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69 records · Page 4

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.

59 BASIC BIOLOGICAL SCIENCES↗

Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora

For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC–MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.

Xing, Yanhong↗

Purification and expression of a novel bacteriocin, JUQZ-1, against Pseudomonas syringae pv. Actinidiae (PSA), secreted by Brevibacillus laterosporus Wq-1, isolated from the rhizosphere soil of healthy kiwifruit

Kiwifruit canker, caused by Pseudomonas syringae pv. actinidiae (PSA), has led to significant losses in the kiwifruit industry each year. Due to the drug resistance feature of PSA, biological control is currently the most promising method. Developing biocontrol bacteria against PSA could help solve the issue of drug resistance generated during the chemical control of PSA to a certain extent. In this research, a Wq-1 strain that demonstrated excellent inhibitory activity against PSA was isolated from the rhizosphere soil of healthy kiwifruit. Based on the morphological characteristics and phylogenetic analysis of the 16S rRNA gene sequence, the isolated strain was identified as Brevibacillus laterosporus Wq-1. Bacteriostatic proteins were isolated from the cell-free culture filtrate of strain Wq-1 and were found to have a molecular weight of approximately 12 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Liquid chromatography–tandem mass spectrometry (LC–MS/MS) detection revealed that there were several peptides in the target band that were consistent with protein 01021 in the genome. The gene of the 01021 protein was cloned into the plasmid pPICZa, and the recombinant bacteriocin was successfully expressed using the Pichia pastoris X33 expression system. The recombinant protein 01021 effectively inhibited the growth of PSA. This is the first report of the protein’s antimicrobial activity, distinguishing it from previously identified bacteriocins. Therefore, we named this bacteriocin JUQZ-1. In addition, our results showed that the protein JUQZ-1 not only exhibited a broad bacteriostatic spectrum but also high thermal and pH stability suitable for harsh environmental conditions., JUQZ-1, a protein with antimicrobial properties and strong environmental tolerance, may serve as a promising alternative to antibiotics.

Shuai, Yang↗

Cloning and Characterization of Aedes aegypti Trypsin Modulating Oostatic Factor (TMOF) Gut Receptor

Trypsin Modulating Oostatic Factor (TMOF) receptor was solubilized from the guts of female Ae. Aegypti and cross linked to His6-TMOF and purified by Ni affinity chromatography. SDS PAGE identified two protein bands (45 and 61 kDa). The bands were cut digested and analyzed using MS/MS identifying a protein sequence (1306 amino acids) in the genome of Ae. aegypti. The mRNA of the receptor was extracted, the cDNA sequenced and cloned into pTAC-MAT-2. E. coli SbmA− was transformed with the recombinant plasmid and the receptor was expressed in the inner membrane of the bacterial cell. The binding kinetics of TMOF-FITC was then followed showing that the cloned receptor exhibits high affinity to TMOF (KD = 113.7 ± 18 nM ± SEM and Bmax = 28.7 ± 1.8 pmol ± SEM). Incubation of TMOF-FITC with E. coli cells that express the receptor show that the receptor binds TMOF and imports it into the bacterial cells, indicating that in mosquitoes the receptor imports TMOF into the gut epithelial cells. A 3D modeling of the receptor indicates that the receptor has ATP binding sites and TMOF transport into recombinant E. coli cells is inhibited with ATPase inhibitors Na Arsenate and Na Azide.

Borovsky, Dov↗

Assessment of Hydroxyl Radical Reactivity in Sulfur-Containing Amino Acid Models Under Acidic pH

Methionine residues in proteins and peptides are frequently oxidized by losing one electron. The presence of nearby amide groups is crucial for this process, enabling methionine to participate in long-range electron transfer. Hydroxyl radical (HO•) plays an important role being generated in aerobic organisms by cellular metabolisms as well as by exogenous sources such as ionizing radiations. The reaction of HO• with methionine mainly affords the one-electron oxidation of the thioether moiety through two consecutive steps (HO• addition to the sulfur followed by HO− elimination). We recently investigated the reaction of HO• with model peptides mimicking methionine and its cysteine-methylated counterpart, i.e., CH3C(O)NHCHXC(O)NHCH3, where X = CH2CH2SCH3 or CH2SCH3 at pH 7. The reaction mechanism varied depending on the distance between the sulfur atom and the peptide backbone, but, for a better understanding of various suggested equilibria, the analysis of the flux of protons is required. We extended the previous study to the present work at pH 4 using pulse radiolysis techniques with conductivity and optical detection of transient species, as well as analysis of final products by LC-MS and high-resolution MS/MS following γ-radiolysis. Comparing all the data provided a better understanding of how the presence of nearby amide groups influences the one-electron oxidation mechanism.

