Proteomic analysis of red blood cells and the potential for the clinic: what have we learned so far?

Introduction: Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating ‘bags of hemoglobin’. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease.

Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology. We thus focus on translational/clinical applications, such as transfusion medicine, hematology (e.g. hemoglobinopathies) and personalized medicine. Synergy of omics technologies – especially proteomics and metabolomics – are highlighted as a hallmark of clinical metabolomics applications for the foreseeable future.

Expert commentary: The introduction of advanced proteomics technologies, especially quantitative and redox proteomics, and the integration of proteomics data with omics information gathered through orthogonal technologies (especially metabolomics) promise to revolutionize many biomedical areas, from hematology and transfusion medicine to personalized medicine and clinical biochemistry.     

Resolving subcellular plant metabolism

Plant cells are characterized by a high degree of compartmentalization and a diverse proteome and metabolome. Only a very limited number of studies has addressed combined subcellular proteomics and metabolomics which strongly limits biochemical and physiological interpretation of large‐scale ’omics data. Our study presents a methodological combination of nonaqueous fractionation, shotgun proteomics, enzyme activities and metabolomics to reveal subcellular diurnal dynamics of plant metabolism. Subcellular marker protein sets were identified and enzymatically validated to resolve metabolism in a four‐compartment model comprising chloroplasts, cytosol, vacuole and mitochondria. These marker sets are now available for future studies that aim to monitor subcellular metabolome and proteome dynamics. Comparing subcellular dynamics in wild type plants and HXK1‐deficient gin2‐1 mutants revealed a strong impact of HXK1 activity on metabolome dynamics in multiple compartments. Glucose accumulation in the cytosol of gin2‐1 was accompanied by diminished vacuolar glucose levels. Subcellular dynamics of pyruvate, succinate and fumarate amounts were significantly affected in gin2‐1 and coincided with differential mitochondrial proteome dynamics. Lowered mitochondrial glycine and serine amounts in gin2‐1 together with reduced abundance of photorespiratory proteins indicated an effect of the gin2‐1 mutation on photorespiratory capacity. Our findings highlight the necessity to resolve plant metabolism to a subcellular level to provide a causal relationship between metabolites, proteins and metabolic pathway regulation.     

植物代谢组学中几种重要的次生代谢物液质分析技术研究进展

代谢组学（metabolomics）主要是研究生物体、组织、细胞的代谢物组分及检测其动态变化过程,是继基因组和蛋白组学后新兴的一门组学技术。代谢物是细胞调节过程中的最终产物,其水平被视为生物系统对遗传或环境变化的最终反映。通过合适的分析平台,准确定性、定量在复杂的生物中具有化学多样性的次生代谢物是代谢组学的一项重要工作。液相色谱-串联质谱技术（liquid chromatography-tandem mass spectrometry,LC-MS/MS）是代谢物质检测平台最常用的方法,也为植物次生代谢物的广泛应用研究提供了基础。本文主要从植物激素类、叶酸类、黄酮类等次生代谢物方面进行阐述,结合液质联用技术,简要论述不同次生代谢物检测技术的研究进展。     

基于比较代谢组学的理性优化方法提高阿维菌素产量

【目的】利用比较代谢组学的分析方法,研究不同发酵培养基中阿维链霉菌的胞内代谢差异,揭示合成阿维菌素的关键代谢物和代谢途径,再通过理性优化添加主要关键代谢物,提高阿维菌素产量。【方法】对M1和M2培养基中生长的菌体进行基于GC-MS的胞内代谢组学分析,通过理性添加强化前体代谢物,确定阿维菌素高产培养基。【结果】GC-MS共检测到232种物质,能够精确匹配70种胞内代谢物,通过PCA和PLS分析,最终确定了21种已知的胞内代谢物与阿维菌素的生物合成密切相关。其中乳酸、丙酮酸、琥珀酸、苏氨酸、异亮氨酸、缬氨酸和油脂类物质对阿维菌素的产量影响较为显著。通过单独或组合优化添加这些前体,阿维菌素的产量从5.36 g/L提高到了5.92 g/L,增加了10.4%。【结论】基于比较代谢组学分析的理性优化培养基的方法可有效提高阿维菌素的产量,并为提高当下生物基产品的产量提供了新思路。     

微生物代谢组学及其在工业中的应用

微生物代谢组学是系统生物学的重要组成部分,其与基因组学、转录组学和蛋白质组学相互补充,近年来受到越来越多人的重视。其主要对细胞生长或生长周期某一时刻细胞内外所有低分子量代谢物进行定性和定量分析,直接反映了细胞的生理状态,对理解细胞功能十分重要。由于代谢物的复杂性,研究者需根据不同的目的及对象选择合适的分析方法。对微生物代谢组学近年来的研究方法进行综述,包括样品处理、分析手段、数据分析,并讨论了微生物代谢组学在工业中的应用及所面临的挑战。     

