Skip to main content
SpringerLink
Log in

Gene Network Holography of the Soil Bacterium Bacillus subtilis

  • Chapter
  • First Online:
Biocommunication in Soil Microorganisms

Part of the book series: Soil Biology ((SOILBIOL,volume 23))

Abstract

Microarray technology has played an important role in promoting the understanding of gene network regulations. Different supervised and unsupervised analysis methods have been devised to extract meaningful information from gene-expression data. In this chapter, we introduce the Genome Holography method (GH) for the analysis of gene-expression data and discuss some of its possible applications, such as clique finding technique and Functional Holography Minimal Spanning Tree (FHMST). We employ this new technique to analyze a database of gene expression of Bacillus subtilis exposed to sublethal levels of 37 different antibiotics. Using this method, we present a new way to visualize and investigate the relationships between genes in different gene regulatory networks, and how these relationships change over time due to an environmental stress.

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

Access this chapter

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 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

  • Albert A, Barabási AL (2002) Statistical mechanics of complex networks. Rev Mod Phys 47:47–97

    Article  Google Scholar 

  • Alon U, Barkai N, Notterman DA, Gish K, Ybarra S et al (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745–6750

    Article  CAS  PubMed  Google Scholar 

  • Atsuhiro A, Eiji K, Michihiro H, Mitsuo O (2003) Inhibition of Bacillus subtilis aprE expression by lincomycin at the posttranscriptional level through inhibition of ppGpp synthesis. J Biochem 134:691–697

    Article  Google Scholar 

  • Azevedo V, Sorokin A, Ehrlich SD, Serror P (1993) The transcriptional organization of the Bacillus subtilis 168 chromosome region between the spoVAF and serA genetic loci. Mol Microbiol 10:397–405

    Article  CAS  PubMed  Google Scholar 

  • Baruchi I, Ben-Jacob E (2004) Functional holography of recorded neuronal networks activity. Neuroinformatics 2:333–352

    Article  PubMed  Google Scholar 

  • Baruchi I, Grossman D, Volman V, Shein M, Hunter J et al (2006) Functional holography analysis: simplifying the complexity of dynamical networks. Chaos 16(1):015112

    Article  PubMed  Google Scholar 

  • Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6:281–297

    Article  CAS  PubMed  Google Scholar 

  • Burbulys D, Trach K, Hoch J (1991) Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay. Cell 8:545–552

    Article  Google Scholar 

  • Caldwell R, Sapolsky R, Weyler W, Maile RR, Causey SC et al (2001) Correlation between Bacillus subtilis scoC phenotype and gene expression determined using microarrays for transcriptome analysis. J Bacteriol 183:7329–7340

    Article  CAS  PubMed  Google Scholar 

  • Chander P, Halbig KM, Miller JK, Fields CJ, Bonner HK et al (2005) Structure of the nucleotide complex of PyrR, the pyr attenuation protein from Bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides. J Bacteriol 187:1773–1782

    Article  CAS  PubMed  Google Scholar 

  • Claverys J, Prudhomme M, Martin B (2006) Induction of competence regulons as a general response to stress in gram-positive bacteria. Annu Rev Microbiol 60:451–475

    Article  CAS  PubMed  Google Scholar 

  • Coronnello C, Tumminello M, Lillo F, Micciche S, Mantegna RN (2005) Sector identification in a set of stock return time series traded at the London Stock Exchange. Acta Phys Pol B 36:2653–2679

    CAS  Google Scholar 

  • Dahl MK, Msadek T, Kunst F, Rapoport G (1992) The phosphorylation state of the DegU response regulator acts as a molecular switch allowing either degradative enzyme synthesis or expression of genetic competence in Bacillus subtilis. J Biol Chem 267:14509–14514

    CAS  PubMed  Google Scholar 

  • de Jong H (2002) Modelling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9:67–103

    Article  PubMed  Google Scholar 

  • Donetti L, Hurtado PI, Munoz MA (2005) Entangled networks, synchronization, and optimal network topology. Phys Rev Lett 95:188701

    Article  PubMed  Google Scholar 

  • Dowds B, Murphy P, McConnell D (1987) Relationship among oxidative stress, growth cycle, and sporulation in Bacillus subtilis. J Bacteriol 169:5771–5775

