Skip to main content
SpringerLink
Log in
Book cover

In Silico Approach for Sustainable Agriculture pp 141–159Cite as

In Silico Approach to Analyze the Biochemical Pathways of Bacterial Metabolite Synthesis

  • Chapter
  • First Online:

Abstract

Plant growth-promoting bacteria are well known to produce various bacterial secondary metabolites (BSM) which are much diversified in their origin and structure. These metabolites provide beneficial effect to crops which lead to sustainable agriculture. Each BSM is produced inside the bacterial cell by the regulation of specific biochemical pathways. To increase the yield of crops, there is a need to understand the metabolic pathway for the synthesis of secondary metabolites. Experimental approach to study the metabolic pathway was found to be limiting in terms of time and money. Development in the genome sequencing technologies and computational methods shifts the focus of researchers toward in silico approaches to reconstruct the biochemical pathways of metabolite production in genome-scale metabolic level. There are varieties of computational databases and tools available for the analysis of biosynthetic gene clusters including the prediction of non-ribosomal peptide synthetases (NRPS) and polyketide synthase (PKS) enzymes which encode for bacterial metabolites. These tools are developed to analyze the biochemical pathways for metabolite production. The present chapter gives a comprehensive overview on the in silico approach for the reconstruction of biochemical pathway and different databases and computational tools associated with it.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Bachmann BO, Van Lanen SG, Baltz RH (2014) Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol 41(2):175–184

    Article  CAS  PubMed  Google Scholar 

  • Barea J, Navarro E, Montoya E (1976) Production of plant growth regulators by rhizosphere phosphate-solubilizing bacteria. J Appl Microbiol 40(2):129–134

    CAS  Google Scholar 

  • Bashan Y, De-Bashan L (2005) Plant growth-promoting. Encycl Soils Environ 1:103–115

    Article  Google Scholar 

  • Bibb MJ (2005) Regulation of secondary metabolism in streptomycetes. Curr Opin Microbiol 8(2):208–215

    Article  CAS  PubMed  Google Scholar 

  • Bode HB (2009) Entomopathogenic bacteria as a source of secondary metabolites. Curr Opin Chem Biol 13(2):224–230

    Article  CAS  PubMed  Google Scholar 

  • Bottini R, Cassán F, Piccoli P (2004) Gibberellin production by bacteria and its involvement in plant growth promotion and yield increase. Appl Microbiol Biotechnol 65(5):497–503

    Article  CAS  PubMed  Google Scholar 

  • Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chaudhary AK, Dhakal D, Sohng JK (2013) An insight into the “-omics” based engineering of streptomycetes for secondary metabolite overproduction. BioMed Res Int 2013

    Google Scholar 

  • Chen G, Li X, Waters B, Davies J (2000) Enhanced production of microbial metabolites in the presence of dimethyl sulfoxide. J Antibiot 53(10):1145–1153

    Article  CAS  Google Scholar 

  • Cimermancic P, Medema MH, Claesen J, Kurita K, Brown LCW, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J (2014) Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158(2):412–421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Compant S, Duffy B, Nowak J, Clément C, Barka EA (2005) Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 71(9):4951–4959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conde M, do Rosario P, Sauter T, Pfau T (2016) Constraint based modeling going multicellular. Front Mol Biosci 3:3

    Google Scholar 

  • Conway KR, Boddy CN (2012) Clustermine360: a database of microbial pks/nrps biosynthesis. Nucleic Acids Res 41(D1):D402–D407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO (2001) Metabolic modeling of microbial strains in silico. Trends Biochem Sci 26(3):179–186

    Article  CAS  PubMed  Google Scholar 

  • Diminic J, Zucko J, Ruzic IT, Gacesa R, Hranueli D, Long PF, Cullum J, Starcevic A (2013) Databases of the thiotemplate modular systems (csdb) and their in silico recombinants (r-csdb). J Ind Microbiol Biotechnol 40(6):653–659

    Article  CAS  PubMed  Google Scholar 

  • Durot M, Bourguignon P-Y, Schachter V (2008) Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 33(1):164–190

    Article  CAS  PubMed  Google Scholar 

  • Edwards JS, Palsson BO (2000) Metabolic flux balance analysis and the in silico analysis of Escherichia coli k-12 gene deletions. BMC Bioinforma 1(1):1

    Article  CAS  Google Scholar 

  • Edwards JS, Covert M, Palsson B (2002) Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 4(3):133–140

    Article  PubMed  Google Scholar 

  • Franco-Correa M, Chavarro-Anzola V (2016) Actinobacteria as plant growth-promoting rhizobacteria. In: Actinobacteria-basics and biotechnological applications. InTech

    Google Scholar 

  • Gamalero E, Glick BR (2015) Bacterial modulation of plant ethylene levels. Plant Physiol 169(1):13–22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gaspar T, Kevers C, Penel C, Greppin H, Reid DM, Thorpe TA (1996) Plant hormones and plant growth regulators in plant tissue culture. In Vitro Cell Dev Biol-Plant 32(4):272–289

