High Accuracy Mass Spectrometry Research Articles

Identification and Functional Analysis of Lysine 2-Hydroxyisobutyrylation in Cyanobacteria.

Cyanobacteria are the oldest prokaryotic photoautotrophic microorganisms and have evolved complicated post-translational modification (PTM) machinery to respond to environmental stress. Lysine 2-hydroxyisobutyrylation (Khib) is a newly identified PTM that is reported to play important roles in diverse biological processes, however, its distribution and function in cyanobacteria have not been reported. Here, we performed the first systematic studies of Khib in a model cyanobacterium Synechococcus sp. strain PCC 7002 (Syn7002) using peptide prefractionation, pan-Khib antibody enrichment, and high-accuracy mass spectrometry (MS) analysis. A total of 1875 high-confidence Khib sites on 618 proteins were identified, and a large proportion of Khib sites are present on proteins in the cellular metabolism, protein synthesis, and photosynthesis pathways. Using site-directed mutagenesis and functional studies, we showed that Khib of glutaredoxin (Grx) affects the efficiency of the PS II reaction center and H2O2 resistance in Syn7002. Together, this study provides novel insights into the functions of Khib in cyanobacteria and suggests that reversible Khib may influence the stress response and photosynthesis in both cyanobacteria and plants.

Toward a More Comprehensive Approach for Dissolved Organic Matter Chemical Characterization Using an Orbitrap Fusion Tribrid Mass Spectrometer Coupled with Ion and Liquid Chromatography Techniques.

Dissolved organic matter (DOM) represents one of the largest active organic carbon pools in the global carbon cycle. Although extensively studied, only <10% of DOM has been chemically characterized into individual dissolved compounds due to its molecular complexity. This study introduced a more comprehensive DOM characterization method by coupling both ion chromatography (IC) and liquid chromatography (LC) with high mass accuracy and resolution mass spectrometry. We presented a new on-the-fly mass calibration of the Orbitrap technique by utilizing the "lock mass" function in the Orbitrap Fusion Tribrid mass spectrometer (OT-FTMS), which assures high mass accuracy at every scan by a postcolumn introduction of internal labeled standards. With both IC and LC, tested unlabeled standards of amino acids, small peptides, and organic acids were consistently below 1.0 ppm mass error, giving the OT-FTMS the potential of reaching mass accuracy of the Fourier-transform ion cyclotron resonance mass spectrometer. In addition to mass accuracy, a pooled quality control sample (QC) was used to increase reproducibility by applying systematic error removal using random forest (SERRF). Using an untargeted mass spectrometry approach, estuarine DOM samples were analyzed by OT-FTMS coupled to IC in negative mode and LC in positive mode detection to cover a wide range of highly cationic to highly anionic molecules. As a proof of concept, we focused on elucidating the structures of three distinct DOM compound classes with varied acidities and basicities. In UPLC-OT-FTMS, a total of 915 compounds were detected. We putatively elucidated 44 small peptides and 33 deaminated peptides of these compounds. With IC-OT-FTMS, a total of 1432 compounds were detected. We putatively elucidated 20 peptides, 268 deaminated peptides, and 188 organic acids. Except for five compounds, all putatively elucidated compounds were uniquely detected in their corresponding chromatography technique. These results highlight the need for combining these two techniques to provide a more comprehensive method for DOM characterization. Application of the combined IC and LC techniques is not limited to DOM chemical characterization. It can analyze other complex compound mixtures, such as metabolites, and anthropogenic pollutants, such as pesticides and endocrine-disrupting chemicals, in environmental and biological samples.

Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi.