代谢组及其在真菌研究中的应用

代谢组学是利用现代分析化学手段对一定条件下生物体内小分子代谢产物（初级和次级代谢产物）定性及定量,从而揭示生命现象及其内在规律的学科。相对于基因组、转录组和蛋白质组,代谢组是一定条件下生物学过程完成后的最终代谢产物的集合,因而是各种组学研究中最接近表型的一种组学,可以直接动态地反映出细胞的生理生化过程,从而有效地检测和发现特定的生化途径,准确地解释生理或者病理现象。代谢组学作为系统生物学中基因组学、转录组学以及蛋白质组学三大组学的延伸和补充,是目前的研究热点之一。目前代谢组学在真菌领域的研究得到日益重视和发展。本文首先从历史发展和技术路线简述了代谢组学的发展历程和常见的代谢组学研究方法。接着从真菌的分类鉴定、生物膜研究、代谢途径、代谢工程、天然产物发现与植物互作这6个方面介绍了代谢组学在真菌研究领域的应用。     

Metabolite profiling of Neptunia oleracea and correlation with antioxidant and α-glucosidase inhibitory activities using 1H NMR-based metabolomics

Neptunia oleracea is a plant consumed as vegetable and used as a traditional herb to treat several ailments. This study evaluated metabolite variations among N. oleracea leaf and stem subjected to air drying (AD), freeze drying (FD) and oven drying (OD) using proton nuclear magnetic resonance (¹H NMR) based metabolomics. The correlation was also studied for the metabolite content with total phenolic content (TPC), DPPH free radical scavenging and α-glucosidase inhibitory activities. A total of 18 metabolites were identified from N. oleracea extracts, including 10 primary metabolites, 5 flavonoids and 3 phenolic acids using NMR. Ultra-high performance liquid chromatography tandem mass spectrometry analysis (UHPLC-MS/MS) confirmed the presence of the secondary metabolites and revealed the flavonoid derivatives present. All the identified phenolics are first reported from this plant. Multivariate data analysis (MVDA) showed strong correlation between the metabolites with the antioxidant and α-glucosidase inhibitory activities of FD N. oleracea leaves. The compounds suggested to be responsible for the high activity of FD leaves include vitexin-2-O-rhamnoside, catechin, caffeic acid, gallic acid and derivatives of quercetin, kaempferol and myricetin. This study demonstrates that FD N. oleracea leaves are a potential natural source for antioxidant and α-glucosidase inhibitors.     

多组学分析在昆虫滞育中的应用

组学技术将生物的相关问题分别展现在基因、蛋白质和代谢物等不同层次水平上,已成为解读生命过程的重要工具。本文分别从转录组学、蛋白质组学、代谢组学以及组学间的联合应用等方面概括总结了组学技术在昆虫滞育研究中的应用情况,阐述了以转录组学、蛋白质组学和代谢组学为代表的多组学技术在昆虫滞育调控分子机制中取得的重要成果,并针对当前研究现状,对昆虫滞育中组学技术应用的前景和局限性进行了总结和展望,以期为昆虫滞育调控分子机制的研究提供参考依据。     

Genomic,transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites

Plants accumulate a vast array of secondary metabolites,which constitute a natural resource for pharmaceuticals.Oldenlandia corymbosa belongs to the Rubiaceae family,and has been used in traditional medicine to treat different diseases,including cancer.However,the active metabolites of the plant,their biosynthetic pathway and mode of action in cancer are unknown.To fill these gaps,we exposed this plant to eight different stress conditions and combined different omics data capturing gene expressi...     

6种植物次生物质对斜纹夜蛾解毒酶活性的影响

草食性昆虫取食植物时遇到宿主植物中大量次生物质的化学防御,研究昆虫适应植物毒素的反防御策略具有重要的科学意义。分别添加0.01%肉桂酸、0.01%水杨酸、0.01%花椒毒素、0.02%槲皮素、0.05%黄酮和0.1%香豆素等6种植物次生物质的人工饲料饲养斜纹夜蛾(Spodoptera litura)五龄幼虫48 h后,测定斜纹夜蛾幼虫中肠和脂肪体中谷胱甘肽S-转移酶(GSTs)、羧酸酯酶(CarE)、P450的酶含量及头部乙酰胆碱酯酶(AChE)的活性,利用半定量RT-PCR检测中肠和脂肪体中CYP4M14和CYP4S9的基因表达水平。结果表明:取食肉桂酸和香豆素后,斜纹夜蛾中肠中CarE的酶活性分别提高了1.67和1.37倍,取食6种次生物质均能显著提高斜纹夜蛾脂肪体中GSTs酶活性。取食肉桂酸和香豆素48 h后,脂肪体中P450酶含量比对照增加2.93和14.50倍。取食肉桂酸、花椒毒素、槲皮素和香豆素后,斜纹夜蛾头部AchE酶活性与对照相比提高了1.53、1.80、2.36和1.56倍。6种次生物质均可诱导脂肪体中CYP4M14基因表达,槲皮素、肉桂酸和香豆素强烈诱导CYP4S9在脂肪体中表达。表明,斜纹夜蛾具有利用植物次生物质诱导其解毒酶的能力,进而提高其对毒素的抗性。     

