1
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Vélez N, Monteoliva L, Sánchez-Quitian ZA, Amador-García A, García-Rodas R, Ceballos-Garzón A, Gil C, Escandón P, Zaragoza Ó, Parra-Giraldo CM. The Combination of Iron and Copper Increases Pathogenicity and Induces Proteins Related to the Main Virulence Factors in Clinical Isolates of Cryptococcus neoformans var. grubii. J Fungi (Basel) 2022; 8:jof8010057. [PMID: 35049997 PMCID: PMC8778102 DOI: 10.3390/jof8010057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/31/2021] [Indexed: 01/09/2023] Open
Abstract
In fungi, metals are associated with the expression of virulence factors. However, it is unclear whether the uptake of metals affects their pathogenicity. This study aimed to evaluate the effect of iron/copper in modulating pathogenicity and proteomic response in two clinical isolates of C. neoformans with high and low pathogenicity. Methods: In both isolates, the effect of 50 µM iron and 500 µM copper on pathogenicity, capsule induction, and melanin production was evaluated. We then performed a quantitative proteomic analysis of cytoplasmic extracts exposed to that combination. Finally, the effect on pathogenicity by iron and copper was evaluated in eight additional isolates. Results: In both isolates, the combination of iron and copper increased pathogenicity, capsule size, and melanin production. Regarding proteomic data, proteins with increased levels after iron and copper exposure were related to biological processes such as cell stress, vesicular traffic (Ap1, Vps35), cell wall structure (Och1, Ccr4, Gsk3), melanin biosynthesis (Hem15, Mln2), DNA repair (Chk1), protein transport (Mms2), SUMOylation (Uba2), and mitochondrial transport (Atm1). Increased pathogenicity by exposure to metal combination was also confirmed in 90% of the eight isolates. Conclusions: The combination of these metals enhances pathogenicity and increases the abundance of proteins related to the main virulence factors.
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Affiliation(s)
- Nórida Vélez
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (L.M.); (A.A.-G.); (C.G.)
| | - Zilpa-Adriana Sánchez-Quitian
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
| | - Ahinara Amador-García
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (L.M.); (A.A.-G.); (C.G.)
| | - Rocío García-Rodas
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, 28013 Madrid, Spain; (R.G.-R.); (Ó.Z.)
| | - Andrés Ceballos-Garzón
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
- Department of Parasitology and Medical Mycology, Faculty of Pharmacy, University of Nantes, 44200 Nantes, France
| | - Concha Gil
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain; (L.M.); (A.A.-G.); (C.G.)
| | - Patricia Escandón
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá 111321, Colombia;
| | - Óscar Zaragoza
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Carretera Majadahonda-Pozuelo, 28013 Madrid, Spain; (R.G.-R.); (Ó.Z.)
| | - Claudia-Marcela Parra-Giraldo
- Unidad de Proteómica y Micosis Humanas, Grupo de Enfermedades Infecciosas, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia; (N.V.); (Z.-A.S.-Q.); (A.C.-G.)
- Correspondence:
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2
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Tian F, Shi J, Li Y, Gao H, Chang L, Zhang Y, Gao L, Xu P, Tang S. Proteogenomics Study of Blastobotrys adeninivorans TMCC 70007-A Dominant Yeast in the Fermentation Process of Pu-erh Tea. J Proteome Res 2021; 20:3290-3304. [PMID: 34008989 DOI: 10.1021/acs.jproteome.1c00205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Blastobotrys adeninivorans plays an essential role in pile-fermenting of Pu-erh tea. Its ability to assimilate various carbon and nitrogen sources makes it available for application in a wide range of industry sectors. The genome of B. adeninivorans TMCC 70007 isolated from pile-fermented Pu-erh tea was sequenced and assembled. Proteomics analysis indicated that 4900 proteins in TMCC 70007 were expressed under various culture conditions. Proteogenomics mapping revealed 48 previously unknown genes and corrected 118 gene models predicted by GeneMark-ES. Ortho-proteogenomics analysis identified 17 previously unidentified genes in B. adeninivorans LS3, the first strain with a sequenced genome among the genus Blastobotrys as well. More importantly, five species specific genes were identified from TMCC 70007, which could serve as a barcode for strain typing and were applicable for fermentation process protection of this industrial species. The datasets generated from tea aqueous extract culture not only increased the proteome coverage and accuracy but also contributed to the identification of proteins related to polyphenols and caffeine, which were considered to change greatly during the microbial fermentation of Pu-erh tea. This study provides a proteome perspective on TMCC 70007, which was considered to be an important strain in the production of Pu-erh tea. The systematic proteogenomics analysis not only made a better annotation on the genome of B. adeninivorans TMCC 70007 as previous proteogenomics study but also provided solution for fermentation process protection on valuable industrial species with species specific genes uniquely identified from proteogenomics study.
