Abstract
The importance of the pathogenic mycobacteria has mainly focused the omic analyses on different aspects of their clinical significance. In contrast, those industrially relevant mycobacteria have received less attention, even though the steroids market sales in 2011, in example, were estimated in $8 billion.
The extra-cellular proteome, due to its relevance in the sterols processing and uptake; as well as the intra-cellular proteome, because of its role in steroids bioconversion, are the core of the present chapter. As a proof of concept, the obtaining methods for both sub-proteomes of Mycobacterium neoaurum NRRL B-3805, a relevant industrial strain involved in steroids production, have been developed. Thus, procedures and relevant key points of these proteomes analyses are fully described.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bott M (2007) Corynebacteria: the good guys and the bad guys. Microbiol Today 34:74–77
Barreiro C, Martín JF (2015) Corynebacterium genus, a dual group of clinical and industrial relevant bacteria. In: Barreiro C (ed) New trends in Corynebacterium glutamicum: beyond the amino acids. Nova Science Publishers, Inc, New York
Shtratnikova VY, Bragin EY, Dovbnya DV et al (2014) Complete genome sequence of sterol-transforming Mycobacterium neoaurum strain VKM Ac-1815D. Genome Announc 2:12–13
Tortoli E (2014) Microbiological features and clinical relevance of new species of the genus Mycobacterium. Clin Microbiol Rev 27:727–752
Euzéby JP. List of Prokaryotic names with standing in nomenclature. http://www.bacterio.net/
Goodfellow M, Kämpfer P, Busse HJ, et al. (2012) Bergey’s manual of systematic bacteriology. The actinobacteria, part B, vol 5. Springer, New York.
Cole ST, Brosch R, Parkhill J et al (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544
Mattow J, Siejak F, Hagens K et al (2009) Two-dimensional gel electrophoresis-based proteomics of mycobacteria. Methods Mol Biol (Clifton, NJ) 465:111–142
Uhía I, Galán B, Kendall SL et al (2012) Cholesterol metabolism in Mycobacterium smegmatis. Environ Microbiol Rep 4:168–182
Liu M, Zhu ZT, Tao XY et al (2016) RNA-Seq analysis uncovers non-coding small RNA system of Mycobacterium neoaurum in the metabolism of sterols to accumulate steroid intermediates. Microb Cell Fact 15:64
World Health Organisation (WHO) (2014) Global tuberculosis report 2014
Korb VC, Chuturgoon AA, Moodley D (2016) Mycobacterium tuberculosis: manipulator of protective immunity. Int J Mol Sci 17:131
Kumar B (2015) World Leprosy Day 2015: Renewing commitment for a leprosy free world! Indian J Med Res 141(1):1–4
Wasinger VC, Cordwell SJ, Cerpa-Poljak A et al (1995) Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16:1090–1094
Wilkins MR, Sanchez JC, Gooley A et al (1996) Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol Genet Eng Rev 13:19–50
Wilkins MR, Pasquali C, Appel RD et al (1996) From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14:61–65
James P (1997) Protein identification in the post-genome era: the rapid rise of proteomics. Q Rev Biophys 30:279–331
Barreiro C (2015) Methods in proteomics applied to Corynebacterium glutamicum. In: Barreiro C (ed) New trends in Corynebacterium glutamicum: beyond the amino acids. Nova Science Publishers, Inc, New York
Bisht D, Singhal N, Sharma P et al (2006) Analysis of mycobacterial strains by two-dimensional gel electrophoresis. J Commun Dis 38:255–262
Betts JC, Dodson P, Quan S et al (2000) Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology 146:3205–3216
Jungblut PR, Schaible UE, Mollenkopf HJ et al (1999) Comparative proteome analysis of Mycobacterium tuberculosis and Mycobacterium bovis BCG strains: towards functional genomics of microbial pathogens. Mol Microbiol 33:1103–1117
Kruh NA, Troudt J, Izzo A et al (2010) Portrait of a pathogen: the Mycobacterium tuberculosis proteome in vivo. PLoS One 5:e13938
Schmidt F, Donahoe S, Hagens K et al (2004) Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol Cell Proteomics 3:24–42
Gupta MK, Subramanian V, Yadav JS (2009) Immunoproteomic identification of secretory and subcellular protein antigens and functional evaluation of the secretome fraction of Mycobacterium immunogenum a newly recognized species of the Mycobacterium chelonae–Mycobacterium abscessus group. J Proteome Res 8:2319–2330
Kruh-Garcia NA, Murray M, Prucha JG et al (2014) Antigen 85 variation across lineages of Mycobacterium tuberculosis—implications for vaccine and biomarker success. J Proteomics 97:141–150
Mattow J, Schaible UE, Schmidt F et al (2003) Comparative proteome analysis of culture supernatant proteins from virulent Mycobacterium tuberculosis H37Rv and attenuated M. bovis BCG Copenhagen. Electrophoresis 24:3405–3420
Ranganathan S, Garg G (2009) Secretome: clues into pathogen infection and clinical applications. Genome Med 1:113