Tyrosine sulfation in the Golgi of secreted and membrane proteins is an important post-translational modification (PTM). However, its labile nature has limited analysis by mass spectrometry (MS), a major reason why no sulfoproteome studies have been previously reported. Here, we show that a phosphoproteomics experimental workflow, which includes serial enrichment followed by high resolution, high mass accuracy MS, and tandem MS (MS/MS) analysis, enables sulfopeptide coenrichment and identification via accurate precursor ion mass shift open MSFragger database search. This approach, supported by manual validation, allows the confident identification of sulfotyrosine-containing peptides in the presence of high levels of phosphorylated peptides, thus enabling these two sterically and ionically similar isobaric PTMs to be distinguished and annotated in a single proteomic analysis. We applied this approach to isolated interphase and mitotic rat liver Golgi membranes and identified 67 tyrosine sulfopeptides, corresponding to 26 different proteins. This work discovered 23 new sulfoproteins with functions related to, for example, Ca2+-binding, glycan biosynthesis, and exocytosis. In addition, we report the first preliminary evidence for crosstalk between sulfation and phosphorylation in the Golgi, with implications for functional control.

Hybrid liquid chromatography high resolution and accuracy mass spectrometry approach for quantification of antibody-drug conjugates at the intact protein level in biological samples

Preclinical in vivo and in vitro characterization of Antibody-Drug Conjugates (ADCs) involves the development of several bioanalytical methods to address many drug exposure questions. The current pharma industry approach requires at least three different assays that must be run, i.e., total antibody (mAb), conjugated payload or conjugated mAb, and free payload assays. Herein we present analytical performances of a quantitative hybrid Ligand Binding/Liquid Chromatography High Resolution and Accuracy Mass Spectrometry (LB/LCHRAM) method that can condense much of the necessary bioanalytical information in one method. The method includes an immuno-capture step, and it detects whole ADC molecules. It was applied to plasma mouse samples and showed reliable bioanalytical performance according to full method validation standards. Quantitation using extracted ion chromatograms and deconvoluted mass peaks was evaluated. The limit of quantitation resulted in 0.5ng of protein on column with a linear dynamic range spanning from 0.5 to 10μg/mL. Moreover, lower drug-to-antibody ratio (DAR) ADC species can be simultaneously detected, also enabling qualitative characterization of in vivo ADC conjugation.

Combination of High-Resolution Multistage Ion Mobility and Tandem MS with High Energy of Activation to Resolve the Structure of Complex Chemoenzymatically Synthesized Glycans.

Carbohydrates, in particular microbial glycans, are highly structurally diverse biomolecules, the recognition of which governs numerous biological processes. Of special interest, glycans of known monosaccharide composition feature multiple possible isomers, differentiated by the anomerism and position of their glycosidic linkages. Robust analytical tools able to circumvent this extreme structural complexity are increasing in demand to ensure not only the correct determination of naturally occurring glycans but also to support the rapid development of enzymatic and chemoenzymatic glycan synthesis. In support to the later, we report the use of complementary strategies based on mass spectrometry (MS) to evaluate the ability of 14 engineered mutants of sucrose-utilizing α-transglucosylases to produce type/group-specific Shigella flexneri pentasaccharide bricks from a single lightly protected non-natural tetrasaccharide acceptor substrate. A first analysis of the reaction media by UHPLC coupled to high-accuracy MS led to detect six reaction products of enzymatic glucosylation out of the eight possible ones. A seventh structure was evidenced by an additional step of ion mobility at a resolving power (Rp) of approximately 100. Finally, a Rp of about 250 in ion mobility made it possible to detect the eighth and last of the expected structures. Complementary to these measurements, tandem MS with high activation energy charge transfer dissociation (CTD) allowed us to unambiguously characterize seven regioisomers out of the eight possible products of enzymatic glucosylation. This work illustrates the potential of the recently described powerful IMS and CTD-MS methods for the precise structural characterization of complex glycans.

Alternative method\u2019s results for the non targeted determination of xenobiotics in food by means of high resolution and accuracy mass spectrometry

The application of a high resolution and accurate mass spectrometry (HRAMS) approach to detect xenobiotics in different food matrices by means of non targeted determination by UHPLC-Orbitrap followed by data processing analysis was described. Three case studies were reported to demonstrate the possibility to identify unexpected substances in different food commodities overcomes targeted method. This innovative approach could lay the foundation for its applicability to routine analysis in the near future giving the possibility to open new horizons to the research of a wide range of xenobiotics.

