BACKGROUNDQuantitative co-localization studies strengthen the analysis of fluorescence microscopy-based assays and are essential for illustrating and understanding many cellular processes and ...interactions. In our earlier study, we presented a rank-based intensity weighting scheme for the quantification of co-localization between structures in fluorescence microscopy images. This method, which uses a combined pixel co-occurrence and intensity correlation approach, is superior to conventional algorithms and provides a more accurate quantification of co-localization. FINDINGSIn this brief report we provide the source code and implementation of the rank-weighted co-localization (RWC) algorithm in three (two open source and one proprietary) image analysis platforms. The RWC algorithm has been implemented as a plugin for ImageJ, a module for CellProfiler and an Acapella script for Columbus image analysis software tools. CONCLUSIONSWe have provided with a web resource from which users can download plugins and modules implementing the RWC algorithm in various commonly used image analysis platforms. The implementations have been designed for easy incorporation into existing tools in a 'ready-for-use' format. The resources can be accessed through the following web link: http://simpsonlab.pbworks.com/w/page/48541482/Bioinformatic_Tools.
Anaerobic gut fungi (Neocallimastigomycetes) live in the digestive tract of large herbivores, where they are vastly outnumbered by bacteria. It has been suggested that anaerobic fungi challenge ...growth of bacteria owing to the wealth of biosynthetic genes in fungal genomes, although this relationship has not been experimentally tested. Here, we cocultivated the rumen bacteria
strain UWB7 with the anaerobic gut fungi
or
on a range of carbon substrates and quantified the bacterial and fungal transcriptomic response. Synthetic cocultures were established for at least 24 h, as verified by active fungal and bacterial transcription.
upregulated components of its secondary metabolism in the presence of
strain UWB7, including six nonribosomal peptide synthetases, one polyketide synthase-like enzyme, and five polyketide synthesis O-type methyltransferases. Both
and
cocultures upregulated
-adenosyl-l-methionine (SAM)-dependent methyltransferases, histone methyltransferases, and an acetyltransferase. Fungal histone 3 lysine 27 trimethylation marks were more abundant in coculture, and heterochromatin protein-1 was downregulated. Together, these findings suggest that fungal chromatin remodeling occurs when bacteria are present.
strain UWB7 upregulated four genes in coculture encoding drug efflux pumps, which likely protect the cell against toxins. Furthermore, untargeted nonpolar metabolomics data revealed at least one novel fungal metabolite enriched in coculture, which may be a defense compound. Taken together, these data suggest that
and
produce antimicrobials when exposed to rumen bacteria and, more broadly, that anaerobic gut fungi are a source of novel antibiotics.
Anaerobic fungi are outnumbered by bacteria by 4 orders of magnitude in the herbivore rumen. Despite their numerical disadvantage, they are resilient members of the rumen microbiome. Previous studies mining the genomes of anaerobic fungi identified genes encoding enzymes to produce natural products, which are small molecules that are often antimicrobials. In this work, we cocultured the anaerobic fungus
or
with rumen bacteria
strain UWB7 and sequenced fungal and bacterial active genes via transcriptome sequencing (RNA-seq). Consistent with production of a fungal defense compound, bacteria upregulated genes encoding drug efflux pumps, which often export toxic molecules, and fungi upregulated genes encoding biosynthetic enzymes of natural products. Furthermore, tandem mass spectrometry detected an unknown fungal metabolite enriched in the coculture. Together, these findings point to an antagonistic relationship between anaerobic fungi and rumen bacteria resulting in the production of a fungal compound with potential antimicrobial activity.
Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases ...typically relies on breeding programs that can take decades to complete. To demonstrate how this process can be accelerated, we employed a genome-wide association mapping of ca. 1,000 resequenced Populus trichocarpa trees individually challenged with Sphaerulina musiva, an invasive fungal pathogen. Among significant associations, three loci associated with resistance were identified and predicted to encode one putative membrane-bound L-type receptor-like kinase and two receptor-like proteins. A susceptibility-associated locus was predicted to encode a putative G-type D-mannose–binding receptor-like kinase. Multiple lines of evidence, including allele analysis, transcriptomics, binding assays, and overexpression, support the hypothesized function of these candidate genes in the P. trichocarpa response to S. musiva.
Lignocellulosic plant biomass is an important feedstock for bio-based economy. In particular, it is an abundant renewable source of aromatic compounds, which are present as part of lignin, as ...side-groups of xylan and pectin, and in other forms, such as tannins. As filamentous fungi are the main organisms that modify and degrade lignocellulose, they have developed a versatile metabolism to convert the aromatic compounds that are toxic at relatively low concentrations to less toxic ones. During this process, fungi form metabolites some of which represent high-value platform chemicals or important chemical building blocks, such as benzoic, vanillic, and protocatechuic acid. Especially basidiomycete white-rot fungi with unique ability to degrade the recalcitrant lignin polymer are expected to perform highly efficient enzymatic conversions of aromatic compounds, thus having huge potential for biotechnological exploitation. However, the aromatic metabolism of basidiomycete fungi is poorly studied and knowledge on them is based on the combined results of studies in variety of species, leaving the overall picture in each organism unclear. Dichomitus squalens is an efficiently wood-degrading white-rot basidiomycete that produces a diverse set of extracellular enzymes targeted for lignocellulose degradation, including oxidative enzymes that act on lignin. Our recent study showed that several intra- and extracellular aromatic compounds were produced when D. squalens was cultivated on spruce wood, indicating also versatile aromatic metabolic abilities for this species. In order to provide the first molecular level systematic insight into the conversion of plant biomass derived aromatic compounds by basidiomycete fungi, we analyzed the transcriptomes of D. squalens when grown with 10 different lignocellulose-related aromatic monomers. Significant differences for example with respect to the expression of lignocellulose degradation related genes, but also putative genes encoding transporters and catabolic pathway genes were observed between the cultivations supplemented with the different aromatic compounds. The results demonstrate that the transcriptional response of D. squalens is highly dependent on the specific aromatic compounds present suggesting that instead of a common regulatory system, fine-tuned regulation is needed for aromatic metabolism.
