The roles of polyamines in microorganisms

Curcumin inhibits growth of Porphyromonas gingivalis by arrest of bacterial dipeptidyl peptidase activity

Background

Curcumin is a multi-functional polyphenol with anti-bacterial and anti-inflammatory effects and may have potential for treatment of periodontal diseases. The present study was conducted to examine the molecular basis of the anti-bacterial effect of curcumin against Porphyromonas gingivalis using metabolome analysis.

Materials and Methods

P. gingivalis were incubated with 10 µg/mL curcumin, and then metabolites were analyzed with CE-TOF/MS. Expression levels of sigma factors were also evaluated using RT-PCR assays. The activities of dipeptidyl peptidases (DPPs) were assessed by examining the degradation reactions of MCA-labeled peptides.

Results

The relative amounts of various glycogenic amino acids were significantly decreased when P. gingivalis was incubated with curcumin. Furthermore, the metabolites on the amino acid degradation pathway, including high-energy compounds such as ATP, various intermediate metabolites of RNA/DNA synthesis, nucleoside sugars and amino sugars were also decreased. Additionally, the expression levels of sigma-54 and sigma-70 were significantly decreased, and the same results as noted following nutrient starvation. Curcumin also significantly suppressed the activities of some DPPs, while the human DPP-4 inhibitors markedly inhibited the growth of P. gingivalis and activities of the DPPs.

Conclusions

Curcumin suppresses the growth of P. gingivalis by inhibiting DPPs and also interferes with nucleic acid synthesis and central metabolic pathways, beginning with amino acid metabolism.

Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

Characterization of an Arginine Decarboxylase from Streptococcus pneumoniae by Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry

Polyamines are polycations derived from amino acids that play an important role in proliferation and growth in almost all living cells. In Streptococcus pneumoniae (the pneumococcus), modulation of polyamine metabolism not only plays an important regulatory role in central metabolism, but also impacts virulence factors such as the capsule and stress responses that affect survival in the host. However, functional annotation of enzymes from the polyamine biosynthesis pathways in the pneumococcus is based predominantly on computational prediction. In this study, we cloned SP_0166, predicted to be a pyridoxal-dependent decarboxylase, from the Orn/Lys/Arg family pathway in S. pneumoniae TIGR4 and expressed and purified the recombinant protein. We performed biochemical characterization of the recombinant SP_0166 and confirmed the substrate specificity. For polyamine analysis, we developed a simultaneous quantitative method using hydrophilic interaction liquid chromatography (HILIC)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) without derivatization. SP_0166 has apparent Km, kcat, and kcat/Km values of 11.3 mM, 715,053 min-1, and 63,218 min-1 mM-1, respectively, with arginine as a substrate at pH 7.5. We carried out inhibition studies of SP_0166 enzymatic activity with arginine as a substrate using chemical inhibitors DFMO and DFMA. DFMO is an irreversible inhibitor of ornithine decarboxylase activity, while DFMA inhibits arginine decarboxylase activity. Our findings confirm that SP_0166 is inhibited by DFMA and DFMO, impacting agmatine production. The use of arginine as a substrate revealed that the synthesis of putrescine by agmatinase and N-carbamoylputrescine by agmatine deiminase were both affected and inhibited by DFMA. This study provides experimental validation that SP_0166 is an arginine decarboxylase in pneumococci.

The alleviation of salt stress on rice through increasing photosynthetic capacity, maintaining redox homeostasis and regulating soil enzyme activities by Enterobacter sp. JIV1 assisted with putrescine

The detrimental impact of soil salinization on crop productivity and agricultural economy has garnered significant attention. A rhizosphere bacterium with favorable salt tolerance and plant growth-promoting (PGP) functions was isolated in this work. The bacterium was identified as Enterobacter through 16 S rDNA sequencing analysis and designated as Enterobacter sp. JIV1. Interestingly, the presence of putrescine (Put), which had been shown to contribute in reducing abiotic stress damage to plants, significantly promoted strain JIV1 to generate 1-aminocyclopropane-1-carboxylic (ACC) deaminase, dissolve phosphorus and secrete indole-3-acetic acid (IAA). However, the synergy of plant growth promoting rhizobacteria (PGPR) and Put in improving plant salt resistance has not been extensively studied. In this study, strain JIV1 and exogenous Put effectively mitigated the inhibitory impact of salt stress simulated by 200 mM NaCl on rice (Oryza sativa L.) growth. The chlorophyll accumulation, photosynthetic efficiency and antioxidant capacity of rice were also significantly strengthened. Notably, the combined application of strain JIV1 and Put outperformed individual treatments. Moreover, the co-addition of strain JIV1 and Put increased soil protease and urease activities by 451.97% and 51.70% compared to that of salt treatment group. In general, Put-assisted PGPR JIV1 provides a new perspective on alleviating the salt-induced negative impacts on plants.

In-situ substitution and community dynamics modeling for enhanced safety in Chinese rice wine brewing

This research paper focuses on the application of the "Design-Build-Test-Learn" framework to design and evaluate a synthetic microbial community aimed at studying the impact of Lactic Acid Bacteria (LAB) interactions and fitness on the formation of biogenic amines (BAs) in Chinese rice wine (CRW). The study reveals a close correlation between the assembly model of LAB and the accumulation of BAs in CRW, and multiple interactions were observed between amine-producing and non-amine-producing LAB, including commensalism, amensalism, and competition. The commensalism among amine-producing LAB was found to promote BAs accumulation through metabolic cross-feeding of amino acids. Moreover, the higher-order interaction community was designed to regulate the BAs formation effectively. For instance, the interference of Lactiplantibacillus plantarum (ACBC271) resulted in the elimination of amine-producing LAB viability, resulting in a 22% decrease (not exceeding 43.54 mg/L) in the total amount of BAs. Simulation of community dynamics models further suggests that LAB with quantitative social interactions can effectively control LAB accumulation in CRW by forecasting fluctuation in BAs generation through fitness competition and metabolic interference. Overall, this study provides valuable insights into the complex interaction networks within microbial communities in traditional fermentation ecosystems. It also proposes a novel approach for quality control of nitrogen food safety factors in fermented foods.

Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature

In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

Potential functions of the shared bacterial taxa in the citrus leaf midribs determine the symptoms of Huanglongbing

Instruction

Citrus is a globally important fruit tree whose microbiome plays a vital role in its growth, adaptability, and resistance to stress.

Methods

With the high throughput sequencing of 16S rRNA genes, this study focused on analyzing the bacterial community, especially in the leaf midribs, of healthy and Huanglongbing (HLB)-infected plants.

Results

We firstly identified the shared bacterial taxa in the midribs of both healthy and HLB-infected plants, and then analyzed their functions. Results showed that the shared bacterial taxa in midribs belonged to 62 genera, with approximately 1/3 of which modified in the infected samples. Furthermore, 366 metabolic pathways, 5851 proteins, and 1833 enzymes in the shared taxa were predicted. Among these, three metabolic pathways and one protein showed significant importance in HLB infection. With the random forest method, six genera were identified to be significantly important for HLB infection. Notably, four of these genera were also among the significantly different shared taxa. Further functional characterization of these four genera revealed that Pseudomonas and Erwinia likely contributed to plant defense against HLB, while Streptomyces might have implications for plant defense against HLB or the pathogenicity of Candidatus Liberibacter asiaticus (CLas).

