Exploiting Charge State Distribution To Probe Intramolecular Interactions in Gas-Phase Phosphopeptides and Enhance Proteomics Analyses

Charging of analytes is a prerequisite for performing mass spectrometry analysis. In proteomics, electrospray ionization is the dominant technique for this process. Although the observation of differences in the peptide charge state distribution (CSD) is well-known among experimentalists, its analytical value remains underexplored. To investigate the utility of this dimension, we analyzed several public data sets, comprising over 250,000 peptide CSD profiles from the human proteome. We found that the dimensions of the CSD demonstrate high reproducibility across multiple laboratories, mass analyzers, and extensive time intervals. The general observation was that the CSD enabled effective partitioning of the peptide property space, resulting in enhanced discrimination between sequence and constitutional peptide isomers. Next, by evaluating the CSD values of phosphorylated peptides, we were able to differentiate between phosphopeptides that indicate the formation of intramolecular structures in the gas phase and those that do not. The reproducibility of the CSD values (mean cosine similarity above 0.97 for most of the experiments) qualified CSD data suitable to train a deep-learning model capable of accurately predicting CSD values (mean cosine similarity - 0.98). When we applied the CSD dimension to MS1- and MS2-based proteomics experiments, we consistently observed around a 5% increase in protein and peptide identification rate. Even though the CSD dimension is not as effective a discriminator as the widely used retention time dimension, it still holds the potential for application in direct infusion proteomics.

Svx Peptidases of Phytopathogenic Pectolytic Bacteria: Structural, Catalytic and Phytoimmune Properties

Svx proteins are virulence factors secreted by phytopathogenic bacteria of the Pectobacterium genus into the host plant cell wall. Svx-encoding genes are present in almost all species of the soft rot Pectobacteriaceae (Pectobacterium and Dickeya genera). The Svx of P. atrosepticum (Pba) has been shown to be a gluzincin metallopeptidase that presumably targets plant extensins, proteins that contribute to plant cell wall rigidity and participate in cell signaling. However, the particular "output" of the Pba Svx action in terms of plant-pathogen interactions and plant immune responses remained unknown. The Svx proteins are largely unexplored in Dickeya species, even though some of them have genes encoding two Svx homologs. Therefore, our study aims to compare the structural and catalytic properties of the Svx proteins of Pba and D. solani (Dso) and to test the phytoimmune properties of these proteins. Two assayed Dso Svx proteins, similar to Pba Svx, were gluzincin metallopeptidases with conservative tertiary structures. The two domains of the Svx proteins form electronegative clefts where the active centers of the peptidase domains are located. All three assayed Svx proteins possessed phytoimmunosuppressory properties and induced ethylene-mediated plant susceptible responses that play a decisive role in Pba-caused disease.

RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum

The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.

A Switch from Latent to Typical Infection during Pectobacterium atrosepticum-Tobacco Interactions: Predicted and True Molecular Players

Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both fundamental science and disease management. No studies to date have compared, at the systemic molecular level, the physiological portraits of plants when different infection types (typical and latent) are developed. The only phytopathogenic bacterium for which latent infections were not only widely described but also at least fluently characterized at the molecular level is Pectobacterium atrosepticum (Pba). The present study aimed at the comparison of plant transcriptome responses during typical and latent infections caused by Pba in order to identify and then experimentally verify the key molecular players that act as switchers, turning peaceful plant-Pba coexistence into a typical infection. Based on RNA-Seq, we predicted plant cell wall-, secondary metabolism-, and phytohormone-related genes whose products contributed to the development of the disease or provided asymptomatic plant-Pba interactions. By treatment tests, we confirmed that a switch from latent to typical Pba-caused infection is determined by the plant susceptible responses mediated by the joint action of ethylene and jasmonates.

Potential of Negative-Ion-Mode Proteomics: An MS1-Only Approach

Current proteomics approaches rely almost exclusively on using the positive ionization mode, resulting in inefficient ionization of many acidic peptides. This study investigates protein identification efficiency in the negative ionization mode using the DirectMS1 method. DirectMS1 is an ultrafast data acquisition method based on accurate peptide mass measurements and predicted retention times. Our method achieves the highest rate of protein identification in the negative ion mode to date, identifying over 1000 proteins in a human cell line at a 1% false discovery rate. This is accomplished using a single-shot 10 min separation gradient, comparable to lengthy MS/MS-based analyses. Optimizing separation and experimental conditions was achieved by utilizing mobile buffers containing 2.5 mM imidazole and 3% isopropanol. The study emphasized the complementary nature of data obtained in positive and negative ion modes. Combining the results from all replicates in both polarities increased the number of identified proteins to 1774. Additionally, we analyzed the method's efficiency using different proteases for protein digestion. Among the four studied proteases (LysC, GluC, AspN, and trypsin), trypsin and LysC demonstrated the highest protein identification yield. This suggests that digestion procedures utilized in positive-mode proteomics can be effectively applied in the negative ion mode. Data are deposited to ProteomeXchange: PXD040583.

The Role of Intercellular Signaling in the Regulation of Bacterial Adaptive Proliferation

Bacterial adaptation is regulated at the population level with the involvement of intercellular communication (quorum sensing). When the population density is insufficient for adaptation under starvation, bacteria can adjust it to a quorum level through cell divisions at the expense of endogenous resources. This phenomenon has been described for the phytopathogenic bacterium Pectobacterium atrosepticum (Pba), and it is called, in our study, adaptive proliferation. An important attribute of adaptive proliferation is its timely termination, which is necessary to prevent the waste of endogenous resources when the required level of population density is achieved. However, metabolites that provide the termination of adaptive proliferation remained unidentified. We tested the hypothesis of whether quorum sensing-related autoinducers prime the termination of adaptive proliferation and assessed whether adaptive proliferation is a common phenomenon in the bacterial world. We showed that both known Pba quorum sensing-related autoinducers act synergistically and mutually compensatory to provide the timely termination of adaptive proliferation and formation of cross-protection. We also demonstrated that adaptive proliferation is implemented by bacteria of many genera and that bacteria with similar quorum sensing-related autoinducers have similar signaling backgrounds that prime the termination of adaptive proliferation, enabling the collaborative regulation of this adaptive program in multispecies communities.