Biochemistry & Molecular Biology↗

Revisiting Five Years of CASMI Contests with EPA Identification Tools

Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency’s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.

97 MATHEMATICS AND COMPUTING↗

Liquid Chromatography Coupled to Refractive Index or Mass Spectrometric Detection for Metabolite Profiling in Lysate-based Cell-free Systems

Engineering cellular metabolism for targeted biosynthesis can require extensive design-build-test-learn (DBTL) cycles as the engineer works around the cell's survival requirements. Alternatively, carrying out DBTL cycles in cell-free environments can accelerate this process and alleviate concerns with host compatibility. A promising approach to cell-free metabolic engineering (CFME) leverages metabolically active crude cell extracts as platforms for biomanufacturing and for rapidly discovering and prototyping modified proteins and pathways. Realizing these capabilities and optimizing CFME performance requires methods to characterize the metabolome of lysate-based cell-free platforms. That is, analytical tools are necessary for monitoring improvements in targeted metabolite conversions and in elucidating alterations to metabolite flux when manipulating lysate metabolism. In this work, metabolite analyses using high-performance liquid chromatography (HPLC) coupled with either optical or mass spectrometric detection were applied to characterize metabolite production and flux in E. coli S30 lysates. Specifically, this report describes the preparation of samples from CFME lysates for HPLC analyses using refractive index detection (RID) to quantify the generation of central metabolic intermediates and by-products in the conversion of low-cost substrates (i.e., glucose) to various high-value products. The analysis of metabolite conversion in CFME reactions fed with 13 C-labeled glucose through reversed-phase liquid chromatography coupled to tandem mass spectrometry (MS/MS), a powerful tool for characterizing specific metabolite yields and lysate metabolic flux from starting materials, is also presented. Altogether, applying these analytical methods to CFME lysate metabolism enables the advancement of these systems as alternative platforms for executing faster or novel metabolic engineering tasks.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing intracellular proteomes for microbes: An experimental approach using label-free protein quantitation

Genomic and transcriptomic studies generate a rich source of molecular information; however, neither a static genome nor the presence of a messenger RNA provides the most direct insight into the functional state of a microbial cell at any given time. Rather, it is the ensemble of proteins (i.e., proteome) that is the primary workhorse for most biological processes that are concurrent and coordinately active in a living cell. Currently, mass-spectrometry-based (MS) technologies provide unprecedented information into the composition of the proteome, shedding light on the numerous complex biological processes actively shaping observed phenotypes. Herein, we detail a protocol for the exploration of intracellular proteomes through the large-scale, unbiased identification of proteins and their relative abundances using liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS). In general, this protocol is applicable to both microbial and eukaryotic systems.

Abraham, Paul↗

The Curious Case of Pu + : Insight on 5f Orbital Activity from Inductively Coupled Plasma Tandem Mass Spectrometry (ICP-MS/MS) Reactions

A comprehensive understanding of when and how 5f orbitals participate in complex chemical bonding is important for a variety of applications. The actinides are unique in that they possess 5f orbitals and can access high oxidation states, which make them attractive for use in catalysis. Fundamental studies of actinide–ligand interactions offer a mechanism to examine the activation of the 5f orbitals so that the selectivity of 5f orbitals can be assessed. A previous study examined the reaction of Pu + + CO 2 and determined that the reaction efficiency is restricted by a barrier, namely, promotion from the Pu + ground-state configuration, 5f 6 7s, to a reactive-state configuration, 5f 5 6d 2 . Here, the present study illustrates the benefit of activation of Pu’s 5f orbitals when studying the reaction of Pu + + NO. In this reaction, PuO + forms in an exothermic, barrierless process. The 5f orbitals can and do participate in forming a linear intermediate, [N-Pu-O] + , and this drives the exothermic reaction. Understanding the conditions under which 5f orbitals are active in chemical bonding is the key to exploiting the actinides’ selective catalytic capabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry

The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product’s primary structure reliably and reproducibly. The major objective of the present study was to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up approaches, such as confirming protein integrity, sequencing variable domains, ruling out artefacts, and revealing modifications and their locations. A panel of three mAbs was selected and centrally provided to twenty laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). A variety of different MS instrument platforms and ion dissociation techniques were employed. Overall, the present study confirms that MD/TD MS strategies are valuable and readily available tools in laboratories worldwide. They provide complementary information to the bottom-up approach and can add unique information, which may be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. One of the limitations revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS, but the number of TD/MD MS experts is still very low.

