Inferring metabolic pathway activity levels from RNA-Seq data

Temate‐Tiagueu, Yvette; Seesi, Sahar Al; Mathew, Meril; Mandric, Igor; Rodríguez, Álex; Bean, Kayla; Cheng, Qiong; Glebova, Olga; Măndoiu, Ion; Lopanik, Nicole B.; Zelikovsky, Alexander

doi:10.1186/s12864-016-2823-y

Cited by 12 publications

(7 citation statements)

References 28 publications

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“…DEGs belonging to the same group (profile) were anticipated to have similar patterns of expression over exposure concentrations. DEGs were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis …”

Section: Methodsmentioning

confidence: 99%

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Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2′,4,4′-Tetrabromodiphenyl Ether (BDE-47) Biotransformation

Zhang

Mao

Liu

et al. 2022

Environ. Sci. Technol.

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The brominated flame retardant 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47) is extensively used, stable, and difficult to degrade in the environment. The existence of BDE-47 could pose a certain risk to the environment and human health. However, the biotransformation mechanisms of BDE-47 by microorganisms remain unclear. In this study, aerobic degradation of BDE-47 by Stenotrophomonas sp. strain WZN-1 and transcriptome analysis were carried out. BDE-47 degradation by Stenotrophomonas sp. strain WZN-1 was mainly through the biological action of intracellular enzymes via the route of debromination and hydroxylation. The results of the transcriptome sequencing indicated the differentially expressed genes were related to transport, metabolism, and stress response. The key processes involved the microbial transmembrane transportation of BDE-47, energy anabolism, synthesis, and metabolism of functional enzymes, stress response, and other biological processes of gene regulation. In particular, bacterial chemotaxis played a potential role in biodegradation of BDE-47 by Stenotrophomonas sp. strain WZN-1. This study provides the first insights into the biotransformation of Stenotrophomonas sp. strain WZN-1 to BED-47 stress and shows potential for application in remediation of polluted environments.

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Section: Methodsmentioning

confidence: 99%

“…DEGs were then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. 29 2.8. Quality Assurance and Quality Control.…”

Section: Dual Chamber Experimentmentioning

confidence: 99%

Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2′,4,4′-Tetrabromodiphenyl Ether (BDE-47) Biotransformation

Zhang

Mao

Liu

et al. 2022

Environ. Sci. Technol.

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“…Three biological replicates were analyzed using the Power SYBR Green PCR Master Mix (Applied Biosystems, Foster City, CA, USA) on a 7500 Real-Time PCR System machine (Applied Biosystems) according to the manufacturer’s protocol. The gene-specific primers were designed using the Primer 3 software [ 61 ]. The relative values for the expression levels were calculated by the 2 −ΔΔCt method [ 62 ].…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Analysis of Pyrus betulaefolia Seedling Root Responses to Short-Term Potassium Deficiency

Han

Jin

et al. 2020

IJMS

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Potassium (K) plays a crucial role in multiple physiological and developmental processes in plants. Its deficiency is a common abiotic stress that inhibits plant growth and reduces crop productivity. A better understanding of the mechanisms involved in plant responses to low K could help to improve the efficiency of K use in plants. However, such responses remain poorly characterized in fruit tree species such as pears (Pyrus sp). We analyzed the physiological and transcriptome responses of a commonly used pear rootstock, Pyrus betulaefolia, to K-deficiency stress (0 mM). Potassium deprivation resulted in apparent changes in root morphology, with short-term low-K stress resulting in rapidly enhanced root growth. Transcriptome analyses indicated that the root transcriptome was coordinately altered within 6 h after K deprivation, a process that continued until 15 d after treatment. Potassium deprivation resulted in the enhanced expression (up to 5-fold) of a putative high-affinity K+ transporter, PbHAK5 (Pbr037826.1), suggesting the up-regulation of mechanisms associated with K+ acquisition. The enhanced root growth in response to K-deficiency stress was associated with a rapid and sustained decrease in the expression of a transcription factor, PbMYB44 (Pbr015309.1), potentially involved in mediating auxin responses, and the increased expression of multiple genes associated with regulating root growth. The concentrations of several phytohormones including indoleacetic acid (IAA), ABA, ETH, gibberellin (GA3), and jasmonic acid (JA) were higher in response to K deprivation. Furthermore, genes coding for enzymes associated with carbon metabolism such as SORBITOL DEHYDROGENASE (SDH) and SUCROSE SYNTHASE (SUS) displayed greatly enhanced expression in the roots under K deprivation, presumably indicating enhanced metabolism to meet the increased energy demands for growth and K+ acquisition. Together, these data suggest that K deprivation in P. betulaefolia results in the rapid re-programming of the transcriptome to enhance root growth and K+ acquisition. These data provide key insights into the molecular basis for understanding low-K-tolerance mechanisms in pears and in other related fruit trees and identifying potential candidates that warrant further analyses.

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“…Finally, the XPathway was used based to compare metabolic pathways across experimental conditions. The XPathway is able to detect and quantify the metabolic differentiation between the two conditions (Temate-tiagueu et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

Assessing the Effect of Pretreatments on the Structure and Functionality of Microbial Communities for the Bioconversion of Microalgae to Biogas

et al. 2018

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Microalgae biomethanization is driven by anaerobic sludge associated microorganisms and is generally limited by the incomplete hydrolysis of the microalgae cell wall, which results in a low availability of microalgal biomass for the methanogenic community. The application of enzymatic pretreatments, e.g., with hydrolytic enzymes, is among the strategies used to work around the incomplete hydrolysis of the microalgae cell wall. Despite the proven efficacy of these pretreatments in increasing biomethanization, the changes that a given pretreatment may cause to the anaerobic sludge associated microorganisms during biomethanization are still unknown. This study evaluated the changes in the expression of the metatranscriptome of anaerobic sludge associated microorganisms during Chlorella sorokiniana biomethanization without pretreatment (WP) (control) and pretreated with commercial cellulase in order to increase the solubilization of the microalgal organic matter. Pretreated microalgal biomass experienced significant increases in biogas the production. The metatranscriptomic analysis of control samples showed functionally active microalgae cells, a bacterial community dominated by γ- and δ-proteobacteria, and a methanogenic community dominated by Methanospirillum hungatei. In contrast, pretreated samples were characterized by the absence of active microalgae cells and a bacteria population dominated by species of the Clostridia class. These differences are also related to the differential activation of metabolic pathways e.g., those associated with the degradation of organic matter during its biomethanization.

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Inferring metabolic pathway activity levels from RNA-Seq data

Cited by 12 publications

References 28 publications

Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2′,4,4′-Tetrabromodiphenyl Ether (BDE-47) Biotransformation

Transcriptome Profiling of Stenotrophomonas sp. Strain WZN-1 Reveals Mechanisms of 2,2′,4,4′-Tetrabromodiphenyl Ether (BDE-47) Biotransformation

Transcriptome Analysis of Pyrus betulaefolia Seedling Root Responses to Short-Term Potassium Deficiency

Assessing the Effect of Pretreatments on the Structure and Functionality of Microbial Communities for the Bioconversion of Microalgae to Biogas

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