Characterizing the Host Coral Proteome of <i>Platygyra carnosa</i> Using Suspension Trapping (S-Trap)

Ma, Heng; Liao, Herui; Dellisanti, Walter; Sun, Yanni; Chan, Leo Lai; Zhang, Liang

doi:10.1021/acs.jproteome.0c00812

Cited by 5 publications

(5 citation statements)

References 26 publications

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“…LC–MS/MS analysis was done as described previously ( Ma et al, 2021 ). The concentration was estimated by measuring absorbance at 280 nm (NanoDrop 2000, Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

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Exogenous L-lactate administration in rat hippocampus increases expression of key regulators of mitochondrial biogenesis and antioxidant defense

Akter

Hasan

et al. 2023

Front. Mol. Neurosci.

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L-lactate plays a critical role in learning and memory. Studies in rats showed that administration of exogenous L-lactate into the anterior cingulate cortex and hippocampus (HPC) improved decision-making and enhanced long-term memory formation, respectively. Although the molecular mechanisms by which L-lactate confers its beneficial effect are an active area of investigations, one recent study found that L-lactate supplementation results in a mild reactive oxygen species burst and induction of pro-survival pathways. To further investigate the molecular changes induced by L-lactate, we injected rats with either L-lactate or artificial CSF bilaterally into the dorsal HPC and collected the HPC after 60 minutes for mass spectrometry. We identified increased levels of several proteins that include SIRT3, KIF5B, OXR1, PYGM, and ATG7 in the HPC of the L-lactate treated rats. SIRT3 (Sirtuin 3) is a key regulator of mitochondrial functions and homeostasis and protects cells against oxidative stress. Further experiments identified increased expression of the key regulator of mitochondrial biogenesis (PGC-1α) and mitochondrial proteins (ATPB, Cyt-c) as well as increased mitochondrial DNA (mtDNA) copy number in the HPC of L-lactate treated rats. OXR1 (Oxidation resistance protein 1) is known to maintain mitochondrial stability. It mitigates the deleterious effects of oxidative damage in neurons by inducing a resistance response against oxidative stress. Together, our study suggests that L-lactate can induce expression of key regulators of mitochondrial biogenesis and antioxidant defense. These findings create new research avenues to explore their contribution to the L-lactate’s beneficial effect in cognitive functions as these cellular responses might enable neurons to generate more ATP to meet energy demand of neuronal activity and synaptic plasticity as well as attenuate the associated oxidative stress.

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“…LC–MS/MS analysis was done as described previously ( Ma et al, 2021 ). The concentration was estimated by measuring absorbance at 280 nm (NanoDrop 2000, Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

“…Data processing and analysis were done as described previously ( Ma et al, 2021 ). Raw MS data were processed using the Proteome Discoverer software v2.2 and proteins were identified by searching MS/MS spectra against in tryptic digest of Rattus norvegicus (Rat) database downloaded from UniProt.…”

Section: Methodsmentioning

confidence: 99%

Exogenous L-lactate administration in rat hippocampus increases expression of key regulators of mitochondrial biogenesis and antioxidant defense

Akter

Hasan

et al. 2023

Front. Mol. Neurosci.

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“…The field of proteomics, i.e. identification and quantification of cellular proteins, has been recently advancing with the aim to identify key physiological processes for uncovering cellular responses under environmental changes [61]. The expression of cellular stress molecular biomarkers represents a useful diagnostic tool to analyze changes in the cellular structural integrity and in the functional cellular pathways [62].…”

Section: Energy Reservesmentioning

confidence: 99%

Nutrition of Corals and Their Trophic Plasticity under Future Environmental Conditions

Dellisanti¹,

Seveso²,

Fang³

2023

Corals - Habitat Formers in the Anthropocene

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Scleractinian corals obtain metabolic energy from their endosymbiotic autotrophic microalgae, and from remineralization of organic matter by bacteria and viruses, along with the heterotrophic food sources. The mutualistic symbiosis is generally stable but can be disrupted when environmental conditions surrounding the corals, such as increasing seawater temperature, become unfavorable to sustain each component of the holobiont. In this connection, the effects of global stressors such as climate change, and local stressors such as pollution, and their combination, are posing serious threats to the metabolic resistance of corals. However, some more resilient coral species have developed specific mechanisms to cope with fluctuating environmental conditions according to the trophic strategy (autotrophy, heterotrophy, or mixotrophy), and by modulating their energy expenditure. In this chapter, the role of nutrition in the coral symbiosis as the energetic budget for metabolic performance will be discussed, with a focus on the role of acquisition of nutrients through feeding, regulation of energy reserves (lipids, proteins, and carbohydrates), and adaptation capability in the natural environment, including the expression of heat-shock proteins (Hsps). Future environmental conditions under a combination of global changes and local impacts will also be discussed, with the aim of identifying the trophic niches of corals and geographical areas as possible refugia.

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“…Ma et al. established a straightforward and reproducible workflow to profile the proteomes of stony corals Platygyra carnosa using the S‐Trap digestion method [88]. S‐Trap is superior to acetone and TCA precipitation methods for recovering the coral host proteome, as evidenced by the number of proteins identified (2779 vs. 647 and 521, respectively).…”

Section: Applications Of Suspension Trapping In Recent Proteomics Stu...mentioning

confidence: 99%

A review of suspension trapping digestion method in bottom‐up proteomics

Duong

Park

Lee

2022

J of Separation Science

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The standard bottom‐up proteomic workflow is comprised of sample preparation, data acquisition, and data analysis. While the latter two parts have made considerable advances in the last decade, sample preparation has remained an important challenge within the workflow due to the multi‐step nature of complex biological samples, and still requires much development. Several sample preparation methods have been developed and used in the last two decades, including in‐gel, in‐solution, on‐bead, filter‐aided sample preparation, and suspension trapping, to improve reproducibility, efficiency, scalability, and reduce the handling time of this process. One of the most recent methods developed and applied in proteomics studies in recent years is suspension trapping, which combines rapid detergent removal, reactor‐type protein digestion, and peptide clean‐up in a tip or spin column. Suspension trapping is a simple, rapid, and reproducible digestion method that can effectively handle proteins in low microgram or sub‐microgram amounts. This review discusses the benefits of the suspension trapping digestion method in relation to its development and application in bottom‐up proteomics studies. We also discuss recent applications of suspension trapping digestion to different sample types and the features of the suspension trapping digestion method compared with other sample preparation methods.

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Characterizing the Host Coral Proteome of Platygyra carnosa Using Suspension Trapping (S-Trap)

Cited by 5 publications

References 26 publications

Exogenous L-lactate administration in rat hippocampus increases expression of key regulators of mitochondrial biogenesis and antioxidant defense

Exogenous L-lactate administration in rat hippocampus increases expression of key regulators of mitochondrial biogenesis and antioxidant defense

Nutrition of Corals and Their Trophic Plasticity under Future Environmental Conditions

A review of suspension trapping digestion method in bottom‐up proteomics

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