiol. 2013;88:537–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiuhua P, Phong V, Byrd TF, Saleena G, Patricia S, Mukamolova GV, Shiping W, Buka S, Howard ST. Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. Microbiology. 2007;153:1229.
Article
CAS
Google Scholar
Fernandes P, Ferreira BS, Cabral JMS. Solvent tolerance in bacteria: role of efflux pumps and cross-resistance with antibiotics. Int J Antimicrob Agents. 2003;22:211–6.
Article
CAS
PubMed
Google Scholar
Marteyn BS, Gouzel K, Fenton AK, Gazi AD, Nicholas W, Lhousseine T, Marie-Christine P, Jean-Michel B, Oemer P, Daniel L. ZapE is a novel cell division protein interacting with FtsZ and modulating the Z-ring dynamics. MBio. 2014;5:00022-14.
Article
CAS
Google Scholar
Xiangmin L, Liqun K, Hui L, Xuanxian P. Fluctuation of multiple metabolic pathways is required for Escherichia coli in response to chlortetracycline stress. Mol BioSyst. 2014;10:901–8.
Article
Google Scholar
Harms A, Maisonneuve E, Gerdes K. Mechanisms of bacterial persistence during stress and antibiotic exposure. Science. 2016;354:aaf4268.
Article
PubMed
CAS
Google Scholar
Poole K. Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria. Trends Microbiol. 2012;20:227–34.
Article
CAS
PubMed
Google Scholar
Sutton M, Jan-Erik L, Christopher H, Hanjo H. Vitamin B6: a long known compound of surprising complexity. Molecules. 2009;14:329–51.
Article
CAS
Google Scholar
Carl B, Sylvie E, Swem LR, Swem DL, Shinji M. Redox and light regulation of gene expression in photosynthetic prokaryotes. Philos Trans R Soc Lond B Biol Sci. 2003;358:147–53.
Article
CAS
Google Scholar
Lushchak VI. Adaptive response to oxidative stress: bacteria, fungi, plants and animals. Comp Biochem Physiol C Toxicol Pharmacol, vol 153. 2010/10/21 edition; 2011; p. 175–90.
Wang X, Kim Y, Ma Q, Hong SH, Pokusaeva K, Sturino JM, Wood TK. Cryptic prophages help bacteria cope with adverse environments. Nat Commun. 2010;1:147.
Article
PubMed
CAS
Google Scholar
Sharma S, Cavallaro G, Rosato A. A systematic investigation of multiheme c-type cytochromes in prokaryotes. J Biol Inorg Chem. 2010;15:559–71.
Article
CAS
PubMed
Google Scholar
Tschowri N, Lindenberg S, Hengge R. Molecular function and potential evolution of the biofilm-modulating blue light-signalling pathway of Escherichia coli. Mol Microbiol. 2012;85:893–906.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harwani D. Regulation of gene expression: cryptic β-glucoside (bgl) operon of Escherichia coli as a paradigm. Braz J Microbiol. 2014;45:1139–44.
Article
CAS
PubMed
Google Scholar
Toba FA, Thompson MG, Campbell BR, Junker LM, Rueggeberg K-G, Hay AG. Role of DLP12 lysis genes in Escherichia coli biofilm formation. Microbiology. 2011;157:1640–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Salscheider SL, Jahn A, Schnetz K. Transcriptional regulation by BglJ–RcsB, a pleiotropic heteromeric activator in Escherichia coli. Nucleic Acids Res. 2014;42:2999–3008.
Article
CAS
PubMed
Google Scholar
Ackerley DF, Barak Y, Lynch SV, Curtin J, Matin A. Effect of chromate stress on Escherichia coli K-12. J Bacteriol. 2006;188:3371.
Article
CAS
PubMed
PubMed Central
Google Scholar
Choe D, Lee JH, Yoo M, Hwang S, Sung BH, Cho S, Palsson B, Kim SC, Cho B-K. Adaptive laboratory evolution of a genome-reduced Escherichia coli. Nat Commun. 2019;10:935.
Article
PubMed
PubMed Central
CAS
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc B. 1995;57:289–300.
Google Scholar
Mater methods 2013;3:203 https://www.labome.com/method/RNA-seq-Using-Next-Generation-Sequencing.html, Accessed 6 Sept 2019.
Li Y, Lin Z, Huang C, Zhang Y, Wang Z, Tang Y-J, Chen T, Zhao X. Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng. 2015;31:13–21.
Article
PubMed
CAS
Google Scholar
Chen M, Liu T, Chen X, Chen L, Zhang W, Wang J, Gao L, Chen Y, Peng X. Subcritical co-solvents extraction of lipid from wet microalgae pastes of Nannochloropsis sp. Eur J Lipid Sci Tech. 2012;114:205–12.
Article
CAS
Google Scholar