Disccusion

Overall, our study highlights that the functions of the shared taxa in leaf midribs are distinguished between healthy and HLB-infected plants, and these microbiome-based findings can contribute to the management and protection of citrus crops against CLas.

A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine

Spermidine, a ubiquitous polyamine, is known to be required for critical physiological functions in bacteria. Two principal pathways are known for spermidine biosynthesis, both of which involve aminopropylation of putrescine. Here, we identified a spermidine biosynthetic pathway via a previously unknown metabolite, carboxyaminopropylagmatine (CAPA), in a model cyanobacterium Synechocystis sp. PCC 6803 through an approach combining 13C and 15N tracers, metabolomics, and genetic and biochemical characterization. The CAPA pathway starts with reductive condensation of agmatine and l-aspartate-β-semialdehyde into CAPA by a previously unknown CAPA dehydrogenase, followed by decarboxylation of CAPA to form aminopropylagmatine, and ends with conversion of aminopropylagmatine to spermidine by an aminopropylagmatine ureohydrolase. Thus, the pathway does not involve putrescine and depends on l-aspartate-β-semialdehyde as the aminopropyl group donor. Genomic, biochemical, and metagenomic analyses showed that the CAPA-pathway genes are widespread in 15 different phyla of bacteria distributed in marine, freshwater, and other ecosystems.

Alishewanella maricola sp. nov., isolated from seawater of the Yellow Sea

A Gram-stain-negative and facultative aerobic bacterium, strain 16-MAT, was isolated from seawater of Yellow Sea in South Korea. Cells were catalase- and oxidase-positive and non-motile rods. Growth occurred at 4-37 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, 8.0), and in the presence of 0-7.0% NaCl (optimum, 3 %). Strain 16-MAT contained ubiquinone-8 as the sole isoprenoid quinone, C16 : 0 and summed feature three as the major fatty acids (>10 %), and phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid, and an unidentified polar lipid as the major polar lipids. The genome size and DNA G+C content of strain 16-MAT were 3.69 Mb and 46.0 mol%, respectively. Strain 16-MAT was most closely related to Alishewanella alkalitolerans LNK-7.1T with a 97.9 % 16S rRNA gene sequence similarity. A phylogenomic tree based on whole genome sequences showed that strain 16-MAT formed a phylogenetic lineage within the genus Alishewanella. Based on the phenotypic, chemotaxonomic, and molecular analyses, strain 16-MAT represents a novel species of the genus Alishewanella, for which the name Alishewanella maricola is proposed. The type strain is 16-MAT (=KACC 22238T =JCM 34596T).

Specific Gene Expression in Pseudomonas Putida U Shows New Alternatives for Cadaverine and Putrescine Catabolism

Pseudomonas putida strain U can be grown using, as sole carbon sources, the biogenic amines putrescine or cadaverine, as well as their catabolic intermediates, ɣ-aminobutyrate or δ-aminovalerate, respectively. Several paralogs for the genes that encode some of the activities involved in the catabolism of these compounds, such as a putrescine-pyruvate aminotransferase (spuC1 and spuC2 genes) and a ɣ-aminobutyrate aminotransferase (gabT1 and gabT2 genes) have been identified in this bacterium. When the expression pattern of these genes is analyzed by qPCR, it is drastically conditioned by supplying the carbon sources. Thus, spuC1 is upregulated by putrescine, whereas spuC2 seems to be exclusively induced by cadaverine. However, gabT1 increases its expression in response to different polyamines or aminated catabolic derivatives from them (i.e., ɣ-aminobutyrate or δ-aminovalerate), although gabT2 does not change its expression level concerning no-amine unrelated carbon sources (citrate). These results reveal differences between the mechanisms proposed for polyamine catabolism in P. aeruginosa and Escherichia coli concerning P. putida strain U, as well as allow a deeper understanding of the enzymatic systems used by this last strain during polyamine metabolism.

Genome-Wide Identification and Characterization of the Biosynthesis of the Polyamine Gene Family in Citrus unshiu

Polyamines (PAs) contribute to diverse plant processes, environmental interaction, and stress responses. In citrus, the mechanism underlying the biosynthesis of polyamines is poorly understood. The present study aims to identify the biosynthesis of PA gene family members in satsuma mandarin (Citrus unshiu) and investigate their response against various stresses. The identified biosynthesis of PA genes in C. unshiu showed clustering in six groups, i.e., SPMS, SPDS, ACL5, ADC, ODC, and SAMDC. Syntenic analysis revealed that segmental duplication was prevalent among the biosynthesis of PA genes compared to tandem duplication. Thus, it might be the main reason for diversity in the gene family in C. unshiu. Almost all biosynthesis of PA gene family members in C. unshiu showed syntenic blocks in the genome of Arabidopsis, Citrus sinensis, Poncirus trifoliata, and Citrus reticulata. Analysis of Cis-regulatory elements (CREs) indicated the occurrence of hormones, light, defense, and environmental stress responses as well as the development and other plant mechanisms-related elements in the upstream sequence of the biosynthesis of PA genes. Expression profiling revealed that the biosynthesis of PA gene expression modulates in different organs during various developmental stages and stress in C. unshiu. This information will provide a deep understanding of genomic information and its expression in multiple tissues to better understand its potential application in functional genomics.

Polyamine as a microenvironment factor in resistance to antibiotics

One of the main issues in modern medicine is the decrease in the efficacy of antibiotic therapy against resistant microorganisms. The advent of antimicrobial resistance has added significantly to the impact of infectious diseases, in number of infections, as well as added healthcare costs. The development of antibiotic tolerance and resistance is influenced by a variety of environmental variables, and it is important to identify these environmental factors as part of any strategy for combating antibiotic resistance. The review aims to emphasize that biogenic polyamines are one of such environmental cues that impacts the antibiotic resistance in bacteria. The biogenic polyamines can help bacteria acquire resistance to antibiotics either by regulating the level of number of porin channels in the outer membrane, by modifying the outer membrane liposaccharides or by protecting macromolecule from antibiotic stress. Thus, understanding the way polyamines function in bacteria can thus be beneficial while designing the drugs to combat diseases.

Genome-Wide Characterization of Light-Regulated Gene Expression in Botrytis cinerea Reveals Underlying Complex Photobiology

Botrytis cinerea is a necrotrophic fungus characterized mainly by its wide host range of infected plants. The deletion of the white-collar-1 gene (bcwcl1), which encodes for a blue-light receptor/transcription factor, causes a decrease in virulence, particularly when assays are conducted in the presence of light or photocycles. However, despite ample characterization, the extent of the light-modulated transcriptional responses regulated by BcWCL1 remains unknown. In this study, pathogen and pathogen:host RNA-seq analyses, conducted during non-infective in vitro plate growth and when infecting Arabidopsis thaliana leaves, respectively, informed on the global gene expression patterns after a 60 min light pulse on the wild-type B05.10 or ∆bcwcl1 B. cinerea strains. The results revealed a complex fungal photobiology, where the mutant did not react to the light pulse during its interaction with the plant. Indeed, when infecting Arabidopsis, no photoreceptor-encoding genes were upregulated upon the light pulse in the ∆bcwcl1 mutant. Differentially expressed genes (DEGs) in B. cinerea under non-infecting conditions were predominantly related to decreased energy production in response to the light pulse. In contrast, DEGs during infection significantly differ in the B05.10 strain and the ∆bcwcl1 mutant. Upon illumination at 24 h post-infection in planta, a decrease in the B. cinerea virulence-associated transcripts was observed. Accordingly, after a light pulse, biological functions associated with plant defense appear enriched among light-repressed genes in fungus-infected plants. Taken together, our results show the main transcriptomic differences between wild-type B. cinerea B05.10 and ∆bcwcl1 after a 60 min light pulse when growing saprophytically on a Petri dish and necrotrophically over A. thaliana.

