1
|
Anjos L, Estêvão J, Infante C, Mantecón L, Power DM. Extracting protein from microalgae (Tetraselmis chuii) for proteome analysis. MethodsX 2022; 9:101637. [PMID: 35242618 PMCID: PMC8886058 DOI: 10.1016/j.mex.2022.101637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/10/2022] [Indexed: 11/26/2022] Open
|
2
|
Fu J, Luo Y, Mou M, Zhang H, Tang J, Wang Y, Zhu F. Advances in Current Diabetes Proteomics: From the Perspectives of Label- free Quantification and Biomarker Selection. Curr Drug Targets 2021; 21:34-54. [PMID: 31433754 DOI: 10.2174/1389450120666190821160207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Due to its prevalence and negative impacts on both the economy and society, the diabetes mellitus (DM) has emerged as a worldwide concern. In light of this, the label-free quantification (LFQ) proteomics and diabetic marker selection methods have been applied to elucidate the underlying mechanisms associated with insulin resistance, explore novel protein biomarkers, and discover innovative therapeutic protein targets. OBJECTIVE The purpose of this manuscript is to review and analyze the recent computational advances and development of label-free quantification and diabetic marker selection in diabetes proteomics. METHODS Web of Science database, PubMed database and Google Scholar were utilized for searching label-free quantification, computational advances, feature selection and diabetes proteomics. RESULTS In this study, we systematically review the computational advances of label-free quantification and diabetic marker selection methods which were applied to get the understanding of DM pathological mechanisms. Firstly, different popular quantification measurements and proteomic quantification software tools which have been applied to the diabetes studies are comprehensively discussed. Secondly, a number of popular manipulation methods including transformation, pretreatment (centering, scaling, and normalization), missing value imputation methods and a variety of popular feature selection techniques applied to diabetes proteomic data are overviewed with objective evaluation on their advantages and disadvantages. Finally, the guidelines for the efficient use of the computationbased LFQ technology and feature selection methods in diabetes proteomics are proposed. CONCLUSION In summary, this review provides guidelines for researchers who will engage in proteomics biomarker discovery and by properly applying these proteomic computational advances, more reliable therapeutic targets will be found in the field of diabetes mellitus.
Collapse
Affiliation(s)
- Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongning Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University, Chongqing 401331, China
| |
Collapse
|
3
|
Chakdar H, Hasan M, Pabbi S, Nevalainen H, Shukla P. High-throughput proteomics and metabolomic studies guide re-engineering of metabolic pathways in eukaryotic microalgae: A review. BIORESOURCE TECHNOLOGY 2021; 321:124495. [PMID: 33307484 DOI: 10.1016/j.biortech.2020.124495] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 06/12/2023]
Abstract
Eukaryotic microalgae are a rich source of commercially important metabolites including lipids, pigments, sugars, amino acids and enzymes. However, their inherent genetic potential is usually not enough to support high level production of metabolites of interest. In order to move on from the traditional approach of improving product yields by modification of the cultivation conditions, understanding the metabolic pathways leading to the synthesis of the bioproducts of interest is crucial. Identification of new targets for strain engineering has been greatly facilitated by the rapid development of high-throughput sequencing and spectroscopic techniques discussed in this review. Despite the availability of high throughput analytical tools, examples of gathering and application of proteomic and metabolomic data for metabolic engineering of microalgae are few and mainly limited to lipid production. The present review highlights the application of contemporary proteomic and metabolomic techniques in eukaryotic microalgae for redesigning pathways for enhanced production of algal metabolites.
Collapse
Affiliation(s)
- Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Maunath Bhanjan, Uttar Pradesh 275103, India
| | - Mafruha Hasan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi 110 012
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, NSW 2109, Australia; Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India; School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
4
|
Li Y, Lammi C, Boschin G, Arnoldi A, Aiello G. Recent Advances in Microalgae Peptides: Cardiovascular Health Benefits and Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:11825-11838. [PMID: 31588750 DOI: 10.1021/acs.jafc.9b03566] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There is now great interest in food protein hydrolysates and food-derived peptides, because they may provide numerous health benefits. Among other foodstuffs, microalgae appear to be sustainable sources of proteins and bioactive peptides that can be exploited in foods and functional formulations. This review considers protein hydrolysates and individual peptides that may be relevant in cardiovascular disease prevention because they mimic the functions of mediators involved in pathologic processes that represent relevant risk factors for cardiovascular disease development, such as hypercholesterolemia, hypertension, diabetes, inflammation, and oxidative status. Some of these peptides are also multifunctional (i.e., they offer more than one benefit). Moreover, the most efficient techniques for protein extraction and hydrolyzation are commented on, as well as the best methodologies for high-throughput detection and quantification. Finally, current challenges and critical issues are discussed.
