Extracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies

Elagamey, Eman; Narula, Kanika; Chakraborty, Niranjan; Chakraborty, Subhra

doi:10.1007/978-1-4939-9790-9_14

Cited by 3 publications

(2 citation statements)

References 25 publications

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“…ECM fraction was isolated and purified as described by Elagamey et al ( 2020 ). Briefly, 15 g tissue was ground in liquid nitrogen with .3% (w/w) polyvinylpolypyrollidone (PVPP).…”

Section: Methodsmentioning

confidence: 99%

Combining extracellular matrix proteome and phosphoproteome of chickpea and meta‐analysis reveal novel proteoforms and evolutionary significance of clade‐specific wall‐associated events in plant

Narula,

Sinha,

Choudhary

et al. 2024

Plant Direct

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Extracellular matrix (ECM) plays central roles in cell architecture, innate defense and cell wall integrity (CWI) signaling. During transition to multicellularity, modular domain structures of ECM proteins and proteoforms have evolved due to continuous adaptation across taxonomic clades under different ecological niche. Although this incredible diversity has to some extent been investigated at protein level, extracellular phosphorylation events and molecular evolution of ECM proteoform families remains unexplored. We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta‐analyses of 74 plant matrisomes. MS/MS analysis identified 1,424 proteins and 315 phosphoproteins involved in diverse functions. Cross‐species ECM protein network identified proteoforms associated with CWI maintenance system. Phylogenetic characterization of eighteen matrix protein families highlighted the role of taxon‐specific paralogs and orthologs. Novel information was acquired on gene expansion and loss, co‐divergence, sub functionalization and neofunctionalization during evolution. Modular networks of matrix protein families and hub proteins showed higher diversity across taxonomic clades than among organs. Furthermore, protein families differ in nonsynonymous to synonymous substitution rates. Our study pointed towards the matrix proteoform functionality, sequence divergence variation, interactions between wall remodelers and molecular evolution using a phylogenetic framework. This is the first report on comprehensive matrisome proteoform network illustrating presence of CWI signaling proteins in land plants.

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“…ECM fraction was isolated and purified as described by Elagamey et al ( 2020 ). Briefly, 15 g tissue was ground in liquid nitrogen with .3% (w/w) polyvinylpolypyrollidone (PVPP).…”

Section: Methodsmentioning

confidence: 99%

Combining extracellular matrix proteome and phosphoproteome of chickpea and meta‐analysis reveal novel proteoforms and evolutionary significance of clade‐specific wall‐associated events in plant

Narula,

Sinha,

Choudhary

et al. 2024

Plant Direct

Self Cite

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“…Over the past few years, mass spectrometry has become the method of choice for the characterization of ECM composition [ 40 , 88 , 89 ] and has been shown to offer new bioinformatic approaches of translating data from the putative biomarkers to the elucidation of new therapeutic targets [ 90 , 91 , 92 ]. The experimental strategies, new bioinformatic tools, and methods for matrix isolation have been described for the research on the ECM composition and mechanisms of degradation/renewal [ 40 , 43 , 44 , 93 , 94 ]. The new MatrisomeDB version contains selected proteomic data from 17 studies with ECM from 15 various tissues and includes 847 human ECM proteoforms and over 350,000 peptide-to-spectrum matches [ 44 ].…”

Section: Proteomic Profile Of Human Matrisome-associated Proteins Under Real and Simulated Microgravitymentioning

confidence: 99%

Microgravity Effects on the Matrisome

Буравкова

Ларина

Андреева

et al. 2021

Cells

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Gravity is fundamental factor determining all processes of development and vital activity on Earth. During evolution, a complex mechanism of response to gravity alterations was formed in multicellular organisms. It includes the “gravisensors” in extracellular and intracellular spaces. Inside the cells, the cytoskeleton molecules are the principal gravity-sensitive structures, and outside the cells these are extracellular matrix (ECM) components. The cooperation between the intracellular and extracellular compartments is implemented through specialized protein structures, integrins. The gravity-sensitive complex is a kind of molecular hub that coordinates the functions of various tissues and organs in the gravitational environment. The functioning of this system is of particular importance under extremal conditions, such as spaceflight microgravity. This review covers the current understanding of ECM and associated molecules as the matrisome, the features of the above components in connective tissues, and the role of the latter in the cell and tissue responses to the gravity alterations. Special attention is paid to contemporary methodological approaches to the matrisome composition analysis under real space flights and ground-based simulation of its effects on Earth.

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