Abstract
Information in public sequence databases on the genomes and metagenomes of microbes and plants has grown rapidly. In conjunction with technological developments in computational identification of biosynthetic gene clusters, molecular biology, synthetic biology, and analytical tools, this has revealed genes for enzymes with optimal and targeted function, as well as a rich pool of uncharacterized metabolic pathways. This chapter discusses different approaches to discovery of genes and metabolic pathways in microbes and plants in nature, such as genomic mining, transcriptome analysis, and metabolite profiling.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW (2012) Transforming clinical microbiology with bacterial genome sequencing. Nat Rev Genet 13:601–612
Rutledge PJ, Challis GL (2015) Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13:509–523
Chica RA, Doucet N, Pelletier JN (2005) Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Curr Opin Biotechnol 16:378–384
Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D et al (2015) Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun 6. https://doi.org/10.1038/ncomms10005
Heins RA, Cheng X, Nath S (2014) Phylogenomically guided identification of industrially relevant GH1 beta-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol 9:2082–2091
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–W37
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Letunic I, Bork P (2007) Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127–128
Letunic I, Bork P (2011) Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:475–478
Huang Y, Niu B, Gao Y, Fu L, Li W (2010) CD-HIT suite: a web server for clustering and comparing biological sequences. Bioinformatics 26:680–682
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649
Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette TJ et al (2013) High-resolution comparative modeling with RosettaCM. Structure 21:1735–1742
Oberortner E, Cheng J, Hillson NJ, Deutsch S (2016) Streamlining the design-to-build transition with build-optimization software tools. ACS Synth Biol. https://doi.org/10.1021/acssynbio.6b00200
Enquist-Newman M, Faust AME, Bravo DD, Santos CN, Raisner RM, Hanel A (2014) Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform. Nature 505:239–243
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR et al (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L (2013) Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotech 31:46–53
Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CNS, Kim PB et al (2012) An engineered microbial platform for direct biofuel production from brown macroalgae. Science 335:308–313
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R et al (2015) AntiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C et al (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 39(suppl 1):D225–D229
Malcolmson J, Meek SJ, Sattely ES, Schrock RR, Hoveyda AH (2008) Highly efficient molybdenum-based catalysts for enantioselective alkene metathesis. Nature 456:933–937
Klein P, Sattely ES (2015) Two cytochromes P450 catalyze S-heterocyclizations in cabbage phytoalexin biosynthesis. Nat Chem Biol 11:837–839
Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78:779–787
De Vos RC, Moco S, Lommen A, Keurentjes JJ, Bino RJ, Hall RD (2007) Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc 2:778–791
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J et al (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:D1178–D1186
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Ke, J., Yoshikuni, Y. (2019). Pathway and Gene Discovery from Natural Hosts and Organisms. In: Santos, C., Ajikumar, P. (eds) Microbial Metabolic Engineering. Methods in Molecular Biology, vol 1927. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9142-6_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9142-6_1
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-9141-9
Online ISBN: 978-1-4939-9142-6
eBook Packages: Springer Protocols