First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale

Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.

GIP Affects Hepatic Fat and Brown Adipose Tissue Thermogenesis but Not White Adipose Tissue Transcriptome in Type 1 Diabetes

CONTEXT

Glucose-dependent insulinotropic polypeptide (GIP) has been proposed to exert insulin-independent effects on lipid and bone metabolism.

OBJECTIVE

We investigated the effects of a 6-day subcutaneous GIP infusion on circulating lipids, white adipose tissue (WAT), brown adipose tissue (BAT), hepatic fat content, inflammatory markers, respiratory exchange ratio (RER), and bone homeostasis in patients with type 1 diabetes.

METHODS

In a randomized, placebo-controlled, double-blind, crossover study, 20 men with type 1 diabetes underwent a 6-day continuous subcutaneous infusion with GIP (6 pmol/kg/min) and placebo (saline), with an interposed 7-day washout period.

RESULTS

During GIP infusion, participants (26 ± 8 years [mean ± SD]; BMI 23.8 ± 1.8 kg/m2; glycated hemoglobin A1c 51 ± 10 mmol/mol [6.8 ± 3.1%]) experienced transiently increased circulating concentrations of nonesterified fatty acid (NEFA) (P = 0.0005), decreased RER (P = 0.009), indication of increased fatty acid β-oxidation, and decreased levels of the bone resorption marker C-terminal telopeptide (P = 0.000072) compared with placebo. After 6 days of GIP infusion, hepatic fat content was increased by 12.6% (P = 0.007) and supraclavicular skin temperature, a surrogate indicator of BAT activity, was increased by 0.29 °C (P < 0.000001) compared with placebo infusion. WAT transcriptomic profile as well as circulating lipid species, proteome, markers of inflammation, and bone homeostasis were unaffected.

CONCLUSION

Six days of subcutaneous GIP infusion in men with type 1 diabetes transiently decreased bone resorption and increased NEFA and β-oxidation. Further, hepatic fat content, and supraclavicular skin temperature were increased without affecting WAT transcriptomics, the circulating proteome, lipids, or inflammatory markers.

Resistance to Snow Mold as a Target Trait for Rye Breeding

Winter rye is a versatile crop widely used for food and industry. Although rye is resistant to abiotic stressors and many phytopathogens, it is severely damaged by pink snow mold (SM)—a progressive disease caused by the psychrotolerant fungus Microdochium nivale under the snow cover or during prolonged periods of wet and cool conditions. Due to little use of the SM resistance sources in contemporary breeding, varieties with at least moderate resistance to SM are limited. Our study aimed to integrate field assessment under natural conditions and an artificially enriched infection background with laboratory techniques for testing rye accessions and selecting SM resistant sources for applied breeding programs and genetic research. We revealed valuable sources of SM resistance and split rye accessions, according to the level of the genetic divergence of the SM resistance phenotype. This allowed us to select the most distinct donors of the SM resistance, for their use as parental forms, to include novel variability sources in the breeding program for achieving high genetic variability, as well as enhanced and durable SM resistance, in progeny. The rye accessions analyzed here, and the suggested options for their use in breeding, are valuable tools for rye breeding.

DirectMS1Quant: Ultrafast Quantitative Proteomics with MS/MS-Free Mass Spectrometry

Recently, we presented the DirectMS1 method of ultrafast proteome-wide analysis based on minute-long LC gradients and MS1-only mass spectra acquisition. Currently, the method provides the depth of human cell proteome coverage of 2500 proteins at a 1% false discovery rate (FDR) when using 5 min LC gradients and 7.3 min runtime in total. While the standard MS/MS approaches provide 4000-5000 protein identifications within a couple of hours of instrumentation time, we advocate here that the higher number of identified proteins does not always translate into better quantitation quality of the proteome analysis. To further elaborate on this issue, we performed a one-on-one comparison of quantitation results obtained using DirectMS1 with three popular MS/MS-based quantitation methods: label-free (LFQ) and tandem mass tag quantitation (TMT), both based on data-dependent acquisition (DDA) and data-independent acquisition (DIA). For comparison, we performed a series of proteome-wide analyses of well-characterized (ground truth) and biologically relevant samples, including a mix of UPS1 proteins spiked at different concentrations into an Echerichia coli digest used as a background and a set of glioblastoma cell lines. MS1-only data was analyzed using a novel quantitation workflow called DirectMS1Quant developed in this work. The results obtained in this study demonstrated comparable quantitation efficiency of 5 min DirectMS1 with both TMT and DIA methods, yet the latter two utilized a 10-20-fold longer instrumentation time.

Phosphoproteomic studies of alamandine signaling in CHO-MrgD and human pancreatic carcinoma cells: An antiproliferative effect is unveiled

Alamandine is a heptapeptide from the renin-angiotensin system (RAS) with similar structure/function to angiotensin-(1-7) [ang-(1-7)], but they act via different receptors. It remains elusive whether alamandine is an antiproliferative agent like ang-(1-7). The goal of this study was to evaluate the potential antiproliferative activity of alamandine and the underlying cellular signaling. We evaluated alamandine effect in the tumoral cell lines Mia PaCa-2 and A549, and in the nontumoral cell lines HaCaT, CHO and CHO transfected with the alamandine receptor MrgD (CHO-MrgD). Alamandine was able to reduce the proliferation of the tumoral cell lines in a MrgD-dependent fashion. We did not observe any effect in the nontumoral cell lines tested. We also performed proteomics and phosphoproteomics to study the alamandine signaling in Mia PaCa-2 and CHO-MrgD. Data suggest that alamandine induces a shift from anaerobic to aerobic metabolism in the tumoral cells, induces a negative regulation of PI3K/AKT/mTOR pathway and activates the transcriptional factor FoxO1; events that could explain, at least partially, the observed antiproliferative effect of alamandine. This study provides for the first time a comprehensive investigation of the alamandine signaling in tumoral (Mia PaCa-2) and nontumoral (CHO-MrgD) cells, highlighting the antiproliferative activity of alamandine/MrgD and its possible antitumoral effect.

