Advances in purification and separation of posttranslationally modified proteins

Černý, Martin; Skalák, Jan; Cerná, H; Brzobohatý, Břetislav

doi:10.1016/j.jprot.2013.05.040

Cited by 52 publications

(25 citation statements)

References 263 publications

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“…Ongoing advances in hormonome analyses will undoubtedly improve our understanding [252], but another limitation is that most presented findings are based solely on transcriptomic analyses, in some cases supplemented with results of knocking out or overexpressing specific genes. Furthermore, posttranslational modifications play important roles in regulatory networks [253], and thus abiotic responses [254]. Thus, they must also be considered.…”

Section: Discussionmentioning

confidence: 99%

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

Pavlů

Novák

Koukalová

et al. 2018

IJMS

Self Cite

136

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Cytokinin is a multifaceted plant hormone that plays major roles not only in diverse plant growth and development processes, but also stress responses. We summarize knowledge of the roles of its metabolism, transport, and signalling in responses to changes in levels of both macronutrients (nitrogen, phosphorus, potassium, sulphur) and micronutrients (boron, iron, silicon, selenium). We comment on cytokinin’s effects on plants’ xenobiotic resistance, and its interactions with light, temperature, drought, and salinity signals. Further, we have compiled a list of abiotic stress-related genes and demonstrate that their expression patterns overlap with those of cytokinin metabolism and signalling genes.

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Section: Discussionmentioning

confidence: 99%

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

Pavlů

Novák

Koukalová

et al. 2018

IJMS

Self Cite

136

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“…Post-translational modifications (PTMs) of proteins are the key step responsible for regulation of protein activity and function [48,49]. Therefore although our proteomes analysis provide an insight into differences between protein expression due to disease and anatomical location, knowledge of PTMs is essential for making firm conclusions as to whether these differences are relevant functionally.…”

Section: Discussionmentioning

confidence: 99%

The effect of disease on human cardiac protein expression profiles in paired samples from right and left ventricles

et al. 2014

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BackgroundCardiac diseases (e.g. coronary and valve) are associated with ventricular cellular remodeling. However, ventricular biopsies from left and right ventricles from patients with different pathologies are rare and thus little is known about disease-induced cellular remodeling in both sides of the heart and between different diseases. We hypothesized that the protein expression profiles between right and left ventricles of patients with aortic valve stenosis (AVS) and patients with coronary artery disease (CAD) are different and that the protein profile is different between the two diseases. Left and right ventricular biopsies were collected from patients with either CAD or AVS. The biopsies were processed for proteomic analysis using isobaric tandem mass tagging and analyzed by reverse phase nano-LC-MS/MS. Western blot for selected proteins showed strong correlation with proteomic analysis.ResultsProteomic analysis between ventricles of the same disease (intra-disease) and between ventricles of different diseases (inter-disease) identified more than 500 proteins detected in all relevant ventricular biopsies. Comparison between ventricles and disease state was focused on proteins with relatively high fold (±1.2 fold difference) and significant (P < 0.05) differences. Intra-disease protein expression differences between left and right ventricles were largely structural for AVS patients and largely signaling/metabolism for CAD. Proteins commonly associated with hypertrophy were also different in the AVS group but with lower fold difference. Inter-disease differences between left ventricles of AVS and CAD were detected in 9 proteins. However, inter-disease differences between the right ventricles of CAD and AVS patients were associated with differences in 73 proteins. The majority of proteins which had a significant difference in one ventricle compared to the other pathology also had a similar trend in the adjacent ventricle.ConclusionsThis work demonstrates for the first time that left and right ventricles have a different proteome and that the difference is dependent on the type of disease. Inter-disease differential expression was more prominent for right ventricles. The finding that a protein change in one ventricle was often associated with a similar trend in the adjacent ventricle for a large number of proteins suggests cross-talk proteome remodeling between adjacent ventricles.

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“…On several occasions, we pointed out difficulties in analysing and identifying PTMs by (standard) proteomics, especially since identification of each type of PTM requires its own strategy (see for reviews on methodological aspects: Č erný, Skalák, Cerna, & Brzobohatý, 2013;Kettenbach, Rush, & Gerber, 2011;Young et al, 2010;Zhao & Jensen, 2009). Consequently, identification of PTMs could only be addressed within the field of proteomics after the development of methods that enabled (1) the routine enrichment of modified peptides from complex biological samples, (2) robust MS analysis and (3) analyses on a high-throughput basis.…”

Section: Posttranslational Modificationsmentioning

confidence: 99%

Bacterial Electron Transfer Chains Primed by Proteomics

Wessels¹,

Almeida²,

Kartal³

et al. 2016

Advances in Bacterial Electron Transport Systems and Their Regulation

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Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.

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Advances in purification and separation of posttranslationally modified proteins

Cited by 52 publications

References 263 publications

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways

The effect of disease on human cardiac protein expression profiles in paired samples from right and left ventricles

Bacterial Electron Transfer Chains Primed by Proteomics

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