Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan

Kok Jun Liew; Neil C. Bruce; Rajesh Kumar Sani; Chun Shiong Chong; Amira Suriaty Yaakop; Mohd Shahir Shamsir; Kian Mau Goh

doi:10.3390/microorganisms8070976

Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan

Microorganisms ◽

10.3390/microorganisms8070976 ◽

2020 ◽

Vol 8 (7) ◽

pp. 976

Author(s):

Kok Jun Liew ◽

Neil C. Bruce ◽

Rajesh Kumar Sani ◽

Chun Shiong Chong ◽

Amira Suriaty Yaakop ◽

...

Keyword(s):

New Genus ◽

Enzymatic Activities ◽

Glycosyl Hydrolases ◽

Marine Broth ◽

Beechwood Xylan ◽

Transcriptomic Responses ◽

Membrane Components ◽

Upregulated Genes ◽

Current Report

The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis.

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Transcriptomic responses to hypoxia in endometrial and decidual stromal cells

10.1101/2019.12.21.885657 ◽

2019 ◽

Author(s):

Kalle T. Rytkönen ◽

Taija Heinosalo ◽

Mehrad Mahmoudian ◽

Xinghong Ma ◽

Antti Perheentupa ◽

...

Keyword(s):

Transcription Factors ◽

Stromal Cells ◽

Epithelial Mesenchymal Transition ◽

Cell Types ◽

Core Gene ◽

Stromal Fibroblasts ◽

Mesenchymal Transition ◽

The Core ◽

Transcriptomic Responses ◽

Upregulated Genes

AbstractHuman reproductive success depends on a properly decidualized uterine endometrium that allows implantation and the formation of the placenta. At the core of the decidualization process are endometrial stromal fibroblasts (ESF) that differentiate to decidual stromal cells (DSC). As variations in oxygen levels are functionally relevant in endometrium both upon menstruation and during placentation, we assessed the transcriptomic responses to hypoxia in ESF and DSC. In both cell types hypoxia upregulated genes in classical hypoxia pathways such as glycolysis and the epithelial mesenchymal transition. In DSC hypoxia restored an ESF like transcriptional state for a subset of transcription factors that are known targets of the progesterone receptor, suggesting that hypoxia partially interferes with progesterone signaling. In both cell types hypoxia modified transcription of several inflammatory transcription factors that are known regulators of decidualization, including decreased transcription of STATs and increased transcription of CEBPs. We observed that hypoxia upregulated genes had a significant overlap with genes previously detected to be upregulated in endometriotic stromal cells. Promoter analysis of the genes in this overlap suggested the hypoxia upregulated Jun/Fos and CEBP transcription factors as potential drivers of endometriosis-associated transcription. Using immunohistochemistry we observed increased expression of JUND and CEBPD in endometriosis lesions compared to healthy endometria. Overall the findings suggest that hypoxic stress establishes distinct transcriptional states in ESF and DSC, and that hypoxia influences the expression of genes that contribute to the core gene regulation of endometriotic stromal cells.

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The Endo-β-1,4-Xylanase Xyn11A Is Required for Virulence in Botrytis cinerea

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-19-0025 ◽

2006 ◽

Vol 19 (1) ◽

pp. 25-32 ◽

Cited By ~ 156

Author(s):

Nélida Brito ◽

José Juan Espino ◽

Celedonio González

Keyword(s):

Extracellular Enzymes ◽

Lesion Size ◽

Phytopathogenic Fungi ◽

Glycosyl Hydrolases ◽

Plant Cell Walls ◽

Wild Type ◽

In Planta ◽

Polymer Backbone ◽

Beechwood Xylan ◽

Type Gene

Phytopathogenic fungi can degrade xylan, an abundant hemicellulose in plant cell walls, by the coordinate action of a group of extracellular enzymes. Among these, endo-β-1,4-xylanases carry out the initial breakdown by cleaving internal bonds in the polymer backbone. We have isolated and characterized a gene, xyn11A coding for an endo-β-1,4-xylanase belonging to family 11 of glycosyl hydrolases. xyn11A was shown to be induced by xylan and repressed by glucose and to be expressed in planta. The disruption of xyn11A caused only a moderate decrease, about 30%, in the level of extracellular endo-β-1-4-xy-lanase activity and in the growth rate, with beechwood xylan as the only carbon source. However, deletion of the gene had a more pronounced effect on virulence, delaying the appearance of secondary lesions and reducing the average lesion size by more than 70%. Reintroducing the wild-type gene into the mutant strains reversed this phenotype back to wild type.