Proteomic analysis reveals stage-specific reprogramed metabolism for the primary breast cancer cell lines MGSO-3 and MACL-1

Breast cancer is the most prevalent cancer in women worldwide. Its molecular subtypes are based on the presence/absence of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2). MACL-1 and MGSO-3 are cell lines derived from primary tumor sites of patients diagnosed with luminal A subtype carcinoma (ER+ / PR+ / HER2-) and ductal carcinoma in situ (ER- / PR- / HER2+), respectively. However, these cell lines lost the expression of these markers over cell culturing, and both have triple-negative phenotypes (ER- / PR- / HER2-), which has the poorest prognosis. Here, we sought to study the proteome signature of MGSO-3 and MACL-1, comparing them with the epithelial cell line MCF-10A and the well-established metastatic-derived breast cancer cell line MDA-MB-231. Our results showed that proteins associated with the tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS) were upregulated in MGSO-3 and MACL-1 cells. These cell lines also showed upregulation of pro-apoptotic proteins when compared with MDA-MB-231. The molecular differences highlighted in this study may clarify the molecular basis behind cancer cells functioning and may reveal novel signatures across the breast cancer cell models. This article is protected by copyright. All rights reserved.

Characterization of Differentially Abundant Proteins Among Leishmania (Viannia) braziliensis Strains Isolated From Atypical or Typical Lesions

Leishmania (Viannia) braziliensis is the main etiological agent of cutaneous and mucocutaneous leishmaniasis in Latin America. Non-ulcerated atypical tegumentary leishmaniasis cases caused by L. braziliensis have been reported in several regions of the American continent, including the Xacriabá indigenous reserve in São João das Missões/Minas Gerais, Brazil. Parasites isolated from these atypical clinical lesions are resistant to antimony-based therapeutics. In the present study, proteins displaying differential abundance in two strains of L. braziliensis isolated from patients with atypical lesions compared with four strains isolated from patients with typical lesions were identified using a quantitative proteomics approach based on tandem mass tag labeling (TMT) and mass spectrometry. A total of 532 (P<0.05) differentially abundant proteins were identified (298 upregulated and 234 downregulated) in strains from atypical lesions compared to strains from typical lesions. Prominent positively regulated proteins in atypical strains included those that may confer greater survival inside macrophages, proteins related to antimony resistance, and proteins associated with higher peroxidase activity. Additionally, we identified proteins showing potential as new drug and vaccine targets. Our findings contribute to the characterization of these intriguing L. braziliensis strains and provide a novel perspective on Atypical Cutaneous Leishmaniasis (ACL) cases that have been associated with therapeutic failures.

DFT Quantum-Chemical Calculation of Thermodynamic Parameters and DSC Measurement of Thermostability of Novel Benzofuroxan Derivatives Containing Triazidoisobutyl Fragments

New derivatives of benzofuroxan containing triazidoisobutyl fragments, opening the way for the creation of highly effective compositions with an increased value of energy characteristics, were synthesized for the first time. Such compounds are also an excellent platform for further modification and for the preparation of new biologically-active compounds containing tetrazole and triazole fragments. Calculations of heats of formation performed with the DFT (density functional theory) method showed that the studied compounds are high-energetic density ones, the enthalpies of formation of which are comparable to the enthalpies of formation of similar benzofuroxan derivatives and exceeds experimental enthalpy of formation of CL-14 (5,7-diamino-4,6-dinitrobenzofuroxan). The analysis of DSC indicates a sufficiently high thermal stability of the synthesized azidobenzofuroxans, which are acceptable for their use as components in the creation of highly efficient compositions with an increased value of energy characteristics.

Biological and Molecular Effects of Trypanosoma cruzi Residence in a LAMP-Deficient Intracellular Environment

Trypanosoma cruzi invades non-professional phagocytic cells by subverting their membrane repair process, which is dependent on membrane injury and cell signaling, intracellular calcium increase, and lysosome recruitment. Cells lacking lysosome-associated membrane proteins 1 and 2 (LAMP1 and LAMP2) are less permissive to parasite invasion but more prone to parasite intracellular multiplication. Several passages through a different intracellular environment can significantly change T. cruzi's gene expression profile. Here, we evaluated whether one single passage through LAMP-deficient (KO) or wild-type (WT) fibroblasts, thus different intracellular environments, could influence T. cruzi Y strain trypomastigotes' ability to invade L6 myoblasts and WT fibroblasts host cells. Parasites released from LAMP2 KO cells (TcY-L2-/-) showed higher invasion, calcium signaling, and membrane injury rates, for the assays in L6 myoblasts, when compared to those released from WT (TcY-WT) or LAMP1/2 KO cells (TcY-L1/2-/-). On the other hand, TcY-L1/2-/- showed higher invasion, calcium signaling, and cell membrane injury rates, for the assays in WT fibroblasts, compared to TcY-WT and TcY-L1/2-/-. Albeit TcY-WT presented an intermediary invasion and calcium signaling rates, compared to the others, in WT fibroblasts, they induced lower levels of injury, which reinforces that signals mediated by surface membrane protein interactions also have a significant contribution to trigger host cell calcium signals. These results clearly show that parasites released from WT or LAMP KO cells are distinct from each other. Additionally, these parasites' ability to invade the cell may be distinct depending on which cell type they interact with. Since these alterations most likely would reflect differences among parasite surface molecules, we also evaluated their proteome. We identified few protein complexes, membrane, and secreted proteins regulated in our dataset. Among those are some members of MASP, mucins, trans-sialidases, and gp63 proteins family, which are known to play an important role during parasite infection and could correlate to TcY-WT, TcY-L1/2-/-, and TcY-L2-/- biological behavior.

Alterations in the Transcriptome of Rye Plants following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the M. nivale-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to M. nivale. Phytohormone abscisic acid was shown to promote plant tolerance to M. nivale. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in M. nivale-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-M. nivale interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.