PIPERADE: A double Penning trap for mass separation and mass spectrometry at DESIR/SPIRAL2

A double Penning trap is being commissioned at CENBG Bordeaux for the future DESIR/SPIRAL2 facility of GANIL. The setup is designed to perform both high-resolution mass separation of the ion beam for trap-assisted spectroscopy, and high-accuracy mass spectrometry of short-lived nuclides. In this paper, the technical details of the new device are described. First offline tests with the purification trap are also presented, showing a mass resolving power of about 105.

Labeling and label-free quantitative proteomics in plant biology

Proteins not only construct cellular structures but also play regulatory functions in plant development and growth. Accurate quantification of protein dynamics, turnover rates, and post-translational modifications provide crucial insights into the molecular mechanisms of biological systems. While early studies only consisted of listing proteins identified in given organs or under specific conditions. There is growing need to apply quantitative proteomic techniques to be biased or unbiased studies of plant protein dynamic changes. With rapid improvements in mass spectrometry (MS) technologies, various proteomic quantification methods have been developed and widely used in biological research. In the meantime, MS-based quantitative proteomics has emerged as a powerful approach for gaining insights into functional aspects of proteins in biological systems. MS is not inherently quantitative; thus, several strategies have been developed to assist MS for protein quantification. These strategies can be distinguished not only by the method of quantification, such as labeled or label-free method, but also by the quantitative goal, such as relative or absolute quantification. They can be also distinguished by the scopes of the experiments performed, such as unbiased or targeted studies. Even within these different research goals, numerous options exist, since each strategy has advantages and disadvantages. For example, labeling methods can tag proteins/peptides with chemical, metabolic, or enzymatic reagents, whereas label-free quantitation methods use spectra ion counting, or peak intensity-based analysis. In comparison with labeling strategies, label-free methods are widely used because of the dynamic quantitative range, costing less, and without labeling steps. However, label-free methods are limited in the sample multiplex capacity and quantitative accuracy. For labeling-based quantitation, materials or samples are labeled by different isotope reagents, the paired MS spectra ions are extracted for relative or absolute quantification. In combination with high accuracy MS instruments, various labeling strategies can be used in quantitative proteome analysis, these methods can be distinguished by quantification ions, such as precursor ion-based, reporter ion-based, peptide-coupled reporter ion-based, and fragment ion-based quantitation. For stable isotope labeled methods, proteins or peptides labeled with different stable isotopes are combined into one vial for LC-MS analysis. These strategies have gained popularity due to the diversity and flexibility of stable isotope reactions, the power to analyze multiple samples simultaneously, and the high quantification accuracy. In this review, we discuss the most widely used label-free and stable isotope-labeling-based proteomic strategies for relative and absolute quantitative proteomics in plants. We compare their strengths and weaknesses in terms of quantitation accuracy, proteome coverage and robustness. We summarize the most promising recent developments and their applications for solving plant biological complexities.

Proteogenomic Characterization of the Pathogenic Fungus Aspergillus flavus Reveals Novel Genes Involved in Aflatoxin Production

AbstractAspergillus flavus (A. flavus), a pathogenic fungus, can produce carcinogenic and toxic aflatoxins that are a serious agricultural and medical threat worldwide. Attempts to decipher the aflatoxin biosynthetic pathway have been hampered by the lack of a high-quality genome annotation for A. flavus. To address this gap, we performed a comprehensive proteogenomic analysis using high-accuracy mass spectrometry data for this pathogen. The resulting high-quality data set confirmed the translation of 8724 previously predicted genes and identified 732 novel proteins, 269 splice variants, 447 single amino acid variants, 188 revised genes. A subset of novel proteins was experimentally validated by RT-PCR and synthetic peptides. Further functional annotation suggested that a number of the identified novel proteins may play roles in aflatoxin biosynthesis and stress responses in A. flavus. This comprehensive strategy also identified a wide range of posttranslational modifications (PTMs), including 3461 modification sites from 1765 proteins. Functional analysis suggested the involvement of these modified proteins in the regulation of cellular metabolic and aflatoxin biosynthetic pathways. Together, we provided a high-quality annotation of A. flavus genome and revealed novel insights into the mechanisms of aflatoxin production and pathogenicity in this pathogen.

