scholarly journals A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites

2021 ◽  
Vol 9 (8) ◽  
pp. 1680
Author(s):  
Domenico Davolos ◽  
Fabiana Russo ◽  
Loredana Canfora ◽  
Eligio Malusà ◽  
Małgorzata Tartanus ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Removal Capacity ◽  
Trichoderma Hamatum ◽  
Enhanced Solubility ◽  
Polluted Sites ◽  
Transmembrane Transporters

Trichoderma hamatum FBL 587 isolated from DDT-contaminated agricultural soils stands out as a remarkable strain with DDT-resistance and the ability to enhance DDT degradation process in soil. Here, whole genome sequencing and RNA-Seq studies for T. hamatum FBL 587 under exposure to DDT were performed. In the 38.9 Mb-genome of T. hamatum FBL 587, 10,944 protein-coding genes were predicted and annotated, including those of relevance to mycoremediation such as production of secondary metabolites and siderophores. The genome-scale transcriptional responses of T. hamatum FBL 587 to DDT exposure showed 1706 upregulated genes, some of which were putatively involved in the cellular translocation and degradation of DDT. With regards to DDT removal capacity, it was found upregulation of metabolizing enzymes such as P450s, and potentially of downstream DDT-transforming enzymes such as epoxide hydrolases, FAD-dependent monooxygenases, glycosyl- and glutathione-transferases. Based on transcriptional responses, the DDT degradation pathway could include transmembrane transporters of DDT, antioxidant enzymes for oxidative stress due to DDT exposure, as well as lipases and biosurfactants for the enhanced solubility of DDT. Our study provides the first genomic and transcriptomic data on T. hamatum FBL 587 under exposure to DDT, which are a base for a better understanding of mycoremediation strategies for DDT-polluted sites.

scholarly journals The Role of Chaperone-Mediated Autophagy in Hepatitis C Virus-Induced Pathogenesis

2021 ◽  
Vol 11 ◽  
Author(s):  
Chieko Matsui ◽  
Putu Yuliandari ◽  
Lin Deng ◽  
Takayuki Abe ◽  
Ikuo Shoji
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Hepatocyte Nuclear Factor ◽  
Selective Degradation ◽  
Substrate Protein ◽  
Hepatocyte Nuclear Factor 1Α ◽  
Chaperone Mediated Autophagy

Lysosome incorporate and degrade proteins in a process known as autophagy. There are three types of autophagy; macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA). Although autophagy is considered a nonselective degradation process, CMA is known as a selective degradation pathway. All proteins internalized in the lysosome via CMA contain a pentapeptide KFERQ-motif, also known as a CMA-targeting motif, which is necessary for selectivity. CMA directly delivers a substrate protein into the lysosome lumen using the cytosolic chaperone HSC70 and the lysosomal receptor LAMP-2A for degradation. Hepatitis C virus (HCV) NS5A protein interacts with hepatocyte-nuclear factor 1α (HNF-1α) together with HSC70 and promotes the lysosomal degradation of HNF-1α via CMA, resulting in HCV-induced pathogenesis. HCV NS5A promotes recruitment of HSC70 to the substrate protein HNF-1α. HCV NS5A plays a crucial role in HCV-induced CMA. Further investigations of HCV NS5A-interacting proteins containing CMA-targeting motifs may help to elucidate HCV-induced pathogenesis.

scholarly journals Steroid Degradation in Comamonas testosteroni TA441: Identification of the Entire β-Oxidation Cycle of the Cleaved B Ring

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Masae Horinouchi ◽  
Hiroyuki Koshino ◽  
Michal Malon ◽  
Hiroshi Hirota ◽  
Toshiaki Hayashi
Keyword(s):  
Gene Clusters ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Comamonas Testosteroni ◽  
Content Type ◽  
Coa Transferase ◽  
Degrading Bacteria ◽  
Globally Distributed

