Skip to main content

Systems and Synthetic Biology Approach to Understand the Importance of Host-Pathogen Interaction

  • Chapter
  • First Online:
Microbial Interventions in Agriculture and Environment

Abstract

In this chapter, we have discussed the basic factors required to understand the systems biology of host-pathology interaction, which can be applied for modeling and simulating the interaction between plant and pathogens and to get an idea about drug discovery and metabolic engineering. Further, we highlight the high-throughput technologies, such as omics technologies (genomics, transcriptomics, proteomics, and metabolomics), which can be used as a tool for identifying molecular mechanisms of the cell and biochemical pathway of the host-pathogen system. Several mathematical models, such as genome-scale metabolic modeling (constrain-based modeling) and interaction-based modeling (e.g., gene regulatory networks and protein-protein-based interactions) have been demonstrated which help in understanding the genotypic-phenotypic relationship of the host-pathogen interactions.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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

Institutional subscriptions

References

  • Aderem A et al (2011) A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. MBio 2(1):e00325–e00310

    Article  PubMed  PubMed Central  Google Scholar 

  • Antoniewicz MR (2015) Methods and advances in metabolic flux analysis: a mini-review. J Ind Microbiol Biotechnol 42(3):317–325

    Article  CAS  PubMed  Google Scholar 

  • Bose B (2013) Systems biology: a biologist’s viewpoint. Prog Biophys Mol Biol 113(3):358–368

    Article  PubMed  Google Scholar 

  • Brown SA, Palmer KL, Whiteley M (2008) Revisiting the host as a growth medium. Nat Rev Microbiol 6(9):657–666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Çalık P, Özdamar TH (2011) Bioreaction network flux analysis for industrial microorganisms: a review. Rev Chem Eng 18(6):553–604

    Google Scholar 

  • Chae TU, Choi SY, Kim JW, Ko Y-S, Lee SY (2017) Recent advances in systems metabolic engineering tools and strategies. Curr Opin Biotechnol 47:67–82

    Article  CAS  PubMed  Google Scholar 

  • Chai LE, Loh SK, Low ST, Mohamad MS, Deris S, Zakaria Z (2014) A review on the computational approaches for gene regulatory network construction. Comput Biol Med 48:55–65

    Article  CAS  PubMed  Google Scholar 

  • Chavali AK, D’Auria KM, Hewlett EL, Pearson RD, Papin JA (2012) A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol 20(3):113–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen X, Shachar-Hill Y (2012) Insights into metabolic efficiency from flux analysis. J Exp Bot 63(6):2343–2351

    Article  CAS  PubMed  Google Scholar 

  • Chen R et al (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148(6):1293–1307

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chuang H-Y, Hofree M, Ideker T (2010) A decade of systems biology. Annu Rev Cell Dev Biol 26:721–744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Colizza V, Flammini A, Maritan A, Vespignani A (2005) Characterization and modeling of protein–protein interaction networks. Phys Stat Mech Appl 352(1):1–27

    Article  CAS  Google Scholar 

  • Dai Z, Locasale JW (2016) Understanding metabolism with flux analysis: from theory to application. Metab Eng 43:94–102

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Das S, Kalpana GV (2009) Reverse two-hybrid screening to analyze protein-protein interaction of HIV-1 viral and cellular proteins. Methods Mol Biol (Clifton NJ) 485:271–293

    Article  CAS  Google Scholar 

  • de Chassey B et al (2008) Hepatitis C virus infection protein network. Mol Syst Biol 4:230

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Deidda M, Piras C, Bassareo PP, Cadeddu Dessalvi C, Mercuro G (2015) Metabolomics, a promising approach to translational research in cardiology. IJC Metab Endocr 9:31–38

    Article  Google Scholar 

  • Del Chierico F et al (2014) Proteomics boosts translational and clinical microbiology. J Proteome 97:69–87

    Article  CAS  Google Scholar 

  • Dorogovtsev SN, Mendes JFF (2002) Evolution of networks. Adv Phys 51(4):1079–1187

    Article  Google Scholar 

  • Durmuş S, Çakır T, Özgür A, Guthke R (2015) A review on computational systems biology of pathogen–host interactions. Front Microbiol 6:235

    PubMed  PubMed Central  Google Scholar 

  • Durmuş S, Çakır T, Guthke R (2016) Editorial: computational systems biology of pathogen-host interactions. Front Microbiol 7:21

    Article  PubMed  PubMed Central  Google Scholar 

  • Eisenreich W, Heesemann J, Rudel T, Goebel W (2013) Metabolic host responses to infection by intracellular bacterial pathogens. Front Cell Infect Microbiol 3:24

    Article  PubMed  PubMed Central  Google Scholar 

  • Eriksson S, Lucchini S, Thompson A, Rhen M, Hinton JCD (2003) Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbiol 47(1):103–118