An accuracy-based proficiency testing programme with metrological reference values for the mass fraction of acesulfame potassium and sucralose in cake mix flour

This paper describes a metrological approach to evaluate the measurement capability of laboratories participating in a then Asia Pacific Laboratory Accreditation Cooperation [APLAC, now Asia Pacific Accreditation Cooperation] proficiency testing (PT) programme on mass fraction of acesulfame potassium and sucralose in cake mix flour. The programme was jointly organised by the Chemical Metrology Laboratory of the Health Sciences Authority, Singapore, and the Singapore Accreditation Council. Through the extensive APLAC network of accreditation bodies, 41 nominated laboratories from 32 economies registered, of which 40 laboratories submitted their results. Reference values of artificial sweeteners in the programme for performance evaluation were obtained from a high-accuracy liquid chromatography isotope dilution mass spectrometry (LC-IDMS) method. One of the unique features of this PT programme was the provision of pure substance certified reference materials (CRMs) of acesulfame potassium and sucralose to the participating laboratories as calibration standards to ensure comparability and metrological traceability of results. The participating laboratories’ performance, based on z-scores, were evaluated using the assigned reference value determined from IDMS. Five and one of the laboratories’ results would be incorrectly evaluated using consensus value calculated from the laboratories’ results for performance evaluation and using commercial standard as calibrant, respectively. This PT programme demonstrates the importance of the use of metrologically traceable reference values as the assigned values for appropriate evaluation of accuracy and reliable assessment. The provision of CRMs also heightened the testing laboratories’ awareness on the importance of using CRMs as calibrants for accurate measurements.

In-depth quantitative proteomics uncovers specie-specific metabolic programs in Leishmania (Viannia) species.

Leishmania species are responsible for a broad spectrum of diseases, denominated Leishmaniasis, affecting over 12 million people worldwide. During the last decade, there have been impressive efforts for sequencing the genome of most of the pathogenic Leishmania spp. as well as hundreds of strains, but large-scale proteomics analyses did not follow these achievements and the Leishmania proteome remained mostly uncharacterized. Here, we report a comprehensive comparative study of the proteomes of strains representing L. braziliensis, L. panamensis and L. guyanensis species. Proteins extracted by SDS-mediated lysis were processed following the multi-enzyme digestion-filter aided sample preparation (FASP) procedure and analysed by high accuracy mass spectrometry. "Total Protein Approach" and "Proteomic Ruler" were applied for absolute quantification of proteins. Principal component analysis demonstrated very high reproducibility among biological replicates and a very clear differentiation of the three species. Our dataset comprises near 7000 proteins, representing the most complete Leishmania proteome yet known, and provides a comprehensive quantitative picture of the proteomes of the three species in terms of protein concentration and copy numbers. Analysis of the abundance of proteins from the major energy metabolic processes allow us to highlight remarkably differences among the species and suggest that these parasites depend on distinct energy substrates to obtain ATP. Whereas L. braziliensis relies the more on glycolysis, L. panamensis and L. guyanensis seem to depend mainly on mitochondrial respiration. These results were confirmed by biochemical assays showing opposite profiles for glucose uptake and O2 consumption in these species. In addition, we provide quantitative data about different membrane proteins, transporters, and lipids, all of which contribute for significant species-specific differences and provide rich substrate for explore new molecules for diagnosing purposes. Data are available via ProteomeXchange with identifier PXD017696.