    CAS  PubMed  Google Scholar 

  • Eisen M, Spellman P, Brown P (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–14868

    Article  CAS  PubMed  Google Scholar 

  • Engelberg-Kulka H, Hazan R (2003) Microbiology. Cannibals defy starvation and avoid sporulation. Science 301:467–468

    Article  CAS  PubMed  Google Scholar 

  • Errington J (1993) Bacillus subtilis sporulation: regulation of gene expression and control of morphogenesis. Microbiol Rev 57:1–33

    CAS  PubMed  Google Scholar 

  • Everitt BS (1993) Cluster analysis. Edward Arnold, London

    Google Scholar 

  • Fawcett P, Eichenberger P, Losick R, Youngman P (2000) The transcriptional profile of early to middle sporulation in Bacillus subtilis. Proc Natl Acad Sci USA 97:8063–8068

    Article  CAS  PubMed  Google Scholar 

  • Fuchs E, Ayali A, Ben-Jacob E, Boccaletti S (2009) Formation of synchronization cliques during development of modular neural networks. Phys Biol 6(3):036018

    Article  PubMed  Google Scholar 

  • Fujita M, Losick R (2005) Evidence that entry into sporulation in Bacillus subtilis is governed by a gradual increase in the level and activity of the master regulator Spo0A. Genes Dev 19:2236–2244

    Article  CAS  PubMed  Google Scholar 

  • Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M et al (2000) Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16:906–914

    Article  CAS  PubMed  Google Scholar 

  • Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M et al (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531–537

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez-Pastor JE, Hobbs EC, Losick R (2003) Cannibalism by sporulating bacteria. Science 301:510–513

    Article  CAS  PubMed  Google Scholar 

  • Graham RL, Hell P (1985) On the history of the minimum spanning tree problem. IEEE Ann Hist Comput 7:43–57

    Article  Google Scholar 

  • Grossman A (1995) Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Annu Rev Genet 29:477–508

    Article  CAS  PubMed  Google Scholar 

  • Hamoen LW, Smits WK, de Jong A, Holsappel S, Kuipers OP (2002) Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Res 30:5517–5528

    Article  CAS  PubMed  Google Scholar 

  • Hamoen LW, Van Werkhoven AF, Venema G, Dubnau D (2000) The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis. Proc Natl Acad Sci USA 97:9246–9251

    Article  CAS  PubMed  Google Scholar 

  • Hansen P, Jaumard B (1997) Cluster analysis and mathematical programming. Math Program 79:191–215

    Google Scholar 

  • Hartigan JA (1975) Clustering algorithms. Wiley, New York

    Google Scholar 

  • Hartuv E, Shami R (2000) A clustering algorithm based on graph connectivity. Inf Process Lett 76:175–181

    Article  Google Scholar 

  • Herwig R, Poustka AJ, Müller C, Bull C, Lehrach H et al (1999) Large-scale clustering of cDNA-fingerprinting data. Genome Res 9:1093–1105

    Article  CAS  PubMed  Google Scholar 

  • Hoch J (1993) Regulation of the phosphorelay and the initiation of sporulation in Bacillus subtilis. Annu Rev Microbiol 47:441–465

    Article  CAS  PubMed  Google Scholar 

  • Hutter B, Schaab C, Albrecht S, Borgmann M, Brunner NA et al (2004) Prediction of mechanisms of action of antibacterial compounds by gene expression profiling. Antimicrob Agents Chemother 48(8):2838–2844

    Article  CAS  PubMed  Google Scholar 

  • Jiang M, Shao W, Perego M, Hoch J (2000) Multiple histidine kinases regulate entry into stationary phase and sporulation in Bacillus subtilis. Mol Microbiol 38:535–542

    Article  CAS  PubMed  Google Scholar 

  • Jonas R, Holt S, Haldenwang W (1990) Effects of antibiotics on synthesis and persistence of sigma E in sporulating Bacillus subtilis. J Bacteriol 172:4616–4623

    CAS  PubMed  Google Scholar 

  • Kocabas P, Calik P, Calik G, Ozdamar TH (2009) Microarray studies in Bacillus subtilis. Biotechnol J 4:1012–1027