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Affiliation(s)
- Fei Tian
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Huiying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Linrui Gao
- Yunnan Pu-erh Tea Fermentation Engineering Research Center, Yunnan TAETEA Microbial Technology Co., Ltd., Kunming 650217, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Shukun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China.,Yunnan Pu-erh Tea Fermentation Engineering Research Center, Yunnan TAETEA Microbial Technology Co., Ltd., Kunming 650217, China
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3
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Patil S, Subbannayya T, Mohan SV, Babu N, Advani J, Sathe G, Rajagopalan P, Patel K, Bhandi S, Solanki H, Sidransky D, Gowda H, Chatterjee A, Ferrari M. Proteomic Changes in Oral Keratinocytes Chronically Exposed to Shisha (Water Pipe). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:86-97. [PMID: 30767727 DOI: 10.1089/omi.2018.0173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Shisha (water pipe) smoking is falsely believed to be a hazard-free habit and has become a major public health concern. Studies have reported shisha smoking to be associated with oral lesions, as well as carcinomas of the lung, esophagus, bladder, and pancreas. A deeper understanding of the underlying molecular mechanisms would contribute to identification of biomarkers for targeted public health screening, therapeutic innovation, and better prognosis of associated diseases. In this study, we have established an in vitro chronic cellular model of shisha-exposed oral keratinocytes to study the effect of shisha on oral cells. Normal nontransformed, immortalized oral keratinocytes were chronically exposed to shisha extract for 8 months. This resulted in significant increase in cellular proliferation and cell invasion in shisha-exposed cells compared to the parental cells. Quantitative proteomic analysis of OKF6/TERT1-Parental and OKF6/TERT1-Shisha cells resulted in the identification of 5515 proteins. Forty-three differentially expressed proteins were found to be common across all conditions. Bioinformatic analysis of the dysregulated proteins identified in the proteomic study revealed dysregulation of interferon pathway, upregulation of proteins involved in cell growth, and downregulation of immune processes. The present findings reveal that chronic exposure of normal oral keratinocytes to shisha leads to cellular transformation and dysregulation of immune response. To the best of our knowledge, this is the first report that has developed a model of oral keratinocytes chronically exposed to shisha and identified proteomic alterations associated with shisha exposure. However, further research is required to evaluate the health burden of shisha smoking.
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Affiliation(s)
- Shankargouda Patil
- 1 Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy.,2 Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | | | - Niraj Babu
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | | | | | | | | | - Shilpa Bhandi
- 5 Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | | | - David Sidransky
- 6 Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harsha Gowda
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | - Aditi Chatterjee
- 3 Institute of Bioinformatics, Bangalore, India.,4 Manipal Academy of Higher Education, Manipal, India
| | - Marco Ferrari
- 1 Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy.,7 Department of Restorative Dentistry, School of Dentistry, University of Leeds, Leeds, West Yorkshire, United Kingdom
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4
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Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A. Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. PLoS Pathog 2019; 15:e1007945. [PMID: 31356623 PMCID: PMC6687208 DOI: 10.1371/journal.ppat.1007945] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/08/2019] [Accepted: 06/27/2019] [Indexed: 01/22/2023] Open
Abstract
Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce Cryptococcus neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy in C. neoformans. We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial mass increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC. Altogether, these data show that we were able to generate for the first time VBNC phenotype in C. neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.