ABSTRACT Comamonas testosteroni TA441 degrades steroids via aromatization of the A ring, followed by degradation of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, mainly by β-oxidation. In this study, we revealed that 7β,9α-dihydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostanoic acid-coenzyme A (CoA) ester is dehydrogenated by (3S)-3-hydroxylacyl CoA-dehydrogenase, encoded by scdE (ORF27), and then the resultant 9α-hydroxy-7,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid-CoA ester is converted by 3-ketoacyl-CoA transferase, encoded by scdF (ORF23). With these results, the whole cycle of β-oxidation on the side chain at C-8 of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid is clarified; 9-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid-CoA ester is dehydrogenated at C-6 by ScdC1C2, followed by hydration by ScdD. 7β,9α-Dihydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostanoic acid-CoA ester then is dehydrogenated by ScdE to be converted to 9α-hydroxy-17-oxo-1,2,3,4,5,6,10,19-octanorandrostan-7-oic acid-CoA ester and acetyl-CoA by ScdF. ScdF is an ortholog of FadA6 in Mycobacterium tuberculosis H37Rv, which was reported as a 3-ketoacyl-CoA transferase involved in C ring cleavage. We also obtained results suggesting that ScdF is also involved in C ring cleavage, but further investigation is required for confirmation. ORF25 and ORF26, located between scdF and scdE, encode enzymes belonging to the amidase superfamily. Disrupting either ORF25 or ORF26 did not affect steroid degradation. Among the bacteria having gene clusters similar to those of tesB to tesR, some have both ORF25- and ORF26-like proteins or only an ORF26-like protein, but others do not have either ORF25- or ORF26-like proteins. ORF25 and ORF26 are not crucial for steroid degradation, yet they might provide clues to elucidate the evolution of bacterial steroid degradation clusters. IMPORTANCE Studies on bacterial steroid degradation were initiated more than 50 years ago primarily to obtain materials for steroid drugs. Steroid-degrading bacteria are globally distributed, and the role of bacterial steroid degradation in the environment as well as in relation to human health is attracting attention. The overall aerobic degradation of the four basic steroidal rings has been proposed; however, there is still much to be revealed to understand the complete degradation pathway. This study aims to uncover the whole steroid degradation process in Comamonas testosteroni TA441 as a model of steroid-degrading bacteria. C. testosteroni is one of the most studied representative steroid-degrading bacteria and is suitable for exploring the degradation pathway, because the involvement of degradation-related genes can be determined by gene disruption. Here, we elucidated the entire β-oxidation cycle of the cleaved B ring. This cycle is essential for the following C and D ring cleavage.

scholarly journals Stability and Degradation Mechanismof Si-based Photocathodes for Water Splitting with Ultrathin TiO2 Protection Layer

2019 ◽  
Vol 0 (0) ◽  
Author(s):  
Emanuel Ronge ◽  
Thorsten Cottre ◽  
Katharina Welter ◽  
Vladimir Smirnov ◽  
Natalie Jacqueline Ottinger ◽  
...  
Keyword(s):  
Water Splitting ◽  
Atomic Layer ◽  
Degradation Process ◽  
Alkaline Media ◽  
Semiconductor Surface ◽  
Nucleation Sites ◽  
Enhanced Solubility ◽  
High Structural Perfection ◽  
Protection Layer ◽  
The Stability

Abstract Using transmission and scanning electron microscopy, we study mechanisms which determine the stability of Silicon photocathodes for solar driven water splitting. Such tandem or triple devices can show a promising stability as photocathodes if the semiconductor surface is protected by an ultrathin TiO2 protection layer. Using atomic layer deposition (ALD) with Cl-precursors, 4–7 nm thick TiO2 layers can be grown with high structural perfection. The layer can be electrochemically covered by Pt nanoparticels serving as electro-catalysts. However, Cl-remnants which are typically present in such layers due to incomplete oxidation, are the origin of an electrochemical degradation process. After 1 h AM1.5G illumination in alkaline media, circular shaped corrosion craters appear in the topmost Si layer, although the TiO2 layer is intact in most parts of the crater. The crater development is stopped at local inhomogenities with a higher Pt coverage. The observations suggests that reduced Titanium species due to Cl−/O2− substitution are nucleation sites of the initial corrosion steps due to enhanced solubility of reduced Ti in the electrolyte. This process is followed by electrochemical dissolution of Si, after direct contact between the electrolyte and the top Si layer surface. To increase the stability of TiO2 protected photocathodes, formation of reduced Ti species must be avoided.

