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Mallick B, Dutta A, Mondal P, Dutta M. Proteomic analysis and protein structure prediction of Shigella phage Sfk20 based on a comparative study using structure prediction approaches. Proteins 2024; 92:637-648. [PMID: 38146101 DOI: 10.1002/prot.26653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Bacteriophages are the natural predators of bacteria and are available abundantly everywhere in nature. Lytic phages can specifically infect their bacterial host (through attachment to the receptor) and use their host replication machinery to replicate rapidly, a feature that enables them to kill a disease-causing bacteria. Hence, phage attachment to the host bacteria is the first important step of the infection process. It is reported in this study that the receptor could be an LPS which is responsible for the attachment of the Sfk20 phage to its host (Shigella flexneri 2a). Phage Sfk20 bacteriolytic activity was examined for preliminary optimization of phage titer. The phage Sfk20 viability at different saline conditions was conducted. The LC-MS/MS technique used here for detecting and identifying 40 Sfk20 phage proteins helped us to get an initial understanding of the structural landscape of phage Sfk20. From the identified proteins, six structurally significant proteins were selected for structure prediction using two neural network systems: AlphaFold2 and ESMFold, and one homology modeling software: Phyre2. Later the performance of these modeling systems was compared using various metrics. We conclude from the available and generated information that AlphaFold2 and Phyre2 perform better than ESMFold for predicting Sfk20 phage protein structures.
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Affiliation(s)
- Bani Mallick
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Aninda Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Payel Mondal
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Moumita Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
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2
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Ngashangva N, Mukherjee PK, Sharma C, Kalita MC, Sarangthem I. Integrated genomics and proteomics analysis of Paenibacillus peoriae IBSD35 and insights into its antimicrobial characteristics. Sci Rep 2022; 12:18861. [PMID: 36344671 PMCID: PMC9640621 DOI: 10.1038/s41598-022-23613-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance has been developing fast and incurring a loss of human life, and there is a need for new antimicrobial agents. Naturally occurring antimicrobial peptides offer the characteristics to counter AMR because the resistance development is low or no resistance. Antimicrobial peptides from Paenibacillus peoriae IBSD35 cell-free supernatant were salted out and purified using chromatography and characterized with liquid chromatography-tandem-mass spectrometry. The extract has shown a high and broad spectrum of antimicrobial activity. Combining the strain IBSD35 genome sequence with its proteomic data enabled the prediction of biosynthetic gene clusters by connecting the peptide from LC-MS/MS data to the gene that encode. Antimicrobial peptide databases offered a platform for the effective search, prediction, and design of AMPs and expanded the studies on their isolation, structure elucidation, biological evaluation, and pathway engineering. The genome-based taxonomy and comparisons have shown that P. peoriae IBSD35 is closely related to Paenibacillus peoriae FSL J3-0120. P. peoriae IBSD35 harbored endophytic trait genes and nonribosomal peptide synthases biosynthetic gene clusters. The comparative genomics revealed evolutionary insights and facilitated the discovery of novel SMs using proteomics from the extract of P. peoriae IBSD35. It will increase the potential to find novel bio-molecules to counter AMR.
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Affiliation(s)
- Ng Ngashangva
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Pulok K. Mukherjee
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Chandradev Sharma
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
| | - Mohan C. Kalita
- grid.411779.d0000 0001 2109 4622Department of Biotechnology, Gauhati University, Jalukbari, Guwahati, Assam 781014 India
| | - Indira Sarangthem
- grid.464584.f0000 0004 0640 0101A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Takyelpat, Imphal, Manipur 795001 India
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3
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Ngashangva N, Mukherjee P, Sharma KC, Kalita MC, Indira S. Analysis of Antimicrobial Peptide Metabolome of Bacterial Endophyte Isolated From Traditionally Used Medicinal Plant Millettia pachycarpa Benth. Front Microbiol 2021; 12:656896. [PMID: 34149644 PMCID: PMC8208310 DOI: 10.3389/fmicb.2021.656896] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022] Open
Abstract
Increasing prevalence of antimicrobial resistance (AMR) has posed a major health concern worldwide, and the addition of new antimicrobial agents is diminishing due to overexploitation of plants and microbial resources. Inevitably, alternative sources and new strategies are needed to find novel biomolecules to counter AMR and pandemic circumstances. The association of plants with microorganisms is one basic natural interaction that involves the exchange of biomolecules. Such a symbiotic relationship might affect the respective bio-chemical properties and production of secondary metabolites in the host and microbes. Furthermore, the discovery of taxol and taxane from an endophytic fungus, Taxomyces andreanae from Taxus wallachiana, has stimulated much research on endophytes from medicinal plants. A gram-positive endophytic bacterium, Paenibacillus peoriae IBSD35, was isolated from the stem of Millettia pachycarpa Benth. It is a rod-shaped, motile, gram-positive, and endospore-forming bacteria. It is neutralophilic as per Joint Genome Institute’s (JGI) IMG system analysis. The plant was selected based on its ethnobotany history of traditional uses and highly insecticidal properties. Bioactive molecules were purified from P. peoriae IBSD35 culture broth using 70% ammonium sulfate and column chromatography techniques. The biomolecule was enriched to 151.72-fold and the yield percentage was 0.05. Peoriaerin II, a highly potent and broad-spectrum antimicrobial peptide against Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, and Candida albicans ATCC 10231 was isolated. LC-MS sequencing revealed that its N-terminal is methionine. It has four negatively charged residues (Asp + Glu) and a total number of two positively charged residues (Arg + Lys). Its molecular weight is 4,685.13 Da. It is linked to an LC-MS/MS inferred biosynthetic gene cluster with accession number A0A2S6P0H9, and blastp has shown it is 82.4% similar to fusaricidin synthetase of Paenibacillus polymyxa SC2. The 3D structure conformation of the BGC and AMP were predicted using SWISS MODEL homology modeling. Therefore, combining both genomic and proteomic results obtained from P. peoriae IBSD35, associated with M. pachycarpa Benth., will substantially increase the understanding of antimicrobial peptides and assist to uncover novel biological agents.
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Affiliation(s)
- Ng Ngashangva
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
| | - Pulok Mukherjee
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
| | - K Chandradev Sharma
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
| | - M C Kalita
- Department of Biotechnology, Gauhati University, Guwahati, India
| | - Sarangthem Indira
- A National Institute of Department of Biotechnology, Institute of Bioresources and Sustainable Development (IBSD), Govt. of India, Imphal, India
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Kleikamp HBC, Pronk M, Tugui C, Guedes da Silva L, Abbas B, Lin YM, van Loosdrecht MCM, Pabst M. Database-independent de novo metaproteomics of complex microbial communities. Cell Syst 2021; 12:375-383.e5. [PMID: 34023022 DOI: 10.1016/j.cels.2021.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/16/2021] [Accepted: 04/07/2021] [Indexed: 11/30/2022]
Abstract
Metaproteomics has emerged as one of the most promising approaches for determining the composition and metabolic functions of complete microbial communities. Conventional metaproteomics approaches rely on the construction of protein sequence databases and efficient peptide-spectrum-matching algorithms, an approach that is intrinsically biased towards the content of the constructed sequence database. Here, we introduce a highly efficient, database-independent de novo metaproteomics approach and systematically evaluate its quantitative performance using synthetic and natural microbial communities comprising dozens of taxonomic families. Our work demonstrates that the de novo sequencing approach can vastly expand many metaproteomics applications by enabling rapid quantitative profiling and by capturing unsequenced community members that otherwise remain inaccessible for further interpretation. Kleikamp et al., describe a novel de novo metaproteomics pipeline (NovoBridge) that enables rapid community profiling without the need for constructing protein sequence databases.
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Affiliation(s)
- Hugo B C Kleikamp
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mario Pronk
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Claudia Tugui
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Leonor Guedes da Silva
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Ben Abbas
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Yue Mei Lin
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Martin Pabst
- Delft University of Technology, Department of Biotechnology, van der Maasweg 9, 2629 HZ Delft, the Netherlands.
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Dorschner BW, Wiedemuth R, Funke AC, Gentzel M, Rogers ML, Brenner S, Thieme S. Listening to the Whispers in Neuroimmune Crosstalk: A Comprehensive Workflow to Investigate Neurotrophin Receptor p75NTR Under Endogenous, Low Abundance Conditions. Front Immunol 2021; 12:648283. [PMID: 33936068 PMCID: PMC8085361 DOI: 10.3389/fimmu.2021.648283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/22/2021] [Indexed: 11/24/2022] Open
Abstract
Inflammatory conditions are critically influenced by neuroimmune crosstalk. Cytokines and neurotrophic factors shape the responses of both nervous and immune systems. Although much progress has been made, most findings to date are based on expression of recombinant (tagged) proteins. The examination of receptor interactions by immunoprecipitation (IP) at endogenous levels provides further insight into the more subtle regulations of immune responses. Here, we present a comprehensive workflow and an optimized IP protocol that provide step-by-step instructions to investigate neurotrophin receptor p75NTR at endogenous, low abundance levels: from lysate preparation and confirmation of receptor expression to antibody validation and successful detection of protein-protein interactions. We employ human melanoma cell line A375 to validate specific antibodies and IP conditions, and apply these methods to explore p75NTR interactions in human leukemic plasmacytoid dendritic cell line PMDC05 detecting 14-3-3ϵ:p75NTR interaction in this cell type. With p75NTR as an exemplary protein, our approach provides a strategy to detect specific interaction partners even under endogenous, low abundance expression conditions.
