Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source.

In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.

Transient drought during flowering modifies the grain proteome of bread winter wheat.

Drought is among the most limiting factors for sustainable agricultural production. Water shortage at the onset of flowering severely affects the quality and quantity of grain yield of bread wheat (Triticum aestivum). Herein, we measured oxidative stress and photosynthesis-related parameters upon applying transient drought on contrasting wheat cultivars at the flowering stage of ontogenesis. The sensitive cultivar (Darunok Podillia) showed ineffective water management and a more severe decline in photosynthesis. Apparently, the tolerant genotype (Odeska 267) used photorespiration to dissipate excessive light energy. The tolerant cultivar sooner induced superoxide dismutase and showed less inhibited photosynthesis. Such a protective effect resulted in less affected yield and spectrum of seed proteome. The tolerant cultivar had a more stable gluten profile, which defines bread-making quality, upon drought. Water deficit caused the accumulation of medically relevant proteins: (i) components of gluten in the sensitive cultivar and (ii) metabolic proteins in the tolerant cultivar. We propose specific proteins for further exploration as potential markers of drought tolerance for guiding efficient breeding: thaumatin-like protein, 14-3-3 protein, peroxiredoxins, peroxidase, FBD domain protein, and Ap2/ERF plus B3 domain protein.

Determination of short-chain fatty acids as putative biomarkers of cancer diseases by modern analytical strategies and tools: a review.

Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of non-digestible carbohydrates in the gastrointestinal tract. They can be seen as the major flow of carbon from the diet, through the microbiome to the host. SCFAs have been reported as important molecules responsible for the regulation of intestinal homeostasis. Moreover, these molecules have a significant impact on the immune system and are able to affect inflammation, cardiovascular diseases, diabetes type II, or oncological diseases. For this purpose, SCFAs could be used as putative biomarkers of various diseases, including cancer. A potential diagnostic value may be offered by analyzing SCFAs with the use of advanced analytical approaches such as gas chromatography (GC), liquid chromatography (LC), or capillary electrophoresis (CE) coupled with mass spectrometry (MS). The presented review summarizes the importance of analyzing SCFAs from clinical and analytical perspective. Current advances in the analysis of SCFAs focused on sample pretreatment, separation strategy, and detection methods are highlighted. Additionally, it also shows potential areas for the development of future diagnostic tools in oncology and other varieties of diseases based on targeted metabolite profiling.

Antibiotic resistance and biofilm-forming ability of α-toxin-positive Clostridium septicum isolates worsen patient prognosis.

A total of, 78 Clostridium septicum (CLSE) isolates were screened for genes encoding: α-toxin, flagellin, and resistance to vancomycin (VANg). The isolates were also tested for their ability to form biofilm and their antibiotic susceptibility. All isolates were positive for α-toxin and flagellin genes. However, only 19 isolates (24.3%) showed prevalence for VANg. We observed the strongest capacity to form a biofilm (100%) in isolates from patients with oncologic or septic and febrile diagnoses. This percentage was also very high in patients with colitis and gastrointestinal hemorrhage (72.7%). No less than 43 isolates showed antibiotic resistance, and 21 were multidrug-resistant (MDR). Interestingly, our studies showed a correlation between antibiotic resistance and biofilm formation. A statistically significant difference was observed between biofilm-forming MDR isolates and those with low/no biofilm-forming ability. However, the most impressive observation was the correlation with mortality rate. While the overall mortality rate for CLSE infections was 16.7% (13/78), the mortality rate for patients infected with MDR isolates forming biofilm moderately or strongly reached 38.1% (8/21). This number increased even further when only infections with the biofilm-forming VANg-positive isolates were considered (61.5%; 8/13). Therefore, the ability of a VANg-positive CLSE isolate to form a biofilm has been suggested as a biomarker of poor prognosis.

Rickettsia Deregulates Genes Coding for the Neurotoxic Cell Response Pathways in Cerebrocortical Neurons In Vitro.