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Affiliation(s)
- Benjamin Hommel
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Stevenn Volant
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | | | - Magalie Duchateau
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Véronique Hourdel
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Hugo Varet
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur - Transcriptome and Epigenome Platform - Biomics Pole - C2RT, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Françoise Dromer
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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5
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Subbannayya T, Leal-Rojas P, Zhavoronkov A, Ozerov IV, Korzinkin M, Babu N, Radhakrishnan A, Chavan S, Raja R, Pinto SM, Patil AH, Barbhuiya MA, Kumar P, Guerrero-Preston R, Navani S, Tiwari PK, Kumar RV, Prasad TSK, Roa JC, Pandey A, Sidransky D, Gowda H, Izumchenko E, Chatterjee A. PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40). J Cell Commun Signal 2019; 13:163-177. [PMID: 30666556 DOI: 10.1007/s12079-018-00503-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022] Open
Abstract
Gallbladder cancer (GBC) is a rare malignancy, associated with poor disease prognosis with a 5-year survival of only 20%. This has been attributed to late presentation of the disease, lack of early diagnostic markers and limited efficacy of therapeutic interventions. Elucidation of molecular events in GBC can contribute to better management of the disease by aiding in the identification of therapeutic targets. To identify aberrantly activated signaling events in GBC, tandem mass tag-based quantitative phosphoproteomic analysis of five GBC cell lines was carried out. Proline-rich Akt substrate 40 kDa (PRAS40) was one of the proteins found to be hyperphosphorylated in all the invasive GBC cell lines. Tissue microarray-based immunohistochemical labeling of phospho-PRAS40 (T246) revealed moderate to strong staining in 77% of the primary gallbladder adenocarcinoma cases. Regulation of PRAS40 activity by inhibiting its upstream kinase PIM1 resulted in a significant decrease in cell proliferation, colony forming and invasive ability of GBC cells. Our results support the role of PRAS40 phosphorylation in GBC cell survival and aggressiveness. This study also elucidates phospho-PRAS40 as a clinical marker in GBC and the role of PIM1 as a therapeutic target in GBC.
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Affiliation(s)
- Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Pamela Leal-Rojas
- Center of Excellence in Translational Medicine (CEMT) &Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alex Zhavoronkov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, 21218, USA
| | - Ivan V Ozerov
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, 21218, USA
| | - Mikhail Korzinkin
- Insilico Medicine, Inc., Emerging Technology Centers, Johns Hopkins University at Eastern, Baltimore, MD, 21218, USA
| | - Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Aneesha Radhakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Arun H Patil
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,School of Biotechnology, KIIT (Deemed to be University), Bhubaneswar, Odisha, 751024, India
| | - Mustafa A Barbhuiya
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India
| | - Rafael Guerrero-Preston
- Department of Otolaryngology, Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II, 5M05C, Baltimore, MD, 21231, USA
| | | | - Pramod K Tiwari
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior, 474011, India.,School of Studies in Zoology, Jiwaji University, Gwalior, 474011, India
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka, 560029, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India.,NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, 560029, India
| | - Juan Carlos Roa
- Department of Pathology, Millenium Institute on Immunology and Immunotherapy (IMII), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - David Sidransky
- Department of Otolaryngology, Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II, 5M05C, Baltimore, MD, 21231, USA
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Evgeny Izumchenko
- Department of Otolaryngology, Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II, 5M05C, Baltimore, MD, 21231, USA.
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, 560066, India. .,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India.