Structural Analysis of Spermidine Synthase from Kluyveromyces lactis

Spermidine is a polyamine molecule that performs various cellular functions, such as DNA and RNA stabilization, autophagy modulation, and eIF5A formation, and is generated from putrescine by aminopropyltransferase spermidine synthase (SpdS). During synthesis, the aminopropyl moiety is donated from decarboxylated S-adenosylmethionine to form putrescine, with 5'-deoxy-5'-methylthioadenosine being produced as a byproduct. Although the molecular mechanism of SpdS function has been well-established, its structure-based evolutionary relationships remain to be fully understood. Moreover, only a few structural studies have been conducted on SpdS from fungal species. Here, we determined the crystal structure of an apo-form of SpdS from Kluyveromyces lactis (KlSpdS) at 1.9 Å resolution. Structural comparison with its homologs revealed a conformational change in the α6 helix linked to the gate-keeping loop, with approximately 40° outward rotation. This change caused the catalytic residue Asp170 to move outward, possibly due to the absence of a ligand in the active site. These findings improve our understanding of the structural diversity of SpdS and provide a missing link that expands our knowledge of the structural features of SpdS in fungal species.

Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity

Polyamines and polyamine-containing metabolites are involved in many cellular processes related to bacterial cell growth and survival. In Escherichia coli, the bifunctional enzyme glutathionylspermidine synthetase/amidase (GspSA) controls the production of glutathionylspermidine, which has a protective role against oxidative stress. E. coli also encodes two enzymes with homology to the synthetase domain of GspSA, YgiC, and YjfC; however, these do not catalyze the formation of glutathionylspermidine, and their catalytic function remained unknown. Here, we detail the structural and functional characterization of YgiC and YjfC. Using X-ray crystallography, the high-resolution crystal structures of YgiC and YjfC were obtained. This revealed that YgiC and YjfC possess multiple substitutions in key residues required for binding of glutathione in GspSA. Despite this difference, these enzymes share a similar active site structure to GspSA, suggesting that they catalyze the formation of an alternate peptide─spermidine conjugate. As the physiological substrates of YgiC and YjfC are unknown, this was probed using the peptide triglycine as a model substrate. A combination of enzyme activity assays and mass spectrometry revealed that YgiC and YjfC can function as peptide-spermidine ligases, forming a triglycine-spermidine conjugate. For both enzymes, conjugate formation was only observed in the presence of spermidine, but not other common polyamines, supporting that spermidine or a spermidine derivative is the physiological substrate. Importantly, since YgiC and YjfC are widely distributed in Gram-negative bacterial species, this suggests that these enzymes function in a conserved cellular process, representing a currently unknown aspect of bacterial polyamine metabolism.

A genomic approach to analyze the cold adaptation of yeasts isolated from Italian Alps

Microorganisms including yeasts are responsible for mineralization of organic matter in cold regions, and their characterization is critical to elucidate the ecology of such environments on Earth. Strategies developed by yeasts to survive in cold environments have been increasingly studied in the last years and applied to different biotechnological applications, but their knowledge is still limited. Microbial adaptations to cold include the synthesis of cryoprotective compounds, as well as the presence of a high number of genes encoding the synthesis of proteins/enzymes characterized by a reduced proline content and highly flexible and large catalytic active sites. This study is a comparative genomic study on the adaptations of yeasts isolated from the Italian Alps, considering their growth kinetics. The optimal temperature for growth (OTG), growth rate (Gr), and draft genome sizes considerably varied (OTG, 10°C–20°C; Gr, 0.071–0.0726; genomes, 20.7–21.5 Mpb; %GC, 50.9–61.5). A direct relationship was observed between calculated protein flexibilities and OTG, but not for Gr. Putative genes encoding for cold stress response were found, as well as high numbers of genes encoding for general, oxidative, and osmotic stresses. The cold response genes found in the studied yeasts play roles in cell membrane adaptation, compatible solute accumulation, RNA structure changes, and protein folding, i.e., dihydrolipoamide dehydrogenase, glycogen synthase, omega-6 fatty acid, stearoyl-CoA desaturase, ATP-dependent RNA helicase, and elongation of very-long-chain fatty acids. A redundancy for several putative genes was found, higher for P-loop containing nucleoside triphosphate hydrolase, alpha/beta hydrolase, armadillo repeat-containing proteins, and the major facilitator superfamily protein. Hundreds of thousands of small open reading frames (SmORFs) were found in all studied yeasts, especially in Phenoliferia glacialis. Gene clusters encoding for the synthesis of secondary metabolites such as terpene, non-ribosomal peptide, and type III polyketide were predicted in four, three, and two studied yeasts, respectively.

The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges

Protein phosphorylation is the most common and versatile post-translational modification occurring in eukaryotes. In yeast, protein phosphorylation is fundamental for maintaining cell growth and adapting to sudden changes in environmental conditions by regulating cellular processes and activating signal transduction pathways. Protein kinases catalyze the reversible addition of phosphate groups to target proteins, thereby regulating their activity. In Saccharomyces cerevisiae, kinases are classified into six major groups based on structural and functional similarities. The NPR/Hal family of kinases comprises nine fungal-specific kinases that, due to lack of similarity with the remaining kinases, were classified to the “Other” group. These kinases are primarily implicated in regulating fundamental cellular processes such as maintaining ion homeostasis and controlling nutrient transporters’ concentration at the plasma membrane. Despite their biological relevance, these kinases remain poorly characterized and explored. This review provides an overview of the information available regarding each of the kinases from the NPR/Hal family, including their known biological functions, mechanisms of regulation, and integration in signaling pathways in S. cerevisiae. Information gathered for non-Saccharomyces species of biotechnological or clinical relevance is also included.

Polyamine and Ethanolamine Metabolism in Bacteria as an Important Component of Nitrogen Assimilation for Survival and Pathogenicity

Nitrogen is an essential element required for bacterial growth. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Bacteria have developed the ability to use various nitrogen sources and possess two enzyme systems for nitrogen assimilation involving glutamine synthetase/glutamate synthase and glutamate dehydrogenase. Microorganisms living in habitats with changeable availability of nutrients have developed strategies to survive under nitrogen limitation. One adaptation is the ability to acquire nitrogen from alternative sources including the polyamines putrescine, cadaverine, spermidine and spermine, as well as the monoamine ethanolamine. Bacterial polyamine and monoamine metabolism is not only important under low nitrogen availability, but it is also required to survive under high concentrations of these compounds. Such conditions can occur in diverse habitats such as soil, plant tissues and human cells. Strategies of pathogenic and non-pathogenic bacteria to survive in the presence of poly- and monoamines offer the possibility to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This work aims to summarize the knowledge on poly- and monoamine metabolism in bacteria and its role in nitrogen metabolism.