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•Mechanisms of white-rot fungal plant polysaccharide degradation are mostly unknown.•White-rot fungus Dichomitus squalens shows cellobiose-based response to ...cellulose.•Pectin-polysaccharides trigger a broad targeted pectinolytic response in D. squalens.•Co-expression analysis reveals candidate regulators of polysaccharide degradation.•Plant polysaccharides induce complete transcriptional response in white-rot fungi.
Wood-degrading white-rot fungi can efficiently degrade all plant biomass components, but the molecular mechanisms behind the degradation of plant polysaccharides remain poorly understood. For example, the gene sets and expression levels induced by the plant polysaccharide-derived monosaccharides in white-rot fungi do not reflect those induced by crude plant biomass substrates. To explore the molecular response of the white-rot fungus Dichomitus squalens to plant-derived oligo- and polysaccharides, we investigated the transcriptomes from mono- and dikaryotic strains of the fungus on 10 substrates and compared the expression of carbohydrate-active enzyme-encoding genes to that previously reported for different monosaccharides and cellobiose. Our results revealed that in D. squalens, a robust response to cellulose leads to its effective depolymerization, with an orthologue of the ascomycete Trichoderma reesei ACE3 likely acting as a central transcriptional regulator. The conserved response between cellulose and cellobiose further confirms cellobiose as the main cellulase inducer in D. squalens. Surprisingly, despite low abundance of pectin in the natural wood substrate of D. squalens, we identified polygalacturonic acid as a major inducer of a broad-targeted pectinolytic response including pectinase, pectin-related sugar transporter and catabolism genes, and four fungal specific transcription factors. This indicates that D. squalens has not only maintained its ability to degrade minor polysaccharide components in its biotope, but also a regulatory system spanning from extracellular degradation to metabolic conversion. Our study contributes to a deeper understanding of the molecular mechanisms behind white-rot fungal plant polysaccharide degradation and provides leads for functional studies of potential transcriptional regulators in basidiomycetes.
Microalgae that are of interest for biofuel production must be able to tolerate environmental changes that occur in outdoor cultivation systems. While algal cultures may experience daily temperature ...fluctuations and seasonal environmental changes, the underlying mechanisms that control and regulate physiological responses and adaptation to environmental pressures are largely unknown. Systems-level characterization enabled by functional genomics can help identify biochemical pathways that promote stability and productivity of algae in various environmental conditions. Monoraphidium minutum 26B-AM, a freshwater green microalga, was identified as a top performer in biomass production in winter season screens. We sequenced the genome of M. minutum 26B-AM and applied our multi-omics pipeline to profile this high potential strain under high salt and cold temperature perturbations. Through comparative analysis, including other green algae in the class Chlorophyceae, we identified gene families unique to the genus Monoraphidium, including a desaturase that has been linked to cold tolerance in plants. We observed that osmolytes, such as trehalose, proline and betaine, accumulate under salt stress, coinciding with upregulation of genes involved in biosynthesis of these metabolites. From the genome annotation, we reconstructed a metabolic model to provide a detailed map of the metabolic pathways and can be used to simulate growth and reaction fluxes. This multi-omics analysis provides a foundation to explore algal strain potential for biofuel applications, guides strain engineering, and expands our understanding of metabolic and regulatory mechanisms of algae in applied systems.
•Analysis of Monoraphidium minutum genome identifies lineage-specific gene families.•Transcriptomics profiling reveals response of conserved genes to abiotic stress.•Known osmolytes, like proline, betaine, and trehalose, accumulate under salt stress.•Metabolic modeling predicts essential genes for the growth of M. minutum.
Dinitrogen (N2)-fixation by cyanobacteria in symbiosis with feather mosses represents the main pathway of biological N input into boreal forests. Despite its significance, little is known about the ...gene repertoire needed for the establishment and maintenance of the symbiosis. To determine gene acquisitions or regulatory rewiring allowing cyanobacteria to form this symbiosis, we compared closely related Nostoc strains that were either symbiosis-competent or non-competent, using a proteogenomics approach and a unique experimental setup allowing for controlled chemical and physical contact between partners. Thirty-two protein families were only in the genomes of competent strains, including some never before associated with symbiosis. We identified conserved orthologs that were differentially expressed in competent strains, including gene families involved in chemotaxis and motility, NO regulation, sulfate/phosphate transport, sugar metabolism, and glycosyl-modifying and oxidative stress-mediating exoenzymes. In contrast to other cyanobacteria-plant symbioses, the moss-cyanobacteria epiphytic symbiosis is distinct, with the symbiont retaining motility and chemotaxis, and not modulating N-fixation, photosynthesis, GS-GOGAT cycle, and heterocyst formation. Our work expands our knowledge of plant cyanobacterial symbioses, provides an interaction model of this ecologically significant symbiosis, and suggests new currencies, namely nitric oxide and aliphatic sulfonates, may be involved in establishing and maintaining this symbiosis.
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