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6
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Advani J, Verma R, Chatterjee O, Devasahayam Arokia Balaya R, Najar MA, Ravishankara N, Suresh S, Pachori PK, Gupta UD, Pinto SM, Chauhan DS, Tripathy SP, Gowda H, Prasad TK. Rise of Clinical Microbial Proteogenomics: A Multiomics Approach to Nontuberculous Mycobacterium—The Case ofMycobacterium abscessusUC22. ACTA ACUST UNITED AC 2019; 23:1-16. [DOI: 10.1089/omi.2018.0116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Oishi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rex Devasahayam Arokia Balaya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohd Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Namitha Ravishankara
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bangalore, India
| | - Sneha Suresh
- Department of Biotechnology, M.S. Ramaiah Institute of Technology, Bangalore, India
| | - Praveen Kumar Pachori
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Umesh D. Gupta
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Sneha M. Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Devendra S. Chauhan
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Srikanth Prasad Tripathy
- Department of Microbiology and Molecular Biology, ICMR-National JALMA Institute for Leprosy & Other Mycobacterial Diseases, Agra, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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7
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Proteomic approach and expression analysis revealed the differential expression of predicted leptospiral proteases capable of ECM degradation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:712-721. [DOI: 10.1016/j.bbapap.2018.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/22/2018] [Accepted: 04/10/2018] [Indexed: 12/22/2022]
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8
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Dammalli M, Dey G, Kumar M, Madugundu AK, Gopalakrishnan L, Gowrishankar BS, Mahadevan A, Shankar SK, Prasad TSK. Proteomics of the Human Olfactory Tract. ACTA ACUST UNITED AC 2018; 22:77-87. [DOI: 10.1089/omi.2017.0155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Manjunath Dammalli
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, India
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya University, Mangalore, India
- School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Lathika Gopalakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya University, Mangalore, India
- School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | | | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
- Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Susarla Krishna Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
- Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Center, Yenepoya University, Mangalore, India
- NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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9
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Yelamanchi SD, Kumar M, Madugundu AK, Gopalakrishnan L, Dey G, Chavan S, Sathe G, Mathur PP, Gowda H, Mahadevan A, Shankar SK, Prasad TSK. Characterization of human pineal gland proteome. MOLECULAR BIOSYSTEMS 2017; 12:3622-3632. [PMID: 27714013 DOI: 10.1039/c6mb00507a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pineal gland is a neuroendocrine gland located at the center of the brain. It is known to regulate various physiological functions in the body through secretion of the neurohormone melatonin. Comprehensive characterization of the human pineal gland proteome has not been undertaken to date. We employed a high-resolution mass spectrometry-based approach to characterize the proteome of the human pineal gland. A total of 5874 proteins were identified from the human pineal gland in this study. Of these, 5820 proteins were identified from the human pineal gland for the first time. Interestingly, 1136 proteins from the human pineal gland were found to contain a signal peptide domain, which indicates the secretory nature of these proteins. An unbiased global proteomic profile of this biomedically important organ should benefit molecular research to unravel the role of the pineal gland in neuropsychiatric and neurodegenerative diseases.
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Affiliation(s)
- Soujanya D Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and School of Biotechnology, KIIT University, Bhubaneswar 751 024, India.