Strategies for anti-oxidative stress and anti-acid stress in bioleaching of LiCoO2 using an acidophilic microbial consortium

High metal ion concentrations and low pH cause severely inhibit the activity of an acidophilic microbial consortium (AMC) in bioleaching. This work investigated the effects of exogenous spermine on biofilm formation and the bioleaching efficiency of LiCoO₂ by AMC in 9K medium. After the addition of 1 mM spermine, the activities of glutathione peroxidase and catalase increased, while the amount of H₂O₂, intracellular reactive oxygen species (ROS) and malondialdehyde in AMC decreased. These results indicated that the ability of AMC biofilm to resist oxidative stress introduced by 3.5 g/L Li⁺ and 30.1 g/L Co²⁺ was improved by spermine. The activity of glutamate decarboxylase was promoted to restore the intracellular pH buffering ability of AMC. Electrochemical measurements showed that the oxidation rate of pyrite was increased by exogenous spermine. As a result, high bioleaching efficiencies of 97.1% for Li⁺ and 96.1% for Co²⁺ from a 5.0% (w v^-1) lithium cobalt oxide powder slurry were achieved. This work demonstrated that Tafel polarization can be used to monitor the AMC biofilm's ability of uptaking electrons from pyrite during bioleaching. The corrosion current density increased with 1 mM spermine, indicating enhanced electron uptake by the biofilm from pyrite.

Molecular mechanisms of Shigella effector proteins: a common pathogen among diarrheic pediatric population

Different gastrointestinal pathogens cause diarrhea which is a very common problem in children aged under 5 years. Among bacterial pathogens, Shigella is one of the main causes of diarrhea among children, and it accounts for approximately 11% of all deaths among children aged under 5 years. The case-fatality rates for Shigella among the infants and children aged 1 to 4 years are 13.9% and 9.4%, respectively. Shigella uses unique effector proteins to modulate intracellular pathways. Shigella cannot invade epithelial cells on the apical site; therefore, it needs to pass epithelium through other cells rather than the epithelial cell. After passing epithelium, macrophage swallows Shigella, and the latter should prepare itself to exhibit at least two types of responses: (I) escaping phagocyte and (II) mediating invasion of and injury to the recurrent PMN. The presence of PMN and invitation to a greater degree resulted in gut membrane injuries and greater bacterial penetration. Infiltration of Shigella to the basolateral space mediates (A) cell attachment, (B) cell entry, (C) evasion of autophagy recognition, (D) vacuole formation and and vacuole rapture, (E) intracellular life, (F) Shiga toxin, and (G) immune response. In this review, an attempt is made to explain the role of each factor in Shigella infection.

Inferring the Significance of the Polyamine Metabolism in the Phytopathogenic Bacteria Pseudomonas syringae: A Meta-Analysis Approach

To succeed in plant invasion, phytopathogenic bacteria rely on virulence mechanisms to subvert plant immunity and create favorable conditions for growth. This process requires a precise regulation in the production of important proteins and metabolites. Among them, the family of compounds known as polyamines have attracted considerable attention as they are involved in important cellular processes, but it is not known yet how phytopathogenic bacteria regulate polyamine homeostasis in the plant environment. In the present study, we performed a meta-analysis of publicly available transcriptomic data from experiments conducted on bacteria to begin delving into this topic and better understand the regulation of polyamine metabolism and its links to pathogenicity. We focused our research on Pseudomonas syringae, an important phytopathogen that causes disease in many economically valuable plant species. Our analysis discovered that polyamine synthesis, as well as general gene expression activation and energy production are induced in the early stages of the disease. On the contrary, synthesis of these compounds is inhibited whereas its transport is upregulated later in the process, which correlates with the induction of virulence genes and the metabolism of nitrogen and carboxylic acids. We also found that activation of plant defense mechanisms affects bacterial polyamine synthesis to some extent, which could reduce bacterial cell fitness in the plant environment. Furthermore, data suggest that a proper bacterial response to oxidative conditions requires a decrease in polyamine production. The implications of these findings are discussed.

Nitratireductor rhodophyticola sp. nov., isolated from marine red algae

Two Gram-stain-negative, strictly aerobic bacteria, strains L1-7-SET and R6, isolated from marine red algae, were characterized. They shared 99.9 % 16S rRNA gene sequence similarity and a 100 % digital DNA–DNA hybridization (DDH) value, representing members of a single species. Cells of strains L1-7-SET and R6 were catalase- and oxidase-positive motile rods with a single polar flagellum. Strains L1-7-SET and R6 optimally grew at 30–35 °C, pH 7.0–8.0 and with 1.0–2.0 % (w/v) NaCl. Ubiquinone-10 was the sole isoprenoid quinone and C19 : 0 cyclo ω8c and summed feature 8 (comprising C18 : 1  ω7c and/or C18 : 1  ω6c) were detected as the major cellular fatty acids. The DNA G+C contents of strains L1-7-SET and R6 were both 61.62 mol%. The polar lipids of strain L1-7-SET consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and two unidentified polar lipids. Phylogenetic analyses based on 16S rRNA gene and 120 protein marker sequences revealed that strains L1-7-SET and R6 formed a phyletic lineage within the genus Nitratireductor and they were most closely related to Nitratireductor aquibiodomus NL21T and Nitratireductor kimnyeongensis KY 101T with both 98.8 % 16S rRNA gene sequence similarities. Digital DDH values between strain L1-7-SET and the type strains of N. aquibiodomus and N. kimnyeongensis were 60.3 and 29.5 %, respectively. The phenotypic, chemotaxonomic and molecular features support that strains L1-7-SET and R6 represents a novel species of the genus Nitratireductor , for which the name Nitratireductor rhodophyticola sp. nov. is proposed. The type strain is L1-7-SET (=KACC 19076T=KCTC 92231T=JCM 31802T).

Polyamines: Α bioenergetic smart switch for plant protection and development

The present review highlights the bioenergetic role of polyamines in plant protection and development and proposes a universal model for describing polyamine-mediated stress responses. Any stress condition induces an excitation pressure on photosystem II by reforming the photosynthetic apparatus. To control this phenomenon, polyamines act directly on the molecular structure and function of the photosynthetic apparatus as well as on the components of the chemiosmotic proton-motive force (ΔpH/Δψ), thus regulating photochemical (qP) and non-photochemical quenching (NPQ) of energy. The review presents the mechanistic characteristics that underline the key role of polyamines in the structure, function, and bioenergetics of the photosynthetic apparatus upon light adaptation and/or under stress conditions. By following this mechanism, it is feasible to make stress-sensitive plants to be tolerant by simply altering their polyamine composition (especially the ratio of putrescine to spermine), either chemically or by light regulation.

The Periplasmic Oxidoreductase DsbA Is Required for Virulence of the Phytopathogen Dickeya solani

In bacteria, the DsbA oxidoreductase is a crucial factor responsible for the introduction of disulfide bonds to extracytoplasmic proteins, which include important virulence factors. A lack of proper disulfide bonds frequently leads to instability and/or loss of protein function; therefore, improper disulfide bonding may lead to avirulent phenotypes. The importance of the DsbA function in phytopathogens has not been extensively studied yet. Dickeya solani is a bacterium from the Soft Rot Pectobacteriaceae family which is responsible for very high economic losses mainly in potato. In this work, we constructed a D. solani dsbA mutant and demonstrated that a lack of DsbA caused a loss of virulence. The mutant bacteria showed lower activities of secreted virulence determinants and were unable to develop disease symptoms in a potato plant. The SWATH-MS-based proteomic analysis revealed that the dsbA mutation led to multifaceted effects in the D. solani cells, including not only lower levels of secreted virulence factors, but also the induction of stress responses. Finally, the outer membrane barrier seemed to be disturbed by the mutation. Our results clearly demonstrate that the function played by the DsbA oxidoreductase is crucial for D. solani virulence, and a lack of DsbA significantly disturbs cellular physiology.

Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach

Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.

Gut Microbiota Signature of Obese Adults Across Different Classifications

PURPOSE

Obesity is currently a major global public health issue. It has been shown by many that gut microbiota and microbial factors regulate the pathogenesis of obesity and metabolic abnormalities, but little is known about their roles in the different degrees of obesity. Here, we sought to investigate the microbial signatures of obesity of various severities.

PATIENTS AND METHODS

We did this by characterizing the intestinal microbiome signature in a Chinese cohort of obese patients and healthy controls using 16S rRNA gene sequencing. To this end, obesity was sub-divided into four subgroups, including "Overweight", Class I, Class II, and Class III obesity, based on body mass index (BMI).

RESULTS

Microbial diversity decreased in obese subjects, and the reduction trend was correlated with the severity of obesity. We detected an expansion of Escherichia shigella in obese patients compared to healthy controls. The family Eubacterium coprostanoligenes and Tannerellaceae, the genera Eubacterium coprostanoligenes, Lachnospiraceae NK4A136, Parabacteroides, and Akkermansia, and the species Prevotella copri were microbial biomarkers of healthy people. Gammaproteobacteria and Enterobacterales were biomarkers of being "Overweight". Erysipelatoclostridiaceae was a biomarker of Class I obesity. The class Bacilli and the order Lactobacillales were both biomarkers of Class II obesity. Negativicutes was a biomarker of Class III obesity. We further established relationships between this microbiome data and other biochemical data, including albumin, low-density lipoprotein (LDL), high-density lipoprotein (HDL), vitamin folic acid (FA) and vitamin B12 (VB12), and Interleukin-6 (IL-6) levels. Function prediction results showed a marked energy metabolism dysbiosis in obesity, especially in patients with Class III obesity.

CONCLUSION

These results suggested that people with different levels of obesity had distinct gut microbial signatures. Decreased microbial diversity, depletion of some specific taxa, and deviation in potential functions mirrored the severity of obesity in this cohort.

Performance of halotolerant bacteria associated with Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L. ameliorate tomato plant growth and tolerance to saline stress: from selective isolation to genomic analysis of potential determinants

The use of halotolerant beneficial plant-growth-promoting (PGP) bacteria is considered as a promising eco-friendly approach to improve the salt tolerance of cash crops. One strategy to enhance the possibility of obtaining stress-alleviating bacteria is to screen salt impacted soils. In this study, amongst the 40 endophytic bacteria isolated from the roots of Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L., 8 showed interesting NaCl tolerance in vitro. Their evaluation, through different tomato plant trials, permitted the isolate IS26 to be distinguished as the most effective seed inoculum for both plant growth promotion and mitigation of salt stress. On the basis of 16S rRNA gene sequence, the isolate was closely related to Stenotrophomonas rhizophila. It was then screened in vitro for multiple PGP traits and the strain-complete genome was sequenced and analysed to further decipher the genomic basis of the putative mechanisms underlying its osmoprotective and plant growth abilities. A remarkable number of genes putatively involved in mechanisms responsible for rhizosphere colonization, plant association, strong competition for nutrients, and the production of important plant growth regulator compounds, such as AIA and spermidine, were highlighted, as were substances protecting against stress, including different osmolytes like trehalose, glucosylglycerol, proline, and glycine betaine. By having genes related to complementary mechanisms of osmosensing, osmoregulation and osmoprotection, the strain confirmed its great capacity to adapt to highly saline environments. Moreover, the presence of various genes potentially related to multiple enzymatic antioxidant processes, able to reduce salt-induced overproduction of ROS, was also detected.

Untargeted Metabolomics Investigation on Selenite Reduction to Elemental Selenium by Bacillus mycoides SeITE01

Bacillus mycoides SeITE01 is an environmental isolate that transforms the oxyanion selenite (SeO 3 2 - ) into the less bioavailable elemental selenium (Se0) forming biogenic selenium nanoparticles (Bio-SeNPs). In the present study, the reduction of sodium selenite (Na2SeO3) by SeITE01 strain and the effect ofSeO 3 2 - exposure on the bacterial cells was examined through untargeted metabolomics. A time-course approach was used to monitor both cell pellet and cell free spent medium (referred as intracellular and extracellular, respectively) metabolites in SeITE01 cells treated or not withSeO 3 2 - . The results show substantial biochemical changes in SeITE01 cells when exposed toSeO 3 2 - . The initial uptake ofSeO 3 2 - by SeITE01 cells (3h after inoculation) shows both an increase in intracellular levels of 4-hydroxybenzoate and indole-3-acetic acid, and an extracellular accumulation of guanosine, which are metabolites involved in general stress response adapting strategies. Proactive and defensive mechanisms againstSeO 3 2 - are observed between the end of lag (12h) and beginning of exponential (18h) phases. Glutathione and N-acetyl-L-cysteine are thiol compounds that would be mainly involved in Painter-type reaction for the reduction and detoxification ofSeO 3 2 - to Se0. In these growth stages, thiol metabolites perform a dual role, both acting against the toxic and harmful presence of the oxyanion and as substrate or reducing sources to scavenge ROS production. Moreover, detection of the amino acids L-threonine and ornithine suggests changes in membrane lipids. Starting from stationary phase (24 and 48h), metabolites related to the formation and release of SeNPs in the extracellular environment begin to be observed. 5-hydroxyindole acetate, D-[+]-glucosamine, 4-methyl-2-oxo pentanoic acid, and ethanolamine phosphate may represent signaling strategies following SeNPs release from the cytoplasmic compartment, with consequent damage to SeITE01 cell membranes. This is also accompanied by intracellular accumulation of trans-4-hydroxyproline and L-proline, which likely represent osmoprotectant activity. The identification of these metabolites suggests the activation of signaling strategies that would protect the bacterial cells fromSeO 3 2 - toxicity while it is converting into SeNPs.

Clp is a "busy" transcription factor in the bacterial warrior, Lysobacter enzymogenes

Cyclic AMP receptor protein (CRP) is a well-characterized group of global transcription factors in bacteria. They are known to regulate numerous cellular processes by binding DNA and/or cAMP (a ligand called bacterial second messenger) to control target gene expression. Gram-negative Lysobacter enzymogenes is a soilborne, plant-beneficial bacterium without flagella that can fight against filamentous fungi and oomycete. Driven by the type IV pilus (T4P) system, this bacterium moves to nearby pathogens and uses a “mobile-attack” antifungal strategy to kill them via heat-stable antifungal factor (HSAF) and abundant lyases. This strategy is controlled by a unique “busy” transcription factor Clp, which is a CRP-like protein that is inactivated by binding of c-di-GMP, another ubiquitous second messenger of bacteria. In this review, we summarize the current progress in how Clp initiates a “mobile-attack” strategy through a series of previously uncharacterized mechanisms, including binding to DNA in a unique pattern, directly interacting with or responding to various small molecules, and interacting specifically with proteins adopting distinct structure. Together, these characteristics highlight the multifunctional roles of Clp in L. enzymogenes, a powerful bacterial warrior against fungal pathogens.