A metabolomics and proteomics study of the <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis> in the grass carp fermentation

Background

Lactobacillus plantarum, a versatile lactic acid-fermenting bacterium, isolated from the traditional pickles in Ningbo of China, was chosen for grass carp fermentation, which could also improve the flavor of grass carp. We here explored the central metabolic pathways of L. plantarum by using metabolomic approach, and further proved the potential for metabolomics combined with proteomics approaches for the basic research on the changes of metabolites and the corresponding fermentation mechanism of L. plantarum fermentation.

Results

This study provides a cellular material footprinting of more than 77 metabolites and 27 proteins in L. plantarum during the grass carp fermentation. Compared to control group, cells displayed higher levels of proteins associated with glycolysis and nucleotide synthesis, whereas increased levels of serine, ornithine, aspartic acid, 2-piperidinecarboxylic acid, and fumarate, along with decreased levels of alanine, glycine, threonine, tryptophan, and lysine.

Conclusions

Our results may provide a deeper understanding of L. plantarum fermentation mechanism based on metabolomics and proteomic analysis and facilitate future investigations into the characterization of L. plantarum during the grass carp fermentation.

     

NMR metabolomic of frontal cortex extracts: First study comparing two neurodegenerative diseases,Alzheimer disease and amyotrophic lateral sclerosis

ObjectiveThis study was designed to assess the brain metabolites’ variability between two neurodegenerative diseases in frontal cortex samples obtained post-mortem. NMR metabolomics was used for the first time in this context.Materials and methods¹H NMR metabolomic was applied to tissue extracts from patients with Alzheimer disease (ALZ) and patients with amyotrophic lateral sclerosis (ALS) to investigate qualitative and quantitative variations of brain metabolites.ResultsThe Alzheimer disease metabolic signature was characterized by a high concentration of alanine, acetate, glutamate and glutamine, and low concentrations of lactate and creatine, while the ALS metabolic signature appears to be marked by high concentrations of lactate, N-acetyl aspartate, creatine, choline and myo-inositol. Moreover, in vitro ¹H NMR could detect metabolites such as 3-hydroxybutyrate, alanine, succinate and aspartate that cannot be detected with in vivo NMR.DiscussionThe neurodegenerative diseases exhibit diverging metabolic pathways. Some of the metabolites responsible for the discrimination between the two diseases were detected before in vivo. However, this in vitro metabolomic investigation demonstrates the involvement of metabolites not detected with in vivo studies.ConclusionUpon these findings, in vitro metabolomics appears to be an efficient tool to investigate the fundamentals of the metabolic pathway modulations in these neurodegenerative diseases to help the interpretation of clinical data obtained with in vivo NMR spectroscopy.     

Nitrogen nutrition and the accumulation of free and sinapoyl-bound malic acid in Raphanus sativus cotyledons

Seedlings of red radish (Raphanus sativus L. var. sativus) accumulated high amounts of free malic acid and sinapoylmalate, when grown on nitrate as the sole N-source. In the presence of ammonium (NO ₃ ^– : NH ₄ ⁺ , 1:2) both metabolites failed to accumulate, and the levels of arginine, asparagine, glutamine, histidine, and serine were greatly increased. The extractable activity of 1-sinapoylglucose: l-malate sinapoyltransferase, an enzyme which plays a key role in channelling malic acid into the sinapic-acid metabolism of this plant, was positively correlated with the malic-acid level in cotyledons. The possibility is discussed that free malic acid might be the likely candidate for regulating the activity of 1-sinapoylglucose: l-malate sinapoyltransferase.Abbreviation SMT sinapoylglucose: L-malate sinapoyltransferase     

Purification by Immunoadsorption and Immunochemical Properties of NADP-Dependent Malic Enzymes from Leaves of C(3), C(4), and Crassulacean Acid Metabolism Plants