The Role of Pectobacterium atrosepticum Exopolysaccharides in Plant-Pathogen Interactions

The phytopathogenic bacterium Pectobacterium atrosepticum (Pba), one of the members of the soft rot Pectobacteriaceae, forms biofilm-like structures known as bacterial emboli when colonizing the primary xylem vessels of the host plants. The initial extracellular matrix of the bacterial emboli is composed of the host plant's pectic polysaccharides, which are gradually substituted by the Pba-produced exopolysaccharides (Pba EPS) as the bacterial emboli "mature". No information about the properties of Pba EPS and their possible roles in Pba-plant interactions has so far been obtained. We have shown that Pba EPS possess physical properties that can promote the maintenance of the structural integrity of bacterial emboli. These polymers increase the viscosity of liquids and form large supramolecular aggregates. The formation of Pba EPS aggregates is provided (at least partly) by the acetyl groups of the Pba EPS molecules. Besides, Pba EPS scavenge reactive oxygen species (ROS), the accumulation of which is known to be associated with the formation of bacterial emboli. In addition, Pba EPS act as suppressors of the quantitative immunity of plants, repressing PAMP-induced reactions; this property is partly lost in the deacetylated form of Pba EPS. Overall, our study shows that Pba EPS play structural, protective, and immunosuppressive roles during Pba-plant interactions and thus should be considered as virulence factors of these bacteria.

Stringent Response in Bacteria and Plants with Infection

Stringent response (SR), a primary stress reaction in bacteria and plant chloroplasts, is a molecular switch that provides operational stress-induced reprogramming of transcription under conditions of abiotic and biotic stress. Because the infection is a stressful situation for both partners (the host plant and the pathogen), we analyzed the expression of bacterial and plastid SR-related genes during plant-microbial interaction. In the phytopathogenic bacterium Pectobacterium atrosepticum, SpoT-dependent SR was induced after contact with potato or tobacco plants. In plants, two different scenarios of molecular events developed under bacterial infection. Plastid SR was not induced in the host plant potato Solanum tuberosum, which co-evolved with the pathogen for a long time. In this case, the salicylic acid defense pathway was activated and plants were more resistant to bacterial infection. SR was activated in the tobacco Nicotiana tabacum (experimental host) along with activation of jasmonic acid-related genes, resulting in plant death. These results are important to more fully understand the evolutionary interactions between plants and symbionts/pathogens.

The Knockout of Enterobactin-Related Gene in Pectobacterium atrosepticum Results in Reduced Stress Resistance and Virulence towards the Primed Plants

Siderophores produced by microorganisms to scavenge iron from the environment have been shown to contribute to virulence and/or stress resistance of some plant pathogenic bacteria. Phytopathogenic bacteria of Pectobacterium genus possess genes for the synthesis of siderophore enterobactin, which role in plant-pathogen interactions has not been elucidated. In the present study we characterized the phenotype of the mutant strain of Pba deficient for the enterobactin-biosynthetic gene entA. We showed that enterobactin may be considered as a conditionally beneficial virulence factor of Pba. The entA knockout did not reduce Pba virulence on non-primed plants; however, salicylic acid-primed plants were more resistant to ΔentA mutant than to the wild type Pba. The reduced virulence of ΔentA mutant towards the primed plants is likely explained by its compromised resistance to oxidative stress.

Plant susceptible responses: the underestimated side of plant-pathogen interactions

Plant susceptibility to pathogens is usually considered from the perspective of the loss of resistance. However, susceptibility cannot be equated with plant passivity since active host cooperation may be required for the pathogen to propagate and cause disease. This cooperation consists of the induction of reactions called susceptible responses that transform a plant from an autonomous biological unit into a component of a pathosystem. Induced susceptibility is scarcely discussed in the literature (at least compared to induced resistance) although this phenomenon has a fundamental impact on plant-pathogen interactions and disease progression. This review aims to summarize current knowledge on plant susceptible responses and their regulation. We highlight two main categories of susceptible responses according to their consequences and indicate the relevance of susceptible response-related studies to agricultural practice. We hope that this review will generate interest in this underestimated aspect of plant-pathogen interactions.

The Modification of Plant Cell Wall Polysaccharides in Potato Plants during Pectobacterium atrosepticum-Caused Infection

Our study is the first to consider the changes in the entire set of matrix plant cell wall (PCW) polysaccharides in the course of a plant infectious disease. We compared the molecular weight distribution, monosaccharide content, and the epitope distribution of pectic compounds and cross-linking glycans in non-infected potato plants and plants infected with Pectobacterium atrosepticum at the initial and advanced stages of plant colonization by the pathogen. To predict the gene products involved in the modification of the PCW polysaccharide skeleton during the infection, the expression profiles of potato and P. atrosepticum PCW-related genes were analyzed by RNA-Seq along with phylogenetic analysis. The assemblage of P. atrosepticum biofilm-like structures—the bacterial emboli—and the accumulation of specific fragments of pectic compounds that prime the formation of these structures were demonstrated within potato plants (a natural host of P. atrosepticum). Collenchyma was shown to be the most “vulnerable” tissue to P. atrosepticum among the potato stem tissues. The infection caused by the representative of the Soft Rot Pectobacteriaceae was shown to affect not only pectic compounds but also cross-linking glycans; the content of the latter was increased in the infected plants compared to the non-infected ones.

Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

Proteome-wide analyses rely on tandem mass spectrometry and the extensive separation of proteolytic mixtures. This imposes considerable instrumental time consumption, which is one of the main obstacles in the broader acceptance of proteomics in biomedical and clinical research. Recently, we presented a fast proteomic method termed DirectMS1 based on ultrashort LC gradients as well as MS1-only mass spectra acquisition and data processing. The method allows significant reduction of the proteome-wide analysis time to a few minutes at the depth of quantitative proteome coverage of 1000 proteins at 1% false discovery rate (FDR). In this work, to further increase the capabilities of the DirectMS1 method, we explored the opportunities presented by the recent progress in the machine-learning area and applied the LightGBM decision tree boosting algorithm to the scoring of peptide feature matches when processing MS1 spectra. Furthermore, we integrated the peptide feature identification algorithm of DirectMS1 with the recently introduced peptide retention time prediction utility, DeepLC. Additional approaches to improve the performance of the DirectMS1 method are discussed and demonstrated, such as using FAIMS for gas-phase ion separation. As a result of all improvements to DirectMS1, we succeeded in identifying more than 2000 proteins at 1% FDR from the HeLa cell line in a 5 min gradient LC-FAIMS/MS1 analysis. The data sets generated and analyzed during the current study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD023977.