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Centre for Bioinformatics, Pondicherry University, Puducherry 605 014, India
| | | | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Sandip Chavan
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and Manipal University, Madhav Nagar, Manipal 576 104, India
| | - Premendu P Mathur
- School of Biotechnology, KIIT University, Bhubaneswar 751 024, India. and Centre for Bioinformatics, Pondicherry University, Puducherry 605 014, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and School of Biotechnology, KIIT University, Bhubaneswar 751 024, India. and YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575 018, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India. and Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India
| | - Susarla K Shankar
- Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India. and Human Brain Tissue Repository, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India and Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India. and YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575 018, India and Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore 560 029, India
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10
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Datta KK, Patil AH, Patel K, Dey G, Madugundu AK, Renuse S, Kaviyil JE, Sekhar R, Arunima A, Daswani B, Kaur I, Mohanty J, Sinha R, Jaiswal S, Sivapriya S, Sonnathi Y, Chattoo BB, Gowda H, Ravikumar R, Prasad TSK. Proteogenomics of Candida tropicalis--An Opportunistic Pathogen with Importance for Global Health. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:239-47. [PMID: 27093108 DOI: 10.1089/omi.2015.0197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The frequency of Candida infections is currently rising, and thus adversely impacting global health. The situation is exacerbated by azole resistance developed by fungal pathogens. Candida tropicalis is an opportunistic pathogen that causes candidiasis, for example, in immune-compromised individuals, cancer patients, and those who undergo organ transplantation. It is a member of the non-albicans group of Candida that are known to be azole-resistant, and is frequently seen in individuals being treated for cancers, HIV-infection, and those who underwent bone marrow transplantation. Although the genome of C. tropicalis was sequenced in 2009, the genome annotation has not been supported by experimental validation. In the present study, we have carried out proteomics profiling of C. tropicalis using high-resolution Fourier transform mass spectrometry. We identified 2743 proteins, thus mapping nearly 44% of the computationally predicted protein-coding genes with peptide level evidence. In addition to identifying 2591 proteins in the cell lysate of this yeast, we also analyzed the proteome of the conditioned media of C. tropicalis culture and identified several unique secreted proteins among a total of 780 proteins. By subjecting the mass spectrometry data derived from cell lysate and conditioned media to proteogenomic analysis, we identified 86 novel genes, 12 novel exons, and corrected 49 computationally-predicted gene models. To our knowledge, this is the first high-throughput proteomics study of C. tropicalis validating predicted protein coding genes and refining the current genome annotation. The findings may prove useful in future global health efforts to fight against Candida infections.
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Affiliation(s)
- Keshava K Datta
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,2 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Arun H Patil
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,2 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Krishna Patel
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,3 Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham , Kollam, India
| | - Gourav Dey
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,4 Manipal University , Madhav Nagar, Manipal, India
| | - Anil K Madugundu
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,5 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | - Santosh Renuse
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,3 Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham , Kollam, India
| | - Jyothi E Kaviyil
- 6 Department of Neuromicrobiology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India
| | - Raja Sekhar
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,5 Centre for Bioinformatics, School of Life Sciences, Pondicherry University , Puducherry, India
| | | | - Bhavna Daswani
- 7 National Institute for Research in Reproductive Health (ICMR) , Parel, Mumbai, India
| | - Inderjeet Kaur
- 8 Malaria Research Group, International Center for Genetic Engineering and Biotechnology (ICGEB) , New Delhi, India
| | - Jyotirmaya Mohanty
- 9 ICAR-Central Institute of Freshwater Aquaculture , Kausalyaganga, Bhubaneswar, India
| | | | | | - S Sivapriya
- 11 Department of Ocular Pathology, Vision Research Foundation , Chennai, India
| | | | - Bharat B Chattoo
- 13 Centre for Genome Research, Department of Microbiology and Biotechnology Centre, Faculty of Science, The M. S. University of Baroda , Vadodara, India
| | - Harsha Gowda
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,2 School of Biotechnology, KIIT University , Bhubaneswar, India .,14 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
| | - Raju Ravikumar
- 6 Department of Neuromicrobiology, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India
| | - T S Keshava Prasad
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India.,14 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .,15 NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India
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11
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Subbannayya Y, Pinto SM, Gowda H, Prasad TSK. Proteogenomics for understanding oncology: recent advances and future prospects. Expert Rev Proteomics 2016; 13:297-308. [PMID: 26697917 DOI: 10.1586/14789450.2016.1136217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The concept of proteogenomics has emerged rapidly as a valuable approach to integrate mass spectrometry-derived proteomic data with genomic and transcriptomic data. It is used to harness the full potential of the former dataset in the discovery of potential biomarkers, therapeutic targets and novel proteins associated with various biological processes including diseases. Proteogenomic strategies have been successfully utilized to identify novel genes and redefine annotation of existing gene models in various genomes. In recent years, this approach has been extended to the field of cancer biology to unravel complexities in the tumor genomes and proteomes. Standard proteomics workflows employing translated cancer genomes and transcriptomes can potentially identify peptides from mutant proteins, splice variants and fusion proteins in the tumor proteome, which in addition to the currently available biomarker panels can serve as potential diagnostic and prognostic biomarkers, besides having therapeutic utility. This review focuses on the role of proteogenomics to understand cancer biology.