Bacterial infection reinforces host metabolic flux from arginine to spermine for NLRP3 inflammasome evasion

Hosts recognize cytosolic microbial infection via the nucleotide-binding domain-like receptor (NLR) protein family, triggering inflammasome complex assembly to provoke pyroptosis or cytokine-related caspase-1-dependent antimicrobial responses. Pathogens have evolved diverse strategies to antagonize inflammasome activation. Here, Edwardsiella piscicida gene-defined transposon library screening for lactate dehydrogenase (LDH) release in nlrc4^-/- bone marrow-derived macrophages (BMDMs) demonstrates that genes clustered in the bacterial arginine metabolism pathway participate in NLRP3 inflammasome inhibition. Blocking arginine uptake or putrescine export significantly relieves NLRP3 inflammasome inhibition, indicating that this bacterium rewires its arginine metabolism network during infection. Moreover, intracellular E. piscicida recruits the host arginine importer (mCAT-1) and putrescine exporter (Oct-2) to bacterium-containing vacuoles, accompanied by reduced arginine and accumulated cytosolic spermine. Neutralizing E. piscicida-induced cytosolic spermine enhancement by spermine synthetase or extracellular spermine significantly alters NLRP3 inflammasome activation. Importantly, accumulated cytosolic spermine inhibits K⁺ efflux-dependent NLRP3 inflammasome activation. These data highlight the mechanism of bacterial gene-mediated arginine metabolism control for NLRP3 inflammasome evasion.

Spot 42 RNA regulates putrescine catabolism in Escherichia coli by controlling the expression of puuE at the post-transcription level

Putrescine, a typical polyamine compound important for cell growth and stress resistance, can be utilized as an energy source. However, the regulation of its catabolism is unclear. Here the small RNA (sRNA) Spot 42, an essential regulator of carbon catabolite repression (CCR), was confirmed to participate in the post-transcriptional regulation of putrescine catabolism in Escherichia coli. Its encoding gene spf exclusively exists in the γ-proteobacteria and contains specific binding sites to the 5'-untranslated regions of the puuE gene, which encodes transaminase in the glutamylated putrescine pathway of putrescine catabolism converting γ-aminobutyrate (GABA) into succinate semialdehyde (SSA). The transcription of the spf gene was induced by glucose, inhibited by putrescine, and unaffected by PuuR, the repressor of puu genes. Excess Spot 42 repressed the expression of PuuE significantly in an antisense mechanism through the direct and specific base-pairing between the 51`-57 nt of Spot 42 and the 5'-UTR of puuE. Interestingly, Spot 42 mainly influenced the stability of the puuCBE transcript. This work revealed the regulatory role of Spot 42 in putrescine catabolism, in the switch between favorable and non-favorable carbon source utilization, and in the balance of metabolism of carbon and nitrogen sources.

The Roles of Microbial Cell-Cell Chemical Communication Systems in the Modulation of Antimicrobial Resistance

Rapid emergence of antimicrobial resistance (AMR) has become a critical challenge worldwide. It is of great importance to understand how AMR is modulated genetically in order to explore new antimicrobial strategies. Recent studies have unveiled that microbial communication systems, which are known to play key roles in regulation of bacterial virulence, are also associated with the formation and regulation of AMR. These microbial cell-to-cell chemical communication systems, including quorum sensing (QS) and pathogen-host communication mechanisms, rely on detection and response of various chemical signal molecules, which are generated either by the microbe itself or host cells, to activate the expression of virulence and AMR genes. This article summarizes the generic signaling mechanisms of representative QS and pathogen-host communications systems, reviews the current knowledge regarding the roles of these chemical communication systems in regulation of AMR, and describes the strategies developed over the years for blocking bacterial chemical communication systems in disease control. The research progress in this field suggests that the bacterial cell-cell communication systems are a promising target not only for disease control but also for curbing the problem of microbial drug resistance.

DNA supercoiling differences in bacteria result from disparate DNA gyrase activation by polyamines

DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E. coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro, Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E. coli enzyme was not. In vivo, putrescine activated the Salmonella DNA gyrase and spermidine the E. coli enzyme. High extracellular Mg2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E. coli and Salmonella, define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.

SP_0916 Is an Arginine Decarboxylase That Catalyzes the Synthesis of Agmatine, Which Is Critical for Capsule Biosynthesis in Streptococcus pneumoniae

The global burden of invasive pneumococcal diseases, including pneumonia and sepsis, caused by Streptococcus pneumoniae, a Gram-positive bacterial pathogen, remains a major global health risk. The success of pneumococcus as a pathogen can be attributed to its ability to regulate the synthesis of capsular polysaccharide (CPS) during invasive disease. We previously reported that deletion of a putative lysine decarboxylase (LDC; ΔSP_0916) in pneumococcal serotype 4 (TIGR4) results in reduced CPS. SP_0916 locus is annotated as either an arginine or a LDC in pneumococcal genomes. In this study, by biochemical characterization of the recombinant SP_0916, we determined the substrate specificity of SP_0916 and show that it is an arginine decarboxylase (speA/ADC). We also show that deletion of the polyamine transporter (potABCD) predicted to import putrescine and spermidine results in reduced CPS, while deletion of spermidine synthase (speE) for the conversion of putrescine to spermidine had no impact on the capsule. Targeted metabolomics identified a correlation between reduced levels of agmatine and loss of capsule in ΔspeA and ΔpotABCD, while agmatine levels were comparable between the encapsulated TIGR4 and ΔspeE. Exogenous supplementation of agmatine restored CPS in both ΔpotABCD and ΔspeA. These results demonstrate that agmatine is critical for regulating the CPS, a predominant virulence factor in pneumococci.

A class I histone deacetylase is implicated in the encystation of Entamoeba invadens

Epigenetic mechanisms such as histone acetylation and deacetylation participate in regulation of the genes involved in encystation of Entamoeba invadens. However, the histones and target residues involved, and whether the acetylation and deacetylation of the histones leads to the regulation of gene expression associated with the encystation of this parasite, remain unknown. In this study, we found that E. invadens histone H4 is acetylated in both stages of the parasite and is more highly acetylated during the trophozoite stage than in the cyst. Histone hyperacetylation induced by Trichostatin A negatively affects the encystation of E. invadens, and this inhibition is associated with the downregulation of the expression of genes implicated in the synthesis of chitin, polyamines, gamma-aminobutyric acid pathways and cyst wall proteins, all of which are important in the formation of cysts. Finally, in silico analysis and activity assays suggest that a class I histone deacetylase (EiHDAC3) could be involved in control of the expression of a subset of genes that are important in several pathways during encystation. Therefore, the identification of enzymes that acetylate and/or deacetylate histones that control encystation in E. invadens could be a promising therapeutic target for preventing transmission of other amoebic parasites such as E. histolytica, the causative agent of amoebiasis in humans.

Identifying the Molecular Targets of an Anti-pathogenic Hydroalcoholic Extract of Punica granatum Peel Against Multidrug-resistant Serratia marcescens

BACKGROUND

Antibiotic-resistant members of the family Enterobacteriaceae are among the serious threats to human health globally. This study reports the anti-pathogenic activity of Punica granatum peel extract (PGPE) against a multi-drug resistant, beta-lactamase producing member of this family i.e. Serratia marcescens.