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The effect of alkali-soluble lignin on purified core cellulase and hemicellulase activities during hydrolysis of extractive ammonia-pretreated lignocellulosic biomass

Royal Society Open Science ◽

10.1098/rsos.171529 ◽

2018 ◽

Vol 5 (6) ◽

pp. 171529 ◽

Cited By ~ 3

Author(s):

Linchao Zhou ◽

Leonardo da Costa Sousa ◽

Bruce E. Dale ◽

Jia-Xun Feng ◽

Venkatesh Balan

Keyword(s):

Enzymatic Hydrolysis ◽

Biomass Conversion ◽

Enzyme Hydrolysis ◽

Mass Loading ◽

Glycosyl Hydrolases ◽

Fixed Amount ◽

Protein Mass ◽

Beechwood Xylan ◽

Soluble Lignin ◽

Sugar Conversion

Removing alkali-soluble lignin using extractive ammonia (EA) pretreatment of corn stover (CS) is known to improve biomass conversion efficiency during enzymatic hydrolysis. In this study, we investigated the effect of alkali-soluble lignin on six purified core glycosyl hydrolases and their enzyme synergies, adopting 31 enzyme combinations derived by a five-component simplex centroid model, during EA-CS hydrolysis. Hydrolysis experiment was carried out using EA-CS(−) (approx. 40% lignin removed during EA pretreatment) and EA-CS(+) (where no lignin was extracted). Enzymatic hydrolysis experiments were done at three different enzyme mass loadings (7.5, 15 and 30 mg protein g −1 glucan), using a previously developed high-throughput microplate-based protocol, and the sugar yields of glucose and xylose were detected. The optimal enzyme combinations (based on % protein mass loading) of six core glycosyl hydrolases for EA-CS(−) and EA-CS(+) were determined that gave high sugar conversion. The inhibition of lignin on optimal enzyme ratios was studied, by adding fixed amount of alkali-soluble lignin fractions to EA-CS(−), and pure Avicel, beechwood xylan and evaluating their sugar conversion. The optimal enzyme ratios that gave higher sugar conversion for EA-CS(−) were CBH I: 27.2–28.2%, CBH II: 18.2–22.2%, EG I: 29.2–34.3%, EX: 9.0–14.1%, βX: 7.2–10.2%, βG: 1.0–5.0% (at 7.5–30 mg g −1 protein mass loading). Endoglucanase was inhibited to a greater extent than other core cellulases and xylanases by lignin during enzyme hydrolysis. We also found that alkali-soluble lignin inhibits cellulase more strongly than hemicellulase during the course of enzyme hydrolysis.

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Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains

Environmental Pollution ◽

10.1016/j.envpol.2017.12.042 ◽

2018 ◽

Vol 235 ◽

pp. 55-64 ◽

Cited By ~ 14

Author(s):

Michael Dare Asemoloye ◽

Rafiq Ahmad ◽

Segun Gbolagade Jonathan

Keyword(s):

Oil Spill ◽

Enzymatic Activities ◽

Fungal Strains ◽

Catalase Peroxidase ◽

Transcriptomic Responses ◽

Encoding Genes

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Transcriptomic responses to hypoxia in endometrial and decidual stromal cells

Reproduction ◽

10.1530/rep-19-0615 ◽

2020 ◽

Vol 160 (1) ◽

pp. 39-51 ◽

Cited By ~ 1

Author(s):

Kalle T Rytkönen ◽

Taija Heinosalo ◽

Mehrad Mahmoudian ◽

Xinghong Ma ◽

Antti Perheentupa ◽

...

Keyword(s):

Transcription Factors ◽

Stromal Cells ◽

Epithelial Mesenchymal Transition ◽

Cell Types ◽

Core Gene ◽

Stromal Fibroblasts ◽

Mesenchymal Transition ◽

The Core ◽

Transcriptomic Responses ◽

Upregulated Genes

Human reproductive success depends on a properly decidualized uterine endometrium that allows implantation and the formation of the placenta. At the core of the decidualization process are endometrial stromal fibroblasts (ESF) that differentiate to decidual stromal cells (DSC). As variations in oxygen levels are functionally relevant in endometrium both upon menstruation and during placentation, we assessed the transcriptomic responses to hypoxia in ESF and DSC. In both cell types, hypoxia-upregulated genes in classical hypoxia pathways such as glycolysis and the epithelial mesenchymal transition. In DSC, hypoxia restored an ESF-like transcriptional state for a subset of transcription factors that are known targets of the progesterone receptor, suggesting that hypoxia partially interferes with progesterone signaling. In both cell types, hypoxia modified transcription of several inflammatory transcription factors that are known regulators of decidualization, including decreased transcription of STATs and increased transcription of CEBPs. We observed that hypoxia-upregulated genes in ESF and DSC had a significant overlap with genes previously detected to be upregulated in endometriotic stromal cells. Promoter analysis of the genes in this overlap suggested the hypoxia-upregulated Jun/Fos and CEBP transcription factors as potential drivers of endometriosis-associated transcription. Using immunohistochemistry, we observed increased expression of JUND and CEBPD in endometriosis lesions compared to healthy endometria. Overall, the findings suggest that hypoxic stress establishes distinct transcriptional states in ESF and DSC and that hypoxia influences the expression of genes that contribute to the core gene regulation of endometriotic stromal cells.

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Structure of clathrin cages and coats in ice

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010014213x ◽

1986 ◽

Vol 44 ◽

pp. 94-97

Author(s):

G.P.A. Vigers ◽

R.A. Crowther ◽

B.M.F. Pearse

Keyword(s):

Electron Microscopy ◽

Heavy Chain ◽

Outer Part ◽

Coated Vesicles ◽

Eukaryotic Cells ◽

Coat Proteins ◽

Terminal Domain ◽

Clathrin Heavy Chain ◽

Membrane Components

Clathrin forms the polyhedral cage of coated vesicles, which mediate the transfer of selected membrane components within eukaryotic cells. Clathrin cages and coated vesicles have been extensively studied by electron microscopy of negatively stained preparations and shadowed specimens. From these studies the gross morphology of the outer part of the polyhedral coat has been established and some features of the packing of clathrin trimers into the coat have also been described. However these previous studies have not revealed any internal details about the position of the terminal domain of the clathrin heavy chain, the location of the 100kd-50kd accessory coat proteins or the interactions of the coat with the enclosed membrane.

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The organization of cell surface membrane domains

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100155992 ◽

1989 ◽

Vol 47 ◽

pp. 804-805

Author(s):

Michael Edidin

Keyword(s):

Cell Surface ◽

Membrane Lipids ◽

Surface Membrane ◽

Lateral Diffusion ◽

Cell Types ◽

Membrane Domains ◽

Membrane Biology ◽

Morphological Polarity ◽

Discrete Domains ◽

Membrane Components

Cell surface membranes are based on a fluid lipid bilayer and models of the membranes' organization have emphasised the possibilities for lateral motion of membrane lipids and proteins within the bilayer. Two recent trends in cell and membrane biology make us consider ways in which membrane organization works against its inherent fluidity, localizing both lipids and proteins into discrete domains. There is evidence for such domains, even in cells without obvious morphological polarity and organization [Table 1]. Cells that are morphologically polarised, for example epithelial cells, raise the issue of membrane domains in an accute form.The technique of fluorescence photobleaching and recovery, FPR, was developed to measure lateral diffusion of membrane components. It has also proven to be a powerful tool for the analysis of constraints to lateral mobility. FPR resolves several sorts of membrane domains, all on the micrometer scale, in several different cell types.

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