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Affiliation(s)
- Benjamin W Dorschner
- Experimental Hematology, Department of Pediatrics, University Clinic Carl Gustav Carus, Dresden, Germany
| | - Ralf Wiedemuth
- Experimental Hematology, Department of Pediatrics, University Clinic Carl Gustav Carus, Dresden, Germany
| | - Ann-Christin Funke
- Experimental Hematology, Department of Pediatrics, University Clinic Carl Gustav Carus, Dresden, Germany
| | - Marc Gentzel
- Molecular Analysis - Mass Spectrometry, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universitaet Dresden, Dresden, Germany
| | - Mary-Louise Rogers
- Centre for Neuroscience, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Sebastian Brenner
- Experimental Hematology, Department of Pediatrics, University Clinic Carl Gustav Carus, Dresden, Germany
| | - Sebastian Thieme
- Experimental Hematology, Department of Pediatrics, University Clinic Carl Gustav Carus, Dresden, Germany
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Dichloromethane Degradation Pathway from Unsequenced Hyphomicrobium sp. MC8b Rapidly Explored by Pan-Proteomics. Microorganisms 2020; 8:microorganisms8121876. [PMID: 33260855 PMCID: PMC7760279 DOI: 10.3390/microorganisms8121876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/23/2022] Open
Abstract
Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for Hyphomicrobium sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain. For this, we designed a pan-proteomics database comprising the annotated genome sequences of 13 distinct Hyphomicrobium strains. Compared to growth with methanol, growth with DCM induces drastic changes in the proteome of strain MC8b. Dichloromethane dehalogenase DcmA was detected by differential pan-proteomics, but only with poor sequence coverage, suggesting atypical characteristics of the DCM dehalogenation system in this strain. More peptides were assigned to DcmA by error-tolerant search, warranting subsequent sequencing of the genome of strain MC8b, which revealed a highly divergent set of dcm genes in this strain. This suggests that the dcm enzymatic system is less strongly conserved than previously believed, and that substantial molecular evolution of dcm genes has occurred beyond their horizontal transfer in the bacterial domain. Our study showed the power of pan-proteomics for quick characterization of new strains belonging to branches of the Tree of Life that are densely genome-sequenced.
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Mondal S, Swamy MJ. Purification, biochemical/biophysical characterization and chitooligosaccharide binding to BGL24, a new PP2-type phloem exudate lectin from bottle gourd (Lagenaria siceraria). Int J Biol Macromol 2020; 164:3656-3666. [PMID: 32890565 DOI: 10.1016/j.ijbiomac.2020.08.246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 12/20/2022]
Abstract
Phloem Protein 2 (PP2), highly abundant in the sieve elements of plants, plays a significant role in wound sealing and anti-pathogenic responses. In this study, we report the purification and characterization of a new PP2-type lectin, BGL24 from the phloem exudate of bottle gourd (Lagenaria siceraria). BGL24 is a homodimer with a subunit mass of ~24 kDa and exhibits high specificity for chitooligosaccharides. The isoelectric point of BGL24 was estimated from zeta potential measurements as 5.95. Partial amino acid sequence obtained by mass spectrometric studies indicated that BGL24 exhibits extensive homology with other PP2-type phloem exudate lectins. CD spectroscopic measurements revealed that the lectin contains predominantly β-sheets, with low α-helical content. CD spectroscopic and DSC studies showed that BGL24 exhibits high thermal stability with an unfolding temperature of ~82 °C, and that its secondary structure is essentially unaltered between pH 3.0 and 8.0. Fluorescence titrations employing 4-methylumbelliferyl-β-D-N,N',N″-triacetylchitotrioside as an indicator ligand revealed that the association constants for BGL24-chitooligosaccharide interaction increase considerably when the ligand size is increased from chitotriose to chitotetraose, whereas only marginal increase was observed for chitopentaose and chitohexaose. BGL24 exhibited moderate cytotoxicity against MDA-MB-231 breast cancer cells, whereas its effect on normal splenocytes was marginal.
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Affiliation(s)
- Saradamoni Mondal
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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Noor Z, Ranganathan S. Bioinformatics approaches for improving seminal plasma proteome analysis. Theriogenology 2019; 137:43-49. [PMID: 31186128 DOI: 10.1016/j.theriogenology.2019.05.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Reproduction efficiency of male animals is one of the key factors influencing the sustainability of livestock. Mass spectrometry (MS) based proteomics has become an important tool for studying seminal plasma proteomes. In this review, we summarize bioinformatics analysis strategies for current proteomics approaches, for identifying novel biomarkers of reproductive robustness.
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Affiliation(s)
- Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, Australia.
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Nallagangula KS, Lakshmaiah V, Muninarayana C, Deepa KV, Shashidhar KN. A proteomic approach of biomarker candidate discovery for alcoholic liver cirrhosis. J Circ Biomark 2018; 7:1849454418788417. [PMID: 30034555 PMCID: PMC6050617 DOI: 10.1177/1849454418788417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/15/2018] [Indexed: 12/16/2022] Open
Abstract
Alcoholic liver disease (ALD) progresses from steatosis to alcoholic hepatitis to fibrosis and cirrhosis. Liver biopsy is considered as the gold standard method for diagnosis of liver cirrhosis and provides useful information about damaging process which is an invasive procedure with complications. Existing biomarkers in clinical practice have narrow applicability due to lack of specificity and lack of sensitivity. The objective of this article is to identify proteomic biomarker candidates for alcoholic liver cirrhosis by differential expression analysis between alcoholic liver cirrhotic and healthy subjects. Blood samples were collected from 20 subjects (10 alcoholic liver cirrhosis and 10 healthy) from R. L. Jalapa Hospital and Research Centre, Kolar, Karnataka, India. Differential protein analysis was carried out by two-dimensional electrophoresis after albumin depletion, followed by liquid chromatography–mass spectrometry. The image analysis found 46 spots in cirrhotic gel and 69 spots in healthy gel, of which 14 spots were identified with significant altered expression levels. Based on the protein score and clinical significance, among 14 spots, a total of 28 protein biomarker candidates were identified: 13 with increased expression and 15 with decreased expression were categorized in alcoholic liver cirrhosis compared to healthy subjects. Protein biomarker candidates identified by “-omics” approach based on differential expression between alcoholic liver cirrhotic subjects and healthy subjects may give better insights for diagnosis of ALD. Prioritization of candidates identified is a prerequisite for validation regimen. Biomarker candidates require verification that demonstrates the differential expression will remain detectable by assay to be used for validation.
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Affiliation(s)
| | - V Lakshmaiah
- Department of Medicine, Sri Devaraj Urs Medical College, SDUAHER, Kolar, Karnataka, India
| | - C Muninarayana
- Department of Community Medicine, Sri Devaraj Urs Medical College, SDUAHER, Kolar, Karnataka, India
| | - KV Deepa
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bengaluru, Karnataka, India
| | - KN Shashidhar
- Department of Biochemistry, Sri Devaraj Urs Medical College, SDUAHER, Kolar, Karnataka, India
- KN Shashidhar, Department of Biochemistry, Sri Devaraj Urs Medical College, SDUAHER, Tamaka, Kolar, Karnataka, India.
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Nair D, Krishna JG, Panikkar MVN, Nair BG, Pai JG, Nair SS. Identification, purification, biochemical and mass spectrometric characterization of novel phycobiliproteins from a marine red alga, Centroceras clavulatum. Int J Biol Macromol 2018; 114:679-691. [DOI: 10.1016/j.ijbiomac.2018.03.153] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/22/2018] [Accepted: 03/25/2018] [Indexed: 11/30/2022]
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Cordero H, Brinchmann MF, Cuesta A, Esteban MA. Chronic wounds alter the proteome profile in skin mucus of farmed gilthead seabream. BMC Genomics 2017; 18:939. [PMID: 29197330 PMCID: PMC5712093 DOI: 10.1186/s12864-017-4349-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/24/2017] [Indexed: 11/20/2022] Open
Abstract
Background Skin and its mucus are known to be the first barrier of defence against any external stressors. In fish, skin wounds frequently appear as a result of intensive culture and also some diseases have skin ulcers as external clinical signs. However, there is no information about the changes produced by the wounds in the mucosae. In the present paper, we have studied the alterations in the proteome map of skin mucus of gilthead seabream during healing of experimentally produced chronic wounds by 2-DE followed by LC-MS/MS. The corresponding gene expression changes of some identified skin proteins were also investigated through qPCR. Results Our study has successfully identified 21 differentially expressed proteins involved in immunity and stress processes as well as other metabolic and structural proteins and revealed, for the first time, that all are downregulated in the skin mucus of wounded seabream specimens. At transcript level, we found that four of nine markers (ighm, gst3, actb and krt1) were downregulated after causing the wounds while the rest of them remained unaltered in the wounded fish. Finally, ELISA analysis revealed that IgM levels were significantly lower in wounded fish compared to the control fish. Conclusions Our study revealed a decreased-expression at protein and for some transcripts at mRNA levels in wounded fish, which could affect the functionality of these molecules, and therefore, delay the wound healing process and increase the susceptibility to any infection after wounds in the skin of gilthead seabream.