scholarly journals Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation

2020 ◽  
Vol 8 (9) ◽  
pp. 1357
Author(s):  
Mengmeng Wang ◽  
Jiaxi Miao ◽  
Xuanqing Wang ◽  
Tuo Li ◽  
Han Zhu ◽  
...  
Keyword(s):  
Thermophilic Bacterium ◽  
Glycoside Hydrolases ◽  
Lignocellulose Degradation ◽  
Geobacillus Stearothermophilus ◽  
Carbohydrate Active Enzymes ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Clusters Of Orthologous Groups ◽  
Different Temperatures ◽  
Shock Proteins

A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency.

scholarly journals Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT

2019 ◽  
Vol 202 (2) ◽  
pp. 421-426 ◽  
Author(s):  
András Táncsics ◽  
Milán Farkas ◽  
Balázs Horváth ◽  
Gergely Maróti ◽  
Lauren M. Bradford ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mobile Element ◽  
Sole Source ◽  
Degradation Pathway ◽  
Whole Genome Sequence ◽  
Toluene Degradation ◽  
Extradiol Dioxygenase ◽  
Protein Coding ◽  
Microaerobic Conditions ◽  
Rna Genes

Abstract Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain BucT was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z .  oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions.

scholarly journals Degradation of the antibiotic ornidazole in aqueous solution by using nanoscale zero-valent iron particles: kinetics, mechanism, and degradation pathway

RSC Advances ◽  
2018 ◽  
Vol 8 (61) ◽  
pp. 35062-35072 ◽  
Author(s):  
Yanchang Zhang ◽  
Lin Zhao ◽  
Yongkui Yang ◽  
Peizhe Sun
Keyword(s):  
Aqueous Solution ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Zero Valent Iron ◽  
Main Mechanism ◽  
Iron Particles ◽  
Nanoscale Zero Valent Iron ◽  
Nitro Reduction

The whole possible process of ONZ removal by nZVI. The reduction on the surface of nZVI was the main mechanism. A potential pathway including dechlorination, nitro reduction, N-denitration, and cleavage was proposed for the degradation process.

Sonochemical Degradation of Sodium Dodecylbenzene Sulfonate in Aqueous Solutions

2003 ◽  
Vol 56 (10) ◽  
pp. 1045 ◽  
Author(s):  
Muthupandian Ashokkumar ◽  
Tyson Niblett ◽  
Lyndon Tantiongco ◽  
Franz Grieser
Keyword(s):  
Initial Step ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Water Soluble ◽  
Sodium Dodecylbenzene Sulfonate ◽  
Gaseous Hydrocarbon ◽  
Dodecylbenzene Sulfonate ◽  
Volatile Products ◽  
Degradation Step ◽  
Radical Attack

The sonochemical degradation of sodium dodecylbenzene sulfonate (SDBS) has been studied over a wide concentration range spanning the critical micelle concentration (CMC) of the surfactant. The rate of degradation of SDBS increased linearly with increasing concentration below the CMC of SDBS. Above the CMC, the degradation rate continued to increase but at a much slower rate compared with that below the CMC. It was found that the increasing rate of degradation of SDBS correlated closely with the decrease in the air/water surface tension of the surfactant solutions. The results of this study strongly suggest that the initial step in the degradation process is OH• radical attack onto SDBS molecules adsorbed at the cavitation bubble/solution interface. The sonication of SDBS solutions for extended periods of time (ca. 12 h) led to the generation of gaseous hydrocarbon products, such as methane, ethane, ethylene, and acetylene. It is concluded that further radical attack occurs on the intermediates produced from the initial degradation step. This further degradation pathway is responsible for producing both water-soluble species, and volatile products that are pyrolyzed within the cavitation bubbles.

scholarly journals Genome-wide profiling of transcribed enhancers during macrophage activation

2017 ◽  
Author(s):  
Elena Denisenko ◽  
Reto Guler ◽  
Musa Mhlanga ◽  
Harukazu Suzuki ◽  
Frank Brombacher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Transcriptional Control ◽  
Macrophage Activation ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Genome Wide ◽  
Ifn Γ ◽  
Cap Analysis

AbstractMacrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well-known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in mouse macrophages, their time kinetics and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers and find that genes associated to many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli-specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue to further elucidate enhancer regulation in macrophages.

scholarly journals Genomic and transcriptome analyses of a thermophilic bacterium Geobacillus stearothermophilus B5 isolated from compost reveal its enzymatic basis for lignocellulose degradation

2020 ◽  
Author(s):  
Mengmeng Wang ◽  
Jiaxi Miao ◽  
Xuanqing Wang ◽  
Tuo Li ◽  
Han Zhu ◽  
...  
Keyword(s):  
Cellulose Degradation ◽  
Carbon Sources ◽  
Thermophilic Bacterium ◽  
Glycoside Hydrolases ◽  
Lignocellulose Degradation ◽  
Geobacillus Stearothermophilus ◽  
Transcriptional Responses ◽  
Protein Coding ◽  
Thermophilic Microorganisms ◽  
Clusters Of Orthologous Groups

Abstract Background Composting is a special global carbon cycle which sustains various microbes engendering the cellulose degradation. Studies have obtained substantial compost microbiomes, yet the expressions and functions of these lignocellulolytic enzymes remains obscure. Thus, the discovery of thermophilic microorganisms as considerable biochemical catalysts for biofuels is becoming more and more attractive.Results A lignocellulose degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, which could secrete considerable enzymes at the optimal temperature (60°C) and pH (7.5). One single contig of 3.37 Mbp was obtained from raw data and 3371 protein-coding genes were predicted, and the clusters of orthologous groups (COG) analysis revealed various genes with function of polymeric substrates degradation, especially for abundant CAZymes including glycoside hydrolases (GH, 29%) and glycosyl transferases (GT, 36%). Furthermore, the transcriptional responses of B5 at different temperature by using rice straw as sole carbon sources were also analyzed, based on which the mechanism of lignocellulose degradation at high temperature was revealed that B5 could resist the heat by up-regulating the heat shock proteins (HSP) and then secrete various Carbohydrate-Active enzymes (CAZymes) to realize energy balance.Conclusions The comparative whole-genome along with transcriptome analysis indicated that G. stearothermophilus B5 owned the ability of lignocellulose degradation and could be considered as a potential inoculant in composting efficiency, thus are also valuable for the lignocellulosic bioenergy industry.

Identification and targeted disruption of the gene encoding the main 3-ketosteroid dehydrogenase in Mycobacterium smegmatis

Microbiology ◽  
2005 ◽  
Vol 151 (7) ◽  
pp. 2393-2402 ◽  
Author(s):  
Anna Brzostek ◽  
Tomasz Śliwiński ◽  
Anna Rumijowska-Galewicz ◽  
Małgorzata Korycka-Machała ◽  
Jarosław Dziadek
Keyword(s):  
Mycobacterium Smegmatis ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Ring Structure ◽  
Wild Type ◽  
Targeted Disruption ◽  
Gene Encoding ◽  
Key Enzymes ◽  
Catabolic Potential ◽  
Partial Inactivation

The catabolic potential for sterol degradation of fast-growing mycobacteria is well known. However, no genes or enzymes responsible for the steroid degradation process have been identified as yet in these species. One of the key enzymes required for degradation of the steroid ring structure is 3-ketosteroid Δ1-dehydrogenase (KsdD). The recent annotation of the Mycobacterium smegmatis genome (TIGR database) revealed six KsdD homologues. Targeted disruption of the MSMEG5898 (ksdD-1) gene, but not the MSMEG4855 (ksdD-2) gene, resulted in partial inactivation of the cholesterol degradation pathway and accumulation of the intermediate 4-androstene-3,17-dione. This effect was reversible by the introduction of the wild-type ksdD-1 gene into M. smegmatis ΔksdD-1 or overexpression of ksdD-2. The data indicate that KsdD1 is the main KsdD in M. smegmatis, but that KsdD2 is able to perform the cholesterol degradation process when overproduced.

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