Rickettsial infections of the central nervous system (CNS) are manifested by severe neurological symptoms and represent a serious life-threatening condition. Despite the considerable health danger, only a few studies have been conducted focusing on the pathogenesis induced by Rickettsia sp. in CNS. To investigate the signaling pathways associated with the neurotoxic effects of rickettsiae, we employed an experimental model of cerebrocortical neurons combined with molecular profiling and comprehensive bioinformatic analysis. The cytopathic effect induced by Rickettsia akari and Rickettsia slovaca was demonstrated by decreased neuronal viability, structural changes in cell morphology, and extensive fragmentation of neurites in vitro. Targeted profiling revealed the deregulation of genes involved in the neuroinflammatory and neurotoxic cell response pathways. Although quantitative analysis showed differences in gene expression response, functional annotation revealed that the biological processes are largely shared between both Rickettsia species. The identified enriched pathways are associated with cytokine signaling, chemotaxis of immune cells, responses to infectious agents, interactions between neurons, endothelial and glial cells, and regulation of neuronal apoptotic processes. The findings of our study provide new insight into the etiopathogenesis of CNS infection and further expand the understanding of molecular signaling associated with neuroinvasive Rickettsia species.

Culture Isolate of Rickettsia felis from a Tick.

Although the cat flea, Ctenocephalides felis, has been identified as the primary vector of Rickettsia felis, additional flea, tick, mite, and louse species have also been associated with this bacterium by molecular means; however, the role of these arthropods in the transmission of R. felis has not been clarified. Here, we succeeded in culture isolation of R. felis from a host-seeking castor bean tick, Ixodes ricinus, the most common tick in Slovakia. The bacterial isolation was performed on XTC-2 cells at 28 °C using the shell-vial technique. An evaluation of the growth properties was performed for both the XTC-2 and Vero cell lines. We observed R. felis in the infected host cells microscopically by Gimenez staining and immunofluorescence assay. The R. felis isolate was purified by gradient ultracentrifugation and visualized by electron microscopy. Fragments of the genes gltA, ompA, ompB, htrA, rpoB, sca4, rffE, and rrs were amplified and compared with the corresponding sequences of the type strain URRWXCal2 and other R. felis culture -isolated strains. We did not detect any nucleotide polymorphisms; however, plasmid pRFδ, characteristic of the standard strain, was absent in our isolate. Herein, we describe the first successful isolation and characterization of a tick-derived R. felis strain "Danube", obtained from an I. ricinus nymph.

Pathogenic microorganisms in ticks removed from Slovakian residents over the years 2008-2018.

A total of 750 ticks feeding on humans were collected during the years 2008-2018. The majority of ticks (94.8 %) came from Slovakia, with 3.5 % from the Czech Republic, 0.9 % from Austria, and 0.3 % from Hungary. Travellers from Ukraine, Croatia, France, and Cuba also brought one tick from each of these countries. The majority of the analysed ticks were identified as Ixodes ricinus (94.3 %). Dermacentor reticulatus (0.93 %), Haemaphysalis concinna (0.1 %), Haemaphysalis sp. (0.1 %), Ixodes arboricola (0.1 %), and Rhipicephalus sp. (0.1 %) were also encountered. The most frequently found stage of I. ricinus was the nymph (69.9 %) followed by adult females (20.4 %) and larvae (8.3 %). Ticks were predominantly found on children younger than 10 years (46.3 %) and adults between 30-39 years (21.4 %). In children younger than 10 years, the ticks were usually found on the head, while in other age categories, the ticks were predominantly attached to legs. Ticks were further individually analysed for the presence of Rickettsia spp., Coxiella burnetii, Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, Neoehrlichia mikurensis, Bartonella spp. and Babesia spp. The overall prevalences of tick-borne bacteria assessed in I. ricinus ticks acquired in Slovakia were: rickettsiae 25.0 % (95 % CI: 21.7-28.2), B. burgdorferi s.l. 20.5 % (95 % CI: 17.4-23.5), A. phagocytophilum 13.5 % (95 % CI: 10.9-16.0), Babesia spp. 5.2 % (95 % CI: 3.5-6.9), C. burnetii 3.0 % (95 % CI: 1.5-4.6), and N. mikurensis 4.4 % (95 % CI: 2.0-6.8). Pathogenic species Rickettsia raoultii, Rickettsia helvetica, Rickettsia monacensis, A. phagocytophilum, Borrelia garinii, Borrelia afzelii, Borrelia valaisiana, Babesia microti, and Babesia divergens were identified in D. reticulatus and I. ricinus ticks.