Yadav JS, Gupta M (2012) Secretome differences between the taxonomically related but clinically differing mycobacterial species Mycobacterium abscessus and M. chelonae. J Integr OMICS 2(2):64–79
Mollenkopf HJ, Jungblut PR, Raupach B et al (1999) A dynamic two-dimensional polyacrylamide gel electrophoresis database: the mycobacterial proteome via Internet. Electrophoresis 20:2172–2180
He Z, De Buck J (2010) Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155. BMC Microbiol 10:121
Sih CJ, Wang KC (1965) A new route to estrone from sterol. J Am Chem Soc 87:1387–1388
Al Jasem Y, Khan M, Taha A et al (2014) Preparation of steroidal hormones with an emphasis on transformations of phytosterols and cholesterol—a review. Mediterr J Chem 3:796–830
Donova MV, Egorova OV (2012) Microbial steroid transformations: current state and prospects. Appl Microbiol Biotechnol 94:1423–1447
Wang F, Yao K, Wei D (2011) From soybean phytosterols to steroid hormones. In: El-Shemy H (ed) Soybean and health. InTech, Rijeka, Croatia, pp 231–252
Bragin EY, Shtratnikova VY, Dovbnya DV et al (2013) Comparative analysis of genes encoding key steroid core oxidation enzymes in fast-growing Mycobacterium spp. strains. J Steroid Biochem Mol Biol 138:41–53
Rodríguez-García A, Fernández-Alegre E, Morales A et al (2016) Complete genome sequence of “Mycobacterium neoaurum” NRRL B-3805, an androstenedione (AD) producer for industrial biotransformation of sterols. J Biotechnol 224:64–65
Barreiro C, Martín JF, García-Estrada C (2012) Proteomics methodology applied to the analysis of filamentous fungi—new trends for an impressive diverse group of organisms. In: Prasain JK (ed) Tandem mass spectrometry—applications and principles. InTech, Rijeka, Croatia
Jeffery CJ (2014) An introduction to protein moonlighting. Biochem Soc Trans 42:1679–1683
Jeffery CJ (2009) Moonlighting proteins—an update. Mol Biosyst 5:345–350
Marsheck WJ, Kraychy S, Muir RD (1972) Microbial degradation of sterols. Appl Microbiol 23:72–77
Candiano G, Bruschi M, Musante L et al (2004) Blue silver: a very sensitive colloidal Coomassie G-250 staining for proteome analysis. Electrophoresis 25(9):1327–1333
Greenbaum D, Luscombe NM, Jansen R et al (2001) Interrelating different types of genomic data, from proteome to secretome: ’oming in on function. Genome Res 11:1463–1468
Makridakis M, Roubelakis MG, Vlahou A (2013) Stem cells: insights into the secretome. Biochim Biophys Acta 1834:2380–2384
Tjalsma H, Bolhuis A, Jongbloed JD et al (2000) Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol Mol Biol Rev 64:515–547
Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254
Lowry OH, Rosebrough NJ, Farr AL et al (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265–275
Smith PK, Krohn RI, Hermanson GT et al (1985) Measurement of protein using bicinchoninic acid. Anal Biochem 150:76–85
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685
O’Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007–4021
Fazekas de St Groth S, Webster RG, Datyner A (1963) Two new staining procedures for quantitative estimation of proteins on electrophoretic strips. Biochim Biophys Acta 71:377–391
Meyer TS, Lamberts BL (1965) Use of coomassie brilliant blue R250 for the electrophoresis of microgram quantities of parotid saliva proteins on acrylamide-gel strips. Biochim Biophys Acta 107:144–145
Westermeier R, Naven T, Hopker HR (2008) Proteomics in practice: a guide to successful experimental design, 2nd Completely Revised edn. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Westermeier R (2006) Sensitive, quantitative, and fast modifications for Coomassie Blue staining of polyacrylamide gels. Proteomics 6 Suppl 2:61–64
Acknowledgments
This work was fully supported by a grant of the European Union program ERA-IB [MySterI (EIB.12.010)] through the APCIN call of the Spanish Ministry of Economy and Competitiveness (MINECO, Spain) (PCIN-2013-024-C02-01). The authors want to thank the European Union program ERA-IB; the Spanish Ministry of Economy and Competitiveness (MINECO, Spain); and the MySterI Consortium (INBIOTEC, Pharmins Ltd., University of York, SINTEF, Technische Universität Dortmund and Gadea Biopharma S.L.). We thank J. Merino, B. Martín, and A. Casenave for their excellent technical assistance and the degree students of the group A. Ibáñez and A. del Árbol.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Barreiro, C., Morales, A., Vázquez-Iglesias, I., Sola-Landa, A. (2017). Intra- and Extra-cellular Proteome Analyses of Steroid-Producer Mycobacteria. In: Barredo, JL., Herráiz, I. (eds) Microbial Steroids. Methods in Molecular Biology, vol 1645. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7183-1_6
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7183-1_6
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7182-4
Online ISBN: 978-1-4939-7183-1
eBook Packages: Springer Protocols