Collapse
Affiliation(s)
- Yuchen Li
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Carmen Lammi
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Giovanna Boschin
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Anna Arnoldi
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| | - Gilda Aiello
- Department of Pharmaceutical Sciences , University of Milan , Milan , Italy
| |
Collapse
|
5
|
Zocher K, Lackmann JW, Volzke J, Steil L, Lalk M, Weltmann KD, Wende K, Kolb JF. Profiling microalgal protein extraction by microwave burst heating in comparison to spark plasma exposures. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
6
|
Cordara A, Manfredi M, van Alphen P, Marengo E, Pirone R, Saracco G, Branco Dos Santos F, Hellingwerf KJ, Pagliano C. Response of the thylakoid proteome of Synechocystis sp. PCC 6803 to photohinibitory intensities of orange-red light. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:524-534. [PMID: 30316162 DOI: 10.1016/j.plaphy.2018.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
Photoautotrophic growth of Synechocystis sp. PCC 6803 in a flat-panel photobioreactor, run in turbidostat mode under increasing intensities of orange-red light (636 nm), showed a maximal growth rate (0.12 h-1) at 300 μmolphotons m-2 s-1, whereas first signs of photoinhibition were detected above 800 μmolphotons m-2 s-1. To investigate the dynamic modulation of the thylakoid proteome in response to photoinhibitory light intensities, quantitative proteomics analyses by SWATH mass spectrometry were performed by comparing thylakoid membranes extracted from Synechocystis grown under low-intensity illumination (i.e. 50 μmolphotons m-2 s-1) with samples isolated from cells subjected to photoinhibitory light regimes (800, 950 and 1460 μmolphotons m-2 s-1). We identified and quantified 126 proteins with altered abundance in all three photoinhibitory illumination regimes. These data reveal the strategies by which Synechocystis responds to photoinibitory growth irradiances of orange-red light. The accumulation of core proteins of Photosystem II and reduction of oxygen-evolving-complex subunits in photoinhibited cells revealed a different turnover and repair rates of the integral and extrinsic Photosystem II subunits with variation of light intensity. Furthermore, Synechocystis displayed a differentiated response to photoinhibitory regimes also regarding Photosystem I: the amount of PsaD, PsaE, PsaJ and PsaM subunits decreased, while there was an increased abundance of the PsaA, PsaB, Psak2 and PsaL proteins. Photoinhibition with 636 nm light also elicited an increased capacity for cyclic electron transport, a lowering of the amount of phycobilisomes and an increase of the orange carotenoid protein content, all presumably as a photoprotective mechanism against the generation of reactive oxygen species.
Collapse
Affiliation(s)
- Alessandro Cordara
- Applied Science and Technology Department-BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144, Torino, Italy; Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Environment Park, Via Livorno 60, 10144, Torino, Italy
| | - Marcello Manfredi
- ISALIT-Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy; Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Pascal van Alphen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090, GE, Amsterdam, Netherlands
| | - Emilio Marengo
- ISALIT-Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy; Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy
| | - Raffaele Pirone
- Applied Science and Technology Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Guido Saracco
- Applied Science and Technology Department, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090, GE, Amsterdam, Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1090, GE, Amsterdam, Netherlands
| | - Cristina Pagliano
- Applied Science and Technology Department-BioSolar Lab, Politecnico di Torino, Environment Park, Via Livorno 60, 10144, Torino, Italy.
| |
Collapse
|
7
|
Comparative proteomic analysis reveals the regulatory network of the veA gene during asexual and sexual spore development of Aspergillus cristatus. Biosci Rep 2018; 38:BSR20180067. [PMID: 29773679 PMCID: PMC6066658 DOI: 10.1042/bsr20180067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 12/13/2022] Open
Abstract
Aspergillus cristatus is the predominant fungal population during fermentation of Chinese Fuzhuan brick tea, and belongs to the homothallic fungal group that undergoes a sexual stage without asexual conidiation under hypotonic conditions, while hypertonic medium induces initiation of the asexual stage and completely blocks sexual development. However, the veA deletion mutant only produces conidia in hypotonic medium after a 24-h culture, but both asexual and sexual spores are observed after 72 h. The veA gene is one of the key genes that positively regulates sexual and negatively regulates asexual development in A. cristatus. To elucidate the molecular mechanism of how VeA regulates asexual and sexual spore development in A. cristatus, 2D electrophoresis (2-DE) combined with MALDI-tandem ToF MS analysis were applied to identify 173 differentially expressed proteins (DEPs) by comparing the agamotype (24 h) and teleomorph (72 h) with wild-type (WT) A. cristatus strains. Further analysis revealed that the changed expression pattern of Pmk1-MAPK and Ser/Thr phosphatase signaling, heat shock protein (Hsp) 90 (HSP90), protein degradation associated, sulphur-containing amino acid biosynthesis associated, valine, leucine, isoleucine, and arginine biosynthesis involved, CYP450 and cytoskeletal formation associated proteins were involved in the production of conidia in agamotype of A. cristatus. Furthermore, the deletion of veA in A. cristatus resulted in disturbed process of transcription, translation, protein folding, amino acid metabolism, and secondary metabolism. The carbohydrate and energy metabolism were also greatly changed, which lied in the suppression of anabolism through pentose phosphate pathway (PPP) but promotion of catabolism through glycolysis and tricarboxylic acid (TCA) cycle. The energy compounds produced in the agamotype were mainly ATP and NADH, whereas they were NADPH and FAD in the teleomorph. These results will contribute to the existing knowledge on the complex role of VeA in the regulation of spore development in Aspergillus and provide a framework for functional investigations on the identified proteins.
Collapse
|
8
|
Darvish M, Jalili H, Ranaei-Siadat SO, Sedighi M. Potential Cytotoxic Effects of Peptide Fractions from Dunaliella salina Protein Hydrolyzed by Gastric Proteases. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2017. [DOI: 10.1080/10498850.2017.1414095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Maliheh Darvish
- Life Science Engineering Department, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Hasan Jalili
- Life Science Engineering Department, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Seyed-Omid Ranaei-Siadat
- Nano-Biotechnology Engineering Lab., Department of Biotechnology, Faculty of Energy Engineering and New Technologies, Shahid Beheshti University, GC, Tehran, Iran
| | - Mahsa Sedighi
- Life Science Engineering Department, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| |
Collapse
|
9
|
Karthikaichamy A, Deore P, Rai V, Bulach D, Beardall J, Noronha S, Srivastava S. Time for Multiple Extraction Methods in Proteomics? A Comparison of Three Protein Extraction Methods in the Eustigmatophyte Alga Microchloropsis gaditana CCMP526. ACTA ACUST UNITED AC 2017; 21:678-683. [DOI: 10.1089/omi.2017.0128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | - Vineeta Rai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dieter Bulach
- Department of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - John Beardall
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Santosh Noronha
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Mumbai, India
- Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| |
Collapse
|
10
|
Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: From basic research to clinical applications. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600278] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/05/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Sandra Isabel Anjo
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Faculty of Sciences and Technology; University of Coimbra; Coimbra Portugal
| | - Cátia Santa
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Institute for Interdisciplinary Research (III); University of Coimbra; Coimbra Portugal
| | - Bruno Manadas
- CNC - Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| |
Collapse
|
11
|
Qin H, Jiang X, Fan J, Wang J, Liu L, Qiu L, Wang J, Jiang P. Investigation of the weak binding of a tetrahistidine-tagged peptide to quantum dots by using capillary electrophoresis with fluorescence detection. J Sep Sci 2016; 40:567-573. [DOI: 10.1002/jssc.201601183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/04/2016] [Accepted: 11/07/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Haifang Qin
- Institute of Pharmaceutical and Environmental Engineering; Changzhou Vocational Institute of Engineering; Changzhou Jiangsu P.R. China
| | - Xiyuan Jiang
- Kunshan affiliated Hospital of Nanjing University of Chinese Medicine; Kunshan Jiangsu P.R. China
| | - Jie Fan
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P.R. China
| | - Jianpeng Wang
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P.R. China
| | - Li Liu
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P.R. China
| | - Lin Qiu
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P.R. China
| | - Jianhao Wang
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P.R. China
| | - Pengju Jiang
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P.R. China
- Key Laboratory of Synthetic Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai P.R. China
| |
Collapse
|
12
|
Wang J, Zhang C, Liu L, Kalesh KA, Qiu L, Ding S, Fu M, Gao LQ, Jiang P. A capillary electrophoresis method to explore the self-assembly of a novel polypeptide ligand with quantum dots. Electrophoresis 2016; 37:2156-62. [DOI: 10.1002/elps.201600164] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 06/14/2016] [Accepted: 06/14/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Jianhao Wang
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
| | - Chencheng Zhang
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
| | - Li Liu
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
| | - Karunakaran A. Kalesh
- Department of Chemical Engineering, Imperial College London; South Kensington Campus; London UK
| | - Lin Qiu
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
- State Key Laboratory of Coordination Chemistry; Nanjing University; Nanjing Jiangsu P. R. China
| | - Shumin Ding
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
| | - Minli Fu
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
| | - Li-qian Gao
- Department of Chemistry; National University of Singapore; Singapore
| | - Pengju Jiang
- School of Pharmaceutical Engineering and Life Science; Changzhou University; Changzhou Jiangsu P. R. China
- Key Laboratory of Synthetic Biology, Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai P. R. China
| |
Collapse
|