PIMT Binding to C-Terminal Ala459 of CAIX Is Involved in Inside-Out Signaling Necessary for Its Catalytic Activity.

Human carbonic anhydrase IX (CAIX), a unique member of the α carbonic anhydrase family, is a transmembrane glycoprotein with high enzymatic activity by which CAIX contributes to tumorigenesis through pH regulation. Due to its aberrant expression, CAIX is considered to be a marker of tumor hypoxia and a poor prognostic factor of several human cancers. Hypoxia-activated catalytic function of CAIX is dependent on posttranslational modification of its short intracellular domain. In this work, we have identified that C-terminal Ala459 residue, which is common across CAIX of various species as well as additional transmembrane isoforms, plays an important role in CAIX activation and in pH regulation. Moreover, structure prediction I-TASSER analysis revealed involvement of Ala459 in potential ligand binding. Using tandem mass spectrometry, Protein-L-isoaspartyl methyltransferase (PIMT) was identified as a novel interacting partner, further confirmed by an in vitro pulldown assay and an in situ proximity ligation assay. Indeed, suppression of PIMT led to increased alkalinization of culture media of C33a cells constitutively expressing CAIX in hypoxia. We suggest that binding of PIMT represents a novel intracellular signal required for enzymatic activity of CAIX with a potential unidentified downstream function.

Proteomic analysis of Rickettsia akari proposes a 44 kDa-OMP as a potential biomarker for Rickettsialpox diagnosis.

BACKGROUND: Rickettsialpox is a febrile illness caused by the mite-borne pathogen Rickettsia akari. Several cases of this disease are reported worldwide annually. Nevertheless, the relationship between the immunogenicity of R. akari and disease development is still poorly understood. Thus, misdiagnosis is frequent. Our study is aiming to identify immunogenic proteins that may improve disease recognition and enhance subsequent treatment. To achieve this goal, two proteomics methodologies were applied, followed by immunoblot confirmation. RESULTS: Three hundred and sixteen unique proteins were identified in the whole-cell extract of R. akari. The most represented protein groups were found to be those involved in translation, post-translational modifications, energy production, and cell wall development. A significant number of proteins belonged to amino acid transport and intracellular trafficking. Also, some proteins affecting the virulence were detected. In silico analysis of membrane enriched proteins revealed 25 putative outer membrane proteins containing beta-barrel structure and 11 proteins having a secretion signal peptide sequence. Using rabbit and human sera, various immunoreactive proteins were identified from which the 44 kDa uncharacterized protein (A8GP63) has demonstrated a unique detection capability. It positively distinguished the sera of patients with Rickettsialpox from other rickettsiae positive human sera. CONCLUSION: Our proteomic analysis certainly contributed to the lack of knowledge of R. akari pathogenesis. The result obtained may also serve as a guideline for a more accurate diagnosis of rickettsial diseases. The identified 44 kDa uncharacterized protein can be certainly used as a unique marker of rickettsialpox or as a target molecule for the development of more effective treatment.

Soybean recovery from stress imposed by multigenerational growth in contaminated Chernobyl environment.

