Staining Your Way into Cells: Exploring Cell and Organelle Markers

Authors: Aparna Chandrasekaran and Cameron Smurthwaite

Cellular constituents elements are organized into membrane-bound and non-membrane bound compartments called ‘Organelles’. These structurally complex compartments carry out specific biological functions which are determined by the distinct enzymes/proteins they contain. These unique proteins can aid in the study of the morphology and function of the cell and its organelles.

Spatial-temporal mapping and characterization of the protein of interest are essential in interpreting its subcellular location and its role in different cellular mechanisms and functions. Although mass spectrometry and gel-based electrophoresis approaches have been at the forefront of high throughput techniques for proteome analysis, imaging-based techniques have enabled scientists to visualize the proteins in situ in individual cells at a high resolution.

Antibodies as cell and organelle markers

One approach for imaging-based techniques involves co-localization with antibodies that target proteins within a specific organelle called organelle markers to accurately identify the spatial distribution and potential function of the protein of interest within the cell. Co-localization studies using antibodies that demonstrate relationships between different proteins can also aid in visualizing multiple organelles simultaneously by using organelle marker antibodies of different isotypes or from different host species. These markers serve as essential tools in western blot assays to confirm the organelle-specific fractionation of cell lysates. The versatile range of fluorescent colors available for the organelle stains accommodates for co-staining experiments with organelle-specific antibodies to monitor cellular movement and location.

Figure 1 | Immunofluorescence analysis of antibody markers staining different subcellular components. Plasma membrane – Pan-cadherin Polyclonal Antibody (Cat. No. 71-7100), mitochondria – HK1 Recombinant Polyclonal Antibody (Cat. No. 711777), Golgi apparatus – GM130 Recombinant Rabbit Monoclonal Antibody (10H5L5) (Cat. No. 703794) peroxisome – Catalase Recombinant Rabbit Monoclonal Antibody (10H47L17) (Cat. No. 702955), lysosome – LIMP2 Recombinant Rabbit Monoclonal (22H6L14) (Cat. No. 703037), endosome – Caveolin 1 Polyclonal Antibody (Cat. No. PA5-17447), nucleus – LSD Recombinant Rabbit Monoclonal Antibody (3H8L63) (Cat. No.703761), nuclear envelope – Lamin B1 Recombinant Rabbit Monoclonal Antibody (10H34L18) (Cat. No. 702972) and nucleolus – Fibrillarin Monoclonal Antibody (38F3) (Cat. No. 480009).

Invitrogen offers antibodies against organelle-specific proteins that have been validated for use in various applications such as ELISA, western blot, flow cytometry, immunofluorescence, immunohistochemistry, immunocytochemistry, and immunoprecipitation. Key organelle marker targets are summarized in Table 1. Invitrogen antibodies undergo rigorous two-part testing to validate their performance based on sensitivity, specificity and functionality.

Table 1 | Invitrogen antibodies as organelle markers

S. No	Organelle	Protein	Catalog #	Product Description
1	Cell Junctions	ZO-3	701825	ZO-3 Recombinant Rabbit Monoclonal Antibody
2	Plasma Membrane	Pan-Cadherin	71-7100	Pan-cadherin Polyclonal Antibody
3	Mitochondria	Hexokinase 1	711777	HK1 Recombinant Polyclonal Antibody
4	Golgi Apparatus	GM130	703794	GM130 Recombinant Rabbit Monoclonal Antibody
5	Endoplasmic reticulum	Calnexin	PA5-34754	Calnexin Polyclonal Antibody
6	Cytoskeleton	Vimentin	MA1-10459	Vimentin Monoclonal Antibody
7	Peroxisome	Catalase	702955	Catalase Recombinant Rabbit Monoclonal Antibody
8	Lysosome	LIMP2	703037	LIMP2 Recombinant Rabbit Monoclonal Antibody
9	Proteasome	PSMA3	703791	PSMA3 Recombinant Rabbit Monoclonal Antibody
10	Ribosome	RPS6	710405	S6 Recombinant Polyclonal Antibody
11	Endosome	Caveolin 1	PA5-17447	Caveolin 1 Polyclonal Antibody
12	Autophagosome	ATG12	701684	ATG12 Recombinant Rabbit Monoclonal Antibody
13	Nucleus	LSD1	703761	LSD1 Recombinant Rabbit Monoclonal Antibody
14	Nuclear Envelope	Lamin B1	702972	Lamin B1 Recombinant Rabbit Monoclonal Antibody
15	Nucleolus	Fibrillarin	480009	Fibrillarin Monoclonal Antibody

Fluorescent Dyes as cell and organelle markers

Conventional imaging-based approaches utilizes fluorescent dyes as counterstains to identify the subcellular location of a specific protein. Invitrogen offers a versatile range of organelle-specific dyes and stains that are represented in Table 12 for multiplex analysis in live cells or fixed-cells for imaging.

Products listed come with many different fluorescence readouts ranging across the visible spectrum, allowing for multiplexing your imaging experiments with other organelle stains or fluorescently conjugated antibodies.

Table 2 | Organelle dyes for fixed and live cell imaging

S. No	Organelle	Product Description	Catalog #
1	Cell Tracking	CellTracker	C34565, C12881, C7025, C34551, C34552
2	Plasma Membrane	CellLight Plasma Membrane, CellMask Plasma Membrane, Wheat Germ Agglutinin Alexa Fluor™ conjugates	C10606, W11261, C10607, C10045, W11262, C10046
3	Mitochondria	CellLight Mitochondria, MitoTracker	C10508, M7510, M7513, M22426
4	Golgi Apparatus	CellLight Golgi	C10592, B22650, C10593, B34400
5	Endoplasmic reticulum	CellLight ER	C10590, C10591
6	Cytoskeleton	CellLight Actin, CellLight Tubulin, CellMask, Alexa Fluor Phalloidin conjugates, ReadyProbes Reagent	A22281, R37110, A57243, R37112, C10503, A12381, A30105, A57245
7	Peroxisome	CellLight Peroxisome	C10604, S34201
8	Lysosome	CellLight Lysosome	C10596, C10596, C10597
9	Nucleus	CellLight Nucleus, HCS NuclearMask, SYTO, SYTOX, Hoechst	S11368, H21486, H10325, S7020, C10602, S11363, H10326, T3605, S34901