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Fulltext Metaproteomic analysis of human gut microbiota: where are we heading?

Lee PY, Chin SF, Neoh HM, Jamal R

J Biomed Sci, 2017 Jun 12;24(1):36.
PMID: 28606141 DOI: 10.1186/s12929-017-0342-z

The human gut is home to complex microbial populations that change dynamically in response to various internal and external stimuli. The gut microbiota provides numerous functional benefits that are crucial for human health but in the setting of a disturbed equilibrium, the microbial community can cause deleterious outcomes such as diseases and cancers. Characterization of the functional activities of human gut microbiota is fundamental to understand their roles in human health and disease. Metaproteomics, which refers to the study of the entire protein collection of the microbial community in a given sample is an emerging area of research that provides informative details concerning functional aspects of the microbiota. In this mini review, we present a summary of the progress of metaproteomic analysis for studying the functional role of gut microbiota. This is followed by an overview of the experimental approaches focusing on fecal specimen for metaproteomics and is concluded by a discussion on the challenges and future directions of metaproteomic research.

Matched MeSH terms: Proteomics*
Proteomics as a reliable approach for discovery of blood-based Alzheimer's disease biomarkers: A systematic review and meta-analysis

Rehiman SH, Lim SM, Neoh CF, Majeed ABA, Chin AV, Tan MP, et al.

Ageing Res Rev, 2020 07;60:101066.
PMID: 32294542 DOI: 10.1016/j.arr.2020.101066

In order to gauge the impact of proteomics in discovery of Alzheimer's disease (AD) blood-based biomarkers, this study had systematically reviewed articles published between 1984-2019. Articles that fulfilled the inclusion criteria were assessed for risk of bias. A meta-analysis was performed for replicable candidate biomarkers (CB). Of the 1651 articles that were identified, 17 case-control and two cohort studies, as well as three combined case-control and longitudinal designs were shortlisted. A total of 207 AD and mild cognitive impairment (MCI) CB were discovered, with 48 reported in >2 studies. This review highlights six CB, namely alpha-2-macroglobulin (α2M)ps, pancreatic polypeptide (PP)ps, apolipoprotein A-1 (ApoA-1)ps, afaminp, insulin growth factor binding protein-2 (IGFBP-2)ps and fibrinogen-γ-chainp, all of which exhibited consistent pattern of regulation in >three independent cohorts. They are involved in AD pathogenesis via amyloid-beta (Aβ), neurofibrillary tangles, diabetes and cardiovascular diseases (CVD). Meta-analysis indicated that ApoA-1ps was significantly downregulated in AD (SMD = -1.52, 95% CI: -1.89, -1.16, p 

Matched MeSH terms: Proteomics*
Fulltext Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves

Chen X, Yang B, Huang W, Wang T, Li Y, Zhong Z, et al.

Int J Mol Sci, 2018 Dec 05;19(12).
PMID: 30563128 DOI: 10.3390/ijms19123897

Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of PPO, a model with decreased PPO expression and enzymatic activity was constructed on Clematis terniflora DC. using virus-induced gene silencing (VIGS) technology. Proteomics was performed to identify the differentially expressed proteins (DEPs) in the model (VC) and empty vector-carrying plants (VV) untreated or exposed to high levels of UV-B and dark (HUV-B+D). Following integration, it was concluded that the DEPs mainly functioned in photosynthesis, glycolysis, and redox in the PPO silence plants. Mapman analysis showed that the DEPs were mainly involved in light reaction and Calvin cycle in photosynthesis. Further analysis illustrated that the expression level of adenosine triphosphate (ATP) synthase, the content of chlorophyll, and the photosynthesis rate were increased in VC plants compared to VV plants pre- and post HUV-B+D. These results indicate that the silence of PPO elevated the plant photosynthesis by activating the glycolysis process, regulating Calvin cycle and providing ATP for energy metabolism. This study provides a prospective approach for increasing crop yield in agricultural production.

