1
|
Prokai L, Zaman K, Prokai-Tatrai K. Mass spectrometry-based retina proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1032-1062. [PMID: 35670041 PMCID: PMC9730434 DOI: 10.1002/mas.21786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
A subfield of neuroproteomics, retina proteomics has experienced a transformative growth since its inception due to methodological advances in enabling chemical, biochemical, and molecular biology techniques. This review focuses on mass spectrometry's contributions to facilitate mammalian and avian retina proteomics to catalog and quantify retinal protein expressions, determine their posttranslational modifications, as well as its applications to study the proteome of the retina in the context of biology, health and diseases, and therapy developments.
Collapse
Affiliation(s)
- Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Khadiza Zaman
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| |
Collapse
|
2
|
Shimazaki Y, Inoue A, Ikeuchi H. Electrophoretic injection and reaction of dye-bound enzymes to protein and bacteria within gel. J Microbiol Methods 2020; 176:106028. [PMID: 32795638 DOI: 10.1016/j.mimet.2020.106028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/02/2020] [Accepted: 08/05/2020] [Indexed: 11/26/2022]
Abstract
Three-dimensional (3D) cell cultures within gels are used to examine physiological reactions between cells, including bacteria and macromolecules such as enzymes. Using non-denaturing electrophoresis, an anionic Coomassie Brilliant Blue (CBB) dye successfully bound to enzymes such as trypsin and lysozyme, and reacted with a protein and a bacterium within a gel. Both CBB-bound trypsin and lysozyme retained their enzymatic activities and migrated toward the anode in non-denaturing electrophoresis. CBB-bound trypsin successfully digested the iron-binding protein, transferrin, within the gel. Furthermore, the activity of esterase extracted from the bacteria, Bacillus subtilis was analyzed by the non-denaturing electrophoresis containing both the bacteria and the CBB-bound lysozyme after the bacteriolysis of the bacteria by the addition of CBB-bound lysozyme. This method can be applied to deliver enzymes to organisms including bacteria within 3D cell cultures.
Collapse
Affiliation(s)
- Youji Shimazaki
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan; Faculty of Science, Ehime University, Matsuyama, Japan.
| | - Aoshi Inoue
- Faculty of Science, Ehime University, Matsuyama, Japan
| | | |
Collapse
|
3
|
Kawano R, Nakanishi A, Zako T, Shimazaki Y. Analysis of the degradation of amyloid beta fibrils after separation via the combination of non‐denaturing agarose electrophoresis and Congo red dye staining. SEPARATION SCIENCE PLUS 2019. [DOI: 10.1002/sscp.201900049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Risa Kawano
- Faculty of ScienceEhime University Matsuyama Japan
| | - Ayaka Nakanishi
- Department of Chemistry and biologyGraduate School of Science and EngineeringEhime University Matsuyama Japan
| | - Tamotsu Zako
- Department of Chemistry and biologyGraduate School of Science and EngineeringEhime University Matsuyama Japan
- Faculty of ScienceEhime University Matsuyama Japan
| | - Youji Shimazaki
- Department of Chemistry and biologyGraduate School of Science and EngineeringEhime University Matsuyama Japan
- Faculty of ScienceEhime University Matsuyama Japan
| |
Collapse
|
4
|
Funke S, Markowitsch S, Schmelter C, Perumal N, Mwiiri FK, Gabel-Scheurich S, Pfeiffer N, Grus FH. In-Depth Proteomic Analysis of the Porcine Retina by Use of a four Step Differential Extraction Bottom up LC MS Platform. Mol Neurobiol 2016; 54:7262-7275. [PMID: 27796761 DOI: 10.1007/s12035-016-0172-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 09/27/2016] [Indexed: 01/09/2023]
Abstract
The eye of the house swine (Sus scrofa domestica Linnaeus, 1758) represents a promising model for the study of human eye diseases encircling neurodegenerative retina disorders that go along with proteomic changes. To provide an in-depth view into the "normal" (untreated & healthy) porcine retina proteome as an important reference, a proteomic strategy has been developed encircling stepwise/differential extraction, LC MS and peptide de novo sequencing. Accordingly, pooled porcine retina homogenates were processed by stepwise DDM, CHAPS, ASB14 and ACN/TFA extraction. Retinal proteins were fractionated by 1D-SDS PAGE and further analyzed by LC ESI MS following database and de novo sequencing related protein identification and functional analyses. In summary, >2000 retinal proteins (FDR < 1 %) could be identified by use of the highly reproducible and selective extraction procedure. Moreover, an identification surplus of 36 % comparing initial one step extraction to the four step method could be documented. Despite most proteins were identified in the DDM and CHAPS fraction, all extraction steps contributed exclusive proteins with nucleus proteins enriched in the final ACN/TFA fraction. Additionally, for the first time new non-annotated de novo peptides could be documented for the porcine retina. The generated porcine retina proteome reference map contributes importantly to the understanding of the pig eye proteome and the developed workflow has strong translational potential considering retina studies of various species.
Collapse
Affiliation(s)
- Sebastian Funke
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Sascha Markowitsch
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Carsten Schmelter
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Natarajan Perumal
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Francis Kamau Mwiiri
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Silke Gabel-Scheurich
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Norbert Pfeiffer
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany
| | - Franz H Grus
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center, Mainz, Germany.
- Department of Experimental Ophthalmology, University Medical Center (Universitätsmedizin), Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
| |
Collapse
|
5
|
YAMAMOTO S, IWATA T, NISHIWAKI K, KINOSHITA M, SUZUKI S. Synthesis of Quaternary Ammonium Derivatives of Cellulose as the Coating Reagents for Capillary Electrophoresis. CHROMATOGRAPHY 2015. [DOI: 10.15583/jpchrom.2015.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | | | | | | | - Shigeo SUZUKI
- Faculty of Pharmaceutical Sciences, Kinki University
| |
Collapse
|
6
|
De Iuliis A, Arrigoni G, Andersson L, Zambenedetti P, Burlina A, James P, Arslan P, Vianello F. Oxidative metabolism of dopamine: A colour reaction from human midbrain analysed by mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1687-93. [DOI: 10.1016/j.bbapap.2008.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 07/02/2008] [Accepted: 07/03/2008] [Indexed: 10/21/2022]
|
7
|
Shimazaki Y, Kuroda T. Direct analysis of retinal dehydrogenase activity on an electroblotting membrane following separation by non-denaturing two-dimensional electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 860:180-4. [PMID: 17997140 DOI: 10.1016/j.jchromb.2007.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 10/10/2007] [Accepted: 10/18/2007] [Indexed: 10/22/2022]
Abstract
The reaction from retinal to retinoic acid catalyzed by retinal dehydrogenase on a polyvinylidene difluoride (PVDF) membrane was examined using laser desorption ionization time of flight mass spectrometry (LDI-TOF MS) when the enzyme was separated by non-denaturing two-dimensional electrophoresis (2-DE), transferred onto the membrane, and stained without impairing the enzyme activity. Furthermore, the enzyme was analyzed by de novo sequencing using electrospray ionization tandem mass spectrometry (ESI-MS/MS) after proteins from mouse liver were separated by non-denaturing 2-DE, blotted onto the membrane, and stained. The results indicated that the reported methods could be applied for the direct examination of changes in retinoid catalyzed by enzymes on such membranes.
Collapse
Affiliation(s)
- Youji Shimazaki
- Graduate school of Science and Engineering (Science section) and Venture Business Laboratory, Ehime University, Matsuyama, Japan.
| | | |
Collapse
|
8
|
Shimazaki Y. Hydrolytic activity of lipase on anion-exchange solid phase column after separation and electrotransfer by non-denaturing electrophoresis. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2007; 70:487-91. [PMID: 17239955 DOI: 10.1016/j.jbbm.2006.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 10/21/2006] [Accepted: 11/29/2006] [Indexed: 05/13/2023]
Abstract
This study reports the initial separation of phospholipase C-alpha from porcine retina using non-denaturing two-dimensional gel electrophoresis (2-DE). Detection was by negative staining and then its hydrolytic activity was estimated using alpha-naphthyl acetate in a 2-DE gel. A spot of phospholipase C-alpha separated by 2-DE was excised. It was then electrophoretically transferred to an anion-exchange solid phase column after 40 mg, equal to dry weight of the solid resin from the cartridge (Accell Plus QMA, Waters Corporation), was packed into a disposable 1 ml syringe to make an anion-exchange solid phase column. Phosphatidylcholine was hydrolyzed in the anion-exchange solid phase column containing phospholipase C-alpha. The results indicated that a column with hydrolytic activity could be produced once lipases separated by non-denaturing 2-DE were transferred to the solid phase column.
Collapse
Affiliation(s)
- Youji Shimazaki
- Graduate School of Science and Engineering (Science Section) and Venture Business Laboratory, Ehime University, Matsuyama City, 790-8577, Japan.
| |
Collapse
|
9
|
|
10
|
Shimazaki Y, Manabe T. Detection of activity and mass spectrometric identification of mouse liver carboxylesterase and aldehyde dehydrogenase separated by non-denaturing two-dimensional electrophoresis after extraction with detergents. BIOCHIMICA ET BIOPHYSICA ACTA 2005; 1749:95-101. [PMID: 15848140 DOI: 10.1016/j.bbapap.2005.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 02/23/2005] [Accepted: 02/23/2005] [Indexed: 11/19/2022]
Abstract
To examine the activities and identity of enzymes associated with organelles such as microsomes and mitochondria, proteins from mouse liver were extracted using the non-ionic detergents Nonidet P-40 (NP-40), polyoxyethylene sorbitan monooleate (Tween 80), polyoxyethylene isooctylphenyl ester (Triton X), n-octyl beta-D-glucoside (octyl glycoside) or anionic detergent sodium dodecylsulfate (SDS) after the removal of cytosolic proteins. The proteins extracted by detergents were separated by non-denaturing two-dimensional electrophoresis (2-DE). The activities of esterase and aldehyde dehydrogenase were retained by non-denaturing 2-DE after treatment with each non-ionic detergent, but the activities were reduced or lost when the proteins were extracted with more than 0.5% SDS. For proteomic analysis of the organelle-associated proteins in mouse liver, proteins were separated by non-denaturing 2-DE and were identified using electrospray ionization tandem mass spectrometry (ESI-MS/MS) after the proteins were solubilized by octyl glycoside, NP-40 and 0.1% SDS. Several organelle-associated proteins such as carboxylesterase, aldehyde dehydrogenase, glucose regulated protein and HSP60 were identified. These results indicate that the activities and identity of detergent-soluble enzymes can be examined by this non-denaturing 2-DE and mass spectrometry.
Collapse
Affiliation(s)
- Youji Shimazaki
- Department of Chemistry, Faculty of Science and Venture Business Laboratory, Ehime University, Matsuyama, Japan.
| | | |
Collapse
|