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Affiliation(s)
- Yashwanth Subbannayya
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Sneha M Pinto
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Harsha Gowda
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - T S Keshava Prasad
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India.,c NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre , National Institute of Mental Health and Neurosciences , Bangalore , India
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12
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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13
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Abstract
Annotation of protein coding genes in sequenced genomes has been routinely carried out using gene prediction programs guided by available transcript data. The advent of mass spectrometry has enabled the identification of proteins in a high-throughput manner. In addition to searching proteins annotated in public databases, mass spectrometry data can also be searched against conceptually translated genome as well as transcriptome to identify novel protein coding regions. This proteogenomics approach has resulted in the identification of novel protein coding regions in both prokaryotic and eukaryotic genomes. These studies have also revealed that some of the annotated noncoding RNAs and pseudogenes code for proteins. This approach is likely to become a part of most genome annotation workflows in the future. Here we describe a general methodology and approach that can be used for proteogenomics.
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Affiliation(s)
- Keshava K Datta
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- School of Biotechnology, KIIT University, Bhubaneswar, 751024, Odisha, India.
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14
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Renuse S, Madugundu AK, Kumar P, Nair BG, Gowda H, Prasad TSK, Pandey A. Proteomic analysis and genome annotation ofPichia pastoris, a recombinant protein expression host. Proteomics 2014; 14:2769-79. [DOI: 10.1002/pmic.201400267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/01/2014] [Accepted: 10/20/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Santosh Renuse
- Institute of Bioinformatics; International Technology Park; Bangalore India
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam India
| | - Anil K. Madugundu
- Institute of Bioinformatics; International Technology Park; Bangalore India
- Centre of Excellence in Bioinformatics, School of Life Sciences; Pondicherry University; Puducherry India
| | - Praveen Kumar
- Institute of Bioinformatics; International Technology Park; Bangalore India
| | - Bipin G. Nair
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam India
| | - Harsha Gowda
- Institute of Bioinformatics; International Technology Park; Bangalore India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics; International Technology Park; Bangalore India
- Amrita School of Biotechnology; Amrita Vishwa Vidyapeetham; Kollam India
- Centre of Excellence in Bioinformatics, School of Life Sciences; Pondicherry University; Puducherry India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Oncology and Pathology; Johns Hopkins University School of Medicine; Baltimore MD USA
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15
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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16
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Wang X, Liu Q, Zhang B. Leveraging the complementary nature of RNA-Seq and shotgun proteomics data. Proteomics 2014; 14:2676-87. [PMID: 25266668 DOI: 10.1002/pmic.201400184] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/22/2014] [Accepted: 09/25/2014] [Indexed: 12/22/2022]
Abstract
RNA sequencing (RNA-Seq) and MS-based shotgun proteomics are powerful high-throughput technologies for identifying and quantifying RNA transcripts and proteins, respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to achieve a more comprehensive understanding of biological systems. A major analytical challenge for such integrative projects is how to effectively leverage the complementary nature of RNA-Seq and shotgun proteomics data. RNA-Seq provides comprehensive information on mRNA abundance, alternative splicing, nucleotide variation, and structure alteration. Sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in cell and tissue samples and thus improve protein identification. Meanwhile, proteomics data provide essential confirmation of the validity and functional relevance of novel findings from RNA-Seq data. At the quantitative level, mRNA and protein levels are only modestly correlated, suggesting strong involvement of posttranscriptional regulation in controlling gene expression. Here, we review recent studies at the interface of RNA-Seq and proteomics data. We discuss goals, accomplishments, and challenges in RNA-Seq-based proteogenomics. We also examine the current status and future potential of parallel transcriptome and proteome quantification in revealing posttranscriptional regulatory mechanisms.
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Affiliation(s)
- Xiaojing Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN
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