Matched MeSH terms: Proteomics*
The underlying mechanism of nuclear and mitochondrial DNA damages in triggering cancer incidences: Insights into proteomic and genomic sciences

Saadi S, Nacer NE, Saari N, Mohammed AS, Anwar F

J Biotechnol, 2024 Mar 10;383:1-12.
PMID: 38309588 DOI: 10.1016/j.jbiotec.2024.01.013

The attempt of this review article is to determine the impact of nuclear and mitochondrial damages on the propagation of cancer incidences. This review has advanced our understanding to altered genes and their relevant cancerous proteins. The progressive raising effects of free reactive oxygen species ROS and toxicogenic compounds contributed to significant mutation in nuclear and mitochondrial DNA where the incidence of gastric cancer is found to be linked with down regulation of some relevant genes and mutation in some important cellular proteins such as AMP-18 and CA-11. Thereby, the resulting changes in gene mutations induced the apparition of newly polymorphisms eventually leading to unusual cellular expression to mutant proteins. Reduction of these apoptotic growth factors and nuclear damages is increasingly accepted by cell reactivation effect, enhanced cellular signaling and DNA repairs. Acetylation, glycation, pegylation and phosphorylation are among the molecular techniques used in DNA repair for rectifying mutation incidences. In addition, the molecular labeling based fluorescent materials are currently used along with the bioconjugating of signal molecules in targeting disease translocation site, particularly cancers and tumors. These strategies would help in determining relevant compounds capable in overcoming problems of down regulating genes responsible for repair mechanisms. These issues of course need interplay of both proteomic and genomic studies often in combination of molecular engineering to cible the exact expressed gene relevant to these cancerous proteins.

Matched MeSH terms: Proteomics*
Omics approaches to unravel insecticide resistance mechanism in Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae)

Rosli MAF, Syed Jaafar SN, Azizan KA, Yaakop S, Aizat WM

PeerJ, 2024;12:e17843.
PMID: 39247549 DOI: 10.7717/peerj.17843

Bemisia tabaci (Gennadius) whitefly (BtWf) is an invasive pest that has already spread worldwide and caused major crop losses. Numerous strategies have been implemented to control their infestation, including the use of insecticides. However, prolonged insecticide exposures have evolved BtWf to resist these chemicals. Such resistance mechanism is known to be regulated at the molecular level and systems biology omics approaches could shed some light on understanding this regulation wholistically. In this review, we discuss the use of various omics techniques (genomics, transcriptomics, proteomics, and metabolomics) to unravel the mechanism of insecticide resistance in BtWf. We summarize key genes, enzymes, and metabolic regulation that are associated with the resistance mechanism and review their impact on BtWf resistance. Evidently, key enzymes involved in the detoxification system such as cytochrome P450 (CYP), glutathione S-transferases (GST), carboxylesterases (COE), UDP-glucuronosyltransferases (UGT), and ATP binding cassette transporters (ABC) family played key roles in the resistance. These genes/proteins can then serve as the foundation for other targeted techniques, such as gene silencing techniques using RNA interference and CRISPR. In the future, such techniques will be useful to knock down detoxifying genes and crucial neutralizing enzymes involved in the resistance mechanism, which could lead to solutions for coping against BtWf infestation.

Matched MeSH terms: Proteomics/methods
Unlocking the molecular modifications of plasma-activated water-induced oxidation through redox proteomics: In the case of duck myofibrillar protein (Anas platyrhynchos)

Rao W, Ju S, Sun Y, Xia Q, Zhou C, He J, et al.

Food Chem, 2024 Nov 15;458:140173.
PMID: 38943955 DOI: 10.1016/j.foodchem.2024.140173

Plasma-activated water (PAW) contains multiple active species that alter the structure of myofibrillar protein (MP) to enhance their gel properties. This work investigated the impact of PAW on the oxidation of cysteine in MP by label-free quantitative proteomics. PAW treatment caused the oxidation of 8241 cysteine sites on 2815 proteins, and structural proteins such as nebulin, myosin XVIIIB, myosin XVIIIA, and myosin heavy chain were susceptible to oxidation by PAW. Bioinformatics analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, subcellular localization, and STRING analysis, indicated that these proteins with differential oxidation sites were mainly derived from the cytoplasm and membrane, and were involved in multiple GO terms and KEGG pathways. This is one of the first reports of the redox proteomic changes induced by PAW treatment, and the results are useful for understanding the possible mechanism of PAW-induced oxidation of MP.

Matched MeSH terms: Proteomics*
TMT-labelled quantitative proteomics reveals the mechanism of Rhodotorula mucilaginosa on proteolysis of dry-cured ham: Structural protein degradation, amino acid release and taste improvement

Zhang T, Wang Y, Zhu J, Chen C, Jiang T, Fang S, et al.