The Mass Resolution of Ca, K Isotopes and CO, N2 and C2H4 Isobars in Isotopes Separator On-Line trap Mass spectrometry

In Isotopes separator on-line trap, ions are trapped, cooled, accumulated, bunched and isotopes or isobars are separated, cyclotron frequencies are determined, which are followed by time of flight mass resolution. The mass resolution of isotopes in Penning trap mass spectrometry is achieved by the direct excitation of axial motion of ions, driven by RF field at the pure cyclotron frequencies of ions. The design and working of Isotopes separator on-line trap which is used for high-accuracy mass spectrometry in the mass resolution of calcium isotopes (40Ca+, 42Ca+, 44Ca+), potassium isotopes (39K+, 41K+) and [28(CO)]+, [(28N2)]+, [28(C2H4)]+ isobars found in mixtures is achieved from time of flight mass spectrometry are presented here.

Plasmodium berghei LAPs form an extended protein complex that facilitates crystalloid targeting and biogenesis

Passage of malaria parasites through mosquitoes involves multiple developmental transitions, from gametocytes that are ingested with the blood meal, through to sporozoites that are transmitted by insect bite to the host. During the transformation from gametocyte to oocyst, the parasite forms a unique transient organelle named the crystalloid, which is involved in sporozoite formation. In Plasmodium berghei, a complex of six LCCL domain-containing proteins (LAPs) reside in the crystalloid and are required for its biogenesis. However, little else is known about the molecular mechanisms that underlie the crystalloid's role in sporogony. In this study, we have used transgenic parasites stably expressing LAP3 fused to GFP, combined with GFP affinity pulldown and high accuracy mass spectrometry, to identify an extended LAP interactome of some fifty proteins. We show that many of these are targeted to the crystalloid, including members of two protein families with CPW-WPC and pleckstrin homology-like domains, respectively. Our findings indicate that the LAPs are part of an intricate protein complex, the formation of which facilitates both crystalloid targeting and biogenesis. SignificanceReducing malaria parasite transmission by mosquitoes is a key component of malaria eradication and control strategies. This study sheds important new light on the molecular composition of the crystalloid, an enigmatic parasite organelle that is essential for sporozoite formation and transmission from the insect to the vertebrate host. Our findings provide new mechanistic insight into how proteins are delivered to the crystalloid, and indicate that the molecular mechanisms that underlie crystalloid function are complex, involving several protein families unique to Plasmodium and closely related organisms. The new crystalloid proteins identified will form a useful starting point for studies aimed at unravelling how the crystalloid organelle facilitates sporogony and transmission.

The cytosolic isoform of glutaredoxin 2 promotes cell migration and invasion

BackroundCytosolic glutaredoxin 2 (Grx2c) controls axonal outgrowth and is specifically induced in many cancer cell lines. We thus hypothesized that Grx2c promotes cell motility and invasiveness. MethodsWe characterized the impact of Grx2c expression in cell culture models. We combined stable isotope labeling, phosphopeptide enrichment, and high-accuracy mass spectrometry to characterize the underlying mechanisms. ResultsThe most prominent associations were found with actin dynamics, cellular adhesion, and receptor-mediated signal transduction, processes that are crucial for cell motility. For instance, collapsin response mediator protein 2, a protein involved in the regulation of cytoskeletal dynamics, is regulated by Grx2c through a redox switch that controls the phosphorylation state of the protein as well. Cell lines expressing Grx2c showed dramatic alterations in morphology. These cells migrated two-fold faster and gained the ability to infiltrate a collagen matrix. ConclusionsThe expression of Grx2c promotes cell migration, and may negatively correlate with cancer-specific survival. General significanceOur results imply critical roles of Grx2c in cytoskeletal dynamics, cell adhesion, and cancer cell invasiveness.