Ionizing radiation is a genotoxic anthropogenic stressor. It can cause heritable changes in the plant genome, which can be either adaptive or detrimental. There is still considerable uncertainty about the effects of chronic low-intensity doses since earlier studies reported somewhat contradictory conclusions. Our project focused on the recovery from the multiyear chronic ionizing radiation stress. Soybean (Glycine max) was grown in field plots located at the Chernobyl exclusion zone and transferred to the clean ground in the subsequent generation. We profiled proteome of mature seeds by two-dimensional gel electrophoresis. Overall, 15 differentially abundant protein spots were identified in the field comparison and 11 in the recovery generation, primarily belonging to storage proteins, disease/defense, and metabolism categories. Data suggested that during multigenerational growth in a contaminated environment, detrimental heritable changes were accumulated. Chlorophyll fluorescence parameters were measured on the late vegetative state, pointing to partial recovery of photosynthesis from stress imposed by contaminating radionuclides. A plausible explanation for the observed phenomena is insufficient provisioning of seeds by lower quality resources, causing a persistent effect in the offspring generation. Additionally, we hypothesized that immunity against phytopathogens was compromised in the contaminated field, but perhaps even primed in the clean ground, yet this idea requires direct functional validation in future experiments. Despite showing clear signs of physiological recovery, one season was not enough to normalize biochemical processes. Overall, our data contribute to the more informed agricultural radioprotection.

Comprehensive Comparison of Clinically Relevant Grain Proteins in Modern and Traditional Bread Wheat Cultivars.

Bread wheat (Triticum aestivum L.) is one of the most valuable cereal crops for human consumption. Its grain storage proteins define bread quality, though they may cause food intolerances or allergies in susceptible individuals. Herein, we discovered a diversity of grain proteins in three Ukrainian wheat cultivars: Sotnytsia, Panna (both modern selection), and Ukrainka (landrace). Firstly, proteins were isolated with a detergent-containing buffer that allowed extraction of various groups of storage proteins (glutenins, gliadins, globulins, and albumins); secondly, the proteome was profiled by the two-dimensional gel electrophoresis. Using multi-enzymatic digestion, we identified 49 differentially accumulated proteins. Parallel ultrahigh-performance liquid chromatography separation followed by direct mass spectrometry quantification complemented the results. Principal component analysis confirmed that differences among genotypes were a major source of variation. Non-gluten fraction better discriminated bread wheat cultivars. Various accumulation of clinically relevant plant proteins highlighted one of the modern genotypes as a promising donor for the breeding of hypoallergenic cereals.

Proteomic analysis revealed the survival strategy of Coxiella burnetii to doxycycline exposure.

Antibiotic resistance is a global threat with a top concern in healthcare. Doxycycline is an antibiotic highly permeable to cell membrane used for treating a broad variety of bacteria, including Coxiella burnetii. This intracellular pathogen is the causative agent of Q fever, a re-emerging zoonosis found worldwide. Hence, C. burnetii has a considerable impact on the farming industry and public health, it is essential to explore its antibiotic adaptation/tolerance strategy to ensure effective therapy. Herein, we tracked changes in the bacterium induced by doxycycline exposure. Our proteomic analysis detected fifteen significantly altered proteins. Adjustments of some key proteins were verified by gene expression analysis. We also observed an increasing in hydrogen peroxide as a consequence of treatment, indicating deregulation of redox balance. Thus, our data suggests the reduction of protein synthesis to minimal levels, activation of the defense mechanism against oxidative stress and maintenance of cell envelope integrity as the key processes ensuring C. burnetii survival under doxycycline exposure. SIGNIFICANCE: Infection by intracellular microorganisms like C. burnetii requires long periods of treatment, thus antibiotic resistance development is a risk. In this report, 2-DE quantitative proteomics was used to identify changes in the proteome that occurs when C. burnetii is exposed to high concentrations of doxycycline. The identification of pathways impacted by doxycycline could be helpful to understand the mechanism of how C. burnetii is dealing with antibiotic stress.

Comparative proteomics of the vector Dermacentor reticulatus revealed differentially regulated proteins associated with pathogen transmission in response to laboratory infection with Rickettsia slovaca.