NADP:malic enzyme from corn (Zea mays L.) leaves was purified by conventional techniques to apparent homogeneity as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Antibodies raised against this protein in rabbits were purified, coupled covalently to protein A-Sepharose CL-4B, and used as an immunoaffinity resin to purify the NADP:malic enzymes of the C₃ plants spinach (Spinacia oleracea L.) and wheat (Triticum aestivum L.), of the Crassulacean acid metabolism (CAM) plant Bryophyllum daigremontianum R. Hamed et Perr. de la Bathie and the C₄ plants corn, sugarcane (Saccharum officinarum L.), and Portulaca grandiflora L. Such procedures yielded homogeneous protein preparations with a single protein band, as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, except for P. grandiflora L. with two bands. The specific activities of the purified proteins ranged between 56 and 91 units (milligrams per protein). NADP:malic enzyme represented up to 1% of the total soluble protein in C₄ plants, 0.5% in the CAM plant, and less than 0.01% in C₃ plants. In immunotitration tests involving immunoprecipitation and immunoinhibition of activity by an antiserum against the corn leaf enzyme, the NADP:malic enzymes of corn and sugarcane showed virtually full identity of epitopes, while the NADP:malic enzymes of the C₃ and CAM plants exhibited a cross-reaction of one-twentieth and one-fourth by these tests, respectively. The NADP:malic enzyme of P. grandiflora exhibited characteristics more closely related to the enzymes of C₃ and CAM plants than to those of C₄ plants.     

Neuroprotective activity and cytotoxic potential of two Parmeliaceae lichens: Identification of active compounds

BackgroundLichens are symbiotic organisms capable of producing unique secondary metabolites, whose pharmacological activities are attracting much interest.PurposeThe present study aimed to investigate the in vitro neuroprotective effects and anticancer potential of methanol extracts of two Parmeliaceae lichens: Cetraria islandica and Vulpicida canadensis. The chemical composition of the two lichens was also determined.MethodsNeuroprotective activity was studied with respect to the antioxidant properties of the extracts; radical scavenging tests (ORAC and DPPH assays) were performed and oxidative stress markers (intracellular ROS production, caspase-3 activity, MDA and glutathione levels) were assessed in a hydrogen peroxide-induced oxidative stress model in astrocytes. Cytotoxic activity was tested against human HepG2 (hepatocellular carcinoma) and MCF-7 (breast adenocarcinoma) cell lines.ResultsCell viability studies identified a single concentration for each extract that was subsequently used to measure oxidative stress markers. Lichen extracts were able to reverse the oxidative damage caused by hydrogen peroxide, thus promoting astrocyte survival. Both lichen extracts also had anticancer activity in the cell lines, with IC₅₀ values of 19.51–181.05 µg/ml. The extracts had a high total phenolic content, and the main constituents identified by HPLC were fumarprotocetraric acid in Cetraria islandica, and usnic, pinastric and vulpinic acids in Vulpicida canadensis. The biological activities of the lichen extracts can be attributed to these secondary metabolites.ConclusionThe lichen species studied are promising sources of natural compounds with neuroprotective activity and cytotoxic potential, and warrant further research.     

代谢物组学方法及其在植物学研究中的应用

代谢物是生物体受遗传控制和环境影响的最终表达产物,以全体代谢物(代谢物组)为研究对象的代谢物组学是继基因组学和蛋白质组学后必然出现的又一门"组学"技术。该文综述了代谢物组的检测、数据的处理和分析等以及这些技术在植物目标分析、基因功能、代谢途径和代谢工程、整合植物学、信号转导等研究中的应用和前景。     

Update on: proteome analysis in thyroid pathology – part II: overview of technical and clinical enhancement of proteomic investigation of the thyroid lesions

ABSTRACT

Introduction: An accurate diagnostic classification of thyroid lesions remains an important clinical aspect that needs to be addressed in order to avoid ‘diagnostic’ thyroidectomies. Among the several ‘omics’ techniques, proteomics is playing a pivotal role in the search for diagnostic markers. In recent years, different approaches have been used, taking advantage of the technical improvements related to mass spectrometry that have occurred.

Areas covered: The review provides an update of the recent findings in diagnostic classification, in genetic definition and in the investigation of thyroid lesions based on different proteomics approaches and on different type of specimens: cytological, surgical and biofluid samples. A brief section will discuss how these findings can be integrated with those obtained by metabolomics investigations.

Expert commentary: Among the several proteomics approaches able to deepen our knowledge of the molecular alterations of the different thyroid lesions, MALDI-MSI is strongly emerging above all. In fact, MS-imaging has also been demonstrated to be capable of distinguishing thyroid lesions, based on their different molecular signatures, using cytological specimens. The possibility to use the material obtained by the fine needle aspiration makes MALDI-MSI a highly promising technology that could be implemented into the clinical and pathological units.