Food Chem, 2025 Apr 30;472:142991.
PMID: 39848055 DOI: 10.1016/j.foodchem.2025.142991

To investigate the mechanism of Rhodotorula mucilaginosa on structural protein degradation and taste development of Jinhua ham, the effects of Rhodotorula mucilaginosa and Pichia kudriavzevii on proteolytic enzyme activities, surface hydrophobicity, myofibril microstructure, protein degradation, free amino acids and sensory attributes were investigated during the dry-ripening of Jinhua ham. The inoculation of Rhodotorula mucilaginosa EIODSF019 (RE) and Rhodotorula mucilaginosa XZY63-3 (RX) consistently exhibited higher proteolytic enzyme activities compared with Pichia kudriavzevii XS-5 (PK). The decrease of α-helix exposing more internal hydrophobic groups of myofibrillar proteins, contributed to higher surface hydrophobicity of RE compared with PK and RX. RE showed the highest proteolysis index among all groups, which could be attributed to more degradation of myosin, actin and troponin; the changes were confirmed by the intense breakdown of myofibrils observed by atomic force microscopy and transmission electron microscopy. 36 down-regulated proteins mainly derived from myofibrils and catalysis-related enzymes were identified in RE by TMT-labeled quantitative proteomics analysis. The degradation of myosin, actin and troponin showed the most intense response to the accumulation of glutamic acid, lysine and alanine. Partial least square regression analysis and correlation analysis revealed that the breakdown of MYH14, MYH3, TNNI1 and TNNTI was highly correlated with improvement of umami, richness and aftertaste.

Matched MeSH terms: Proteomics*
Advancing optical nanosensors with artificial intelligence: A powerful tool to identify disease-specific biomarkers in multi-omics profiling

Taha BA, Abdulrahm ZM, Addie AJ, Haider AJ, Alkawaz AN, Yaqoob IAM, et al.

Talanta, 2025 May 15;287:127693.
PMID: 39919475 DOI: 10.1016/j.talanta.2025.127693

Multi-omics profiling integrates genomic, epigenomic, transcriptomic, and proteomic data, essential for understanding complex health and disease pathways. This review highlights the transformative potential of combining optical nanosensors with artificial intelligence (AI). It is possible to identify disease-specific biomarkers using real-time and sensitive molecular interactions. These technologies are precious for genetic, epigenetic, and proteomic changes critical to disease progression and treatment response. AI improves multi-omics profiling by analyzing large, diverse data sets and common patterns traditional methods overlook. Machine learning tools Biomarkers Discovery is revolutionizing, drug resistance is being understood, and medicine is being personalized as the combination of AI and nanosensors has advanced the detection of DNA methylation and proteomic signatures and improved our understanding of cancer, cardiovascular disease and vascular disease. Despite these advances, challenges still exist. Difficulties in integrating data sets, retaining sensors, and building scalable computing tools are the biggest obstacles. It also examines various solutions with advanced AI algorithms and innovations, including fabrication in nanosensor design. Moreover, it highlights the potential of nanosensor-assisted, AI-driven multi-omics profiling to revolutionize disease diagnosis and treatment. As technology advances, these tools pave the way for faster diagnosis, more accurate treatment and improved patient outcomes, offering new hope for personalized medicine.

Matched MeSH terms: Proteomics/methods
Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery

Lee PY, Osman J, Low TY, Jamal R

Bioanalysis, 2019 Oct;11(19):1799-1812.
PMID: 31617391 DOI: 10.4155/bio-2019-0145

Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.

Matched MeSH terms: Proteomics
TMT-labeled quantitative proteomic reveals the mechanism of proteolysis and taste improvement of dry-cured bacon with Staphylococcus co-inoculation

Zhou C, Wu X, Pan D, Xia Q, Sun Y, Geng F, et al.

Food Chem, 2024 Mar 15;436:137711.
PMID: 37839122 DOI: 10.1016/j.foodchem.2023.137711

To understand the mechanism of co-inoculation of Staphylococcus xylosus and Staphylococcus vitulinus (SX & SV) on structural protein degradation and taste enhancement of dry-cured bacon, protease activities, protein degradation, surface morphology of proteins and taste parameters of dry-cured bacon with Staphylococcus inoculation were investigated. The dry-cured bacon with co-inoculation of Staphylococcus xylosus and Staphylococcus vitulinus showed the best taste attributes. High residual activities in cathepsin B + L (more than 1.6-fold) and alanyl aminopeptidase (more than 1.4-fold) accelerated structural protein degradation in SX & SV. 32 down-regulated proteins were identified in SX & SV by TMT-labeled quantitative proteomic compared with control group; myosin and actin showed the most intense response to the accumulation of sweet and umami amino acids, and atomic force microscopy confirmed structural proteins breakdown by morphological changes. The accumulation of glutamic acid, alanine and lysine was mainly responsible for taste improvement of dry-cured bacon with Staphylococcus co-inoculation.