Preliminary Study to Develop an Alternative Method for the Non-targeted Determination of Xenobiotics in Food by Means of Ultra High Performance Liquid Chromatography Coupled to High Resolution and Accuracy Mass Spectrometry

This preliminary study describes the use of high resolution and accuracy mass spectrometry techniques combined with new generation chemical software products for detecting and identifying contaminants in food commodities. As a first step, the extracts of routine target analysis samples (obtained in our official laboratory responsible for food residues control) were acquired and processed with this method in order to search unknown and non-targeted contaminants in food. In order to verify the feasibility of the presented method, the research has been firstly addressed to untargeted pesticides and their metabolites in stone fruits commodities and tomatoes. The differential analysis carried with Compound Discoverer 2.0 between the investigated unknown sample and the blank matrix sample allowed to remove all the matrix molecular components; Aggregated Computational Toxicology Resource (ACToR) helped to understand and predict chemical interpretation of substances. The acquisition in FullScan-AIF and FullScan-ddMS2 allowed the clear detection and identification of isobaric compounds such as quinalphos and phoxim. In order to verify that the proposed method is suitable to the scope of application, the main points of SANTE/11813/2017 Document have been followed. The results demonstrate that no false positives and no false negatives have been detected from the analysis of samples spiked with 55 pesticides at 0.010 and 0.10 mg kg−1. This preliminary study has been also tested with a Proficiency Test (EUPT-FV-SM08) and, according to EUPT-FV-SM08 Final Report, our laboratory has been included in the 67% (56) that clearly detected over 70% pesticides. Finally, this method has been extended to other matrices and contaminants.

Determination of serum 25-hydroxyvitamin D status among population in southern China by a high accuracy LC-MS/MS method traced to reference measurement procedure

ObjectiveWe aimed to describe the 25-hydroxyvitamin D (25(OH)D) status of southern Chinese individuals by a high-accuracy liquid chromatography tandem mass spectrometry (LC-MS/MS) method which can trace to reference measurement procedure.Materials and methodsFrom January 2018 to June 2019, a total of 4775 southern Chinese individuals were evaluated in our study. The serum levels of parathyroid hormone (PTH) were detected simultaneously in 162 cases. 25(OH)D was determined by LC-MS/MS, and PTH was detected using routine automated analysers. The distribution of the concentration, prevalence and seasonal variability of 25(OH)D in males and females of different age groups were studied.ResultsThe mean 25(OH)D concentration in our study was 32.57 ng/mL (4.20–101.40 ng/mL). The global 25(OH)D concentration in males was higher than that in females of different age group. The prevalence of vitamin D deficiency (< 20 ng/mL) in females (16.65%) was higher than that in males (6.83%). The prevalence of vitamin D deficiency (< 20 ng/mL) was most common in winter (22.98% of all women and 15.49% of all men). 25(OH)D concentrations were higher in those from whom blood samples were collected in summer and autumn than in winter and spring. 25(OH)D2 was detected in 672 serum samples (14.07%). In addition, there was a negative correlation between the concentrations of 25(OH)D and serum PTH (r = − 0.149, P < 0.05).ConclusionOur study demonstrated that the average serum 25(OH)D concentration in southern Chinese individuals was higher than that in other Chinese cohorts by a high-accuracy LC-MS/MS method. The global 25(OH)D concentration in males was higher than that in females of different ages, and the prevalence of vitamin D deficiency in females was higher than that in males. Seasonal change was an important aspect of 25(OH)D concentration in young and middle-aged people but became less relevant for that in older subjects. 25(OH)D2 detection was of minor practical significance in our study. In addition, we also found that there was a negative correlation between the serum levels of 25(OH)D and PTH in southern Chinese individuals.

Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria

Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.

