Time-dependent transcriptome profile of genes involved in triacylglycerol (TAG) and polyunsaturated fatty acid synthesis in Nannochloropsis gaditana during nitrogen starvation

In this research, the gene expression of genes involved in lipid metabolism of the eustigmatophyte alga Nannochloropsis gaditana was measured by transcriptomic data. This microalga can be used as a source of triacylglycerol (TAG) and the omega-3 fatty acid eicosapentaenoic acid (EPA). Insight in TAG and EPA production and regulation are needed to improve their productivity. Nitrogen starvation induces TAG accumulation in N. gaditana. Previous research showed that during nitrogen starvation, EPA was translocated from the polar lipids to TAG and de novo synthesized in N. gaditana. Therefore, the expression levels of genes involved in fatty acid translocation and de novo TAG synthesis were measured. Furthermore, the genes involved in de novo EPA synthesis such as elongases and desaturases were studied. The expression levels were measured during the first hours of nitrogen starvation and the subsequent period of 14 days. One phospholipid:diacylglycerol acyltransferase (PDAT) gene involved in translocation of fatty acids from membrane lipids to TAG was upregulated. In addition, several lipases were upregulated, suggesting that these enzymes might be responsible for the translocation of EPA to TAG. Most desaturases and elongases involved in de novo EPA synthesis were downregulated during nitrogen starvation, except for Δ9 desaturase which was upregulated. This upregulation correlates with the increase in oleic acid. Due to the presence of many hypothetical genes, improvement in annotation is needed to increase our understanding of these pathways and their regulation.</p

Classical, novel and atypical isoforms of PKC stimulate ANF- and TRE/AP-1-regulated-promoter activity in ventricular cardiomyocytes

Cultured neonatal rat ventricular myocytes were co-transfected with expression plasmids encoding protein kinase C (PKC) isoforms from each of the PKC subfamilies (classical PKC-α, novel PKC-ε or atypical PKC-ξ) together with an atrial natriuretic factor (ANF) reporter plasmid. Each PKC had been rendered constitutively active by a single Ala→Glu mutation or a small deletion in the inhibitory pseudosubstrate site. cPKC-α, nPKC-ε or aPKC-ξ expression plasmids each stimulated ANF-promoter activity and expression of a reporter gene under the control of a 12-O-tetradecanoylphorbol 13-acetate-response element (TRE). Upregulation of the ANF promoter is characteristic of the hypertrophic response in the heart ventricle and a TRE is present in the ANF promoter. Thus all subfamilies of PKC may have the potential to contribute to hypertrophic response in cardiomyocytes

Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets

Graphene nanomaterials have attracted a great interest during the last years for different applications, but their possible impact on different biological systems remains unclear. Here, an assessment to understand the toxicity of commercial polycarboxylate functionalized graphene nanoplatelets (GN) on the unicellular fungal model Saccharomyces cerevisiae was performed. While cell proliferation was not negatively affected even in the presence of 800 mg L−1 of the nanomaterial for 24 hours, oxidative stress was induced at a lower concentration (160 mg L−1), after short exposure periods (2 and 4 hours). No DNA damage was observed under a comet assay analysis under the studied conditions. In addition, to pinpoint the molecular mechanisms behind the early oxidative damage induced by GN and to identify possible toxicity pathways, the transcriptome of S. cerevisiae exposed to 160 and 800 mg L−1 of GN was studied. Both GN concentrations induced expression changes in a common group of genes (337), many of them related to the fungal response to reduce the nanoparticles toxicity and to maintain cell homeostasis. Also, a high number of genes were only differentially expressed in the GN800 condition (3254), indicating that high GN concentrations can induce severe changes in the physiological state of the yeast.European Union’s H2020 research and innovation programme under the Marie Skłodowska-Curie grant agreements N° 691095 and N° 734873; and Junta de Castilla y Leon-FEDER under grants N° BU079U16, and N° UBU-16-B