    Article  CAS  Google Scholar 

  • Glick BR (2014) Bacteria with acc deaminase can promote plant growth and help to feed the world. Microbiol Res 169(1):30–39

    Article  CAS  PubMed  Google Scholar 

  • Gupta G, Parihar SS, Ahirwar NK, Snehi SK, Singh V (2015) Plant growth promoting rhizobacteria (pgpr): current and future prospects for development of sustainable agriculture. J Microb Biochem Technol 7(2):096–102

    CAS  Google Scholar 

  • Haggart CR, Bartell JA, Saucerman JJ, Papin JA (2011) Whole-genome metabolic network reconstruction and constraint-based modeling⋆. In: Methods in enzymology. Elsevier, Amsterdam, pp 411–433

    Google Scholar 

  • Hao Y, Charles TC, Glick BR (2007) Acc deaminase from plant growth-promoting bacteria affects crown gall development. Can J Microbiol 53(12):1291–1299

    Article  CAS  PubMed  Google Scholar 

  • van Heel AJ, de Jong A, Montalban-Lopez M, Kok J, Kuipers OP (2013) Bagel3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides. Nucleic Acids Res 41(W1):W448–W453

    Article  PubMed  PubMed Central  Google Scholar 

  • Hwang K-S, Kim HU, Charusanti P, Palsson BØ, Lee SY (2014) Systems biology and biotechnology of streptomyces species for the production of secondary metabolites. Biotechnol Adv 32(2):255–268

    Article  CAS  PubMed  Google Scholar 

  • Ichikawa N, Sasagawa M, Yamamoto M, Komaki H, Yoshida Y, Yamazaki S, Fujita N (2012) Dobiscuit: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res 41(D1):D408–D414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jasim B, Joseph AA, John CJ, Mathew J, Radhakrishnan E (2014) Isolation and characterization of plant growth promoting endophytic bacteria from the rhizome of Zingiber officinale. 3. Biotech 4(2):197–204

    CAS  Google Scholar 

  • de Jesus Sousa JA, Olivares FL (2016) Plant growth promotion by streptomycetes: ecophysiology, mechanisms and applications. Chem Biolo Technol Agric 3(1):24

    Article  CAS  Google Scholar 

  • Kim HU, Charusanti P, Lee SY, Weber T (2016) Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites. Nat Prod Rep 33(8):933–941

    Article  CAS  PubMed  Google Scholar 

  • Kudoyarova G, Arkhipova T, Melent’ev A (2015) Role of bacterial phytohormones in plant growth regulation and their development. In: Bacterial metabolites in sustainable agroecosystem. Springer, Cham, pp 69–86

    Chapter  Google Scholar 

  • Kumar RR, Prasad S (2011) Metabolic engineering of bacteria. Indian J Microbiol 51(3):403–409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li MH, Ung PM, Zajkowski J, Garneau-Tsodikova S, Sherman DH (2009) Automated genome mining for natural products. BMC Bioinforma 10(1):185

    Article  CAS  Google Scholar 

  • Little PF, Subramaniam S, Jorde LB, Dunn MJ (2005) Encyclopedia of genetics, genomics, proteomics and bioinformatics. Wiley, Hoboken

    Google Scholar 

  • Liu M, Bienfait B, Sacher O, Gasteiger J, Siezen RJ, Nauta A, Geurts JM (2014) Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach “reverse pathway engineering”. PLoS One 9(1):e84769

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Llaneras F, Picó J (2008) Stoichiometric modelling of cell metabolism. J Biosci Bioeng 105(1):1–11

    Article  CAS  PubMed  Google Scholar 

  • Mahadevan R, Edwards JS, Doyle FJ III (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J 83(3):1331–1340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matiru VN, Dakora FD (2004) Potential use of rhizobial bacteria as promoters of plant growth for increased yield in landraces of African cereal crops. Afr J Biotechnol 3(1):1–7

    Article  CAS  Google Scholar 

  • Niu G (2017) Genomics-driven natural product discovery in actinomycetes. Trends Biotechnol 36(3):238–241

    Article  CAS  PubMed  Google Scholar 

  • Odoh CK (2017) Plant growth promoting rhizobacteria (pgpr): a bioprotectant bioinoculant for sustainable agrobiology. Rev Int J Adv Res Biol Sci 4(5):123–142

    Google Scholar 

  • van Pée K-H (1996) Biosynthesis of halogenated metabolites by bacteria. Ann Revin Microbiol 50(1):375–399

    Article  Google Scholar 

  • Price ND, Papin JA, Schilling CH, Palsson BO (2003) Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21(4):162–169

    Article  CAS  PubMed  Google Scholar 

  • Price ND, Reed JL, Palsson BØ (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2(11):886

    Article  CAS  PubMed  Google Scholar 

  • Radhakrishnan R, Hashem A, Abd_Allah EF (2017) Bacillus: a biological tool for crop improvement through bio-molecular changes in adverse environments. Front Physiol 8:667

    Article  PubMed  PubMed Central  Google Scholar 

  • Schippers B, Bakker AW, Bakker PA (1987) Interactions of deleterious and beneficial rhizosphere microorganisms and the effect of cropping practices. Annu Rev Phytopathol 25(1):339–358

