Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Bobek, Jan ^a,b,c   Strakova, Eva ^a   Zikova, Alice ^a   Vohradsky, Jiri ^a  

^a INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c J E PURKINJE UNIVERSITY   (Czech Republic)

Author keywords

Germination; Metabolic pathways; Microarrays; Sigma factors; Streptomyces

Indexed keywords

MESSENGER RNA; SIGMA FACTOR; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL CELL WALL; BACTERIAL METABOLISM; CULTURE MEDIUM; GENE EXPRESSION; NONHUMAN; OSMOTIC STRESS; OXIDATIVE STRESS; PROTEIN AGGREGATION; REHYDRATION; RNA DEGRADATION; RNA SYNTHESIS; SPORE GERMINATION; SPOROGENESIS; STREPTOMYCES COELICOLOR; TIME; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; HEAT SHOCK RESPONSE; METABOLISM; PHYSIOLOGY; TIME FACTOR;

BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; HEAT-SHOCK RESPONSE; STREPTOMYCES COELICOLOR; TIME FACTORS;

EID: 84928235774     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1173     Document Type: Article

References (45)

1. Hopwood DA: How do antibiotic-producing bacteria ensure their self-resistance before antibiotic biosynthesis incapacitates them? Mol Microbiol 2007, 63(4):937-940.
2. Kelemen GH, Buttner MJ: Initiation of aerial mycelium formation in Streptomyces. Curr Opin Microbiol 1998, 1(6):656-662.
3. Claessen D, de Jong W, Dijkhuizen L, Wosten HA: Regulation of Streptomyces development: reach for the sky! Trends Microbiol 2006, 14(7):313-319.
4. Yague P, Lopez-Garcia MT, Rioseras B, Sanchez J, Manteca A: Pre-sporulation stages of Streptomyces differentiation: state-of-the-art and future perspectives. FEMS Microbiol Lett 2013, 342(2):79-88.
5. Hodgson DA: Differentiation in actinomycetes. In Prokaryotic Structure and Function: A New Perspective, CDaJAC, Volume 47. Edited by Mohan S. Cambridge: Cambridge University Press; 1992:407-440.
6. Stewart GS, Johnstone K, Hagelberg E, Ellar DJ: Commitment of bacterial spores to germinate. A measure of the trigger reaction. Biochem J 1981, 198(1):101-106.
7. Miguelez EM, Martin C, Hardisson C, Manzanal MB: Synchronous germination of Streptomyces antibioticus spores: tool for the analysis of hyphal growth in liquid cultures. FEMS Microbiol Lett 1993, 109(2-3):123-129.
8. Mikulik K, Janda I, Maskova H, Stastna J, Jiranova A: Macromolecular synthesis accompanying the transition from spores to vegetative forms of Streptomyces granaticolor. Folia Microbiol (Praha) 1977, 22(4):252-261.
9. Stastna J: A method of rapid wetting and synchronous germination of streptomycete spores. Folia Microbiol (Praha) 1977, 22(2):137-138.
10. Haiser HJ, Yousef MR, Elliot MA: Cell wall hydrolases affect germination, vegetative growth, and sporulation in Streptomyces coelicolor. J Bacteriol 2009, 191(21):6501-6512.
11. Mikulik K, Janda I, Weiser J, Stastna J, Jiranova A: RNA and ribosomal protein patterns during aerial spore germination in Streptomyces granaticolor. Eur J Biochem 1984, 145(2):381-388.
12. Glauert AM, Hopwood DA: The fine structure of Streptomyces violaceoruber (S. coelicolor). III. The walls of the mycelium and spores. J Biophys Biochem Cytol 1961, 10:505-516.
13. Hardisson C, Manzanal MB, Salas JA, Suarez JE: Fine structure, physiology and biochemistry of arthrospore germination in Streptomyces antibioticus. J Gen Microbiol 1978, 105(2):203-214.
14. Vohradsky J, Branny P, Thompson CJ: Comparative analysis of gene expression on mRNA and protein level during development of Streptomyces cultures by using singular value decomposition. Proteomics 2007, 7(21):3853-3866.
15. Vohradsky J, Li X, Dale G, Folcher M, Nguyen L, Viollier PH, Thompson CJ: Developmental control of stress stimulons in streptomyces coelicolor revealed by statistical analyses of global gene expression patterns. J Bacteriol 2000, 182(17):4979-4986.
16. Laing E, Mersinias V, Smith CP, Hubbard SJ: Analysis of gene expression in operons of Streptomyces coelicolor. Genome Biol 2006, 7(6):R46.
17. Vohradsky J, Thompson C: Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions. Proteomics 2006, 6(7):785-793.
18. Basler M, Linhartova I, Halada P, Novotna J, Bezouskova S, Osicka R, Weiser J, Vohradsky J, Sebo P: The iron-regulated transcriptome and proteome of Neisseria meningitidis serogroup C. Proteomics 2006, 6(23):6194-6206.
19. Jayapal KP, Philp RJ, Kok YJ, Yap MG, Sherman DH, Griffin TJ, Hu WS: Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PLoS One 2008, 3(5):e2097.
20. Strakova E, Bobek J, Zikova A, Vohradsky J: Global Features of Gene Expression on the Proteome and Transcriptome Levels in S-coelicolor during Germination. Plos One 2013, 8(9):e72842.
21. Strakova E, Zikova A, Vohradsky J: Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote. Nucleic Acids Res 2014, 42(2):748-763.
22. Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30.
23. Mikulik K, Bobek J, Bezouskova S, Benada O, Kofronova O: Expression of proteins and protein kinase activity during germination of aerial spores of Streptomyces granaticolor. Biochem Biophys Res Commun 2002, 299(2):335-342.
24. Bobek J, Halada P, Angelis J, Vohradsky J, Mikulík K: Activation and expression of proteins during synchronous germination of aerial spores of Streptomyces granaticolor. Proteomics In press.
25. Economou A: Bacterial preprotein translocase: mechanism and conformational dynamics of a processive enzyme. Mol Microbiol 1998, 27(3):511-518.
26. Herrmann KM, Weaver LM: The Shikimate Pathway. Annu Rev Plant Physiol Plant Mol Biol 1999, 50:473-503.
27. Helmann JD: Deciphering a complex genetic regulatory network: the Bacillus subtilis sigmaW protein and intrinsic resistance to antimicrobial compounds. Sci Prog 2006, 89(Pt 3-4):243-266.
28. Takano H, Asker D, Beppu T, Ueda K: Genetic control for light-induced carotenoid production in non-phototrophic bacteria. J Ind Microbiol Biotechnol 2006, 33(2):88-93.
29. Armstrong GA: Eubacteria show their true colors: genetics of carotenoid pigment biosynthesis from microbes to plants. J Bacteriol 1994, 176(16):4795-4802.
30. Hong HJ, Paget MS, Buttner MJ: A signal transduction system in Streptomyces coelicolor that activates the expression of a putative cell wall glycan operon in response to vancomycin and other cell wall-specific antibiotics. Mol Microbiol 2002, 44(5):1199-1211.
31. Paget MS, Chamberlin L, Atrih A, Foster SJ, Buttner MJ: Evidence that the extracytoplasmic function sigma factor sigmaE is required for normal cell wall structure in Streptomyces coelicolor A3(2). J Bacteriol 1999, 181(1):204-211.
32. Paget MS, Leibovitz E, Buttner MJ: A putative two-component signal transduction system regulates sigmaE, a sigma factor required for normal cell wall integrity in Streptomyces coelicolor A3(2). Mol Microbiol 1999, 33(1):97-107.
33. Bobek J, Halada P, Angelis J, Vohradsky J, Mikulik K: Activation and expression of proteins during synchronous germination of aerial spores of Streptomyces granaticolor. Proteomics 2004, 4(12):3864-3880.
34. Kallifidas D, Thomas D, Doughty P, Paget MS: The sigmaR regulon of Streptomyces coelicolor A32 reveals a key role in protein quality control during disulphide stress. Microbiology 2010, 156(Pt 6):1661-1672.
35. Zdanowski K, Doughty P, Jakimowicz P, O'Hara L, Buttner MJ, Paget MS, Kleanthous C: Assignment of the zinc ligands in RsrA, a redox-sensing ZAS protein from Streptomyces coelicolor. Biochemistry 2006, 45(27):8294-8300.
36. Shu D, Chen L, Wang W, Yu Z, Ren C, Zhang W, Yang S, Lu Y, Jiang W: afsQ1-Q2-sigQ is a pleiotropic but conditionally required signal transduction system for both secondary metabolism and morphological development in Streptomyces coelicolor. Appl Microbiol Biotechnol 2009, 81(6):1149-1160.
37. Kelemen GH, Viollier PH, Tenor J, Marri L, Buttner MJ, Thompson CJ: A connection between stress and development in the multicellular prokaryote Streptomyces coelicolor A3(2). Mol Microbiol 2001, 40(4):804-814.
38. Kormanec J, Sevcikova B, Halgasova N, Knirschova R, Rezuchova B: Identification and transcriptional characterization of the gene encoding the stress-response sigma factor sigma(H) in streptomyces coelicolor A3(2). FEMS Microbiol Lett 2000, 189(1):31-38.
39. Sevcikova B, Benada O, Kofronova O, Kormanec J: Stress-response sigma factor sigma(H) is essential for morphological differentiation of Streptomyces coelicolor A3(2). Arch Microbiol 2001, 177(1):98-106.
40. Viollier PH, Weihofen A, Folcher M, Thompson CJ: Post-transcriptional regulation of the Streptomyces coelicolor stress responsive sigma factor, SigH, involves translational control, proteolytic processing, and an anti-sigma factor homolog. J Mol Biol 2003, 325(4):637-649.
41. Sevcikova B, Rezuchova B, Homerova D, Kormanec J: The anti-anti-sigma factor BldG is involved in activation of the stress response sigma factor sigma(H) in Streptomyces coelicolor A3(2). J Bacteriol 2010, 192(21):5674-5681.
42. Karoonuthaisiri N, Weaver D, Huang J, Cohen SN, Kao CM: Regional organization of gene expression in Streptomyces coelicolor. Gene 2005, 353(1):53-66.
43. Fernandez Martinez L, Bishop A, Parkes L, Del Sol R, Salerno P, Sevcikova B, Mazurakova V, Kormanec J, Dyson P: Osmoregulation in Streptomyces coelicolor: modulation of SigB activity by OsaC. Mol Microbiol 2009, 71(5):1250-1262.
44. Krasny L, Tiserova H, Jonak J, Rejman D, Sanderova H: The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis. Mol Microbiol 2008, 69(1):42-54.
45. Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210.