59 BASIC BIOLOGICAL SCIENCES↗

193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI

MALDI imaging allows for the near-cellular profiling of proteoforms directly from microbial, plant, and mammalian samples. Despite detecting hundreds of proteoforms, identification of unknowns with only intact mass information remains a distinct challenge, even with high mass resolving power and mass accuracy. To this end, many supplementary methods have been used to create experimental databases for accurate mass matching, including bulk or spatially resolved bottom-up and/or top-down proteomics. Herein, we describe the application of 193 nm ultraviolet photodissociation (UVPD) for fragmentation of quadrupole isolated singly charged ubiquitin (m/z 8565) by MALDI-UVPD on a UHMR HF Orbitrap. This platform permitted the high-resolution accurate mass measurement of not just terminal fragments but also large internal fragments. Finally, the outlined workflow demonstrates the feasibility of top-down analyses of isolated MALDI protein ions and the potential toward more comprehensive characterization of proteoforms in MALDI imaging applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The balance of orbital overlap and orbital energy in the activation of methane by actinide cations: insights from inductively coupled plasma tandem mass spectrometry

The actinides present a unique challenge to chemical theory. The classical view of covalent bonding is driven by the extent of spatial overlap of valence orbitals. Modern theory has expanded assessments of covalency to include considerations of orbital energy degeneracy to assess orbital energy mixing between metal and ligand valence orbitals. Actinide–ligand (An–L) bonding has more recently been described as a balance between orbital overlap and orbital energy mixing, where 5f and L valence orbital overlap decreases while energy mixing between An 5f and L valence orbitals increases across the series. To test these existing views, we employed inductively coupled plasma tandem mass spectrometry to examine the kinetic energy dependences of reactions of actinide cations, Th + –Am + , with methane. Further, this is the first experimental report of the energy dependences of methane activation reactions involving the cations of Pa, Np, Pu, and Am and the first experimental determination of transuranic An + –D, An + –CD 2 , An + –CD 3 , and An + –CD bond dissociation energies. The correlation of the measured An + –CD 2 bond energies with E p (6d 2 ) indicates that An + 6d orbitals are the dominant contributors in the An + –CD 2 bonds. Close examination of the relative reactivities of An + offers additional support that the balance of classical and modern views of molecular bonding may lie between Np + and Pu + and that the increased reactivity of Th + –Np + may be attributed to the increased spatial extension of the 5f orbitals whereas covalent An + bond formation may be more driven by the decreasing energies of the 5f orbitals across the actinide series.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermodynamic insight into AnO 2 + bonding from ThH + /UH + reactions studied by inductively coupled plasma tandem mass spectrometry

The bonding mechanisms of actinides have been a focus of fundamental research over the past few decades. In the present study, reactions of the simplest actinide-containing species, ThH + and UH + , with O 2 and CO 2 are investigated by inductively coupled plasma tandem mass spectrometry. The reactions of ThH + and UH + with O 2 are efficient, and the reactions of ThH + and UH + with CO 2 display reduced reaction efficiencies. For both reactions involving CO 2 , ThO 2 + and UO 2 + are observed; however, there is a clear barrier to ThO 2 + formation whereas UO 2 + forms through an exothermic, barrierless process. The experimental observations and available thermodynamic information are used to predict the outcomes of reactions involving the later AnH + . The anticipated reaction enthalpies for Pa–Am display a clear correlation with the promotion energy of An + to a 6d 2 electronic configuration, E p (6d 2 ), although a shift in the slope of the correlation of reaction enthalpies and E p (6d 2 ) suggests that there is likely a change in bonding mechanism that starts with Np + . Similar shifts have also been noted in previous studies. Beginning with Np + , the 6d orbitals become less accessible than they are for the earlier An + as measured by E p (6d 2 ), and this accessibility of the 6d orbitals may drive actinide bonding.