OBJECTIVE

This study aimed at assessing the anti-pathogenic activity of PGPE against the gramnegative bacterial pathogen S. marcescens and identifying the molecular targets of this extract in the test bacterium.

METHODS

Effect of PGPE on S. marcescens growth and quorum sensing (QS)-regulated pigment production was assessed through broth dilution assay. In vivo anti-infective and prophylactic activity of PGPE was assessed employing the nematode worm Caenorhabditis elegans as a model host. Differential gene expression in PGPE-exposed S. marcescens was studied through a whole transcriptome approach.

RESULTS

PGPE was able to modulate QS-regulated pigment production in S. marcescens without exerting any heavy growth-inhibitory effect at concentrations as low as ≥2.5 μg/mL. It could attenuate the virulence of the test bacterium towards the worm host by 22-42% (p≤0.01) at even lower concentrations (≥0.5 μg/mL). PGPE also exerted a post-extract effect on S. marcescens. This extract was found to offer prophylactic benefit too, to the host worm, as PGPE-pre-fed worms scored better (34-51%; p≤0.001) survival in face of subsequent bacterial attack. Differential gene expression analysis revealed that PGPE affected the expression of a total of 66 genes in S. marcescens by ≥1.5 fold.

CONCLUSION

The anti-virulence effect of PGPE against S. marcescens is multifaceted, affecting stress-response machinery, efflux activity, iron homeostasis, and cellular energetics of this bacterium notably. Among the major molecular targets identified in this study are LPS export transporter permease (LptF), t-RNA pseudouridine synthase (TruB), etc.

Effect of high hydrostatic pressure challenge on biogenic amines, microbiota, and sensory profile in traditional poultry- and pork-based semidried fermented sausage

The processing of traditional poultry- and pork-based semidried fermented smoked sausages needs to be modernized to improve product quality and further extend its shelf life. The aim of the present study was to apply different combinations of high pressure (300 to 600 MPa) and time (154 to 1,800 s) on the sausages using an experimental design based on response surface methodology. The chemical, microbial, and sensory characteristics of sausages treated with high-pressure processing (HPP) were investigated. HPP application to semidried fermented sausages resulted in color changes, which could be dependent on the ingredients, formulation, and smoking conditions used. Nevertheless, none of the HPP treatments applied resulted in detectable changes in sensory properties, as tested in a triangle test and confirmed by the analysis of focus groups assessment. Significant differences were detected for lactic acid bacteria (LAB) counts from 344 MPa and 1,530 s onward, with a marked decrease for the combination of 600 MPa and 960 s (P < 0.05). Coagulase-negative staphylococci showed higher tolerance to the increase in pressure than LAB. HPP induced a microbial reduction on Enterobacteriaceae, molds, and yeasts, minimizing the production of the main biogenic amines. However, the polyamines (spermine and spermidine) increased since their metabolic use by microorganisms did not occur. Given the reduction of the main spoilage microbial indicators with no detectable sensory changes observed with the binomial condition of 600 MPa and 960 s, this was chosen as the optimal combination to be further applied. PRACTICAL APPLICATION: The results from sensory analysis revealed that any of the HPP treatments applied resulted in detectable changes in sensory properties, as tested in a triangle test and confirmed by the analysis of the focus groups speeches.

The signaling mechanisms involved in the dimorphic phenomenon of the Basidiomycota fungus Ustilago maydis

In the present manuscript, we describe the mechanisms involved in the yeast-to-hypha dimorphic transition of the plant pathogenic Basidiomycota fungus Ustilago maydis. During its life cycle, U. maydis presents two stages: one in the form of haploid saprophytic yeasts that divide by budding and the other that is the product of the mating of sexually compatible yeast cells (sporidia), in the form of mycelial dikaryons that invade the plant host. The occurrence of the involved dimorphic transition is controlled by the two mating loci a and b. In addition, the dimorphic event can be obtained in vitro by different stimuli: change in the pH of the growth medium, use of different carbon sources, and by nitrogen depletion. The presence of other factors and mechanisms may affect this phenomenon; among these, we may cite the PKA and MAPK signal transduction pathways, polyamines, and factors that affect the structure of the nucleosomes. Some of these factors and conditions may affect all these dimorphic events, or they may be specific for only one or more but not all the processes involved. The conclusion reached by these experiments is that U. maydis has constituted a useful model for the analysis of the mechanisms involved in cell differentiation of fungi in general.

The Thiol-polyamine Metabolism of Trypanosoma cruzi: Molecular Targets and Drug Repurposing Strategies

Chagas´ disease continues to be a challenging and neglected public health problem in many American countries. The etiologic agent, Trypanosoma cruzi, develops intracellularly in the mammalian host, which hinders treatment efficacy. Progress in the knowledge of parasite biology and host-pathogen interaction has not been paralleled by the development of novel, safe and effective therapeutic options. It is then urgent to seek for novel therapeutic candidates and to implement drug discovery strategies that may accelerate the discovery process. The most appealing targets for pharmacological intervention are those essential for the pathogen and, whenever possible, absent or significantly different from the host homolog. The thiol-polyamine metabolism of T. cruzi offers interesting candidates for a rational design of selective drugs. In this respect, here we critically review the state of the art of the thiolpolyamine metabolism of T. cruzi and the pharmacological potential of its components. On the other hand, drug repurposing emerged as a valid strategy to identify new biological activities for drugs in clinical use, while significantly shortening the long time and high cost associated with de novo drug discovery approaches. Thus, we also discuss the different drug repurposing strategies available with a special emphasis in their applications to the identification of drug candidates targeting essential components of the thiol-polyamine metabolism of T. cruzi.

Transcriptome and Volatilome Analysis During Growth of Brochothrix thermosphacta in Food: Role of Food Substrate and Strain Specificity for the Expression of Spoilage Functions

Brochothrix thermosphacta is one of the main spoilers in food, responsible for meat and seafood spoilage through the production of malodorous volatile organic compounds. The molecules produced by this bacterium depend on the substrate (meat or seafood) and the storage conditions such as gas mixtures used in the packaging. It seems also that the spoilage potential is strain dependent as production of diacetyl and acetoin, two molecules responsible for seafood spoilage, varies with strains. Therefore, this suggests the involvement of different metabolic functions depending on both food substrate and strain capacities. In this study, we selected two strains with different abilities to produce diacetyl and acetoin and compared their behavior after grown in beef or cooked peeled shrimp juices. We determined the genes upregulated by both strains depending on the growth substrate and those that were specifically upregulated in only one strain. The genes upregulated by both strains in meat or in shrimp juice revealed the importance of the substrate for inducing specific metabolic pathways. The examination of genes that were specifically upregulated in only one of the two strains revealed strain features associated to specific substrates and also strain-specific regulations of metabolic pathways putatively leading to different levels of spoilage molecule production. This shows that the spoilage potential of B. thermosphacta depends on nutrients provided by food substrate and on metabolic activity potential that each strain possesses.