Microbial systems for conversion of syngas to biobased products

Microbiology Centennial Symposium 2017 - Exploring Microbes for the Quality of Life (Book of Abstracts)Synthesis gas, a mixture of CO, H2, and CO2, can be created via gasification of any carbohydrate material. Fermentation of syngas by carboxydotrophic microbes allows for it to be converted into interesting bio-chemicals. Organisms involved in the fermentation of syngas use the CO or H2 in the gas as electron donor, fixating CO2 into the final end products. Currently acetate and ethanol are relatively well established products from syngas fermentation and there is interest to broaden the scope towards production of more complex products. However, genetic engineering of carboxydotrophic organisms and the knowledge of their metabolism is rather limited, making it difficult to create strains producing these products. A possible way to broaden the scope of products is via co-cultivation of microbes which can make use of each others products. We established a co-cultivation of Clostridium autoethanogenum, a well-known carboxydotrophic acetogen, together with Clostridium kluyveri, a well characterized organism employing the reverse -oxidation pathway. C. autoethanogenum uses the syngas to produce a mixture of acetate and ethanol. C. kluyveri subsequently uses these products to perform chain elongation. This results in a co-culture producing a mixture of C4 and C6 acids and alcohols using carbon monoxide as a sole substrate. This co-culture poses an interesting way for production of more complex and valuable products from syngas. Basic characterization of these co-cultures has been done and currently the research focus lies on how the species interact with each other and how environmental factors influence their production patterns and metabolism.info:eu-repo/semantics/publishedVersio

Regulation of three virulence strategies of Mycobacterium tuberculosis : A success story

Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review recent literature to provide a systems level overview of the molecular and cellular components involved in divalent metal homeostasis and their role in regulating the three main virulence strategies of M. tuberculosis: immune modulation, dormancy and phagosomal rupture. We provide a visual and modular overview of these components and their regulation. Our analysis identified a single regulatory cascade for these three virulence strategies that respond to limited availability of divalent metals in the phagosome

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach

Host glycans are paramount in regulating the symbiotic relationship between humans and their gut bacteria. The constant flux of host-secreted mucin at the mucosal layer creates a steady niche for bacterial colonization. Mucin degradation by keystone species subsequently shapes the microbial community. This study investigated the transcriptional response during mucin-driven trophic interaction between the specialised mucin-degrader Akkermansia muciniphila and a butyrogenic gut commensal Anaerostipes caccae. A. muciniphila monocultures and co-cultures with non-mucolytic A. caccae from the Lachnospiraceae family were grown anaerobically in minimal media supplemented with mucin. We analysed for growth, metabolites (HPLC analysis), microbial composition (quantitative reverse transcription PCR), and transcriptional response (RNA-seq). Mucin degradation by A. muciniphila supported the growth of A. caccae and concomitant butyrate production predominantly via the acetyl-CoA pathway. Differential expression analysis (DESeq 2) showed the presence of A. caccae induced changes in the A. muciniphila transcriptional response with increased expression of mucin degradation genes and reduced expression of ribosomal genes. Two putative operons that encode for uncharacterised proteins and an efflux system, and several two-component systems were also differentially regulated. This indicated A. muciniphila changed its transcriptional regulation in response to A. caccae. This study provides insight to understand the mucin-driven microbial ecology using metatranscriptomics. Our findings show that the expression of mucolytic enzymes by A. muciniphila increases upon the presence of a community member. This could indicate its role as a keystone species that supports the microbial community in the mucosal environment by increasing the availability of mucin sugars.Peer reviewe

A genomic view on syntrophic versus non-syntrophic lifestyle of anaerobic fatty acid-degrading bacteria

In sulfate-reducing and methanogenic environments complex biopolymers are degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate reduction. We applied a genomic approach to understand why some bacteria are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases, including their maturation protein are a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production and a second in cell division, shape-determination or sporulation. Some sulfate reducing bacteria have never been tested for syntrophic growth, but as all crucial domains were found in their genomes, it is possible that these are able to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnfcomplex and the formate transporter in syntrophy, and indicates that DUF224 may have a role in electron transfer in bacteria that show syntrophic growth

Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio

Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesised that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival e.g. through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges