Native DIGE for Quantitative and Functional Analysis of Protein Interactomes.

Protein-protein interactions and multiprotein assemblies of water-soluble and membrane proteins are inherent features of the proteome, which also impart functional heterogeneity. One needs to consider this aspect while studying changes in abundance and activities of proteins in response to any physiological stimulus. Abundance changes in the components of a given proteome can be best visualized and efficiently quantified using electrophoresis-based approaches. Here, we describe the method of Blue Native Difference Gel Electrophoresis to quantify changes in abundance and activity of proteins in the context of protein-protein interactions. This method confers an additional advantage to monitor quantitative changes in membrane proteins, which otherwise is a difficult task.

Native DIGE: Efficient Tool to Elucidate Protein Interactomes.

Protein-protein interactions and multi-protein assemblies are inherent features of proteomes, involving soluble and membrane proteins. This imparts structural and functional heterogeneity to the proteome. One needs to consider this aspect while studying changes in abundance or activities of proteins in response to any physiological stimulus. Abundance changes in components of a given proteome can be best visualized and quantified using electrophoresis-based approaches. Here, we describe the method of Blue Native Difference Gel Electrophoresis (BN DIGE) to quantify abundance changes in proteins in the context of protein-protein interactions. This method confers an additional advantage to monitor quantitative changes in membrane proteins, which otherwise is a difficult task.

Modulation of oxidative phosphorylation machinery signifies a prime mode of anti-ageing mechanism of calorie restriction in male rat liver mitochondria.

Mitochondria being the major source and target of reactive oxygen species (ROS) play a crucial role during ageing. We analyzed ageing and calorie restriction (CR)-induced changes in abundance of rat liver mitochondrial proteins to understand key aspects behind the age-retarding mechanism of CR. The combination of blue-native (BN) gel system with fluorescence Difference Gel Electrophoresis (DIGE) facilitated an efficient analysis of soluble and membrane proteins, existing as monomers or multi-protein assemblies. Changes in abundance of specific key subunits of respiratory chain complexes I, IV and V, critical for activity and/or assembly of the complexes were identified. CR lowered complex I assembly and complex IV activity, which is discussed as a molecular mechanism to minimize ROS production at mitochondria. Notably, the antioxidant system was found to be least affected. The GSH:GSSG couple could be depicted as a rapid mean to handle the fluctuations in ROS levels led by reversible metabolic shifts. We evaluated the relative significance of ROS generation against quenching. We also observed parallel and unidirectional changes as effect of ageing and CR, in subunits of ATP synthase, cytochrome P450 and glutathione S-transferase. This is the first report on such 'putatively hormetic' ageing-analogous effects of CR, besides the age-retarding ones.

Native-DIGE: a new look at the mitochondrial membrane proteome.

Respiratory chain proteins play a pivotal role in mitochondrial metabolism and thereby in the aging process. Differential display of the mitochondrial proteome reveals the abundance changes occurring in proteins as response to complex events such as senescence and aging. However, there is an absolute need to implement a detection technique that could potentially encompass the hydrophobic and very basic membrane proteins, along with the soluble ones. It is also important to assess protein-protein interactions, besides changes in abundance. Native-difference gel electrophoresis (DIGE) is an approach that facilitates sensitive quantitative assessment of changes in membrane and soluble proteins. It stretches the boundaries of detecting abundance changes to protein-protein interactions for interpretation of a proteome in a more "meaningful" way. Here we evaluate the benefits of blue-native fluorescence DIGE as a method in differential quantitative proteomics with a focus on critical issues for application and experimental design.

Modularity: a new perspective in biology.

Several decades of research in biochemistry and molecular biology have been devoted for studies on isolated enzymes and proteins. Recent high throughput technologies in genomics and proteomics have resulted in avalanche of information about several genes, proteins and enzymes in variety of living systems. Though these efforts have greatly contributed to the detailed understanding of a large number of individual genes and proteins, this explosion of information has simultaneously brought out the limitations of reductionism in understanding complex biological processes. The genes or gene products do not function in isolation in vivo. A delicate and dynamic molecular architecture is required for precision of the chemical reactions associated with "life". In future, a paradigm shift is, therefore, envisaged, in biology leading to exploration of molecular organizations in physical and genomic context, a subtle transition from conventional molecular biology to modular biology. A module can be defined as an organization of macromolecules performing a synchronous function in a given metabolic pathway. In modular biology, the biological processes of interest are explored as complex systems of functionally interacting macromolecules. The present article describes the perceptions of the concept of modularity, in terms of associations among genes and proteins, presenting a link between reductionist approach and system biology.

Isolation and characterization of a thylakoid membrane module showing partial light and dark reactions.

A functional thylakoid membrane module of photosynthesis was isolated from cell free extracts of Anacystis nidulans by stepwise sequential ultracentrifugation. The thylakoid membrane fractions sedimenting at 40,000 x g, followed by 90,000 x g and finally at 150,000 x g were collected. These fractions had all the components of electron transport chain, ATP synthase, phycobiliproteins, ferredoxin-NADP reductase but no ferredoxin. Five sequential enzymes of Calvin cycle viz phosphoriboisomerase, phosphoribulokinase, RuBP carboxylase, 3-PGA kinase and glyceraldehyde-3-phosphate dehydrogenase were found to be associated with thylakoid membranes. Among the three different thylakoid fractions, the 150,000 x g fraction showed highest activities of these enzymes and also higher rate of whole chain electron transport activity on chlorophyll basis. An important finding was that the 150,000 x g fraction showed appreciably higher rate of R-5-P+ADP+Pi dependent CO2 fixation in light compared to the other two fractions, indicating the efficiency of this fraction in utilizing ATP for Calvin cycle. This thylakoid membrane fraction represents a fully functional module exhibiting a synchronized system of light and dark reactions of photosynthesis. Most of the components of this module remained together even after sucrose density gradient centrifugation. This is the first report on the isolation of a photosynthetic module involving membrane and soluble proteins.

Involvement of thylakoid membranes in supramolecular organisation of Calvin cycle enzymes in Anacystis nidulans.

The cells of unicellular photosynthetic cyanobacterium Anacystis nidulans were permeated with lysozyme, toluene, toluene-triton, toluene-triton-lysozyme. Transmission electron microscopy of semi-thin sections (500 nm) using TEM at 160 kV showed that cells permeated with only lysozyme or toluene showed the typical concentric arrangement of thylakoid membranes. However, when toluene-treated cells were further treated with triton and lysozyme the thylakoid membranes were disrupted. Sequential reactions of Calvin cycle were studied in the differentially permeated cells in vivo, using various intermediates such as 3-PGA, GA-3-P, FDP, SDP, R-5-P, RuBP and cofactors like ATP, NADPH depending on the requirement. RuBP and R-5-P + ATP dependent activities could be observed in all types of permeated cells. Sequential reactions of the entire Calvin cycle using 3-PGA could be detected in the cells that had retained the internal organisation of the thylakoid membranes after permeation and were lost on disruption of this organisation. Light dependent CO2 fixation could be detected only in the cells permeated with lysozyme. This activity was abolished in the cells after treatment with toluene. The results suggested that the integrity of thylakoid membranes may be essential for the organisation of sequential enzymes of the Calvin cycle in vivo and facilitate their functioning.