Biosaur: An open-source Python software for liquid chromatography-mass spectrometry peptide feature detection with ion mobility support

RATIONALE

One of the important steps in initial data processing of peptide mass spectra is the detection of peptide features in full-range mass spectra. Ion mobility offers advantages over previous methods performing this detection by providing an additional structure-specific separation dimension. However, there is a lack of open-source software that utilizes these advantages and detects peptide features in mass spectra acquired along with ion mobility data using new instruments such as timsTOF and/or FAIMS-Orbitrap.

METHODS

Recently, a utility called Dinosaur was presented, which provides an efficient way for feature detection in peptide ion mass spectra. In this work we extended its functionality by developing Biosaur software to fully employ the additional information provided by ion mobility data. Biosaur was developed using the Python 3.8 programming language.

RESULTS

Biosaur supports the processing of data acquired using mass spectrometers with ion mobility capabilities, specifically timsTOF and FAIMS. In addition, it processes mass spectra obtained in negative ion mode and reports cosine correlation table for peptide features which is useful for differentiation between in-source fragments and semi-tryptic peptides.

CONCLUSIONS

Biosaur is a utility for detecting peptide features in liquid chromatography-mass spectra with ion mobility and negative ion supports. The software is distributed with an open-source APACHE 2.0 license and is freely available on Github: https://github.com/abdrakhimov1/Biosaur.

Rye Snow Mold-Associated Microdochium nivale Strains Inhabiting a Common Area: Variability in Genetics, Morphotype, Extracellular Enzymatic Activities, and Virulence

Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant snow mold resistance are not elucidated. Our study aimed to identify comprehensive characteristics of a local community of snow mold-causing Microdochium species colonizing a particular crop culture. By using the next-generation sequencing (NGS) technique, we characterized fungal and bacterial communities of pink snow mold-affected winter rye (Secale cereale) plants within a given geographical location shortly after snowmelt. Twenty-one strains of M. nivale were isolated, classified on the basis of internal transcribed spacer 2 (ITS2) region, and characterized by morphology, synthesis of extracellular enzymes, and virulence. Several types of extracellular enzymatic activities, the level of which had no correlations with the degree of virulence, were revealed for Microdochium species for the first time. Our study shows that genetically and phenotypically diverse M. nivale strains simultaneously colonize winter rye plants within a common area, and each strain is likely to utilize its own, unique strategy to cause the disease using "a personal" pattern of extracellular enzymes.

Design of Novel 4-Aminobenzofuroxans and Evaluation of Their Antimicrobial and Anticancer Activity

A series of novel 4-aminobenzofuroxan derivatives containing aromatic/aliphatic amines fragments was achieved via aromatic nucleophilic substitution reaction of 4,6-dichloro-5-nitrobenzofuroxan. The quantum chemistry calculations were performed to identify the factors affecting the regioselectivity of the reaction. The formation of 4-substituted isomer is favored both by its greater stability and the lower activation barrier. Antimicrobial activity of the obtained compounds has been evaluated and some of them were found to suppress effectively bacterial biofilm growth. Fungistatic activity of 4-aminobenzofuroxans were tested on two genetically distinct isolates of M. nivale. The effect of some benzofuroxan derivatives is likely to be more universal against different varieties of M. nivale compared with benzimidazole and carbendazim. Additionally, their anti-cancer activity in vitro has been tested. 4-aminofuroxans possessing aniline moiety showed a high selectivity towards MCF-7 and M-HeLa tumor cell lines. Moreover, they exhibit a significantly lower toxicity towards normal liver cells compared to Doxorubicin and Tamoxifen. Thus, benzofuroxans containing aromatic amines fragments in their structure are promising candidates for further development both as anti-cancer and anti-microbial agents.

PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety

Protein phosphorylation is a post-translational modification that is essential to cellular signaling, cellular function, and associated disease progression. Bottom-up proteomics based on enzymatic digestion is the most widely used approach for identifying and quantifying phosphoproteins in complex biological samples. Researchers have largely optimized the experimental conditions for trypsin digestion, and it is now a routine procedure. However, trypsin digestion is impaired by the presence of phosphorylated residues in the protein sequence. This impairment arises from the fact that there are commonly salt bridges between a negatively charged phosphate group and the side chain of protonated arginine or lysine. On average, 55% of all phosphopeptides have their phosphosites located less than three amino acid residues from a cleavage site. Salt bridges reduce the cleavage accessibility for trypsin by masking the basic site chain groups of arginine and lysine. Thus, there are frequent missed cleavages in the vicinity of phosphorylation sites, thereby lessening both the depth of proteome coverage and the quantification accuracy of phosphoproteomics. In this work, we propose a method termed PhosphoShield to mitigate salt bridge formation by adding a digallium complex that exhibits a high binding affinity to the phosphate group. We tested our method using quantitative mass spectrometry analysis of the phosphoproteome of human liver cancer cells (HepG2). PhosphoShield enhances the cleavage frequency of at least 17% of tryptic phosphopeptides having cleavage sites close to the phosphate group.

HUMOS: How to Understand My Orbitrap Spectrum?-An Interactive Web-Based Tool to Teach the Basics of Mass-Spectrometry-Based Proteomics

The Orbitrap mass analyzer can provide high mass accuracy and throughput, which has significantly improved proteome research and made this type of instrumentation one of the most frequently applied in proteomics. The efficient use of Orbitrap mass spectrometers requires training. Students in the field of proteomics can benefit from a deeper understanding of the Orbitrap technology to comprehend mass spectral interpretation, troubleshooting, and judgment of experimental settings. Unfortunately, the cost of high-end mass spectrometers limits the implementation of this type of equipment in educational laboratories. Guided by these concerns, we developed an eLearning web application called HUMOS aimed to help teach Orbitrap mass spectrometry. Although a typical proteomics experiment includes the use of several different technologies, such as liquid chromatography, mass spectrometry, and bioinformatics, the learning objectives of HUMOS are focused on mass spectrometry. HUMOS models a mass spectrum of a peptide mixture, allowing us to investigate the influence of mass spectral acquisition parameters. By changing the parameters and observing the differences, students can learn more about the mass spectral resolution, duty cycle, throughput of the analysis, ion accumulation, and spectral dynamic range and get familiar with advanced spectral acquisition methods, such as BoxCar. HUMOS is an open-source software published under the Apache license; the live installation is available at http://humos.bmb.sdu.dk.

Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular "players" in plant-Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by "missed" genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease's development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.

Moving Pieces in a Cellular Puzzle: A Cryptic Peptide from the Scorpion Toxin Ts14 Activates AKT and ERK Signaling and Decreases Cardiac Myocyte Contractility via Dephosphorylation of Phospholamban

Cryptic peptides (cryptides) are biologically active peptides formed after proteolysis of native precursors present in animal venoms, for example. Proteolysis is an overlooked post-translational modification that increases venom complexity. The tripeptide KPP (Lys-Pro-Pro) is a peptide encrypted in the C-terminus of Ts14-a 25-mer peptide from the venom of the Tityus serrulatus scorpion that has a positive impact on the cardiovascular system, inducing vasodilation and reducing arterial blood pressure of hypertensive rats among other beneficial effects. A previous study reported that KPP and its native peptide Ts14 act via activation of the bradykinin receptor B2 (B2R). However, the cellular events underlying the activation of B2R by KPP are unknown. To study the cell signaling triggered by the Ts14 cryptide KPP, we incubated cardiac myocytes isolated from C57BL/6 mice with KPP (10^-7 mol·L^-1) for 0, 5, or 30 min and explored the proteome and phosphoproteome. Our results showed that KPP regulated cardiomyocyte proteins associated with, but not limited to, apoptosis, muscle contraction, protein turnover, and the respiratory chain. We also reported that KPP led to AKT phosphorylation, activating AKT and its downstream target nitric oxide synthase. We also observed that KPP led to dephosphorylation of phospholamban (PLN) at its activation sites (S16 and T17), leading to reduced contractility of treated cardiomyocytes. Some cellular targets reported here for KPP (e.g., AKT, PLN, and ERK) have already been reported to protect the cardiac tissue from hypoxia-induced injury. Hence, this study suggests potential beneficial effects of this scorpion cryptide that needs to be further investigated, for example, as a drug lead for cardiac infarction.

Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution

Nanoparticles (NPs) in contact with protein-containing media such as biological fluids rapidly acquire a surface layer of proteins, known as the protein corona. The protein composition and structural properties of the protein corona are crucial for NP interactions with living cells. Although much has been learned about the protein corona phenomenon, further elucidation could benefit from extensive quantitative proteomics analysis. Herein we report a comprehensive quantitative characterization (>350 proteins) of the corona that formed on 60 nm silver NPs via interaction with human blood plasma, as a function of pH and temperature. By varying the pH and temperature one can access different conformational spaces and charge localizations of the plasma proteins, which in turn provide knowledge pertinent to how the proteome corresponds to binding affinity. Thirty-eight percent of the quantified proteins bind at all temperatures, 47% at all pH values, and of these most persistent proteins, approximately 60% do not significantly change in abundance within the protein corona. Evaluation of 544 protein properties (present in the Kyoto databank) suggests that binding of these proteins to NPs is determined by the extent of hydrophobicity, β-sheet propensity, α-helical structure (and turns), and amino acid composition. Protein binding is promoted by a larger amount of β-sheets, higher hydrophobicity, and a smaller amount of α-helices. Our work enhances researchers' knowledge of a long-standing, vexing aspect of the nano-bio interface.

Transcriptome Analysis of Intrusively Growing Flax Fibers Isolated by Laser Microdissection

The intrusive growth, a type of plant cell elongation occurring in the depths of plant tissues, is characterized by the invasion of a growing cell between its neighbours due to a higher rate of elongation. In order to reveal the largely unknown molecular mechanisms of intrusive growth, we isolated primary flax phloem fibers specifically at the stage of intrusive growth by laser microdissection. The comparison of the RNA-Seq data from several flax stem parts enabled the characterization of those processes occurring specifically during the fiber intrusive elongation. The revealed molecular players are summarized as those involved in the supply of assimilates and support of turgor pressure, cell wall enlargement and modification, regulation by transcription factors and hormones, and responses to abiotic stress factors. The data obtained in this study provide a solid basis for developing approaches to manipulate fiber intrusive elongation, which is of importance both for plant biology and the yield of fiber crops.

Approaching cellular resolution and reliable identification in mass spectrometry imaging of tryptic peptides

On-tissue digestion has become the preferred method to identify proteins in mass spectrometry (MS) imaging. In this study, we report advances in data acquisition and protein identification for MS imaging after on-tissue digestion. Tryptic peptides in a coronal mouse brain section were measured at 50 μm pixel size and revealed detailed histological structures, e.g., the ependyma (consisting of one to two cell layers), which was confirmed by H&E staining. This demonstrates that MS imaging of tryptic peptides at or close to cellular resolution is within reach. We also describe a detailed identification workflow which resulted in the identification of 99 proteins (with 435 corresponding peptides), based on comparison with LC-MS/MS data and in silico digest. These results were obtained with stringent parameters, including high mass accuracy in imaging mode (RSME < 3 ppm) and at least two unique peptides per protein showing consistent spatial distribution. We identified almost 50% of proteins with at least four corresponding peptides. As there is no agreed approach for identification of proteins after on-tissue digestion yet, we discuss our workflow in detail and make the corresponding mass spectral data available as “open data” via ProteomeXchange (identifier PXD003172). With this, we would like to contribute to a more effective discussion and the development of new approaches for tryptic peptide identification in MS imaging. From an experimental point of view, we demonstrate the improvement due to the combination of high spatial resolution and high mass resolution/mass accuracy on a measurement at 25 μm pixel size in mouse cerebellum tissue. A whole body section of a mouse pub imaged at 50 μm pixel size (40 GB, 230,000 spectra) demonstrates the stability of our protocol. For this data set, we developed a workflow that is based on conversion to the common data format imzML and sequential application of freely available software tools. In combination, the presented results for spatial resolution, protein identification, and data processing constitute significant improvements for the field of on-tissue digestion.