    Article  CAS  PubMed  Google Scholar 

  • Faust K, Croes D, van Helden J (2011) Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems 105(2):109–121

    Article  CAS  PubMed  Google Scholar 

  • Gardiner DM, Howlett BJ (2005) Bioinformatic and expression analysis of the putative gliotoxin biosynthetic gene cluster of Aspergillus fumigatus. FEMS Microbiol Lett 248(2):241–248

    Article  CAS  PubMed  Google Scholar 

  • Geng J, Nielsen J (2017) In silico analysis of human metabolism: reconstruction, contextualization and application of genome-scale models. Curr Opin Syst Biol 2:29–38

    Article  Google Scholar 

  • Gouzy A, Poquet Y, Neyrolles O (2014) Nitrogen metabolism in Mycobacterium tuberculosis physiology and virulence. Nat Rev Microbiol 12(11):729–737

    Article  PubMed  CAS  Google Scholar 

  • Grafahrend-Belau E, Junker A, Eschenröder A, Müller J, Schreiber F, Junker BH (2013) Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale. Plant Physiol 163(2):637–647

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guttman DS, McHardy AC, Schulze-Lefert P (2014) Microbial genome-enabled insights into plant-microorganism interactions. Nat Rev Genet 15(12):797–813

    Article  CAS  PubMed  Google Scholar 

  • Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R (2009) Gene regulatory network inference: data integration in dynamic models—a review. Biosystems 96(1):86–103

    Article  CAS  PubMed  Google Scholar 

  • Ikeuchi M et al (2018) A gene regulatory network for cellular reprogramming in plant regeneration. Plant Cell Physiol 59(4):770–782

    Article  CAS  PubMed Central  Google Scholar 

  • Karahalil B (2016) Overview of systems biology and omics technologies. Curr Med Chem 23(37):4221–4230

    Article  CAS  PubMed  Google Scholar 

  • Karahalil B, Kesimci E, Emerce E, Gumus T, Kanbak O (2011) The impact of OGG1, MTH1 and MnSOD gene polymorphisms on 8-hydroxy-2′-deoxyguanosine and cellular superoxide dismutase activity in myocardial ischemia-reperfusion. Mol Biol Rep 38(4):2427–2435

    Article  CAS  PubMed  Google Scholar 

  • Kauffman KJ, Prakash P, Edwards JS (2003) Advances in flux balance analysis. Curr Opin Biotechnol 14(5):491–496

    Article  CAS  PubMed  Google Scholar 

  • Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY (2012) Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol 23(4):617–623

    Article  CAS  PubMed  Google Scholar 

  • Kitano H (2002) Systems biology: a brief overview. Science 295(5560):1662–1664

    Article  CAS  PubMed  Google Scholar 

  • Larance M, Lamond AI (2015) Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol 16(5):269–280

    Article  CAS  PubMed  Google Scholar 

  • Likić VA, McConville MJ, Lithgow T, Bacic A (2010) Systems biology: the next frontier for bioinformatics. Adv Bioinforma 2010:1–10. [Online]. Available: https://www.hindawi.com/journals/abi/2010/268925/. Accessed 08 Sept 2018

    Article  Google Scholar 

  • Mardan-Nik M et al (2016) Association of heat shock protein70-2 (HSP70-2) gene polymorphism with obesity. Ann Hum Biol 43(6):542–546

    Article  PubMed  Google Scholar 

  • Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296(5569):910–913

    Article  CAS  PubMed  Google Scholar 

  • McCourt CM et al (2013) Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One 8(7):e69604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McDermott JE et al (2011) Technologies and approaches to elucidate and model the virulence program of salmonella. Front Microbiol 2:121

    Article  PubMed  PubMed Central  Google Scholar 

  • Milenbachs AA, Brown DP, Moors M, Youngman P (1997) Carbon-source regulation of virulence gene expression in Listeria monocytogenes. Mol Microbiol 23(5):1075–1085

    Article  CAS  PubMed  Google Scholar 

  • Mukhtar MS et al (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science 333(6042):596–601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Niemann GS et al (2011) Discovery of novel secreted virulence factors from Salmonella enterica serovar Typhimurium by proteomic analysis of culture supernatants. Infect Immun 79(1):33–43

    Article  CAS  PubMed  Google Scholar 

  • Orth JD, Thiele I, Palsson BØ (2010) What is flux balance analysis? Nat Biotechnol 28(3):245–248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peng X et al (2010) Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. MBio 1(5):e00206–e00210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prabhu AA, Veeranki VD, Dsilva SJ (2016) Improving the production of human interferon gamma (hIFN-γ) in Pichia pastoris cell factory: an approach of cell level. Process Biochem 51(6):709–718

    Article  CAS  Google Scholar 

  • Prabhu AA, Purkayastha A, Mandal B, Kumar JP, Mandal BB, Dasu VV (2017) A novel reverse micellar purification strategy for histidine tagged human interferon gamma (hIFN-γ) protein from Pichia pastoris. Int J Biol Macromol 107:2512–2524

    Article  PubMed  CAS  Google Scholar 

  • Prabhu AA, Bharali B, Singh AK, Allaka M, Sukumar P, Veeranki VD (2018) Engineering folding mechanism through Hsp70 and Hsp40 chaperones for enhancing the production of recombinant human interferon gamma (rhIFN-γ) in Pichia pastoris cell factory. Chem Eng Sci 181:58–67

    Article  CAS  Google Scholar 

  • Qian C, Cao X (2013) Regulation of toll-like receptor signaling pathways in innate immune responses. Ann N Y Acad Sci 1283:67–74

    Article  CAS  PubMed  Google Scholar 

  • Raghunathan A, Reed J, Shin S, Palsson B, Daefler S (2009) Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol 3:38

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Raja K, Patrick M, Gao Y, Madu D, Yang Y, Tsoi LC (2017) A review of recent advancement in integrating omics data with literature mining towards biomedical discoveries. Int J Genomics 2017:1–10. [Online]. Available: https://www.hindawi.com/journals/ijg/2017/6213474/. Accessed 09 Sept 2018

    Article  CAS  Google Scholar 

  • Raman K, Chandra N (2009) Flux balance analysis of biological systems: applications and challenges. Brief Bioinform 10(4):435–449

    Article  CAS  PubMed  Google Scholar 

  • Ravasz E, Barabasi A-L (2003) Hierarchical organization in complex networks. Phys Rev E 67(2):026112

    Article  CAS  Google Scholar 

  • Sarker M, Talcott C, Galande AK (2013) In silico systems biology approaches for the identification of antimicrobial targets. Methods Mol Biol (Clifton NJ) 993:13–30

    Article  CAS  Google Scholar 

  • Scharf DH, Heinekamp T, Remme N, Hortschansky P, Brakhage AA, Hertweck C (2012) Biosynthesis and function of gliotoxin in Aspergillus fumigatus. Appl Microbiol Biotechnol 93(2):467–472

    Article  CAS  PubMed  Google Scholar 

  • Shao M, Yang Y, Guan J, Zhou S (2012) A comparison study on protein-protein interaction network models. In: 2012 IEEE International Conference on Bioinformatics and Biomedicine, pp 1–4

    Google Scholar 

  • Shapira SD et al (2009) A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139(7):1255–1267

    Article  PubMed  PubMed Central  Google Scholar 

  • Shi L et al (2006) Proteomic analysis of Salmonella enterica serovar typhimurium isolated from RAW 264.7 macrophages: identification of a novel protein that contributes to the replication of serovar typhimurium inside macrophages. J Biol Chem 281(39):29131–29140

    Article  CAS  PubMed  Google Scholar 

  • Thompson D, Regev A, Roy S (2015) Comparative analysis of gene regulatory networks: from network reconstruction to evolution. Annu Rev Cell Dev Biol 31:399–428

    Article  CAS  PubMed  Google Scholar 

  • Varala K et al (2018) Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proc Natl Acad Sci 115:6494–6499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vijesh N, Chakrabarti SK, Sreekumar J (2013) Modeling of gene regulatory networks: a review. J Biomed Sci Eng 06:223

    Article  Google Scholar 

  • Wright PC, Noirel J, Ow S-Y, Fazeli A (2012) A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 77(4):738–765.e52

    Article  CAS  PubMed  Google Scholar 

  • Yağar S, Yavaş S, Karahalil B (2011) The role of the ADRA2A C1291G genetic polymorphism in response to dexmedetomidine on patients undergoing coronary artery surgery. Mol Biol Rep 38(5):3383–3389

    Article  PubMed  CAS  Google Scholar 

  • Yook S-H, Oltvai ZN, Barabási A-L (2004) Functional and topological characterization of protein interaction networks. Proteomics 4(4):928–942

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Gao P, Yuan JS (2010) Plant protein-protein interaction network and interactome. Curr Genomics 11(1):40–46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou H et al (2014) Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. Biol Direct 9:5

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu G et al (2016) PPIM: a protein-protein interaction database for maize. Plant Physiol 170(2):618–626

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to V. Venkatadasu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Prabhu, A.A., Venkatadasu, V. (2019). Systems and Synthetic Biology Approach to Understand the Importance of Host-Pathogen Interaction. In: Singh, D., Prabha, R. (eds) Microbial Interventions in Agriculture and Environment. Springer, Singapore. https://doi.org/10.1007/978-981-32-9084-6_19

Download citation

Publish with us

Policies and ethics