Mitophagy could fight Parkinson's disease through antioxidant action

During aging, the process of mitophagy, a system that allows the removal of dysfunctional mitochondria through lysosomal degradation, starts to malfunction. Because of this defect, damaged mitochondria are not removed correctly, and their decomposing components accumulate inside the cells. Dysfunctional mitochondria that are not removed by mitophagy produce high amounts of reactive oxygen species (ROS) and, thus, cause oxidative stress. Oxidative stress, in turn, is very harmful for the cells, neuronal cells, in particular. Consequently, the process of mitophagy plays a crucial role in mitochondria-related disease. Mitochondrial dysfunctions and oxidative stress are well-established factors contributing to Parkinson's disease (PD), one of the most common neurodegenerative disorders. In this review, we report various known antioxidants for PD treatments and describe the stimulation of mitophagy process as a novel and exciting method for reducing oxidative stress in PD patients. We describe the different mechanisms responsible for mitochondria removal through the mitophagy process. In addition, we review the functional connection between mitophagy induction and reduction of oxidative stress in several in vitro models of PD and also agents (drugs and natural compounds) already known to be antioxidants and to be able to activate mitophagy. Finally, we propose that there is an urgent need to test the use of mitophagy-inducing antioxidants in order to fight PD.

Specific effects of antitumor active norspermidine on the structure and function of DNA

We compared the effects of trivalent polyamines, spermidine (SPD) and norspermidine (NSPD), a chemical homologue of SPD, on the structure of DNA and gene expression. The chemical structures of SPD and NSPD are different only with the number of methylene groups between amine groups, [N-3-N-4-N] and [N-3-N-3-N], respectively. SPD plays vital roles in cell function and survival, including in mammals. On the other hand, NSPD has antitumor activity and is found in some species of plants, bacteria and algae, but not in humans. We found that both polyamines exhibit biphasic effect; enhancement and inhibition on in vitro gene expression, where SPD shows definitely higher potency in enhancement but NSPD causes stronger inhibition. Based on the results of AFM (atomic force microscopy) observations together with single DNA measurements with fluorescence microscopy, it becomes clear that SPD tends to align DNA orientation, whereas NSPD induces shrinkage with a greater potency. The measurement of binding equilibrium by NMR indicates that NSPD shows 4-5 times higher affinity to DNA than SPD. Our theoretical study with Monte Carlo simulation provides the insights into the underlying mechanism of the specific effect of NSPD on DNA.

Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae

Streptococcus pneumoniae (pneumococcus, Spn) colonizes the human nasopharynx asymptomatically but can cause infections such as otitis media, and invasive pneumococcal disease such as community-acquired pneumonia, meningitis, and sepsis. Although the success of Spn as a pathogen can be attributed to its ability to synthesize and regulate capsular polysaccharide (CPS) for survival in the host, the mechanisms of CPS regulation are not well-described. Recent studies from our lab demonstrate that deletion of a putative polyamine biosynthesis gene (ΔcadA) in Spn TIGR4 results in the loss of the capsule. In this study, we characterized the transcriptome and metabolome of ΔcadA and identified specific mechanisms that could explain the regulatory role of polyamines in pneumococcal CPS biosynthesis. Our data indicate that impaired polyamine synthesis impacts galactose to glucose interconversion via the Leloir pathway which limits the availability of UDP-galactose, a precursor of serotype 4 CPS, and UDP-N-acetylglucosamine (UDP-GlcNAc), a nucleotide sugar precursor that is at the intersection of CPS and peptidoglycan repeat unit biosynthesis. Reduced carbon flux through glycolysis, coupled with altered fate of glycolytic intermediates further supports impaired synthesis of UDP-GlcNAc. A significant increase in the expression of transketolases indicates a potential shift in carbon flow toward the pentose phosphate pathway (PPP). Higher PPP activity could constitute oxidative stress responses in ΔcadA which warrants further investigation. The results from this study clearly demonstrate the potential of polyamine synthesis, targeted for cancer therapy in human medicine, for the development of novel prophylactic and therapeutic strategies for treating bacterial infections.

A 2D-DIGE-based proteomic analysis brings new insights into cellular responses of Pseudomonas putida KT2440 during polyhydroxyalkanoates synthesis

Background

Polyhydroxyalkanoates (PHAs) have attracted much attention in recent years as natural alternatives to petroleum-based synthetic polymers that can be broadly used in many applications. Pseudomonas putida KT2440 is a metabolically versatile microorganism that is able to synthesize medium-chain-length PHAs (mcl-PHAs). The phenomena that drive mcl-PHAs synthesis and accumulation seems to be complex and are still poorly understood. Therefore, here we determine new insights into cellular responses of Pseudomonas putida KT2440 during biopolymers production using two-dimensional difference gel-electrophoresis (2D-DIGE) followed by MALDI TOF/TOF mass spectrometry.

Results

The maximum mcl-PHAs content in Pseudomonas putida KT2440 cells was 24% of cell dry weight (CDW) and was triggered by nitrogen depletion. Proteomic analysis allowed the detection of 150 and 131 protein spots differentially regulated at 24 h and 48 h relative to the cell growth stage (8 h), respectively. From those, we successfully identified 84 proteins that had altered expression at 24 h and 74 proteins at 48 h of the mcl-PHAs synthesis process. The protein–protein interactions network indicated that the majority of identified proteins were functionally linkage. The abundance of proteins involved in carbon metabolism were significantly decreased at 24 h and 48 h of the cultivations. Moreover, proteins associated with ATP synthesis were up-regulated suggesting that the enhanced energy metabolism was necessary for the mcl-PHAs accumulation. Furthermore, the induction of proteins involved in nitrogen metabolism, ribosome synthesis and transport was observed. Our results indicate that mcl-PHAs accumulated in the bacterial cells changed the protein abundance involved in stress response and cellular homeostasis.

Conclusions

The presented data allow us to investigate time-course proteome rearrangement in response to nitrogen limitation and biopolyesters accumulation. Our results have pointed out novel proteins that might take part in cellular responses of mcl-PHA-accumulated bacteria. The study provides an additional knowledge that could be helpful to improve the efficiency of the bioprocess and make it more economically feasible.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1146-5) contains supplementary material, which is available to authorized users.

Spermidine plays a significant role in stabilizing a master transcription factor Clp to promote antifungal activity in Lysobacter enzymogenes

Spermidine is a common polyamine compound produced in bacteria, but its roles remain poorly understood. The bacterial SpeD encodes an S-adenosylmethionine decarboxylase that participates in spermidine synthesis. Lysobacter enzymogenes is an efficient environmental predator of crop fungal pathogens by secreting an antifungal antibiotic HSAF (heat-stable antifungal factor), while Clp is a master transcription factor essential for the antifungal activity of L. enzymogenes. In this work, we observed that speD was a close genomic neighbor of the clp gene. This genomic arrangement also seems to occur in many other bacteria, but the underlying reason remains unclear. By using L. enzymogenes OH11 as a working model, we showed that SpeD was involved in spermidine production that was essential for the L. enzymogenes antifungal activity. Spermidine altered the bacterial growth capability and HSAF production, both of which critically contributed to the L. enzymogenes antifungal activity. We further found that spermidine in L. enzymogenes was able to play a crucial, yet indirect role in maintaining the Clp level in vivo, at least partially accounting for its role in the antifungal activity. Thus, our findings suggested that spermidine probably plays an uncharacterized role in maintaining the levels of the master transcription regulator Clp to optimize its role in antifungal activity in an agriculturally beneficial bacterium.