Graphical abstract

Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism

Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode many Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor We identified and quantified 3461 proteins corresponding to 44.3% of the S. coelicolor proteome across three developmental stages: vegetative hypha (first mycelium); secondary metabolite producing hyphae (second mycelium); and sporulating hyphae. A total of 1350 proteins exhibited more than 2-fold expression changes during the bacterial differentiation process. These proteins include 136 regulators (transcriptional regulators, transducers, Ser/Thr/Tyr kinases, signaling proteins), as well as 542 putative proteins with no clear homology to known proteins which are likely to play a role in differentiation and secondary metabolism. Phosphoproteomics revealed 85 unique protein phosphorylation sites, 58 of them differentially phosphorylated during differentiation. Computational analysis suggested that these regulated protein phosphorylation events are implicated in important cellular processes, including cell division, differentiation, regulation of secondary metabolism, transcription, protein synthesis, protein folding and stress responses. We discovered a novel regulated phosphorylation site in the key bacterial cell division protein FtsZ (pSer319) that modulates sporulation and regulates actinorhodin antibiotic production. We conclude that manipulation of distinct protein phosphorylation events may improve secondary metabolite production in industrial streptomycetes, including the activation of cryptic pathways during the screening for new secondary metabolites from streptomycetes.

Co-exposure to silver nanoparticles and cadmium induce metabolic adaptation in HepG2 cells

Although multiple studies have reported the toxicological effects and underlying mechanisms of toxicity of silver nanoparticles (AgNP) in a variety of organisms, the interactions of AgNP with environmental contaminants such as cadmium are poorly understood. We used biochemical assays and mass spectrometry-based proteomics to assess the cellular and molecular effects induced by a co-exposure of HepG2 cells to AgNP and cadmium. Cell viability and energy homeostasis were slightly affected after a 4-h exposure to AgNP, cadmium, or a combination of the two; these endpoints were substantially altered after a 24-h co-exposure to AgNP and cadmium, while exposure to one of the two contaminants led only to minor changes. Proteomics analysis followed the same trend: while a 4-h exposure induced minor protein deregulation, a 24-h exposure to a combination of AgNP and cadmium deregulated 43% of the proteome. The toxicity induced by a combined exposure to AgNP and cadmium involved (1) inactivation of Nrf2, resulting in downregulation of antioxidant defense and proteasome-related proteins, (2) metabolic adaptation and ADP/ATP imbalance, and (3) increased protein synthesis possibly to reestablish homeostasis. The adaptation strategy was not sufficient to restore ADP/ATP homeostasis and to avoid cell death.

Proceedings of the EuBIC developer's meeting 2018

The inaugural European Bioinformatics Community (EuBIC) developer's meeting was held from January 9th to January 12th 2018 in Ghent, Belgium. While the meeting kicked off with an interactive keynote session featuring four internationally renowned experts in the field of computational proteomics, its primary focus were the hands-on hackathon sessions which featured six community-proposed projects revolving around three major topics: Here, we present an overview of the scientific program of the EuBIC developer's meeting and provide a starting point for follow-up on the covered projects.

SuperQuant-assisted comparative proteome analysis of glioblastoma subpopulations allows for identification of potential novel therapeutic targets and cell markers

Glioblastoma (GBM) is a highly aggressive brain cancer with poor prognosis and low survival rate. Invasive cancer stem-like cells (CSCs) are responsible for tumor recurrence because they escape current treatments. Our main goal was to study the proteome of three GBM subpopulations to identify key molecules behind GBM cell phenotypes and potential cell markers for migrating cells. We used SuperQuant-an enhanced quantitative proteome approach-to increase proteome coverage. We found 148 proteins differentially regulated in migrating CSCs and 199 proteins differentially regulated in differentiated cells. We used Ingenuity Pathway Analysis (IPA) to predict upstream regulators, downstream effects and canonical pathways associated with regulated proteins. IPA analysis predicted activation of integrin-linked kinase (ILK) signaling, actin cytoskeleton signaling, and lysine demethylase 5B (KDM5B) in CSC migration. Moreover, our data suggested that microRNA-122 (miR-122) is a potential upstream regulator of GBM phenotypes as miR-122 activation was predicted for differentiated cells while its inhibition was predicted for migrating CSCs. Finally, we validated transferrin (TF) and procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (PLOD2) as potential markers for migrating cells.

Comparative proteomics as a tool for identifying specific alterations within interferon response pathways in human glioblastoma multiforme cells

An acquisition of increased sensitivity of cancer cells to viruses is a common outcome of malignant progression that justifies the development of oncolytic viruses as anticancer therapeutics. Studying molecular changes that underlie the sensitivity to viruses would help to identify cases where oncolytic virus therapy would be most effective. We quantified changes in protein abundances in two glioblastoma multiforme (GBM) cell lines that differ in the ability to induce resistance to vesicular stomatitis virus (VSV) infection in response to type I interferon (IFN) treatment. In IFN-treated samples we observed an up-regulation of protein products of some IFN-regulated genes (IRGs). In total, the proteome analysis revealed up to 20% more proteins encoded by IRGs in the glioblastoma cell line, which develops resistance to VSV infection after pre-treatment with IFN. In both cell lines protein-protein interaction and signaling pathway analyses have revealed a significant stimulation of processes related to type I IFN signaling and defense responses to viruses. However, we observed a deficiency in STAT2 protein in the VSV-sensitive cell line that suggests a de-regulation of the JAK/STAT/IRF9 signaling. The study has shown that the up-regulation of IRG proteins induced by the IFNα treatment of GBM cells can be detected at the proteome level. Similar analyses could be applied for revealing functional alterations within the antiviral mechanisms in glioblastoma samples, accompanying by acquisition of sensitivity to oncolytic viruses. The approach can be useful for discovering the biomarkers that predict a potential sensitivity of individual glioblastoma tumors to oncolytic virus therapy.

Brown Mycelial Mat as an Essential Morphological Structure of the Shiitake Medicinal Mushroom Lentinus edodes (Agaricomycetes)

We show here, to our knowledge for the first time, that the brown mycelial mat of the xylotrophic shiitake medicinal mushroom, Lentinus edodes, not only performs a protective function owing to significant changes in the ultrastructure (thickening of the cell wall, increased density, and pigmentation of the fungal hyphae) but also is a metabolically active stage in the development of the mushroom. The cells of this morphological structure exhibit repeated activation of expression of the genes lcc4, tir, exp1, chi, and exg1, coding for laccase, tyrosinase, a specific transcription factor, chitinase, and glucanase, which are required for fungal growth and morphogenesis. This study revealed the maximum activity of functionally important proteins with phenol oxidase and lectin activities, and the emergence of additional laccases, tyrosinases, and lectins, which are typical of only this stage of morphogenesis and have a regulatory function in the development and formation of fruiting bodies.