    Article  CAS  PubMed  Google Scholar 

  • Kruskal JB (1956) On the shortest spanning subtree of a graph and the traveling salesman problem. Proc Am Math Soc 7:48–50

    Article  Google Scholar 

  • Lorenz M, Wackernagel W (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Mol Biol Rev 58:563–602

    CAS  Google Scholar 

  • Madi A, Friedman Y, Roth D, Regev T, Bransburg-Zabary S et al (2008) Genome holography: deciphering function-form motifs from gene expression data. PLoS ONE 3:e2708

    Article  PubMed  Google Scholar 

  • Madi A, Hect I, Bransburg-Zabary S, Merbl Y, Zucker-Toledano M et al (2009) Organization of the autoantibody repertoire in healthy newborns and adults revealed by system level informatics of antigen microarray data. Proc Natl Acad Sci USA 106:14484–14489

    Article  CAS  PubMed  Google Scholar 

  • Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR (2003) Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113:577–586

    Article  CAS  PubMed  Google Scholar 

  • Mantegna RN (1999) Hierarchical structure in financial markets. Eur Phys J B 11:193–197

    Article  CAS  Google Scholar 

  • Mantegna RN, Stanley HE (2000) An introduction to econophysics: correlation and complexity in finance. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Mirkin B (1996) Mathematical classification and clustering. Kluwer Academic Publishing, Dordrecht, The Netherlands

    Book  Google Scholar 

  • Molle V, Fujita M, Jensen ST, Eichenberger P, Gonzalez-Pastor JE et al (2003) The Spo0A regulon of Bacillus subtilis. Mol Microbiol 50:1683–1701

    Article  CAS  PubMed  Google Scholar 

  • Newman MEJ (2003) The structure and function of complex networks. SIAM Rev 45:167–256

    Article  Google Scholar 

  • Ogura M, Tanaka T (2000) Bacillus subtilis comZ (yjzA) negatively affects expression of comG but not comK. J Bacteriol 182:4992–4994

    Article  CAS  PubMed  Google Scholar 

  • Ortega GJ, Sola RG, Pastor J (2008) Complex network analysis of human ECoG data. Neurosci Lett 147:129–133

    Article  Google Scholar 

  • Parego M, Hanstein C, Welsh KM, Djavakhishvili T, Glaser P et al (1994) Multiple protein-aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in B. subtilis. Cell 79:1047–1055

    Article  Google Scholar 

  • Prudhomme M, Attaiech L, Sanchez G (2006) Antibiotic stress induces genetic transformability in the human pathogen Streptococcus pneumoniae. Science 313(5783):89–92

    Article  CAS  PubMed  Google Scholar 

  • Quinlan J (1992) Programs for machine learning. Morgan Kaufmann, San Mateo, CA

    Google Scholar 

  • Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (2003) Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res 31:6748–6757

    Article  CAS  PubMed  Google Scholar 

  • Rogers P, Liu T, Barker K, Hilliard G (2007) Gene expression profiling of the response of Streptococcus pneumoniae to penicillin. J Antimicrob Chemother 59:616–626

    Article  CAS  PubMed  Google Scholar 

  • Roggiani M, Dubnau D (1993) ComA, a phosphorylated response regulator protein of Bacillus subtilis, binds to the promoter region of srfA. J Bacteriol 175:3182–3187

    CAS  PubMed  Google Scholar 

  • Rumelhart DE, Hinton GE, Williams RJ (1986) Learning internal representations by error propagation. In: Rumelhart DE, McClelland JL (eds) Parallel distributed processing, vol 1. MIT Press, Cambridge, MA, pp 318–362

    Google Scholar 

  • Ruzal S, Sanchez-Rivas C (1998) In Bacillus subtilis DegU-P is a positive regulator of the osmotic response. Curr Microbiol 37:368–372

    Article  CAS  PubMed  Google Scholar 

  • Schultz D, Wolynes PG, Ben Jacob E, Onuchic JN (2009) Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc Natl Acad Sci USA 106:21027–21034

    Article  CAS  PubMed  Google Scholar 

  • Serizawa M, Yamamoto H, Yamaguchi H, Fujita Y, Kobayashi K et al (2004) Systematic analysis of SigD-regulated genes in Bacillus subtilis by DNA microarray and Northern blotting analyses. Gene 329:125–136