5f orbitals↗

2023 American Society for Mass Spectrometry (ASMS) 71st Annual Conference on Mass Spectrometry and Allied Topics

Title (20 words): The investigation of the mechanism for the water splitting by holmium oxide nitrate complex in gas-phase Introduction (120 words): The studies for hydrogen from water splitting is important for clean energy economy as molecular hydrogen is a potential energy carrier. Therefore, understanding the fundamental chemistry of water splitting is essential. The water splitting activated by [Ho(NO3)4]- was previously studied. The suggested mechanism was to first eliminate •NO2 from [Ho(NO3)4]- to make [HoO(NO3)3]-. Then, water was added to form [HoO(NO3)3(H2O)]-, followed by eliminating the •OH to form [HoOH(NO3)3]-. However, we proposed a new mechanism with the formation of [Ho(NO3)3]- prior to the water addition. Once water is added to this intermediate to make [Ho(NO3)3(H2O)]-, the •H is eliminated to form [HoOH(NO3)3]-. Here we have used a labeled experiments with 18-O nitrates. The results to support the new mechanism are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

2023 American Society for Mass Spectrometry (ASMS) 71st Annual Conference on Mass Spectrometry and Allied Topics

Introduction (120 words max) Understanding metal-cluster chemistry occuring at solvent boundaries in the aqueous and organic phases has applications in environments from cellular processes to nuclear fuel reprocessing. Transport of metal ions at the boundaries from aqueous to organic phases involves forming a metal-ligand complex, and wherever the initial metal coordination environment is significantly different from the final one, the metal transitions through a series of transient species in passing from one phase to another. Here an investigation of the role of coordination in the chemistry of the transient species using gas-phase measurements that are free of solvent effects to better understand the binding of complexes of metals with triphenylphosphine chalcogenide ligands, examining metal-ligand homo- and hetero-dimers to better understand transient species. Methods (120 word max) Mass spectrometry and collision induced dissociation (CID) experiments were performed with a Bruker (Billerica, MA, USA) micrOTOF-Q II quadrupole time-of-flight mass spectrometer (QTOF) and Bruker amaZon speed ETD (ion trap). High resolution/high mass accuracy spectra were generated using the QTOF. External calibration was performed with Agilent (Santa Clara, CA, USA) ESI-L Low Concentration tuning mix. Both mass spectrometers were equipped with either the electrospray ionization source or nanospray sources. Metal samples were prepared between 40 – 60 uM of the metal-ligand complex in 25% water and 75% acetonitrile. Metal-ion clusters were isolated and subjected to collision induced dissociation. Density functional theory calculations were performed. Preliminary Data or Plenary Speakers Abstract (300 words max) Metal ion clusters with triphenylphosphine chalcogenide ligands were observed for group I metals with triphenylphosphine chalcogenide samples in the mass spectrum upon electrospray ionization. For each metal ligand complex of interest, the parent ion was isolated and collision induced dissociation fragmentation spectra were acquired. We observed clusters of group I metal with triphenylphosphine oxide, triphenyl phosphine sulfide, and triphenylphosphine selenide, with homodimers and heterodimer formation. In samples where the ligands were mixed, we observed mixed sodium ligand clusters at varying amounts. These mixed ligand clusters were fragmented. Metal clusters of mixed ligand dimers containing triphenylphosphine oxide showed preferential loss of the other ligand, either triphenylphosphine sulfide or triphenyl selenide. In samples with mixed triphenylphosphine sulfide and triphenylphosphine selenium ligands, sodium bound similarly between the ligands, and losses were more evenly split, showing loss ratio upon CID with losses of triphenylphosphine sulfide:triphenylphosphine selenide 43:57 ratio observed on CID. These results suggest that the oxide binds significantly more strongly than either the selenium or sulfur triphenylphosphine ligand, and the sulfur and selenium ligands are more evenly bound. Calculations were performed using density functional theory to calculate likely structures and bond energies between the group I metal and the ligands. Novel Aspect Novel analysis of sodium bound dimers with chalcogenide triphenylphosphine ligands were investigated using mass spectrometry and theoretical calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