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At least 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, although the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of Zn tolerance in the ectomycorrhizal fungus Suillus luteus. We found that Zn tolerance in this species is mainly a constitutive trait that can also be environmentally dependent. Zinc tolerance in S. luteus is associated with differences in the expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus Zn tolerance, while others are reported here for the first time. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of fungal metal tolerance in mycorrhizal associations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F 1 and F 2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F 1 progeny individuals. We show that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Lastly, altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment

Abstract The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption—impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01–4.7 fmol SO42− cell−1 h−1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23–40 nmol h−1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.

Lindsay, Melody R.↗
DOE OSTI2023

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

Abstract Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Network analysis of transcriptomics expands regulatory landscapes in Synechococcus sp. PCC 7002

Cyanobacterial regulation of gene expression must contend with a genome organization that lacks apparent functional context, as the majority of cellular processes and metabolic pathways are encoded by genes found at disparate locations across the genome. In addition, the fact that coordinated regulation of cyanobacterial cellular machinery takes place with significantly fewer transcription factors, compared to other Eubacteria, suggests the involvement of post-transcriptional mechanisms and regulatory adaptations which are not fully understood. Global transcript abundance from model cyanobacterium Synechococcus sp. PCC 7002 grown under 42 different conditions was analyzed using context-likelihood of relatedness. The resulting 903-gene network, which was organized into 11 modules, not only allowed classification of cyanobacterial responses to specific environmental variables but provided insight into the transcriptional network topology and led to the expansion of predicted regulons. When used in conjunction with genome sequence, the global transcript abundance allowed identification of putative post-transcriptional changes in expression as well as novel potential targets of both DNA binding proteins and asRNA regulators. The results offer a new perspective into the multi-level regulation that governs cellular adaptations of fast-growing physiologically robust cyanobacterium Synechococcus sp. PCC 7002 to changing environmental variables. It also extends a methodological knowledge-based framework for studying multi-scale regulatory mechanisms that operate in cyanobacteria. Finally, it provides valuable context for integrating systems-level data to enhance evidence-driven genomic annotation, especially in organisms where traditional context analyses cannot be implemented due to lack of operon-based functional organization.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2016

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome Assembly and Transcriptome of Colletotrichum sublineola CsGL1, a New Resource to Study Anthracnose Disease in Sorghum

Colletotrichum species are globally distributed and well known as members of a destructive phytopathogenic genus, causing the anthracnose disease in a wide variety of crops and fruits. Colletotrichum sublineola is the causal agent of the anthracnose disease in sorghum, causing losses of up to 50% in yield. Here, we used PacBio sequencing combined with RNA-seq to generate a chromosome-level assembly and annotation of the Colletotrichum sublineola strain CsGL1. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Biochemistry & Molecular Biology↗
DOE OSTI2010

Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism

Abstract Desulfovibrio vulgaris is a metabolically flexible microorganism. It can use sulfate as electron acceptor to catabolize a variety of substrates, or in the absence of sulfate can utilize organic acids and alcohols by forming a syntrophic association with hydrogen scavenging partner to relieve inhibition by hydrogen. These alternativemetabolic types increase the chance of survival for D. vulgaris in environments where one of the potential external electron acceptors becomes depleted. In this work, whole-genome D. vulgaris microarrays were used to determine relative transcript levels as D. vulgaris shifted its metabolism from syntroph in a lactate-oxidizing dual-culture with Methanosarcina barkeri to a sulfidogenic metabolism. Syntrophic dual-cultures were grown in two independent chemostats and perturbation was introduced after six volume changes with the addition of sulfate. The results showed that 132 genes were differentially expressed in D. vulgaris 2 hours after addition of sulfate. Functional analyses suggested that genes involved in cell envelope and energy metabolism were the most regulated when comparing syntrophic and sulfidogenic metabolism. Up-regulation was observed for genes encoding ATPase and the membrane-integrated energy conserving hydrogenase (Ech) when cells shifted to a sulfidogenic metabolism. A five-gene cluster encoding several lipo- and membrane-bound proteins was down-regulated when cells were shifted to a sulfidogenic metabolism. Interestingly, this gene cluster has orthologs found only in another syntrophic bacterium Syntrophobacter fumaroxidans and four recently sequenced Desulfovibrio strains. This study also identified several novel c-type cytochrome encoding genes which may be involved in the sulfidogenic metabolism.

08 HYDROGEN↗
DOE OSTI2020

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ~40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

59 BASIC BIOLOGICAL SCIENCES↗