Polyphenol oxidase from Pectobacterium atrosepticum: identification and cloning of gene and characteristics of the enzyme

In the present study, we attempted to elucidate if the harmful phytopathogenic bacteria of Pectobacterium genus (P. atrosepticum) possess the enzymes for oxidation of phenolic compounds. Polyphenol oxidase (laccase) activity was revealed in P. atrosepticum cell lysates. Using bioinformatic analysis, an ORF encoding a putative copper-containing polyphenol oxidase of 241 amino acids with a predicted molecular mass of 25.9 kDa was found. This protein (named Pal1) shares significant level of identity with laccases of a new type described for several bacterial species. Cloning and expression of the pal1 gene and the analysis of corresponding recombinant protein confirmed that Pal1 possessed laccase activity. The recombinant Pal1 protein was characterized in terms of substrate specificity, kinetic parameters, pH and temperature optimum, sensitivity to inhibitors and metal content. Pal1 demonstrated alkali- and thermo-tolerance. The kinetic parameters K_m and kcat for 2,6-dimethoxyphenol were 0.353 ± 0.062 mM and 98.79 ± 4.9 s^-1 , respectively. The protein displayed high tolerance to sodium azide, sodium fluoride, NaCl, SDS and cinnamic acid. The transcript level of the pal1 gene in P. atrosepticum was shown to be induced by plant-derived phenolic compound (ferulic acid) and copper sulfate.

Characterization of Complete Histone Tail Proteoforms Using Differential Ion Mobility Spectrometry

Histone proteins are subject to dynamic post-translational modifications (PTMs) that cooperatively modulate the chromatin structure and function. Nearly all functional PTMs are found on the N-terminal histone domains (tails) of ∼50 residues protruding from the nucleosome core. Using high-definition differential ion mobility spectrometry (FAIMS) with electron transfer dissociation, we demonstrate rapid baseline gas-phase separation and identification of tails involving monomethylation, trimethylation, acetylation, or phosphorylation in biologically relevant positions. These are by far the largest variant peptides resolved by any method, some with PTM contributing just 0.25% to the mass. This opens the door to similar separations for intact proteins and in top-down proteomics.

Transcriptome portrait of cellulose-enriched flax fibres at advanced stage of specialization

Functional specialization of cells is among the most fundamental processes of higher organism ontogenesis. The major obstacle to studying this phenomenon in plants is the difficulty of isolating certain types of cells at defined stages of in planta development for in-depth analysis. A rare opportunity is given by the developed model system of flax (Linum usitatissimum L.) phloem fibres that can be purified from the surrounding tissues at the stage of the tertiary cell wall deposition. The performed comparison of the whole transcriptome profile in isolated fibres and other portions of the flax stem, together with fibre metabolism characterization, helped to elucidate the general picture of the advanced stage of plant cell specialization and to reveal novel participants potentially involved in fibre metabolism regulation and cell wall formation. Down-regulation of all genes encoding proteins involved in xylan and lignin synthesis and up-regulation of genes for the specific set of transcription factors transcribed during tertiary cell wall formation were revealed. The increased abundance of transcripts for several glycosyltransferases indicated the enzymes that may be involved in synthesis of fibre-specific version of rhamnogalacturonan I.

Alteration in the ultrastructural morphology of mycelial hyphae and the dynamics of transcriptional activity of lytic enzyme genes during basidiomycete morphogenesis

The morphogenesis of macromycetes is a complex multilevel process resulting in a set of molecular-genetic, physiological-biochemical, and morphological-ultrastructural changes in the cells. When the xylotrophic basidiomycetes Lentinus edodes, Grifola frondosa, and Ganoderma lucidum were grown on wood waste as the substrate, the ultrastructural morphology of the mycelial hyphal cell walls differed considerably between mycelium and morphostructures. As the macromycetes passed from vegetative to generative development, the expression of the tyr1, tyr2, chi1, chi2, exg1, exg2, and exg3 genes was activated. These genes encode enzymes such as tyrosinase, chitinase, and glucanase, which play essential roles in cell wall growth and morphogenesis.

Global Gene Expression Analysis of Cross-Protected Phenotype of Pectobacterium atrosepticum

The ability to adapt to adverse conditions permits many bacterial species to be virtually ubiquitous and survive in a variety of ecological niches. This ability is of particular importance for many plant pathogenic bacteria that should be able to exist, except for their host plants, in different environments e.g. soil, water, insect-vectors etc. Under some of these conditions, bacteria encounter absence of nutrients and persist, acquiring new properties related to resistance to a variety of stress factors (cross-protection). Although many studies describe the phenomenon of cross-protection and several regulatory components that induce the formation of resistant cells were elucidated, the global comparison of the physiology of cross-protected phenotype and growing cells has not been performed. In our study, we took advantage of RNA-Seq technology to gain better insights into the physiology of cross-protected cells on the example of a harmful phytopathogen, Pectobacterium atrosepticum (Pba) that causes crop losses all over the world. The success of this bacterium in plant colonization is related to both its virulence potential and ability to persist effectively under various stress conditions (including nutrient deprivation) retaining the ability to infect plants afterwards. In our previous studies, we showed Pba to be advanced in applying different adaptive strategies that led to manifestation of cell resistance to multiple stress factors. In the present study, we determined the period necessary for the formation of cross-protected Pba phenotype under starvation conditions, and compare the transcriptome profiles of non-adapted growing cells and of adapted cells after the cross-protective effect has reached the maximal level. The obtained data were verified using qRT-PCR. Genes that were expressed differentially (DEGs) in two cell types were classified into functional groups and categories using different approaches. As a result, we portrayed physiological features that distinguish cross-protected phenotype from the growing cells.

Peptide de novo sequencing of mixture tandem mass spectra

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co‐isolation and thus prone to false identifications. The deconvolution approach matched complementary b‐, y‐ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co‐isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications.