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Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022; 264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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2
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Low TY, Mohtar MA, Ang MY, Jamal R. Connecting Proteomics to Next‐Generation Sequencing: Proteogenomics and Its Current Applications in Biology. Proteomics 2018; 19:e1800235. [DOI: 10.1002/pmic.201800235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/09/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - M. Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - Mia Yang Ang
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI)Universiti Kebangsaan Malaysia 56000 Kuala Lumpur Malaysia
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3
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Müller AK, Föll M, Heckelmann B, Kiefer S, Werner M, Schilling O, Biniossek ML, Jilg CA, Drendel V. Proteomic Characterization of Prostate Cancer to Distinguish Nonmetastasizing and Metastasizing Primary Tumors and Lymph Node Metastases. Neoplasia 2018; 20:140-151. [PMID: 29248718 PMCID: PMC5735259 DOI: 10.1016/j.neo.2017.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Patients with metastatic prostate cancer (PCa) have a poorer prognosis than patients with organ-confined tumors. We strove to uncover the proteome signature of primary PCa and associated lymph node metastases (LNMs) in order to identify proteins that may indicate or potentially promote metastases formation. We performed a proteomic comparative profiling of PCa tissue from radical prostatectomy (RPE) of patients without nodal metastases or relapse at the time of surgical resection (n=5) to PCa tissue from RPE of patients who suffered from nodal relapse (n=5). For the latter group, we also included patient-matched tissue of the nodal metastases. All samples were formalin fixed and paraffin embedded. We identified and quantified more than 1200 proteins by liquid chromatography tandem mass spectrometry with subsequent label-free quantification. An increase of ribosomal or proteasomal proteins in LNM (compared to corresponding PCa) became apparent, while extracellular matrix components rather decreased. Immunohistochemistry (IHC) corroborated accumulation of poly-(ADP-ribose)-polymerase 1 and N-myc-downstream-regulated-gene 3, alpha/beta hydrolase domain-containing protein 11, and protein phosphatase slingshot homolog 3 in LNM. These findings strengthen the present interest in examining PARP inhibitors for the treatment of aggressive PCa. IHC also corroborated increased abundance of retinol dehydrogenase 11 in metastasized primary PCa compared to organ-confined PCa. Generally, metastasizing primary tumors were characterized by an enrichment of proteins involved in cellular lipid metabolic processes with concomitant decrease of cell adhesion proteins. This study highlights the usefulness of a combined proteomic-IHC approach to explore novel aspects in tumor biology. Our initial results open novel opportunities for follow-up studies.
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Key Words
- pca, prostate cancer
- lnm, lymph node metastasis
- tu, primary tumor
- rpe, radical prostatectomy
- lnd, lymph node dissection
- ffpe, formalin-fixed, paraffin-embedded
- ms, mass-spectrometry
- ihc, immunohistochemistry
- fc, fold change
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Affiliation(s)
- Ann-Kathrin Müller
- Department of Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Melanie Föll
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Bianca Heckelmann
- Department of Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Selina Kiefer
- Department of Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Martin Werner
- Department of Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104 Freiburg, Germany.
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Cordula Annette Jilg
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Urology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Vanessa Drendel
- Department of Pathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
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4
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Pettersen VK, Steinsland H, Wiker HG. Comparative Proteomics of Enterotoxigenic Escherichia coli Reveals Differences in Surface Protein Production and Similarities in Metabolism. J Proteome Res 2017; 17:325-336. [DOI: 10.1021/acs.jproteome.7b00593] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Veronika Kuchařová Pettersen
- The Gade Research Group for Infection and Immunity, Department of
Clinical Science, ‡Centre for International Health, Department of Global Public Health
and Primary Care, and §Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Hans Steinsland
- The Gade Research Group for Infection and Immunity, Department of
Clinical Science, ‡Centre for International Health, Department of Global Public Health
and Primary Care, and §Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Harald G. Wiker
- The Gade Research Group for Infection and Immunity, Department of
Clinical Science, ‡Centre for International Health, Department of Global Public Health
and Primary Care, and §Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
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5
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D'Lima NG, Khitun A, Rosenbloom AD, Yuan P, Gassaway BM, Barber KW, Rinehart J, Slavoff SA. Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli. J Proteome Res 2017; 16:3722-3731. [PMID: 28861998 PMCID: PMC5647875 DOI: 10.1021/acs.jproteome.7b00419] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Recent advances in mass spectrometry-based
proteomics have revealed
translation of previously nonannotated microproteins from thousands
of small open reading frames (smORFs) in prokaryotic and eukaryotic
genomes. Facile methods to determine cellular functions of these newly
discovered microproteins are now needed. Here, we couple semiquantitative
comparative proteomics with whole-genome database searching to identify
two nonannotated, homologous cold shock-regulated microproteins in Escherichia coli K12 substr. MG1655, as well as two
additional constitutively expressed microproteins. We apply molecular
genetic approaches to confirm expression of these cold shock proteins
(YmcF and YnfQ) at reduced temperatures and identify the noncanonical
ATT start codons that initiate their translation. These proteins are
conserved in related Gram-negative bacteria and are predicted to be
structured, which, in combination with their cold shock upregulation,
suggests that they are likely to have biological roles in the cell.
These results reveal that previously unknown factors are involved
in the response of E. coli to lowered
temperatures and suggest that further nonannotated, stress-regulated E. coli microproteins may remain to be found. More
broadly, comparative proteomics may enable discovery of regulated,
and therefore potentially functional, products of smORF translation
across many different organisms and conditions.
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Affiliation(s)
- Nadia G D'Lima
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Alexandra Khitun
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Aaron D Rosenbloom
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Peijia Yuan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Brandon M Gassaway
- Department of Cellular and Molecular Physiology, Yale University , New Haven, Connecticut 06520, United States.,Systems Biology Institute, Yale University , West Haven, Connecticut 06511, United States
| | - Karl W Barber
- Department of Cellular and Molecular Physiology, Yale University , New Haven, Connecticut 06520, United States.,Systems Biology Institute, Yale University , West Haven, Connecticut 06511, United States
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology, Yale University , New Haven, Connecticut 06520, United States.,Systems Biology Institute, Yale University , West Haven, Connecticut 06511, United States
| | - Sarah A Slavoff
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06529, United States
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Abstract
Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes may be missed as soon as they are specific and poorly conserved in a given taxon, while important to explain the specific traits of the organism. Translational starts are also poorly predicted in a relatively important number of cases, thus impacting the protein sequence database used in proteomics, comparative genomics, and systems biology. The use of high-throughput proteomics data to improve genome annotation is an attractive option to obtain a more comprehensive molecular picture of a given organism. Here, protocols for reannotating prokaryote genomes are described based on shotgun proteomics and derivatization of protein N-termini with a positively charged reagent coupled to high-resolution tandem mass spectrometry.
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7
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Potgieter MG, Nakedi KC, Ambler JM, Nel AJM, Garnett S, Soares NC, Mulder N, Blackburn JM. Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry. Front Microbiol 2016; 7:427. [PMID: 27092112 PMCID: PMC4821088 DOI: 10.3389/fmicb.2016.00427] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 03/16/2016] [Indexed: 11/30/2022] Open
Abstract
Biochemical evidence is vital for accurate genome annotation. The integration of experimental data collected at the proteome level using high resolution mass spectrometry allows for improvements in genome annotation by providing evidence for novel gene models, while validating or modifying others. Here, we report the results of a proteogenomic analysis of a reference strain of Mycobacterium smegmatis (mc2155), a fast growing model organism for the pathogenic Mycobacterium tuberculosis—the causative agent for Tuberculosis. By integrating high throughput LC/MS/MS proteomic data with genomic six frame translation and ab initio gene prediction databases, a total of 2887 ORFs were identified, including 2810 ORFs annotated to a Reference protein, and 63 ORFs not previously annotated to a Reference protein. Further, the translational start site (TSS) was validated for 558 Reference proteome gene models, while upstream translational evidence was identified for 81. In addition, N-terminus derived peptide identifications allowed for downstream TSS modification of a further 24 gene models. We validated the existence of six previously described interrupted coding sequences at the peptide level, and provide evidence for four novel frameshift positions. Analysis of peptide posterior error probability (PEP) scores indicates high-confidence novel peptide identifications and shows that the genome of M. smegmatis mc2155 is not yet fully annotated. Data are available via ProteomeXchange with identifier PXD003500.
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Affiliation(s)
- Matthys G Potgieter
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Kehilwe C Nakedi
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Jon M Ambler
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Andrew J M Nel
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Shaun Garnett
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, IDM, University of Cape Town Cape Town, South Africa
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