BACKGROUND: Tick-borne rickettsial diseases are caused by pathogens acquired from hard ticks. In particular, Rickettsia slovaca, a zoonotic infectious bacterium causing tick-borne lymphadenopathy (TIBOLA), is transmitted by the vectors Dermacentor spp. that can be found all over Europe. Although recent studies point out the extreme complexity of bacteria-induced effects in these blood-feeding vectors, the knowledge of individual molecules involved in the preservation and transmission of the pathogen is still limited. System biology tools, including proteomics, may contribute greatly to the understanding of pathogen-tick-host interactions. METHODS: Herein, we performed a comparative proteomics study of the tick vector Dermacentor reticulatus that was experimentally infected with the endosymbiotic bacterium R. slovaca. Rickettsia-free ticks, collected in the southern region of Slovakia, were infected with the bacterium by a capillary tube-feeding system, and the dynamics of infection was assessed by quantitative PCR method after 5, 10, 15 and 27 days. RESULTS: At the stage of controlled proliferation (at 27 dpi), 33 (from 481 profiled) differentially abundant protein spots were detected on a two-dimensional gel. From the aforementioned protein spots, 21 were successfully identified by tandem mass spectrometry. CONCLUSIONS: Although a few discovered proteins were described as having structural or housekeeping functions, the vast majority of the affected proteins were suggested to be essential for tick attachment and feeding on the host, host immune system evasion and defensive response modulation to ensure successful pathogen transmission.

Structural and Functional Impact of Seven Missense Variants of Phenylalanine Hydroxylase.

The molecular genetics of well-characterized inherited diseases, such as phenylketonuria (PKU) and hyperphenylalaninemia (HPA) predominantly caused by mutations in the phenylalanine hydroxylase (PAH) gene, is often complicated by the identification of many novel variants, often with no obvious impact on the associated disorder. To date, more than 1100 PAH variants have been identified of which a substantial portion have unknown clinical significance. In this work, we study the functionality of seven yet uncharacterized PAH missense variants p.Asn167Tyr, p.Thr200Asn, p.Asp229Gly, p.Gly239Ala, p.Phe263Ser, p.Ala342Pro, and p.Ile406Met first identified in the Czech PKU/HPA patients. From all tested variants, three of them, namely p.Asn167Tyr, p.Thr200Asn, and p.Ile406Met, exerted residual enzymatic activity in vitro similar to wild type (WT) PAH, however, when expressed in HepG2 cells, their protein level reached a maximum of 72.1% ± 4.9%, 11.2% ± 4.2%, and 36.6% ± 7.3% compared to WT PAH, respectively. Remaining variants were null with no enzyme activity and decreased protein levels in HepG2 cells. The chaperone-like effect of applied BH4 precursor increased protein level significantly for p.Asn167Tyr, p.Asp229Gly, p.Ala342Pro, and p.Ile406Met. Taken together, our results of functional characterization in combination with in silico prediction suggest that while p.Asn167Tyr, p.Thr200Asn, and p.Ile406Met PAH variants have a mild impact on the protein, p.Asp229Gly, p.Gly239Ala, p.Phe263Ser, and p.Ala342Pro severely affect protein structure and function.

Silencing of carbonic anhydrase I enhances the malignant potential of exosomes secreted by prostatic tumour cells.

We report results showing that the silencing of carbonic anhydrase I (siCA1) in prostatic (PC3) tumour cells has a significant impact on exosome formation. An increased diameter, concentration and diversity of the produced exosomes were noticed as a consequence of this knock-down. The protein composition of the exosomes' cargo was also altered. Liquid chromatography and mass spectrometry analyses identified 42 proteins significantly altered in PC3 siCA1 exosomes compared with controls. The affected proteins are mainly involved in metabolic processes, biogenesis, cell component organization and defense/immunity. Interestingly, almost all of them have been described as 'enhancers' of tumour development through the promotion of cell proliferation, migration and invasion. Thus, our results indicate that the reduced expression of the CA1 protein enhances the malignant potential of PC3 cells.

Natural ecotype of Arabidopsis thaliana (L.) Heynh (Chernobyl-07) respond to cadmium stress more intensively than the sensitive ecotypes Oasis and Columbia.