New approaches using mass spectrometry to investigate changes to cytokinin and abscisic acid (ABA) concentrations in soil

Phytohormones such as cytokinins, abscisic acid (ABA) and auxins play a vital role in plant development and regulatory processes. Their role within the plant is a focus for much research, with studies using recent advances in mass spectrometry performance allowing the quantification of low levels of phytohormones extracted from plant tissues. Despite these advances, external factors influencing the production of phytohormones are less well studied. Here, a new approach is presented for the extraction of a range of phytohormones from plant growth media (soil and hydroponic solution), their identification using high mass accuracy mass spectrometry and subsequent quantification using multiple reaction monitoring (MRM). The ability to detect phytohormones in matrices other than plant tissue presents the opportunity to study further the influence of factors such as below ground organisms and soil bacteria on phytohormone production.This novel approach was therefore applied to the plant growth media from a series of experiments comparing plant growth in the presence and absence of earthworms. A small but significant increase in ABA concentration was observed in the presence of earthworms, increasing even further when plants were also present. This finding suggests that earthworms could stimulate plant ABA production. This experiment and its outcomes demonstrate the value of studying phytohormones outside plant tissue, and the potential value of further research in this area.

Distinct Fractions of an Artemisia scoparia Extract Contain Compounds With Novel Adipogenic Bioactivity.

Adipocytes are important players in metabolic health and disease, and disruption of adipocyte development or function contributes to metabolic dysregulation. Hence, adipocytes are significant targets for therapeutic intervention in obesity and metabolic syndrome. Plants have long been sources for bioactive compounds and drugs. In previous studies, we screened botanical extracts for effects on adipogenesis in vitro and discovered that an ethanolic extract of Artemisia scoparia (SCO) could promote adipocyte differentiation. To follow up on these studies, we have used various separation methods to identify the compound(s) responsible for SCO's adipogenic properties. Fractions and subfractions of SCO were tested for effects on lipid accumulation and adipogenic gene expression in differentiating 3T3-L1 adipocytes. Fractions were also analyzed by Ultra Performance Liquid Chromatography- Mass Spectrometry (UPLC-MS), and resulting peaks were putatively identified through high resolution, high mass accuracy mass spectrometry, literature data, and available natural products databases. The inactive fractions contained mostly quercetin derivatives and chlorogenates, including chlorogenic acid and 3,5-dicaffeoylquinic acid, which had no effects on adipogenesis when tested individually, thus ruling them out as pro-adipogenic bioactives in SCO. Based on these studies we have putatively identified the principal constituents in SCO fractions and subfractions that promoted adipocyte development and fat cell gene expression as prenylated coumaric acids, coumarin monoterpene ethers, 6-demethoxycapillarisin and two polymethoxyflavones.

Proteomic and Phosphoproteomic Analysis in Tobacco Mosaic Virus-Infected Tobacco (Nicotiana tabacum)

Tobacco mosaic virus (TMV) is a common source of biological stress that significantly affects plant growth and development. It is also useful as a model in studies designed to clarify the mechanisms involved in plant viral disease. Plant responses to abiotic stress were recently reported to be regulated by complex mechanisms at the post-translational modification (PTM) level. Protein phosphorylation is one of the most widespread and major PTMs in organisms. Using immobilized metal ion affinity chromatography (IMAC) enrichment, high-pH C18 chromatography fraction, and high-accuracy mass spectrometry (MS), a set of proteins and phosphopeptides in both TMV-infected tobacco and control tobacco were identified. A total of 4905 proteins and 3998 phosphopeptides with 3063 phosphorylation sites were identified. These 3998 phosphopeptides were assigned to 1311 phosphoproteins, as some proteins carried multiple phosphorylation sites. Among them, 530 proteins and 337 phosphopeptides corresponding to 277 phosphoproteins differed between the two groups. There were 43 upregulated phosphoproteins, including phosphoglycerate kinase, pyruvate phosphate dikinase, protein phosphatase 2C, and serine/threonine protein kinase. To the best of our knowledge, this is the first phosphoproteomic analysis of leaves from a tobacco cultivar, K326. The results of this study advance our understanding of tobacco development and TMV action at the protein phosphorylation level.