Identification of prolyl hydroxylation modifications in mammalian cell proteins

Arsenault, Patrick R.; Heaton-Johnson, Katherine J.; Li, Linsheng; Song, Daisheng; Ferreira, Vinicius S.; Patel, Nish; Master, Stephen R.; Lee, Frank S.

doi:10.1002/pmic.201400398

Cited by 20 publications

(25 citation statements)

References 29 publications

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“…As noted above, hydroxylation modifications of proline residues, and to a lesser extent lysine residues, is a common observation in proteomics datasets that result from the analysis of extracellular tissues. These have been studied for types I and III [ 46 ], type IV [ 47 ], type V [ 46 , 48 ] as well as a range of non-collagenous proteins such as osteocalcin [ 49 , 50 ]. However, exhaustive maps that attempt to span the entirety of type 1 remain elusive due to issues with reproducibility within such proteomics methods.…”

Section: Discussionmentioning

confidence: 99%

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

Buckley

2016

IJMS

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Collagen is one of the most ubiquitous proteins in the animal kingdom and the dominant protein in extracellular tissues such as bone, skin and other connective tissues in which it acts primarily as a supporting scaffold. It has been widely investigated scientifically, not only as a biomedical material for regenerative medicine, but also for its role as a food source for both humans and livestock. Due to the long-term stability of collagen, as well as its abundance in bone, it has been proposed as a source of biomarkers for species identification not only for heat- and pressure-rendered animal feed but also in ancient archaeological and palaeontological specimens, typically carried out by peptide mass fingerprinting (PMF) as well as in-depth liquid chromatography (LC)-based tandem mass spectrometric methods. Through the analysis of the three most common domesticates species, cow, sheep, and pig, this research investigates the advantages of each approach over the other, investigating sites of sequence variation with known functional properties of the collagen molecule. Results indicate that the previously identified species biomarkers through PMF analysis are not among the most variable type 1 collagen peptides present in these tissues, the latter of which can be detected by LC-based methods. However, it is clear that the highly repetitive sequence motif of collagen throughout the molecule, combined with the variability of the sites and relative abundance levels of hydroxylation, can result in high scoring false positive peptide matches using these LC-based methods. Additionally, the greater alpha 2(I) chain sequence variation, in comparison to the alpha 1(I) chain, did not appear to be specific to any particular functional properties, implying that intra-chain functional constraints on sequence variation are not as great as inter-chain constraints. However, although some of the most variable peptides were only observed in LC-based methods, until the range of publicly available collagen sequences improves, the simplicity of the PMF approach and suitable range of peptide sequence variation observed makes it the ideal method for initial taxonomic identification prior to further analysis by LC-based methods only when required.

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Section: Discussionmentioning

confidence: 99%

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

Buckley

2016

IJMS

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“…Prolyl-hydroxylase and asparagine hydroxylase are both members of the oxygen-dependent hydroxylase families whose catalytic properties are dependent upon oxygen, and are viewed as the cellular detectors for oxygen concentration (Schofield and Ratcliffe, 2004). Under hypoxic conditions, the absence of oxygen, which constitutes the substrate for PHDs and FIH, results in a cessation of the hydroxylation process, preventing the binding of HIF-α to the p-VHL (Arsenault et al, 2015; Maxwell et al, 2017). This leads to the build-up of HIF-1α in its stable isomer, translocation across the nuclear membrane and binding to the β- subunit to generate the active HIF dimer.…”

Section: Hif Hydroxylationmentioning

confidence: 99%

Hypoxia-Modified Cancer Cell Metabolism

Tameemi

Dale

Al-Jumaily

et al. 2019

Front. Cell Dev. Biol.

412

312

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While oxygen is critical to the continued existence of complex organisms, extreme levels of oxygen within a system, known as hypoxia (low levels of oxygen) and hyperoxia (excessive levels of oxygen), potentially promote stress within a defined biological environment. The consequences of tissue hypoxia, a result of a defective oxygen supply, vary in response to the gravity, extent and environment of the malfunction. Persistent pathological hypoxia is incompatible with normal biological functions, and as a result, multicellular organisms have been compelled to develop both organism-wide and cellular-level hypoxia solutions. Both direct, including oxidative phosphorylation down-regulation and inhibition of fatty-acid desaturation, and indirect processes, including altered hypoxia-sensitive transcription factor expression, facilitate the metabolic modifications that occur in response to hypoxia. Due to the dysfunctional vasculature associated with large areas of some cancers, sections of these tumors continue to develop in hypoxic environments. Crucial to drug development, a robust understanding of the significance of these metabolism changes will facilitate our understanding of cancer cell survival. This review defines our current knowledge base of several of the hypoxia-instigated modifications in cancer cell metabolism and exemplifies the correlation between metabolic change and its support of the hypoxic-adapted malignancy.

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“…Approximately 80% of mammalian proteins are modified posttranslationally. For instance, phosphorylation is implicated in cell signaling , acetylation in epigenetics and NDs , ubiquitination in regulation of cellular protein homeostasis , hydroxylation in collagen formation , and glycosylation in the pathophysiology of neurotrauma . The basic findings from studies that demonstrated the role of PTMs in the relevant diseases are summarized in Table .…”

Section: Ptmsmentioning

confidence: 99%

Glycosylation and other PTMs alterations in neurodegenerative diseases: Current status and future role in neurotrauma

et al. 2016

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Traumatic brain injuries (TBIs) present a chief public health threat affecting nations worldwide. As numbers of patients afflicted by TBI are expected to rise, the necessity to increase our understanding of the pathophysiological mechanism(s) as a result of TBI mounts. TBI is known to augment the risk of developing a number of neurodegenerative diseases (NDs) such as Alzheimer’s disease (AD) and Parkinson’s disease (PD). Hence, it is rational to assume that a common mechanistic ground links the pathophysiology of NDs to that of TBIs. Through this review, we aim to identify the protein–protein interactions, differential proteins expression, and PTMs, mainly glycosylation, that are involved in the pathogenesis of both ND and TBI. OVID and PubMed have been rigorously searched to identify studies that utilized advanced proteomic platforms (MS based) and systems biology tools to unfold the mechanism(s) behind ND in an attempt to unveil the mysterious biological processes that occur postinjury. Various PTMs have been found to be common between TBI and AD, whereas no similarities have been found between TBI and PD. Phosphorylated tau protein, glycosylated amyloid precursor protein, and many other modifications appear to be common in both TBI and AD. PTMs, differential protein profiles, and altered biological pathways appear to have critical roles in ND processes by interfering with their pathological condition in a manner similar to TBI. Advancement in glycoproteomic studies pertaining to ND and TBI is urgently needed in order to develop better diagnostic tools, therapies, and more favorable prognoses.

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Identification of prolyl hydroxylation modifications in mammalian cell proteins

Cited by 20 publications

References 29 publications

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods

Hypoxia-Modified Cancer Cell Metabolism

Glycosylation and other PTMs alterations in neurodegenerative diseases: Current status and future role in neurotrauma

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