Matched MeSH terms: Proteomics
Analysis of Entamoeba histolytica Membrane Proteome Using Three Extraction Methods

Ujang J, Sani AAA, Lim BH, Noordin R, Othman N

Proteomics, 2018 12;18(23):e1700397.
PMID: 30284757 DOI: 10.1002/pmic.201700397

Entamoeba histolytica membrane proteins are important players toward the pathogenesis of amoebiasis, but the roles of most of the proteins are not fully understood. Since efficient protein extraction method is crucial for a successful MS analysis, three extractions methods are evaluated for the use in studying the membrane proteome of E. histolytica: Two commercial kits (ProteoExtract from Calbiochem and ProteoPrep from Sigma), and a conventional laboratory method. The results show that ProteoExtract and the conventional method gave higher protein yields compared to ProteoPrep. LC-ESI-MS/MS identifies 456, 482, and 551 membrane fraction proteins extracted using ProteoExtract, ProteoPrep, and a conventional method, respectively. In silico analysis predicts 108 (21%), 235 (45%), and 177 (34%) membrane proteins from the extracts of ProteoExtract, ProteoPrep, and the conventional method, respectively. Furthermore, analysis of the cytosolic and membrane fractions shows the highest selectivity of the membrane proteins using the ProteoPrep extraction kit. Overall, this study reports 828 E. histolytica membrane fraction proteins that include 249 predicted membrane proteins. The data are available via ProteomeXchange with identifier PXD010171.

Matched MeSH terms: Proteomics/methods*
Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions

Abu Bakar N, Chung BLY, Smykla J, Karsani SA, Alias SA

Mycologia, 2024;116(3):449-463.
PMID: 38484286 DOI: 10.1080/00275514.2024.2313429

Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid‑acetone‑phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.

Matched MeSH terms: Proteomics*
Decomplexation proteomic analysis and purity assessment of a biologic for snakebite envenoming: Philippine Cobra Antivenom

Palasuberniam P, Tan KY, Chan YW, Blanco FB, Tan CH

Trans R Soc Trop Med Hyg, 2023 Jun 02;117(6):428-434.
PMID: 36611268 DOI: 10.1093/trstmh/trac125

BACKGROUND: Philippine Cobra Antivenom (PCAV) is the only snake antivenom manufactured in the Philippines. It is used clinically to treat envenoming caused by the Philippine Spitting Cobra (Naja philippinensis). While PCAV is effective pharmacologically, it is crucial to ensure the safety profile of this biologic that is derived from animal plasma.
METHODS: This study examined the composition purity of PCAV through a decomplexation proteomic approach, applying size-exclusion chromatography (SEC), sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and tandem mass spectrometry liquid chromatography-tandem mass spectrometry (LC-MS/MS).
RESULTS: SDS-PAGE and SEC showed that the major protein in PCAV (constituting ∼80% of total proteins) is approximately 110 kDa, consistent with the F(ab')2 molecule. This protein is reducible into two subunits suggestive of the light and heavy chains of immunoglobulin G. LC-MS/MS further identified the proteins as equine immunoglobulins, representing the key therapeutic ingredient of this biologic product. However, protein impurities, including fibrinogens, alpha-2-macroglobulins, albumin, transferrin, fibronectin and plasminogen, were detected at ∼20% of the total antivenom proteins, unveiling a concern for hypersensitivity reactions.
CONCLUSIONS: Together, the findings show that PCAV contains a favorable content of F(ab')2 for neutralization, while the antibody purification process awaits improvement to minimize the presence of protein impurities.

Matched MeSH terms: Proteomics/methods
Integrated transcriptomics and proteomics data analysis identifies CDH17 as a key cell surface target in colorectal cancer

Wong KK

Comput Biol Chem, 2023 Aug;105:107897.
PMID: 37247573 DOI: 10.1016/j.compbiolchem.2023.107897