    Article  Google Scholar 

  • Schuster S, Dandekar T, Fell DA (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 17(2):53–60

    Article  CAS  PubMed  Google Scholar 

  • Seaver S, Bradbury LM, Frelin O, Zarecki R, Ruppin E, Hanson AD, Henry CS (2015) Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. Front Plant Sci 6:142

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh RP, Shelke GM, Kumar A, Jha PN (2015) Corrigendum: biochemistry and genetics of acc deaminase: a weapon to “stress ethylene” produced in plants. Front Microbiol 6:937

    PubMed  PubMed Central  Google Scholar 

  • Souza Rd, Ambrosini A, Passaglia LM (2015) Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol 38(4):401–419

    Article  PubMed  PubMed Central  Google Scholar 

  • Spaepen S, Vanderleyden J (2011) Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol 3(4):a001438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stephanopoulos G, Vallino JJ (1991) Network rigidity and metabolic engineering in metabolite overproduction. Science 252(5013):1675–1681

    Article  CAS  PubMed  Google Scholar 

  • Starcevic A, Zucko J, Simunkovic J, Long PF, Cullum J, Hranueli D (2008) Clustscan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures. Nucleic Acids Res 36(21):6882–6892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stulberg ER, Lozano GL, Morin JB, Park H, Baraban EG, Mlot C, Heffelfinger C, Phillips GM, Rush JS, Phillips AJ (2016) Genomic and secondary metabolite analyses of streptomyces sp. 2aw provide insight into the evolution of the cycloheximide pathway. Front Microbiol 7:573

    Article  PubMed  PubMed Central  Google Scholar 

  • Taffs R, Aston JE, Brileya K, Jay Z, Klatt CG, McGlynn S, Mallette N, Montross S, Gerlach R, Inskeep WP (2009) In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Syst Biol 3(1):114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tak HI, Ahmad F, Babalola OO (2013) Advances in the application of plant growth-promoting rhizobacteria in phytoremediation of heavy metals. In: Reviews of environmental contamination and toxicology, vol 223. Springer, New York, pp 33–52

    Google Scholar 

  • Tatsis EC, O’Connor SE (2016) New developments in engineering plant metabolic pathways. Curr Opin Biotechnol 42:126–132

    Article  CAS  PubMed  Google Scholar 

  • Tounekti T, Hernández I, Munné-Bosch S (2013) Salicylic acid biosynthesis and role in modulating terpenoid and flavonoid metabolism in plant responses to abiotic stress. In: Salicylic acid. Springer, Dordrecht, pp 141–162

    Chapter  Google Scholar 

  • Vessey JK (2003) Plant growth promoting rhizobacteria as biofertilizers. Plant Soil 255(2):571–586

    Article  CAS  Google Scholar 

  • Wang Y, Eddy JA, Price ND (2012) Reconstruction of genome-scale metabolic models for 126 human tissues using mcadre. BMC Syst Biol 6(1):153

    Article  PubMed  PubMed Central  Google Scholar 

  • Weaver DS, Keseler IM, Mackie A, Paulsen IT, Karp PD (2014) A genome-scale metabolic flux model of Escherichia coli k–12 derived from the ecocyc database. BMC Syst Biol 8(1):79

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weber T (2014) In silico tools for the analysis of antibiotic biosynthetic pathways. Int J Med Microbiol 304(3–4):230–235

    Article  CAS  PubMed  Google Scholar 

  • Weber T, Rausch C, Lopez P, Hoof I, Gaykova V, Huson D, Wohlleben W (2009) Clusean: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J Biotechnol 140(1–2):13–17

    Article  CAS  PubMed  Google Scholar 

  • Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W (2015) Antismash 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43(W1):W237–W243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yadav G, Gokhale RS, Mohanty D (2003) Searchpks: a program for detection and analysis of polyketide synthase domains. Nucleic Acids Res 31(13):3654–3658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ziemert N, Alanjary M, Weber T (2016) The evolution of genome mining in microbes–a review. Nat Prod Rep 33(8):988–1005

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India

    Tania, Mehendi Goyal & Manoj Baranwal

Authors
  1. Tania
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mehendi Goyal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Manoj Baranwal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Manoj Baranwal .

Editor information

Editors and Affiliations

  1. Department of Microbiology, Faculty of Life Sciences, PDM University, Bahadurgarh, Haryana, India

    Devendra K. Choudhary

  2. Centre for Life Sciences, Central University of Jharkhand, Ranchi, Jharkhand, India

    Manoj Kumar

  3. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Ram Prasad

  4. Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, India

    Vivek Kumar

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Tania, Goyal, M., Baranwal, M. (2018). In Silico Approach to Analyze the Biochemical Pathways of Bacterial Metabolite Synthesis. In: Choudhary, D., Kumar, M., Prasad, R., Kumar, V. (eds) In Silico Approach for Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-13-0347-0_8

Download citation

Publish with us

Policies and ethics

Search

Navigation