title: Quantitative Proteomic and Phosphoproteomic Analysis of H37Ra and H37Rv Strains of Mycobacterium tuberculosis.
abstract: Mycobacterium tuberculosis, the causative agent of tuberculosis, accounts for 1.5 million human deaths annually worldwide. Despite efforts to eradicate tuberculosis, it still remains a deadly disease. The two best characterized strains of M. tuberculosis, virulent H37Rv and avirulent H37Ra, provide a unique platform to investigate biochemical and signaling pathways associated with pathogenicity. To delineate the biomolecular dynamics that may account for pathogenicity and attenuation of virulence in M. tuberculosis, we compared the proteome and phosphoproteome profiles of H37Rv and H37Ra strains. Quantitative phosphoproteomic analysis was performed using high-resolution Fourier transform mass spectrometry. Analysis of exponential and stationary phases of these strains resulted in identification and quantitation of 2709 proteins along with 512 phosphorylation sites derived from 257 proteins. In addition to confirming the presence of previously described M. tuberculosis phosphorylated proteins, we identified 265 novel phosphorylation sites. Quantitative proteomic analysis revealed more than five-fold upregulation of proteins belonging to virulence associated type VII bacterial secretion system in H37Rv when compared to those in H37Ra. We also identified 84 proteins, which exhibited changes in phosphorylation levels between the virulent and avirulent strains. Bioinformatics analysis of the proteins altered in their level of expression or phosphorylation revealed enrichment of pathways involved in fatty acid biosynthesis and two-component regulatory system. Our data provides a resource for further exploration of functional differences at molecular level between H37Rv and H37Ra, which will ultimately explain the molecular underpinnings that determine virulence in tuberculosis.
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|School of Biotechnology, KIIT University , Bhubaneswar, Odisha 751024, India.
authors.forename: Renu
authors.initials: R
authors.lastname: Verma
authors.affiliation: YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore 575020, India.
authors.forename: Sneha Maria
authors.initials: SM
authors.lastname: Pinto
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|School of Biotechnology, KIIT University , Bhubaneswar, Odisha 751024, India.
authors.forename: Arun Hanumana
authors.initials: AH
authors.lastname: Patil
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|Manipal University, Madhav Nagar, Manipal 576104, India.
authors.forename: Jayshree
authors.initials: J
authors.lastname: Advani
authors.affiliation: YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore 575020, India.
authors.forename: Pratigya
authors.initials: P
authors.lastname: Subba
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|Manipal University, Madhav Nagar, Manipal 576104, India.
authors.forename: Manish
authors.initials: M
authors.lastname: Kumar
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.
authors.forename: Jyoti
authors.initials: J
authors.lastname: Sharma
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|Manipal University, Madhav Nagar, Manipal 576104, India.
authors.forename: Gourav
authors.initials: G
authors.lastname: Dey
authors.forename: Raju
authors.initials: R
authors.lastname: Ravikumar
authors.affiliation: Intermediate Reference Laboratory, State Tuberculosis Training and Demonstration Centre , Someshwaranagar, SDSTRC and RGICD Campus, Bangalore 560029, India.|Department of Cardio Thoracic Surgery, Super Specialty State Referral Hospital for Chest Diseases , Someshwaranagar First Main Road, Dharmaram College Post, Bangalore 560029, India.
authors.forename: Shashidhar
authors.initials: S
authors.lastname: Buggi
authors.forename: Parthasarathy
authors.initials: P
authors.lastname: Satishchandra
authors.affiliation: Department of Medical Microbiology, Postgraduate Institute of Medical Education & Research (PGIMER) , Chandigarh 160012, India.
authors.forename: Kusum
authors.initials: K
authors.lastname: Sharma
authors.affiliation: School of Biotechnology, KIIT University , Bhubaneswar, Odisha 751024, India.
authors.forename: Mrutyunjay
authors.initials: M
authors.lastname: Suar
authors.affiliation: National Institute for Research in Tuberculosis (Indian Council of Medical Research), Chennai 600031, India.
authors.forename: Srikanth Prasad
authors.initials: SP
authors.lastname: Tripathy
authors.affiliation: Department of Microbiology, National JALMA Institute for Leprosy & Other Mycobacterial Diseases (Indian Council of Medical Research) , Agra 282004, India.
authors.forename: Devendra Singh
authors.initials: DS
authors.lastname: Chauhan
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore 575020, India.
authors.forename: Harsha
authors.initials: H
authors.lastname: Gowda
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
authors.affiliation: CSIR-Institute of Genomics & Integrative Biology , SukhdevVihar, New Delhi 110020, India.
authors.forename: Sheetal
authors.initials: S
authors.lastname: Gandotra
authors.affiliation: Institute of Bioinformatics , International Technology Park, Bangalore 560066, India.|YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore 575020, India.
authors.forename: Thottethodi Subrahmanya Keshava
authors.identifier: 0000-0002-6206-2384
authors.initials: TS
authors.lastname: Prasad
mesh_terms: D006801:Humans; D013058:Mass Spectrometry; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000472:pathogenicity; D010750:Phosphoproteins / Q000096:biosynthesis* / Q000235:genetics; D010766:Phosphorylation / Q000235:genetics; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction / Q000235:genetics; D014376:Tuberculosis / Q000235:genetics / Q000382:microbiology* / Q000473:pathology
chemical_list: D010750:Phosphoproteins; D020543:Proteome
keywords: Orbitrap Fusion Tribrid mass spectrometer; chaperones; kinome; proteases; proteasomes; protein abundance