Immunotherapy development against colorectal cancer (CRC) is hindered by the lack of cell surface target highly expressed in cancer cells but with restricted presence in normal tissues to minimize off-tumor toxicities. In this in silico analysis, a longlist of genes (n = 13,488) expressed in CRCs according to the Human Protein Atlas (HPA) database were evaluated to shortlist for potential surface targets based on the following prerequisites: (i) Absent from the brain and lung tissues to minimize the likelihood of neurologic and pulmonary toxicities; (ii) Restricted expression profile in other normal human tissues; (iii) Genes that potentially encode cell surface proteins and; (iv) At least moderately expressed in CRC cases. Fifteen potential targets were shortlisted and subsequently ranked according to the combination of their transcript and protein expression levels in CRCs derived from multiple datasets (i.e. DepMap, TCGA, CPTAC-2, and HPA CRCs). The top-ranked target with the highest and homogenous expression in CRCs was cadherin 17 (CDH17). Downstream analysis of CRC transcriptomics and proteomics datasets showed that CDH17 was significantly correlated with carcinoembryonic antigen expression. Moreover, CDH17 expression was significantly lower in CRC cases with high microsatellite instability, as well as negatively associated with immune response gene sets and the expression of MHC class I and II molecules. CDH17 represents an optimal target for therapeutic development against CRCs, and this study provides a novel framework to identify key cell surface targets for therapeutic development against other malignancies.

Matched MeSH terms: Proteomics*
Fulltext Using the Proteomics Toolbox to Resolve Topology and Dynamics of Compartmentalized cAMP Signaling

Kovanich D, Low TY, Zaccolo M

Int J Mol Sci, 2023 Feb 28;24(5).
PMID: 36902098 DOI: 10.3390/ijms24054667

cAMP is a second messenger that regulates a myriad of cellular functions in response to multiple extracellular stimuli. New developments in the field have provided exciting insights into how cAMP utilizes compartmentalization to ensure specificity when the message conveyed to the cell by an extracellular stimulus is translated into the appropriate functional outcome. cAMP compartmentalization relies on the formation of local signaling domains where the subset of cAMP signaling effectors, regulators and targets involved in a specific cellular response cluster together. These domains are dynamic in nature and underpin the exacting spatiotemporal regulation of cAMP signaling. In this review, we focus on how the proteomics toolbox can be utilized to identify the molecular components of these domains and to define the dynamic cellular cAMP signaling landscape. From a therapeutic perspective, compiling data on compartmentalized cAMP signaling in physiological and pathological conditions will help define the signaling events underlying disease and may reveal domain-specific targets for the development of precision medicine interventions.

Matched MeSH terms: Proteomics*
Proteomic analysis of Moroccan cobra Naja haje legionis venom using tandem mass spectrometry

Malih I, Ahmad rusmili MR, Tee TY, Saile R, Ghalim N, Othman I

J Proteomics, 2014 Jan 16;96:240-52.
PMID: 24269350 DOI: 10.1016/j.jprot.2013.11.012

The proteome of the venom of Naja haje legionis, the only medically important elapid species in Morocco, has been elucidated by using a combination of proteomic techniques that includes size exclusion chromatography, reverse-phase HPLC, Tricine/SDS-Page, tryptic digestion, Q-TOF tandem mass spectrometry and database search. The sequence analysis of venom fractions revealed a highly complex venom proteome which counts a total of 76 proteins identified from database that can be assigned into 9 proteins families. We report the identification of: cobra venom factor (CVF), l-amino-acid oxidases (LAAO), acetylcholinesterase (AChE), snake venom metalloproteinases (SVMP), cysteine rich secretory proteins (CRISP), venom nerve growth factor (vNGF), phospholipases A2 (PLA2), vespryns, kunitz-type inhibitor, short neurotoxins, long neurotoxins, weak neurotoxins, neurotoxin like proteins, muscarinic toxins, cardiotoxins and cytotoxins. Comparison of these proteins showed high sequence homology with proteins from other African and Asian cobras. Further works are needed to assess the contribution of individual toxins in venom toxicity.

Matched MeSH terms: Proteomics*
Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives

Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, et al.

J Proteome Res, 2015 Jul 2;14(7):2723-44.
PMID: 26035454 DOI: 10.1021/acs.jproteome.5b00211

In the rapidly growing economies of Asia and Oceania, food security has become a primary concern. With the rising population, growing more food at affordable prices is becoming even more important. In addition, the predicted climate change will lead to drastic changes in global surface temperature and changes in rainfall patterns that in turn will pose a serious threat to plant vegetation worldwide. As a result, understanding how plants will survive in a changing climate will be increasingly important. Such challenges require integrated approaches to increase agricultural production and cope with environmental threats. Proteomics can play a role in unraveling the underlying mechanisms for food production to address the growing demand for food. In this review, the current status of food crop proteomics is discussed, especially in regard to the Asia and Oceania regions. Furthermore, the future perspective in relation to proteomic techniques for the important food crops is highlighted.

Matched MeSH terms: Proteomics*
Comparative Proteomic Analysis on Fruit Ripening Processes in Two Varieties of Tropical Mango (Mangifera indica)

Chin CF, Teoh EY, Chee MJY, Al-Obaidi JR, Rahmad N, Lawson T

Protein J, 2019 12;38(6):704-715.
PMID: 31552579 DOI: 10.1007/s10930-019-09868-x

Mango (Mangifera indica L.) is an economically important fruit. However, the marketability of mango is affected by the perishable nature and short shelf-life of the fruit. Therefore, a better understanding of the mango ripening process is of great importance towards extending its postharvest shelf life. Proteomics is a powerful tool that can be used to elucidate the complex ripening process at the cellular and molecular levels. This study utilized 2-dimensional gel electrophoresis (2D-GE) coupled with MALDI-TOF/TOF to identify differentially abundant proteins during the ripening process of the two varieties of tropical mango, Mangifera indica cv. 'Chokanan' and Mangifera indica cv 'Golden Phoenix'. The comparative analysis between the ripe and unripe stages of mango fruit mesocarp revealed that the differentially abundant proteins identified could be grouped into the three categories namely, ethylene synthesis and aromatic volatiles, cell wall degradation and stress-response proteins. There was an additional category for differential proteins identified from the 'Chokanan' variety namely, energy and carbohydrate metabolism. However, of all the differential proteins identified, only methionine gamma-lyase was found in both 'Chokanan' and 'Golden Phoenix' varieties. Six differential proteins were selected from each variety for validation by analysing their respective transcript expression using reverse transcription-quantitative PCR (RT-qPCR). The results revealed that two genes namely, glutathione S-transferase (GST) and alpha-1,4 glucan phosphorylase (AGP) were found to express in concordant with protein abundant. The findings will provide an insight into the fruit ripening process of different varieties of mango fruits, which is important for postharvest management.

Matched MeSH terms: Proteomics/methods
Fulltext Proteomic Analysis of the Human Anterior Pituitary Gland

Yelamanchi SD, Tyagi A, Mohanty V, Dutta P, Korbonits M, Chavan S, et al.

OMICS, 2018 12;22(12):759-769.
PMID: 30571610 DOI: 10.1089/omi.2018.0160

The pituitary function is regulated by a complex system involving the hypothalamus and biological networks within the pituitary. Although the hormones secreted from the pituitary have been well studied, comprehensive analyses of the pituitary proteome are limited. Pituitary proteomics is a field of postgenomic research that is crucial to understand human health and pituitary diseases. In this context, we report here a systematic proteomic profiling of human anterior pituitary gland (adenohypophysis) using high-resolution Fourier transform mass spectrometry. A total of 2164 proteins were identified in this study, of which 105 proteins were identified for the first time compared with high-throughput proteomic-based studies from human pituitary glands. In addition, we identified 480 proteins with secretory potential and 187 N-terminally acetylated proteins. These are the first region-specific data that could serve as a vital resource for further investigations on the physiological role of the human anterior pituitary glands and the proteins secreted by them. We anticipate that the identification of previously unknown proteins in the present study will accelerate biomedical research to decipher their role in functioning of the human anterior pituitary gland and associated human diseases.

Matched MeSH terms: Proteomics/methods*
Proteomic Investigations of In Vitro and In Vivo Models of Periodontal Disease

Binti Badlishah Sham NI, Lewin SD, Grant MM

Proteomics Clin Appl, 2020 05;14(3):e1900043.
PMID: 31419032 DOI: 10.1002/prca.201900043

Proteomics has currently been a developing field in periodontal diseases to obtain protein information of certain samples. Periodontal disease is an inflammatory disorder that attacks the teeth, connective tissues, and alveolar bone within the oral cavity. Proteomics information can provide proteins that are differentially expressed in diseased or healthy samples. This review provides insight into approaches researching single species, multi species, bacteria, non-human, and human models of periodontal disease for proteomics information. The approaches that have been taken include gel electrophoresis and qualitative and quantitative mass spectrometry. This review is carried out by extracting information about in vitro and in vivo studies of proteomics in models of periodontal diseases that have been carried out in the past two decades. The research has concentrated on a relatively small but well-known group of microorganisms. A wide range of models has been reviewed and conclusions across the breadth of these studies are presented in this review.

Matched MeSH terms: Proteomics*

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