    Article  CAS  PubMed  Google Scholar 

  • Serror P, Sonenshein A (1996) CodY is required for nutritional repression of Bacillus subtilis genetic competence. J bacteriol 178:5910–5915

    CAS  PubMed  Google Scholar 

  • Serror P, Wong K, Sonenshein A (2001) Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 15:1093–1103

    Article  PubMed  Google Scholar 

  • Shapira Y, Kenett DY, Ben-Jacob E (2009) The index cohesive effect on stock market correlations. Eur Phys J B 72:657–669

    Article  CAS  Google Scholar 

  • Sharan R, Maron-Katz A, Shamir R (2003) CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 19:1787–1799

    Article  CAS  PubMed  Google Scholar 

  • Sonenshein A (2000) Control of sporulation initiation in Bacillus subtilis. Curr Opin Microbiol 3:561–568

    Article  CAS  PubMed  Google Scholar 

  • Stephenson K, Hoch JA (2002) Evolution of signalling in the sporulation phosporelay. Mol Microbiol 2:297–304

    Article  Google Scholar 

  • Stragier P (2006) To kill but not be killed: a delicate balance. Cell 124:461–463

    Article  CAS  PubMed  Google Scholar 

  • Stragier P, Losick R (1996) Molecular genetics of sporulation in Bacillus subtilis. Annu Rev Genet 30:297–341

    Article  CAS  PubMed  Google Scholar 

  • Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S et al (1999) Interpreting patterns of gene expression with self-organizing maps. Proc Natl Acad Sci USA 96:2907–2912

    Article  CAS  PubMed  Google Scholar 

  • Tumminello M, Coronnello C, Lillo F, Micciche S, Mantegna RN (2007) Spanning trees and bootstrap reliability estimation in correlation-based networks. Int J Bifurcat Chaos 17:2319–2329

    Article  Google Scholar 

  • Vazquez-Ramos J, Mandelstam J (1981) Inhibition of sporulation by DNA gyrase inhibitors. Microbiology 127:11–17

    Article  CAS  Google Scholar 

  • Veening JW, Hamoen LW, Kuipers OP (2005) Phosphatases modulate the bistable sporulation gene expression pattern in Bacillus subtilis. Mol Microbiol 56:1481–1494

    Article  CAS  PubMed  Google Scholar 

  • West DB (2001) An introduction to graph theory. Prentice-Hall, Englewood Cliffs, NJ

    Google Scholar 

  • Xu Y, Olman V, Xu D (2001) Minimum spanning trees for gene expression data clustering. Genome Inform 12:24–33

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank Itai Baruchy for his help in applying the Functional holography method to the study of gene-expression data. We also thank Dr. Sharron Bransburg-Zabary, Yonatan Friedman, and Tamar Regev for their contribution to this project. This research has been supported in part by the Maugy-Glass Chair in Physics of Complex Systems and the Tauber Family Foundation at Tel Aviv University, by National Science Foundation-sponsored Center for Theoretical Biological Physics (CTBP) Grants PHY-0216576 and 0225630, and by the University of California at San Diego.

Author information

Authors and Affiliations

  1. Faculty of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel

    Dalit Roth & Asaf Madi

  2. School of Physics and Astronomy, Tel Aviv University, 69978, Tel Aviv, Israel

    Dror Y. Kenett & Eshel Ben-Jacob

  3. The Center for Theoretical and Biological Physics, University of California San Diego, La Jolla, CA, 92093, USA

    Eshel Ben-Jacob

Authors
  1. Dalit Roth
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Asaf Madi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dror Y. Kenett
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Eshel Ben-Jacob
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eshel Ben-Jacob .

Editor information

Editors and Affiliations

  1. Telos - Philosophische Praxis, Vogelsangstr. 18c18c, Bürmoos, 5111, Austria

    Günther Witzany

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Roth, D., Madi, A., Kenett, D.Y., Ben-Jacob, E. (2011). Gene Network Holography of the Soil Bacterium Bacillus subtilis . In: Witzany, G. (eds) Biocommunication in Soil Microorganisms. Soil Biology, vol 23. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-14512-4_10

Download citation

Publish with us

Policies and ethics

Search

Navigation