Large areas polluted with toxic heavy metals or radionuclides were formed as a side product of rapid industrial development of human society. Plants, due to their sessile nature, should adapt to these challenging genotoxic environmental conditions and develop resistance. Herein, we evaluated the response of three natural ecotypes of Arabidopsis thaliana (L.) Heynh (Oasis, Columbia-0, and Chernobyl-07) to cadmium, using discovery gel-based proteomics. These accessions are differing by level of tolerance to heavy metal probably achieved by various exposure to chronic ionizing radiation. Based on the pairwise comparison (control versus cadmium-treated) we recognized 5.8-13.4% of identified proteins as significantly altered at the presence of cadmium. Although the majority of photosynthesis-related proteins were found to be less abundant in all ecotypes it was noted that in contrast to the sensitive variants (Col and Oas), the tolerant Che accession may activate the mechanism preserving photosynthesis and energy production. Also, proteins modulating energy budget through alternative route and mediating higher resistance to heavy metals were upregulated in this ecotype. Although we suggest that regulation of enzymes acting in peptide and protein synthesis, protection of the plants against various abiotic stresses, or those neutralizing the effects of reactive oxygen species are rather associated with general response to cadmium, they were found to be altered more intensively in the Che accession. Thus, the identified affected proteins may represent good candidate molecules for molecular breeding to improve tolerance of crops to heavy metal stress.

Evaluation of the possible use of genus Mentha derived essential oils in the prevention of SENLAT syndrome caused by Rickettsia slovaca.

ETHNOPHARMACOLOGICAL RELEVANCE: Essential oils and essential oil bearing medicinal and culinary plants have a long tradition of being used to combat infection, treat various conditions, and promote and restore health. Mint oils are traditionally applied to repel insects and treat various conditions including wounds, skin infections, inflammation, eczema, urticaria, psoriasis, scabies and insect bites. They are among essential oils promoted as a natural way to prevent tick-borne diseases and recommended as ingredients in various homemade repellent mixtures and tick-bite treatments. AIM OF THE STUDY: The aim of this study was to evaluate the effect of three most common mint oils - peppermint (Mentha x piperita L.), cornmint (M. arvensis L.), and spearmint (M. spicata L.) on obligate intracellular tick-borne bacterium Rickettsia slovaca. MATERIALS AND METHODS: Influence of mint oils on R. slovaca replication in Vero cells initially infected by lower (106) or higher (108) number of rickettsial particles was tested during in vitro cultivation with daily change of medium. qPCR and RT-qPCR based growth curves and linear mixed effect models were applied to evaluate the growth inhibition. Peppermint oil was further tested in pilot in vivo study on experimentally infected ticks. RESULTS: Two of the tested essential oils, peppermint and cornmint, significantly inhibited rickettsial growth. On average, peppermint oil reduced the amount of rickettsiae present on day 4 post infection up to 0.05% of the rickettsial load present in the respective controls. Cornmint oil decreased the amount of rickettsiae to 0.09% of control. Peppermint oil also significantly reduced the number of living rickettsiae in artificially infected ticks. CONCLUSIONS: Present study showed that essential oils with antimicrobial properties may also inhibit tick-transmitted bacteria, and thus their possible use as preventative measures against tick-borne diseases is worth further research.

Low-cost light-induced therapy to treat rickettsial infection.

Antimicrobial photodynamic therapy uses a nontoxic photosensitizer with the assistance of harmless visible light to activate the photosensitizer. Consequently, the excited state of the photosensitizer interacts with molecular oxygen to produce reactive oxygen species, which have the antimicrobial effect. In this study, we evaluated the effect of photodynamic therapy on Vero cells infected with rickettsia using methylene blue as a photosensitizer along with red light. A significant reduction (by 96%) in the number of viable Rickettsia slovaca was determined by quantitative RT-PCR 48 h after the treatment with methylene blue followed by 30 min of red light excitation. A statistically significant reduction of R. slovaca was also recorded with pretreatment (by 99%). To the best of our knowledge, this result is the first one in the literature to confirm the effectiveness of photodynamic therapy for the elimination of R. slovaca and to suggest this technique as a good supportive treatment for rickettsial infections.