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Affiliation(s)
- Héctor Cordero
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain.,Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA.,Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Monica F Brinchmann
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway.
| | - Alberto Cuesta
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain
| | - María A Esteban
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100, Murcia, Spain
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Menschaert G, David F. Proteogenomics from a bioinformatics angle: A growing field. MASS SPECTROMETRY REVIEWS 2017; 36:584-599. [PMID: 26670565 PMCID: PMC6101030 DOI: 10.1002/mas.21483] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/01/2015] [Indexed: 05/16/2023]
Abstract
Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies. Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments. Other proteogenomics studies using a combination of proteomics and genomics techniques focus on antibody sequencing, the identification of immunogenic peptides or venom peptides. Over the years, a growing amount of bioinformatics tools and databases became available to help streamlining these cross-omics studies. Some of these solutions only help in specific steps of the proteogenomics studies, e.g. building custom sequence databases (based on next generation sequencing output) for mass spectrometry fragmentation spectrum matching. Over the last few years a handful integrative tools also became available that can execute complete proteogenomics analyses. Some of these are presented as stand-alone solutions, whereas others are implemented in a web-based framework such as Galaxy. In this review we aimed at sketching a comprehensive overview of all the bioinformatics solutions that are available for this growing research area. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:584-599, 2017.
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Affiliation(s)
- Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics, Department of
Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience
Engineering, Ghent University, Ghent, Belgium
- To whom correspondence should be addressed. Tel:
+32 9 264 99 22; Fax: +32 9 264 6220;
| | - Fenyö David
- Center for Health Informatics and Bioinformatics and Department of
Biochemistry and Molecular Pharmacology, New York University School of Medicine, New
York, New York, USA
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13
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Brinchmann MF. Immune relevant molecules identified in the skin mucus of fish using -omics technologies. MOLECULAR BIOSYSTEMS 2017; 12:2056-63. [PMID: 27173837 DOI: 10.1039/c5mb00890e] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review will give an overview of immune relevant molecules in fish skin mucus. The skin of fish is continuously exposed to a water environment, and unlike that of terrestrial vertebrates, it is a mucosal surface with a thin epidermis of live cells covered by a mucus layer. The mucosa plays an important role in maintaining the homeostasis of the fish and preventing the entry of invading pathogens. This review provides an overview of proteins, RNA, DNA, lipids and carbohydrates found in the skin mucus of studied species. Proteins such as actin, histones, lectins, lysozyme, mucin, and transferrin have extracellular immune relevant functions. Complement complement molecules, heat shock molecules and superoxide dismutase present in mucus show differential expression during pathogen challenge in some species, but their functions in mucus, if any, need to be shown. RNA, DNA, lipids, carbohydrates and metabolites in mucus have been studied to a limited extent in fish, the current knowledge is summarized and knowledge gaps are pointed out.
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14
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Saha B, Bhattacharya SG. Charting novel allergens from date palm pollen (Phoenix sylvestris) using homology driven proteomics. J Proteomics 2017; 165:1-10. [PMID: 28535932 DOI: 10.1016/j.jprot.2017.05.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 05/05/2017] [Accepted: 05/17/2017] [Indexed: 11/19/2022]
Abstract
Pollen grains from Phoenix sylvestris (date palm), a commonly cultivated tree in India has been found to cause severe allergic diseases in an increasing percentage of hypersensitive individuals. To unearth its allergenic components, pollen protein were profiled by two-dimensional gel electrophoresis followed by immunoblotting with date palm pollen sensitive patient sera. Allergens were identified by MALDI-TOF/TOF employing a layered proteomic approach combining conventional database dependent search and manual de novo sequencing followed by homology-based search as Phoenix sylvestris is unsequenced. Derivatization of tryptic peptides by acetylation has been demonstrated to differentiate the 'b' from the 'y' ions facilitating efficient de novo sequencing. Ten allergenic proteins were identified, out of which six showed homology with known allergens while others were reported for the first time. Amongst these, isoflavone reductase, beta-conglycinin, S-adenosyl methionine synthase, 1, 4 glucan synthase and beta-galactosidase were commonly reported as allergens from coconut pollen and presumably responsible for cross-reactivity. One of the allergens had IgE binding epitope recognized by its glycan moiety. The allergenic potency of date palm pollen has been demonstrated using in vitro tests. The identified allergens can be used to develop vaccines for immunotherapy against date palm pollen allergy. THE SIGNIFICANCE OF THE STUDY Identification of allergenic proteins from sources harboring them is essential in developing therapeutic interventions. This is the first comprehensive study on the identification of allergens from Phoenix sylvestris (date palm) pollen, one of the major aeroallergens in India using a proteomic approach. Proteomic methods are being increasingly used to identify allergens. However, since many of these proteins arise from species which are un-sequenced, it becomes difficult to interpret those using conventional proteomics. Date palm being an unsequenced species, the IgE-reactive proteins have been identified using a stratified proteomic workflow incorporating manual de novo sequencing and homology-based proteomics. This study also gives an insight into the presence of glycan nature of the IgE binding epitopes. Five proteins have been found to be common with coconut pollen allergens and presumably responsible for cross-reactivity. These can be used in diagnostics to differentiate patient cohorts allergic to both coconut and date palm pollen from true date palm pollen allergic subjects. This would also determine better specific immunotherapy regimes between the two cohorts. The allergens identified herein have potential towards vaccine development in date palm pollen allergy as well as in enriching the existing catalogue of allergenic proteins.
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Affiliation(s)
- Bodhisattwa Saha
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Swati Gupta Bhattacharya
- Division of Plant Biology, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India.
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Tremblay RR, Bourassa S, Nehmé B, Calvo EL. Daylily protein constituents of the pollen and stigma a proteomics approach. JOURNAL OF PLANT PHYSIOLOGY 2017; 212:1-12. [PMID: 28242413 DOI: 10.1016/j.jplph.2017.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 01/18/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
This study was aimed at the identification and quantification of the protein components of the pollen grains in parallel with the distal stigmatic tissue of tetraploid cultivars. Proteomes were analyzed using iTRAQ 4plex labeling, peptides separation by online RP-nano-LC and analysis by ESI-MS/MS. Protein identification and quantification were made using the Asparagales database as a reference. A total of 524,037 MS/MS spectra were produced from pollen and stigma samples. From these, a total of 8368 peptides wereidentified corresponding to 994 unique peptides and 432 protein groups. Among them, 128 differentially expressed proteins were retained for further analysis. In absence of the daylily genome availability, we exploited numerous databases and bioinformatics resources to exploring the putative biological functions of these proteins. The profile of differentially expressed proteins suggests an important representation of functions associated to the signalling and response against endogenous and environmental stresses, including several enzymes implicated in the biosynthesis of antibiotics. The abundance in stigma of several structural proteins of the ribosomal sub-units as well as of the core histones suggest that the translation processes and the regulation of gene expression in stigma is a more active mechanism than in pollen. In addition, pollen prioritizes the synthesis of fructose and glucose as opposed to sucrose in stigma as a source of energy. Finally, the modulated proteins in Hemerocallis point to several pathways that give potential clues concerning the molecular mechanisms underlying the functions of the pollen and the stigmatic fluid in daylily reproduction.
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Affiliation(s)
- Roland R Tremblay
- CHUL Research Center in Reproduction, Centre de Recherche du CHU de Québec,2705 Boulevard Laurier, Suite T3-67, Quebec City, QC, G1 V 4G2, Canada.
| | - Sylvie Bourassa
- Proteomics Platform Quebec Genomics Center, CRCHUL, Centre de Recherche du CHU de Quebec, Canada.
| | - Benjamin Nehmé
- Proteomics Platform Quebec Genomics Center, CRCHUL, Centre de Recherche du CHU de Quebec, Canada.
| | - Ezequiel L Calvo
- Scientific Consultant in Genomics, 701 Leonard, Quebec City, QC, G1X 4C9, Canada.
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Ghosal K, Saha B, Gupta Bhattacharya S. Clinical and immuno-proteomic approach on Lantana camara pollen allergy-a major health hazard. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2016; 12:33. [PMID: 27471520 PMCID: PMC4963993 DOI: 10.1186/s13223-016-0135-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND The incidence of allergic diseases is increasing gradually and is a global burden affecting the socio-economic quality of life. Identification of allergens is the first step towards paving the way for therapeutic interventions against atopic diseases. Our previous investigation figured out that total pollen load correlated significantly with the rise of respiratory allergy in a subtropical city in India. The most dominant pollen responsible for IgE sensitivity in most patients emerged to be from Lantana camara (LC) an obnoxious weed growing in and around suburban areas of West Bengal. In this study, we identified allergenic components from this shrub using an immunoproteomic approach. METHODS Determination of dominant pollen species was done using aerobiological sampling during two consecutive years and correlated with hospitalization and skin prick test. Serum was collected from LC positive patients and checked for in vitro allergenicity using ELISA and Histamine assay. Total proteome was profiled in SDS-PAGE, 2D PAGE and immunoblotted to detect IgE binding proteins which were further identified using mass spectrometry. RESULTS Lantana camara pollen emerged as a significant contributor from the correlation study with hospital admission of the respiratory allergy sufferers and its extract demonstrated an elevated IgE response in ELISA and histamine release assay tests. Five IgE reactive bands/zones were observed in 1D blot which resolved to 12 allergo-reactive spots in the 2D blot. Mass spectrometric analysis identified nine spots that grouped into four diverse proteins. Pathogenesis-related Thaumatin-like protein was found to be one of the major allergens in Lantana camara. CONCLUSIONS This is to our knowledge the first attempt to identify allergens from Lantana camara using a proteomic approach. The allergens identified thereof can be used to prepare hypoallergenic vaccine candidates and design immunotherapy trials against LC pollen and other aeroallergen carriers which are cross-reactive and harbor similar proteins.
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Affiliation(s)
- Kavita Ghosal
- Division of Plant Biology, Bose Institute, Main Campus, 93/1, A.P.C. Road, Kolkata, West Bengal 700009 India
| | - Bodhisattwa Saha
- Division of Plant Biology, Bose Institute, Main Campus, 93/1, A.P.C. Road, Kolkata, West Bengal 700009 India
| | - Swati Gupta Bhattacharya
- Division of Plant Biology, Bose Institute, Main Campus, 93/1, A.P.C. Road, Kolkata, West Bengal 700009 India
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Kotzsch A, Pawolski D, Milentyev A, Shevchenko A, Scheffel A, Poulsen N, Shevchenko A, Kröger N. Biochemical Composition and Assembly of Biosilica-associated Insoluble Organic Matrices from the Diatom Thalassiosira pseudonana. J Biol Chem 2016; 291:4982-97. [PMID: 26710847 PMCID: PMC4777836 DOI: 10.1074/jbc.m115.706440] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/23/2015] [Indexed: 11/06/2022] Open
Abstract
The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis.
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Affiliation(s)
| | | | - Alexander Milentyev
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Anna Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - André Scheffel
- the Max-Planck-Institute of Plant Physiology, 14476 Potsdam, Germany
| | | | - Andrej Shevchenko
- the Max-Planck-Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany, and
| | - Nils Kröger
- From the B CUBE Center for Molecular Bioengineering and the Department of Chemistry and Food Chemistry, Technische Universität Dresden, 01307 Dresden, Germany,
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Castro D, Cordeiro IB, Taquita P, Eberlin MN, Garcia JS, Souza GHMF, Arruda MAZ, Andrade EV, Filho SA, Crainey JL, Lozano LL, Nogueira PA, Orlandi PP. Proteomic analysis of Chromobacterium violaceum and its adaptability to stress. BMC Microbiol 2015; 15:272. [PMID: 26627076 PMCID: PMC4666173 DOI: 10.1186/s12866-015-0606-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 11/24/2015] [Indexed: 12/15/2022] Open
Abstract
Background Chromobacterium violaceum (C. violaceum) occurs abundantly in a variety of ecosystems, including ecosystems that place the bacterium under stress. This study assessed the adaptability of C. violaceum by submitting it to nutritional and pH stresses and then analyzing protein expression using bi-dimensional electrophoresis (2-DE) and Maldi mass spectrometry. Results Chromobacterium violaceum grew best in pH neutral, nutrient-rich medium (reference conditions); however, the total protein mass recovered from stressed bacteria cultures was always higher than the total protein mass recovered from our reference culture. The diversity of proteins expressed (repressed by the number of identifiable 2-DE spots) was seen to be highest in the reference cultures, suggesting that stress reduces the overall range of proteins expressed by C. violaceum. Database comparisons allowed 43 of the 55 spots subjected to Maldi mass spectrometry to be characterized as containing a single identifiable protein. Stress-related expression changes were noted for C. violaceum proteins related to the previously characterized bacterial proteins: DnaK, GroEL-2, Rhs, EF-Tu, EF-P; MCP, homogentisate 1,2-dioxygenase, Arginine deiminase and the ATP synthase β-subunit protein as well as for the ribosomal protein subunits L1, L3, L5 and L6. The ability of C. violaceum to adapt its cellular mechanics to sub-optimal growth and protein production conditions was well illustrated by its regulation of ribosomal protein subunits. With the exception of the ribosomal subunit L3, which plays a role in protein folding and maybe therefore be more useful in stressful conditions, all the other ribosomal subunit proteins were seen to have reduced expression in stressed cultures. Curiously, C. violeaceum cultures were also observed to lose their violet color under stress, which suggests that the violacein pigment biosynthetic pathway is affected by stress. Conclusions Analysis of the proteomic signatures of stressed C. violaceum indicates that nutrient-starvation and pH stress can cause changes in the expression of the C. violaceum receptors, transporters, and proteins involved with biosynthetic pathways, molecule recycling, energy production. Our findings complement the recent publication of the C. violeaceum genome sequence and could help with the future commercial exploitation of C. violeaceum. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0606-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diogo Castro
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil. .,Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - Isabelle Bezerra Cordeiro
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil. .,Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - Paula Taquita
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
| | - Marcos Nogueira Eberlin
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil.
| | - Jerusa Simone Garcia
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil.
| | | | - Marco Aurélio Zezzi Arruda
- Universidade Estadual de Campinas, Institute of Chemistry, Thomson Mass Spectrometry Laboratory PO and Spectrometry, Sample Preparation and Mechanization Group (GEPAM), 13084-971, Campinas, SP, Brazil.
| | - Edmar V Andrade
- Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - Spartaco A Filho
- Universidade Estadual do Amazonas, 3578 Djalma Batista Av., 69050-010, Manaus, AM, Brazil.
| | - J Lee Crainey
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
| | - Luis Lopez Lozano
- Biotechnology Laboratory/ Universidade Federal do Amazonas, 3000 Rodrigo Octávio Av., 69077-000, Manaus, AM, Brazil.
| | - Paulo A Nogueira
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
| | - Patrícia P Orlandi
- Instituto Leônidas e Maria Deane - ILMD- Fiocruz, 476 Teresina St., 69057-070, Manaus, AM, Brazil.
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Cordero H, Brinchmann MF, Cuesta A, Meseguer J, Esteban MA. Skin mucus proteome map of European sea bass (Dicentrarchus labrax). Proteomics 2015; 15:4007-20. [PMID: 26376207 DOI: 10.1002/pmic.201500120] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 08/07/2015] [Accepted: 09/01/2015] [Indexed: 12/23/2022]
Abstract
Skin mucus is the first barrier of fish defence. Proteins from skin mucus of European sea bass (Dicentrarchus labrax) were identified by 2DE followed by LC-MS/MS. From all the identified proteins in the proteome map, we focus on the proteins associated with several immune pathways in fish. Furthermore, the real-time PCR transcript levels in skin are shown. Proteins found include apolipoprotein A1, calmodulin, complement C3, fucose-binding lectin, lysozyme and several caspases. To our knowledge, this is the first skin mucus proteome study and further transcriptional profiling of the identified proteins done on this bony fish species. This not only contributes knowledge on the routes involved in mucosal innate immunity, but also establishes a non-invasive technique based on locating immune markers with a potential use for prevention and/or diagnosis of fish diseases.
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Affiliation(s)
- Héctor Cordero
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Murcia, Spain
- Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
| | - Monica F Brinchmann
- Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway
| | - Alberto Cuesta
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - José Meseguer
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - María A Esteban
- Fish Innate Immune System Group, Department of Cell Biology and Histology, Faculty of Biology, University of Murcia, Murcia, Spain
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da Veiga Leprevost F, Barbosa VC, Carvalho PC. Using PepExplorer to Filter and Organize
De Novo
Peptide Sequencing Results. ACTA ACUST UNITED AC 2015; 51:13.27.1-13.27.9. [DOI: 10.1002/0471250953.bi1327s51] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Felipe da Veiga Leprevost
- Computational Mass Spectrometry Group, Carlos Chagas Institute–Fiocruz. Curitiba Paraná Brazil
- Department of Pathology, University of Michigan Ann Arbor Michigan
| | - Valmir C. Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Paulo Costa Carvalho
- Computational Mass Spectrometry Group, Carlos Chagas Institute–Fiocruz. Curitiba Paraná Brazil
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Jurado J, Fuentes-Almagro CA, Guardiola FA, Cuesta A, Esteban MÁ, Prieto-Álamo MJ. Proteomic profile of the skin mucus of farmed gilthead seabream (Sparus aurata). J Proteomics 2015; 120:21-34. [DOI: 10.1016/j.jprot.2015.02.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 02/09/2015] [Accepted: 02/20/2015] [Indexed: 01/24/2023]
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22
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Xu L, Tang H, Chen DW, El-Naggar AK, Wei P, Sturgis EM. Genome-wide association study identifies common genetic variants associated with salivary gland carcinoma and its subtypes. Cancer 2015; 121:2367-74. [PMID: 25823930 DOI: 10.1002/cncr.29381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/20/2015] [Accepted: 02/09/2015] [Indexed: 01/20/2023]
Abstract
BACKGROUND Salivary gland carcinomas (SGCs) are a rare malignancy with unknown etiology. The objective of the current study was to identify genetic variants modifying the risk of SGC and its major subtypes: adenoid cystic carcinoma and mucoepidermoid carcinoma. METHODS The authors conducted a genome-wide association study in 309 well-defined SGC cases and 535 cancer-free controls. A single-nucleotide polymorphism (SNP)-level discovery study was performed in non-Hispanic white individuals followed by a replication study in Hispanic individuals. A logistic regression analysis was applied to calculate odds ratios (ORs) and 95% confidence intervals (95% CIs). A meta-analysis of the results was conducted. RESULTS A genome-wide significant association with SGC in non-Hispanic white individuals was detected at coding SNPs in CHRNA2 (cholinergic receptor, nicotinic, alpha 2 [neuronal]) (OR, 8.55; 95% CI, 4.53-16.13 [P = 3.6 × 10(-11)]), OR4F15 (olfactory receptor, family 4, subfamily F, member 15) (OR, 5.26; 95% CI, 3.13-8.83 [P = 3.5 × 10(-10)]), ZNF343 (zinc finger protein 343) (OR, 3.28; 95% CI, 2.12-5.07 [P = 9.1 × 10(-8)]), and PARP4 (poly(ADP-ribose) polymerase family, member 4) (OR, 2.00; 95% CI, 1.54-2.59 [P = 1.7 × 10(-7)]). Meta-analysis of the non-Hispanic white and Hispanic cohorts identified another genome-wide significant SNP in ELL2 (meta-OR, 1.86; 95% CI, 1.48-2.34 [P = 1.3 × 10(-7)]). Risk alleles were largely enriched in mucoepidermoid carcinoma, in which the SNPs in CHRNA2, OR4F15, and ZNF343 had ORs of 15.71 (95% CI, 6.59-37.47 [P = 5.2 × 10(-10)]), 15.60 (95% CI, 6.50-37.41 [P = 7.5 × 10(-10)]), and 6.49 (95% CI, 3.36-12.52 [P = 2.5 × 10(-8)]), respectively. None of these SNPs retained a significant association with adenoid cystic carcinoma. CONCLUSIONS To the best of the authors' knowledge, the current study is the first to identify a panel of SNPs associated with the risk of SGC. Confirmation of these findings along with functional analysis of identified SNPs are needed.
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Affiliation(s)
- Li Xu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hongwei Tang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Diane W Chen
- Clincal Research, Quality Improvement, Baylor College of Medicine, Houston, Texas
| | - Adel K El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peng Wei
- Division of Biostatistics and Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods 2015; 11:1114-25. [PMID: 25357241 DOI: 10.1038/nmeth.3144] [Citation(s) in RCA: 505] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022]
Abstract
Proteogenomics is an area of research at the interface of proteomics and genomics. In this approach, customized protein sequence databases generated using genomic and transcriptomic information are used to help identify novel peptides (not present in reference protein sequence databases) from mass spectrometry-based proteomic data; in turn, the proteomic data can be used to provide protein-level evidence of gene expression and to help refine gene models. In recent years, owing to the emergence of new sequencing technologies such as RNA-seq and dramatic improvements in the depth and throughput of mass spectrometry-based proteomics, the pace of proteogenomic research has greatly accelerated. Here I review the current state of proteogenomic methods and applications, including computational strategies for building and using customized protein sequence databases. I also draw attention to the challenge of false positive identifications in proteogenomics and provide guidelines for analyzing the data and reporting the results of proteogenomic studies.
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Affiliation(s)
- Alexey I Nesvizhskii
- 1] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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Challenges and prospects of proteomics of non-model organisms. J Proteomics 2015; 105:1-4. [PMID: 24952831 DOI: 10.1016/j.jprot.2014.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 03/24/2014] [Accepted: 03/25/2014] [Indexed: 11/23/2022]
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Capriotti AL, Cavaliere C, Piovesana S, Stampachiacchiere S, Ventura S, Zenezini Chiozzi R, Laganà A. Characterization of quinoa seed proteome combining different protein precipitation techniques: Improvement of knowledge of nonmodel plant proteomics. J Sep Sci 2015; 38:1017-25. [PMID: 25580831 DOI: 10.1002/jssc.201401319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 12/25/2014] [Indexed: 12/21/2022]
Abstract
A shotgun proteomics approach was used to characterize the quinoa seed proteome. To obtain comprehensive proteomic data from quinoa seeds three different precipitation procedures were employed: MeOH/CHCl3 /double-distilled H2 O, acetone either alone or with trichloroacetic acid; the isolated proteins were then in-solution digested and the resulting peptides were analyzed by nano-liquid chromatography coupled to tandem mass spectrometry. However, since quinoa is a nonmodel plant species, only a few protein sequences are included in the most widely known protein sequence databases. To improve the data reliability a UniProt subdatabase, containing only proteins of Caryophillales order, was used. A total of 352 proteins were identified and evaluated both from a qualitative and quantitative point of view. This combined approach is certainly useful to increase the final number of identifications, but no particular class of proteins was extracted and identified in spite of the different chemistries and the different precipitation protocols. However, with respect to the other two procedures, from the relative quantitative analysis, based on the number of spectral counts, the trichloroacetic acid/acetone protocol was the best procedure for sample handling and quantitative protein extraction. This study could pave the way to further high-throughput studies on Chenopodium Quinoa.
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Chapman B, Bellgard M. High-throughput parallel proteogenomics: A bacterial case study. Proteomics 2014; 14:2780-9. [DOI: 10.1002/pmic.201400185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/11/2014] [Accepted: 10/22/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Brett Chapman
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
| | - Matthew Bellgard
- Centre for Comparative Genomics; Murdoch University; Western Australia Australia
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Looso M. Opening the genetic toolbox of niche model organisms with high throughput techniques: novel proteins in regeneration as a case study. Bioessays 2014; 36:407-18. [PMID: 24741707 DOI: 10.1002/bies.201300093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Understanding in vivo regeneration of complex structures offers a fascinating perspective for translation into medical applications. Unfortunately, mammals in general lack large-scale regenerative capacity, whereas planarians, newts or Hydra can regenerate complete body parts. Such organisms are, however, poorly annotated because of the lack of sequence information. This leads to limited access for molecular biological investigations. In the last decade, high throughput technologies and new methods enabling the effective generation of transgenic animals have rapidly evolved. These developments have allowed the extensive use of niche model organisms as part of a trend towards the accessibility of a greater panel of model species for scientific research. The case study that follows provides an insight into the impact of high throughput techniques on the landscape of models of regeneration. The cases presented here give evidence of alternative stem cell maintenance pathways, the identification of new protein families and new stem cell markers.
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Armengaud J, Trapp J, Pible O, Geffard O, Chaumot A, Hartmann EM. Non-model organisms, a species endangered by proteogenomics. J Proteomics 2014; 105:5-18. [PMID: 24440519 DOI: 10.1016/j.jprot.2014.01.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Previously, large-scale proteomics was possible only for organisms whose genomes were sequenced, meaning the most common model organisms. The use of next-generation sequencers is now changing the deal. With "proteogenomics", the use of experimental proteomics data to refine genome annotations, a higher integration of omics data is gaining ground. By extension, combining genomic and proteomic data is becoming routine in many research projects. "Proteogenomic"-flavored approaches are currently expanding, enabling the molecular studies of non-model organisms at an unprecedented depth. Today draft genomes can be obtained using next-generation sequencers in a rather straightforward way and at a reasonable cost for any organism. Unfinished genome sequences can be used to interpret tandem mass spectrometry proteomics data without the need for time-consuming genome annotation, and the use of RNA-seq to establish nucleotide sequences that are directly translated into protein sequences appears promising. There are, however, certain drawbacks that deserve further attention for RNA-seq to become more efficient. Here, we discuss the opportunities of working with non-model organisms, the proteomic methods that have been used until now, and the dramatic improvements proffered by proteogenomics. These put the distinction between model and non-model organisms in great danger, at least in terms of proteomics! BIOLOGICAL SIGNIFICANCE Model organisms have been crucial for in-depth analysis of cellular and molecular processes of life. Focusing the efforts of thousands of researchers on the Escherichia coli bacterium, Saccharomyces cerevisiae yeast, Arabidopsis thaliana plant, Danio rerio fish and other models for which genetic manipulation was possible was certainly worthwhile in terms of fundamental and invaluable biological insights. Until recently, proteomics of non-model organisms was limited to tedious, homology-based techniques, but today draft genomes or RNA-seq data can be straightforwardly obtained using next-generation sequencers, allowing the establishment of a draft protein database for any organism. Thus, proteogenomics opens new perspectives for molecular studies of non-model organisms, although they are still difficult experimental organisms. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France.
| | - Judith Trapp
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France; Irstea, UR MALY, F-69626 Villeurbanne, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
| | | | | | - Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze F-30207, France
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Shevchenko A, Yang Y, Knaust A, Thomas H, Jiang H, Lu E, Wang C, Shevchenko A. Proteomics identifies the composition and manufacturing recipe of the 2500-year old sourdough bread from Subeixi cemetery in China. J Proteomics 2013; 105:363-71. [PMID: 24291353 DOI: 10.1016/j.jprot.2013.11.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/18/2013] [Indexed: 11/20/2022]
Abstract
UNLABELLED We report on the geLC-MS/MS proteomics analysis of cereals and cereal food excavated in Subeixi cemetery (500-300BC) in Xinjiang, China. Proteomics provided direct evidence that at the Subexi sourdough bread was made from barley and broomcorn millet by leavening with a renewable starter comprising baker's yeast and lactic acid bacteria. The baking recipe and flour composition indicated that barley and millet bread belonged to the staple food already in the first millennium BC and suggested the role of Turpan basin as a major route for cultural communication between Western and Eastern Eurasia in antiquity. This article is part of a Special Issue entitled: Proteomics of non-model organisms. BIOLOGICAL SIGNIFICANCE We demonstrate that organic residues of thousand year old foods unearthed by archeological excavations can be analyzed by geLC-MS/MS proteomics with good representation of protein source organisms and coverage of sequences of identified proteins. In-depth look into the foods proteome identifies the food type and its individual ingredients, reveals ancient food processing technologies, projects their social and economic impact and provides evidence of intercultural communication between ancient populations. Proteomics analysis of ancient organic residues is direct, quantitative and informative and therefore has the potential to develop into a valuable, generally applicable tool in archaeometry. This article is part of a Special Issue entitled: Proteomics of non-model organisms.
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Affiliation(s)
- Anna Shevchenko
- MPI of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Yimin Yang
- Department of Archaeometry, University of Chinese Academy of Sciences, Beijing 100049, PR China; Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, PR China
| | - Andrea Knaust
- MPI of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Henrik Thomas
- MPI of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Hongen Jiang
- Department of Archaeometry, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Enguo Lu
- Xinjiang Cultural Relics and Archaeology Institute, Ürümchi 830000, PR China
| | - Changsui Wang
- Department of Archaeometry, University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Wang DZ, Xie ZX, Zhang SF. Marine metaproteomics: current status and future directions. J Proteomics 2013; 97:27-35. [PMID: 24041543 DOI: 10.1016/j.jprot.2013.08.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/26/2013] [Accepted: 08/30/2013] [Indexed: 02/06/2023]
Abstract
Metaproteomics is a new field within the 'omics' science which investigates protein expression from a complex biological system and provides direct evidence of physiological and metabolic activities. Characterization of the metaproteome will enhance our understanding of the microbial world and link microbial communities to ecological functions. Recently, the availability of extensive metagenomic sequences from various marine microbial communities has extended the postgenomic era to the field of oceanography. Although still in its infancy, metaproteomics has shown its powerful potential with regard to functional gene expression within microbial habitats and their interactions with the ambient environment as well as their biogeochemical functions. However, the application of metaproteomic approaches to complex marine samples still faces considerable challenges. This review summarizes the recent progress in marine metaproteomics and discusses the limitations of and perspectives for this approach in the study of the marine ecosystem. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China.
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
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Gasulla F, Jain R, Barreno E, Guéra A, Balbuena TS, Thelen JJ, Oliver MJ. The response of Asterochloris erici (Ahmadjian) Skaloud et Peksa to desiccation: a proteomic approach. PLANT, CELL & ENVIRONMENT 2013; 36:1363-78. [PMID: 23305100 DOI: 10.1111/pce.12065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 12/21/2012] [Accepted: 12/26/2012] [Indexed: 05/11/2023]
Abstract
The study of desiccation tolerance of lichens, and of their chlorobionts in particular, has frequently focused on the antioxidant system that protects the cell against photo-oxidative stress during dehydration/rehydration cycles. In this study, we used proteomic and transcript analyses to assess the changes associated with desiccation in the isolated phycobiont Asterochloris erici. Algae were dried either slowly (5-6 h) or rapidly (<60 min), and rehydrated after 24 h in the desiccated state. To identify proteins that accumulated during the drying or rehydration processes, we employed two-dimensional (2D) difference gel electrophoresis (DIGE) coupled with individual protein identification using trypsin digestion and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Proteomic analyses revealed that desiccation caused an increase in relative abundance of only 11-13 proteins, regardless of drying rate, involved in glycolysis, cellular protection, cytoskeleton, cell cycle, and targeting and degradation. Transcripts of five Hsp90 and two β-tubulin genes accumulated primarily at the end of the dehydration process. In addition, transmission electron microscopy (TEM) images indicate that ultrastructural cell injuries, perhaps resulting from physical or mechanical stress rather than metabolic damage, were more intense after rapid dehydration. This occurred with no major change in the proteome. These results suggest that desiccation tolerance of A. erici is achieved by constitutive mechanisms.
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Affiliation(s)
- Franscico Gasulla
- Dpt. Botànica, ICBiBE, Universitat de València, Burjassot 46100, Spain
| | - Renuka Jain
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Eva Barreno
- Dpt. Botànica, ICBiBE, Universitat de València, Burjassot, 46100, Spain
| | - Alfredo Guéra
- Dpto. Biología Vegetal, Universidad de Alcalá, Alcalá de Henares, 28871, Spain
| | - Tiago S Balbuena
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
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Sestili F, Paoletti F, Botticella E, Masci S, Saletti R, Muccilli V, Lafiandra D. Comparative proteomic analysis of kernel proteins of two high amylose transgenic durum wheat lines obtained by biolistic and Agrobacterium-mediated transformations. J Cereal Sci 2013. [DOI: 10.1016/j.jcs.2013.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rubiano-Labrador C, Bland C, Miotello G, Guérin P, Pible O, Baena S, Armengaud J. Proteogenomic insights into salt tolerance by a halotolerant alpha-proteobacterium isolated from an Andean saline spring. J Proteomics 2013; 97:36-47. [PMID: 23727365 DOI: 10.1016/j.jprot.2013.05.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 04/30/2013] [Accepted: 05/16/2013] [Indexed: 01/18/2023]
Abstract
UNLABELLED Tistlia consotensis is a halotolerant Rhodospirillaceae that was isolated from a saline spring located in the Colombian Andes with a salt concentration close to seawater (4.5%w/vol). We cultivated this microorganism in three NaCl concentrations, i.e. optimal (0.5%), without (0.0%) and high (4.0%) salt concentration, and analyzed its cellular proteome. For assigning tandem mass spectrometry data, we first sequenced its genome and constructed a six reading frame ORF database from the draft sequence. We annotated only the genes whose products (872) were detected. We compared the quantitative proteome data sets recorded for the three different growth conditions. At low salinity general stress proteins (chaperons, proteases and proteins associated with oxidative stress protection), were detected in higher amounts, probably linked to difficulties for proper protein folding and metabolism. Proteogenomics and comparative genomics pointed at the CrgA transcriptional regulator as a key-factor for the proteome remodeling upon low osmolarity. In hyper-osmotic condition, T. consotensis produced in larger amounts proteins involved in the sensing of changes in salt concentration, as well as a wide panel of transport systems for the transport of organic compatible solutes such as glutamate. We have described here a straightforward procedure in making a new environmental isolate quickly amenable to proteomics. BIOLOGICAL SIGNIFICANCE The bacterium Tistlia consotensis was isolated from a saline spring in the Colombian Andes and represents an interesting environmental model to be compared with extremophiles or other moderate organisms. To explore the halotolerance molecular mechanisms of the bacterium T. consotensis, we developed an innovative proteogenomic strategy consisting of i) genome sequencing, ii) quick annotation of the genes whose products were detected by mass spectrometry, and iii) comparative proteomics of cells grown in three salt conditions. We highlighted in this manuscript how efficient such an approach can be compared to time-consuming genome annotation when pointing at the key proteins of a given biological question. We documented a large number of proteins found produced in greater amounts when cells are cultivated in either hypo-osmotic or hyper-osmotic conditions. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Carolina Rubiano-Labrador
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá D.C., Colombia; Colombian Center for Genomics and Bioinformatics of Extreme Environments, GeBiX, Colombia
| | - Céline Bland
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Guylaine Miotello
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Philippe Guérin
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá D.C., Colombia; Colombian Center for Genomics and Bioinformatics of Extreme Environments, GeBiX, Colombia
| | - Jean Armengaud
- CEA, DSV, iBEB, SBTN, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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Shabbiri K, Botting CH, Adnan A, Fuszard M. Charting the cellular and extracellular proteome analysis of Brevibacterium linens DSM 20158 with unsequenced genome by mass spectrometry-driven sequence similarity searches. J Proteomics 2013; 83:99-118. [PMID: 23507220 DOI: 10.1016/j.jprot.2013.02.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 02/27/2013] [Indexed: 11/26/2022]
Abstract
UNLABELLED Brevibacterium linens DSM 20158 is an industrially important actinobacterium which is well-known for the production of amino acids and enzymes. However, as this strain has an unsequenced genome, there is no detailed information regarding its proteome although another strain of this microbe, BL2, has a shotgun genome sequence. However, this still does not cover the entire scope of its proteome. The present study is carried out by first identifying proteins by homology matches using the Mascot search algorithm followed by an advanced approach using de novo sequencing and MS BLAST to expand the B. linens proteome. The proteins identified in the secretome and cellular portion appear to be involved in various metabolic and physiological processes of this unsequenced organism. This study will help to enhance the usability of this strain of B. linens in different areas of research in the future rather than mainly in the food industries. BIOLOGICAL SIGNIFICANCE The present study describes the construction of the first detailed proteomic reference map of B. linens DSM 20158 with unsequenced genome by comparative proteome research analysis. This opens new horizons in proteomics to understand the role of proteins involved in the metabolism and physiology of other organisms with unsequenced genomes.
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Affiliation(s)
- Khadija Shabbiri
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, Scotland, United Kingdom
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Chandramouli KH, Sun J, Mok FS, Liu L, Qiu JW, Ravasi T, Qian PY. Transcriptome and quantitative proteome analysis reveals molecular processes associated with larval metamorphosis in the polychaete Pseudopolydora vexillosa. J Proteome Res 2013; 12:1344-58. [PMID: 23294167 DOI: 10.1021/pr3010088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Larval growth of the polychaete worm Pseudopolydora vexillosa involves the formation of segment-specific structures. When larvae attain competency to settle, they discard swimming chaetae and secrete mucus. The larvae build tubes around themselves and metamorphose into benthic juveniles. Understanding the molecular processes, which regulate this complex and unique transition, remains a major challenge because of the limited molecular information available. To improve this situation, we conducted high-throughput RNA sequencing and quantitative proteome analysis of the larval stages of P. vexillosa. Based on gene ontology (GO) analysis, transcripts related to cellular and metabolic processes, binding, and catalytic activities were highly represented during larval-adult transition. Mitogen-activated protein kinase (MAPK), calcium-signaling, Wnt/β-catenin, and notch signaling metabolic pathways were enriched in transcriptome data. Quantitative proteomics identified 107 differentially expressed proteins in three distinct larval stages. Fourteen and 53 proteins exhibited specific differential expression during competency and metamorphosis, respectively. Dramatic up-regulation of proteins involved in signaling, metabolism, and cytoskeleton functions were found during the larval-juvenile transition. Several proteins involved in cell signaling, cytoskeleton and metabolism were up-regulated, whereas proteins related to transcription and oxidative phosphorylation were down-regulated during competency. The integration of high-throughput RNA sequencing and quantitative proteomics allowed a global scale analysis of larval transcripts/proteins associated molecular processes in the metamorphosis of polychaete worms. Further, transcriptomic and proteomic insights provide a new direction to understand the fundamental mechanisms that regulate larval metamorphosis in polychaetes.
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Affiliation(s)
- Kondethimmahalli H Chandramouli
- KAUST Global Collaborative Research, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong
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Silva AJD, Gómez-Mendoza DP, Junqueira M, Domont GB, Ximenes Ferreira Filho E, de Sousa MV, Ricart CAO. Blue native-PAGE analysis of Trichoderma harzianum secretome reveals cellulases and hemicellulases working as multienzymatic complexes. Proteomics 2012; 12:2729-38. [DOI: 10.1002/pmic.201200048] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Adelson Joel da Silva
- Laboratório de Bioquímica e Química de Proteínas,; Departamento de Biologia Celular; Universidade de Brasília; Brasília DF Brazil
| | - Diana Paola Gómez-Mendoza
- Laboratório de Bioquímica e Química de Proteínas,; Departamento de Biologia Celular; Universidade de Brasília; Brasília DF Brazil
| | - Magno Junqueira
- Laboratório de Bioquímica e Química de Proteínas,; Departamento de Biologia Celular; Universidade de Brasília; Brasília DF Brazil
| | | | | | - Marcelo Valle de Sousa
- Laboratório de Bioquímica e Química de Proteínas,; Departamento de Biologia Celular; Universidade de Brasília; Brasília DF Brazil
| | - Carlos André Ornelas Ricart
- Laboratório de Bioquímica e Química de Proteínas,; Departamento de Biologia Celular; Universidade de Brasília; Brasília DF Brazil
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Junqueira M, Carvalho PC. Tools and challenges for diversity-driven proteomics in Brazil. Proteomics 2012; 12:2601-6. [PMID: 22744956 DOI: 10.1002/pmic.201200058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/15/2012] [Accepted: 03/21/2012] [Indexed: 11/12/2022]
Abstract
Our current knowledge in biology has been mostly derived from studying model organisms and cell lines in which only a small fraction of all described species have been extensively studied. Although these model organisms are amenable to genetic manipulations, this blinds researchers to the true variability of life. Groundbreaking discoveries are often achieved by analyzing "noncanonical" species; for example, the characterization of Taq polymerase from Thermus aquaticus ultimately led to a revolution in the field of molecular biology. Brazil possesses a rich biodiversity and a considerable fraction of Brazilian groups use current proteomic techniques to explore this natural treasure-trove. However, in our opinion, much more than the widely adopted peptide spectrum match approach is required to explore this rich "proteomosphere." Here, we provide a critical overview of the available strategies for the analysis of proteomic data from "noncanonical" biological samples (e.g. proteins from unsequenced genomes or genomes with high levels of polymorphisms), and demonstrate some limitations of existing approaches for large-scale protein identification and quantitation. An understanding of the premises behind these computational tools is necessary to properly deal with their limitations and draw accurate conclusions.
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Affiliation(s)
- Magno Junqueira
- Brazilian Center for Protein Research, Department of Cell Biology, University of Brasilia, Brasilia, D.F., Brazil.
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Cunsolo V, Muccilli V, Saletti R, Foti S. Mass spectrometry in the proteome analysis of mature cereal kernels. MASS SPECTROMETRY REVIEWS 2012; 31:448-465. [PMID: 22711440 DOI: 10.1002/mas.20347] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/07/2011] [Accepted: 07/07/2011] [Indexed: 06/01/2023]
Abstract
In the last decade, the improved performance and versatility of the mass spectrometers together with the increasing availability of gene and genomic sequence database, led the mass spectrometry to become an indispensable tool for either protein and proteome analyses in cereals. Mass spectrometric works on prolamins have rapidly evolved from the determination of the molecular masses of proteins to the proteomic approaches aimed to a large-scale protein identification and study of functional and regulatory aspects of proteins. Mass spectrometry coupled with electrophoresis, chromatographic methods, and bioinformatics tools is currently making significant contributions to a better knowledge of the composition and structure of the cereal proteins and their structure-function relationships. Results obtained using mass spectrometry, including characterization of prolamins, investigation of the gluten toxicity for coeliac patients, identification of proteins responsible of cereal allergies, determination of the protein pattern and its modification under environmental or stress effects, investigation of genetically modified varieties by proteomic approaches, are summarized here, to illustrate current trends, analytical troubles and challenges, and suggest possible future perspectives.
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Affiliation(s)
- Vincenzo Cunsolo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Italy
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40
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Mass spectrometry and animal science: Protein identification strategies and particularities of farm animal species. J Proteomics 2012; 75:4190-206. [DOI: 10.1016/j.jprot.2012.04.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/17/2012] [Accepted: 04/08/2012] [Indexed: 12/30/2022]
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Abstract
High-throughput identification of proteins with the latest generation of hybrid high-resolution mass spectrometers is opening new perspectives in microbiology. I present, here, an overview of tandem mass spectrometry technology and bioinformatics for shotgun proteomics that make 2D-PAGE approaches obsolete. Non-labelling quantitative approaches have become more popular than labelling techniques on most proteomic platforms because they are easier to carry out while their quantitative outcome is rather robust. Parameters for recording mass spectrometry data, however, need to be chosen carefully and statistics to assess the confidence of the results should not be neglected. Interestingly, next-generation sequencing methodologies make any microbial model quickly amenable to proteomics, leading to the documentation of a wide range of organisms from diverse environments. Some recent discoveries made using microbial proteomics have challenged some biological dogma, such as: (i) initiation of the translation does not occur predominantly from ATG codons in some microorganisms, (ii) non-canonical initiation codons are used to regulate the production of specific but important proteins and (iii) a gene may code for multiple polypeptide species, heterogeneous in terms of sequences. Microbial diversity and microbial physiology can now be revisited by means of exhaustive comparative proteomic surveys where thousands of proteins are detected and quantified. Proteogenomics, consisting of better annotating of genomes with the help of proteomic evidence, is paving the way for integrated multi-omic approaches in microbiology. Finally, meta-proteomic tools and approaches are emerging for tackling the high complexity of the microbial world as a whole, opening new perspectives for assessing how microbial communities function.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, F-30207 Bagnols-sur-Cèze, France.
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Lázaro-Mixteco PE, Nieto-Sotelo J, Swatek KN, Houston NL, Mendoza-Hernández G, Thelen JJ, Dinkova TD. The absence of heat shock protein HSP101 affects the proteome of mature and germinating maize embryos. J Proteome Res 2012; 11:3246-58. [PMID: 22545728 DOI: 10.1021/pr3000046] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Maize heat shock protein HSP101 accumulates during embryo maturation and desiccation and persists at high levels during the first 24 h following kernel imbibition in the absence of heat stress. This protein has a known function in disaggregation of high molecular weight complexes and has been proposed to be a translational regulator of specific mRNAs. Here, a global proteomic approach was used to identify changes in the maize proteome due to the absence of HSP101 in embryos from mature-dry or 24 h-imbibed kernels. A total of 26 protein spots from the mature dry embryo exhibited statistically significant expression changes in the L10 inbred hsp101 mutant (hsp101-m5::Mu1/hsp101-m5::Mu1) line as compared to the corresponding wild type (Hsp101/Hsp101). Additional six spots reproducibly showed qualitative changes between the mutant and wild-type mature and germinating embryos. Several chaperones, translation-related proteins, actin, and enzymes participating in cytokinin metabolism were identified in these spots by tandem mass-spectrometry (MS). The proteomic changes partially explain the altered root growth and architecture observed in young hsp101 mutant seedlings. In addition, specific protein de novo synthesis was altered in the 24 h-imbibed mutant embryos indicating that maize HSP101 functions as both chaperone and translational regulator during germination. Supporting this, HSP101 was found as part of Cap-binding and translation initiation complexes during early kernel imbibition. Overall, these findings expose the relevance of maize HSP101 for protein synthesis and balance mechanisms during germination.
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Affiliation(s)
- Pedro E Lázaro-Mixteco
- Departamento de Bioquímica, Facultad de Química, ‡Jardín Botánico, Instituto de Biología, and #Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México , 04510, México, D.F., Mexico
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Renard BY, Xu B, Kirchner M, Zickmann F, Winter D, Korten S, Brattig NW, Tzur A, Hamprecht FA, Steen H. Overcoming species boundaries in peptide identification with Bayesian information criterion-driven error-tolerant peptide search (BICEPS). Mol Cell Proteomics 2012; 11:M111.014167. [PMID: 22493179 PMCID: PMC3394943 DOI: 10.1074/mcp.m111.014167] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Currently, the reliable identification of peptides and proteins is only feasible when thoroughly annotated sequence databases are available. Although sequencing capacities continue to grow, many organisms remain without reliable, fully annotated reference genomes required for proteomic analyses. Standard database search algorithms fail to identify peptides that are not exactly contained in a protein database. De novo searches are generally hindered by their restricted reliability, and current error-tolerant search strategies are limited by global, heuristic tradeoffs between database and spectral information. We propose a Bayesian information criterion-driven error-tolerant peptide search (BICEPS) and offer an open source implementation based on this statistical criterion to automatically balance the information of each single spectrum and the database, while limiting the run time. We show that BICEPS performs as well as current database search algorithms when such algorithms are applied to sequenced organisms, whereas BICEPS only uses a remotely related organism database. For instance, we use a chicken instead of a human database corresponding to an evolutionary distance of more than 300 million years (International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716). We demonstrate the successful application to cross-species proteomics with a 33% increase in the number of identified proteins for a filarial nematode sample of Litomosoides sigmodontis.
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Affiliation(s)
- Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin 13353, Germany.
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44
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Allmer J. Algorithms for the de novo sequencing of peptides from tandem mass spectra. Expert Rev Proteomics 2012; 8:645-57. [PMID: 21999834 DOI: 10.1586/epr.11.54] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Proteomics is the study of proteins, their time- and location-dependent expression profiles, as well as their modifications and interactions. Mass spectrometry is useful to investigate many of the questions asked in proteomics. Database search methods are typically employed to identify proteins from complex mixtures. However, databases are not often available or, despite their availability, some sequences are not readily found therein. To overcome this problem, de novo sequencing can be used to directly assign a peptide sequence to a tandem mass spectrometry spectrum. Many algorithms have been proposed for de novo sequencing and a selection of them are detailed in this article. Although a standard accuracy measure has not been agreed upon in the field, relative algorithm performance is discussed. The current state of the de novo sequencing is assessed thereafter and, finally, examples are used to construct possible future perspectives of the field.
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Affiliation(s)
- Jens Allmer
- Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir 35430, Turkey.
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Diz AP, Martínez-Fernández M, Rolán-Alvarez E. Proteomics in evolutionary ecology: linking the genotype with the phenotype. Mol Ecol 2012; 21:1060-80. [PMID: 22268916 DOI: 10.1111/j.1365-294x.2011.05426.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The study of the proteome (proteomics), which includes the dynamics of protein expression, regulation, interactions and its function, has played a less prominent role in evolutionary and ecological investigations in comparison with the study of the genome and transcriptome. There are, however, a number of arguments suggesting that this situation should change. First, the proteome is closer to the phenotype than the genome or the transcriptome, and as such may be more directly responsive to natural selection, and thus closely linked to adaptation. Second, there is evidence of a low correlation between protein and transcript expression levels across genes in many different organisms. Finally, there have been some recent important technological improvements in proteomics methods that make them feasible, practical and useful to address a wide range of evolutionary questions even in nonmodel organisms. The different proteomic methods, their limitations and problems when interpreting empirical data are described and discussed. In addition, the proteomic literature pertaining to evolutionary ecology is reviewed with examples, and potential applications of proteomics in a variety of evolutionary contexts are outlined. New proteomic research trends such as the study of posttranslational modifications and protein-protein interactions, as well as the combined use of the different -omics approaches, are discussed in relation to the development of a more functional and integrated perspective, needed for achieving a more comprehensive knowledge of evolutionary change.
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Affiliation(s)
- Angel P Diz
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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Jayaraman D, Forshey KL, Grimsrud PA, Ané JM. Leveraging proteomics to understand plant-microbe interactions. FRONTIERS IN PLANT SCIENCE 2012; 3:44. [PMID: 22645586 PMCID: PMC3355735 DOI: 10.3389/fpls.2012.00044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 02/21/2012] [Indexed: 05/20/2023]
Abstract
Understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. Proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. The various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. In this review, we discuss how these techniques have been applied to the study of plant-microbe interactions. We also present some areas where this field of study would benefit from the utilization of newly developed methods that overcome previous limitations. Finally, we reinforce the need for expanding, integrating, and curating protein databases, as well as the benefits of combining protein-level datasets with those from genetic analyses and other high-throughput large-scale approaches for a systems-level view of plant-microbe interactions.
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Affiliation(s)
| | - Kari L. Forshey
- Department of Agronomy, University of Wisconsin MadisonMadison, WI, USA
- Department of Genetics, University of Wisconsin MadisonMadison, WI, USA
| | - Paul A. Grimsrud
- Department of Biochemistry, University of Wisconsin MadisonMadison, WI, USA
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin MadisonMadison, WI, USA
- *Correspondence: Jean-Michel Ané, Department of Agronomy, University of Wisconsin Madison, 1575 Linden Drive, Madison, WI 53706, USA. e-mail:
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47
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Carrasco MA, Buechler SA, Arnold RJ, Sformo T, Barnes BM, Duman JG. Investigating the deep supercooling ability of an Alaskan beetle, Cucujus clavipes puniceus, via high throughput proteomics. J Proteomics 2011; 75:1220-34. [PMID: 22094879 DOI: 10.1016/j.jprot.2011.10.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/26/2011] [Accepted: 10/31/2011] [Indexed: 12/27/2022]
Abstract
Cucujus clavipes puniceus is a freeze avoiding beetle capable of surviving the long, extremely cold winters of the Interior of Alaska. Previous studies showed that some individuals typically supercool to mean values of approximately -40 °C, with some individuals supercooling to as low as -58 °C, but these non-deep supercooling (NDSC) individuals eventually freeze if temperatures drop below this. However, other larvae, especially if exposed to very cold temperatures, supercool even further. These deep supercooling (DSC) individuals do not freeze even if cooled to -100 °C. In addition, the body water of the DSC larvae vitrifies (turns to a glass) at glass transition temperatures of -58 to -70 °C. This study examines the proteomes of DSC and NDSC larvae to assess proteins that may contribute to or inhibit the DSC trait. Using high throughput proteomics, we identified 138 proteins and 513 Gene Ontology categories in the DSC group and 104 proteins and 573 GO categories in the NDSC group. GO categories enriched in DSC include alcohol metabolic process, cellular component morphogenesis, monosaccharide metabolic process, regulation of biological quality, extracellular region, structural molecule activity, and antioxidant activity. Proteins unique to DSC include alpha casein precursor, alpha-actinin, vimentin, tropomyosin, beta-lactoglobulin, immunoglobulins, tubulin, cuticle proteins and endothelins.
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Nanavati D, Austin DR, Catapano LA, Luckenbaugh DA, Dosemeci A, Manji HK, Chen G, Markey SP. The effects of chronic treatment with mood stabilizers on the rat hippocampal post-synaptic density proteome. J Neurochem 2011; 119:617-29. [PMID: 21838781 PMCID: PMC3192943 DOI: 10.1111/j.1471-4159.2011.07424.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bipolar disorder is a devastating illness that is marked by recurrent episodes of mania and depression. There is growing evidence that the disease is correlated with disruptions in synaptic plasticity cascades involved in cognition and mood regulation. Alleviating the symptoms of bipolar disorder involves chronic treatment with mood stabilizers like lithium or valproate. These two structurally dissimilar drugs are known to alter prominent signaling cascades in the hippocampus, but their effects on the post-synaptic density complex remain undefined. In this work, we utilized mass spectrometry for quantitative profiling of the rat hippocampal post-synaptic proteome to investigate the effects of chronic mood stabilizer treatment. Our data show that in response to chronic treatment of mood stabilizers there were not gross qualitative changes but rather subtle quantitative perturbations in post-synaptic density proteome linked to several key signaling pathways. Our data specifically support the changes in actin dynamics on valproate treatment. Using label-free quantification methods, we report that lithium and valproate significantly altered the abundance of 21 and 43 proteins, respectively. Seven proteins were affected similarly by both lithium and valproate: Ank3, glutamate receptor 3, dynein heavy chain 1, and four isoforms of the 14-3-3 family. Immunoblotting the same samples confirmed the changes in Ank3 and glutamate receptor 3 abundance. Our findings support the hypotheses that BPD is a synaptic disorder and that mood stabilizers modulate the protein signaling complex in the hippocampal post-synaptic density.
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Affiliation(s)
- Dhaval Nanavati
- Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel R. Austin
- Laboratory of Molecular Pathophysiology and Experimental Therapeutics, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa A. Catapano
- Laboratory of Molecular Pathophysiology and Experimental Therapeutics, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A. Luckenbaugh
- Laboratory of Molecular Pathophysiology and Experimental Therapeutics, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayse Dosemeci
- Laboratory of Neurobiology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Husseini K. Manji
- Laboratory of Molecular Pathophysiology and Experimental Therapeutics, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guang Chen
- Laboratory of Molecular Pathophysiology and Experimental Therapeutics, Mood and Anxiety Disorders Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanford P. Markey
- Laboratory of Neurotoxicology, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
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49
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Carrasco MA, Buechler SA, Arnold RJ, Sformo T, Barnes BM, Duman JG. Elucidating the Biochemical Overwintering Adaptations of Larval Cucujus clavipes puniceus, a Nonmodel Organism, via High Throughput Proteomics. J Proteome Res 2011; 10:4634-46. [DOI: 10.1021/pr200518y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Martin A. Carrasco
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven A. Buechler
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Randy J. Arnold
- Proteomics Facility, Indiana University, Indianapolis, Indiana, United States
| | - Todd Sformo
- University of Alaska, Fairbanks, Alaska, United States
| | - Brian M. Barnes
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, United States
| | - John G. Duman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
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50
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Vertommen A, Møller A, Cordewener J, Swennen R, Panis B, Finnie C, America A, Carpentier S. A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana. J Proteomics 2011; 74:1218-29. [DOI: 10.1016/j.jprot.2011.02.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/03/2011] [Accepted: 02/07/2011] [Indexed: 02/06/2023]
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