Transcriptomic Analysis of Rhodococcus opacus R7 Grown on o-Xylene by RNA-Seq.

Abstract:

:Xylenes are considered one of the most common hazardous sources of environmental contamination. The biodegradation of these compounds has been often reported, rarer the ability to oxidize the ortho-isomer. Among few o-xylene-degrading bacteria, Rhodococcus opacus R7 is well known for its capability to degrade diverse aromatic hydrocarbons and toxic compounds, including o-xylene as only carbon and energy source. This work shows for the first time the RNA-seq approach to elucidate the genetic determinants involved in the o-xylene degradation pathway in R. opacus R7. Transcriptomic data showed 542 differentially expressed genes that are associated with the oxidation of aromatic hydrocarbons and stress response, osmotic regulation and central metabolism. Gene ontology (GO) enrichment and KEGG pathway analysis confirmed significant changes in aromatic compound catabolic processes, fatty acid metabolism, beta-oxidation, TCA cycle enzymes, and biosynthesis of metabolites when cells are cultured in the presence of o-xylene. Interestingly, the most up-regulated genes belong to the akb gene cluster encoding for the ethylbenzene (Akb) dioxygenase system. Moreover, the transcriptomic approach allowed identifying candidate enzymes involved in R7 o-xylene degradation for their likely participation in the formation of the metabolites that have been previously identified. Overall, this approach supports the identification of several oxidative systems likely involved in o-xylene metabolism confirming that R. opacus R7 possesses a redundancy of sequences that converge in o-xylene degradation through R7 peculiar degradation pathway. This work advances our understanding of o-xylene metabolism in bacteria belonging to Rhodococcus genus and provides a framework of useful enzymes (molecular tools) that can be fruitfully targeted for optimized o-xylene consumption.

journal_name

Front Microbiol

authors

Zampolli J,Di Canito A,Manconi A,Milanesi L,Di Gennaro P,Orro A

doi

10.3389/fmicb.2020.01808

subject

Has Abstract

pub_date

2020-08-12 00:00:00

pages

1808

issn

1664-302X

journal_volume

11

pub_type

杂志文章
  • Comparative Insights Into the Complete Genome Sequence of Highly Metal Resistant Cupriavidus metallidurans Strain BS1 Isolated From a Gold-Copper Mine.

    abstract::The highly heavy metal resistant strain Cupriavidus metallidurans BS1 was isolated from the Zijin gold-copper mine in China. This was of particular interest since the extensively studied, closely related strain, C. metallidurans CH34 was shown to not be only highly heavy metal resistant but also able to reduce metal c...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00047

    authors: Mazhar SH,Herzberg M,Ben Fekih I,Zhang C,Bello SK,Li YP,Su J,Xu J,Feng R,Zhou S,Rensing C

    更新日期:2020-02-07 00:00:00

  • Occurrence of the mcr-1 Colistin Resistance Gene and other Clinically Relevant Antibiotic Resistance Genes in Microbial Populations at Different Municipal Wastewater Treatment Plants in Germany.

    abstract::Seven wastewater treatment plants (WWTPs) with different population equivalents and catchment areas were screened for the prevalence of the colistin resistance gene mcr-1 mediating resistance against last resort antibiotic polymyxin E. The abundance of the plasmid-associated mcr-1 gene in total microbial populations d...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01282

    authors: Hembach N,Schmid F,Alexander J,Hiller C,Rogall ET,Schwartz T

    更新日期:2017-07-11 00:00:00

  • Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research.

    abstract::Plants shape distinct, species-specific microbiomes in their rhizospheres. A main premise for evaluating microbial communities associated with root-soil compartments is their successful separation into the rhizosphere (soil-root interface), the rhizoplane (root surface), and the endosphere (inside roots). We evaluated...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00773

    authors: Richter-Heitmann T,Eickhorst T,Knauth S,Friedrich MW,Schmidt H

    更新日期:2016-05-24 00:00:00

  • Biosynthesis and Bioactivity of Prodiginine Analogs in Marine Bacteria, Pseudoalteromonas: A Mini Review.

    abstract::The Prodiginine family consists of primarily red-pigmented tripyrrole secondary metabolites that were first characterized in the Gram-negative bacterial species Serratia marcescens and demonstrates a wide array of biological activities and applications. Derivatives of prodiginine have since been characterized in the m...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2019.01715

    authors: Sakai-Kawada FE,Ip CG,Hagiwara KA,Awaya JD

    更新日期:2019-07-24 00:00:00

  • Epstein-Barr virus-driven lymphomagenesis in the context of human immunodeficiency virus type 1 infection.

    abstract::Epstein-Barr virus (EBV) is a ubiquitous human γ-herpes virus which establishes a life-long asymptomatic infection in immunocompetent hosts. In human immunodeficiency virus type 1 (HIV-1) infected patients, the impaired immunosurveillance against EBV may favor the development of EBV-related diseases, ranging from lymp...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2013.00311

    authors: Petrara MR,Freguja R,Gianesin K,Zanchetta M,De Rossi A

    更新日期:2013-10-18 00:00:00

  • Evidence of New Endemic Clusters of Human T-Cell Leukemia Virus (HTLV) Infection in Bahia, Brazil.

    abstract:Background:Salvador, Bahia (northeastern Brazil), has been identified as the epicenter of Human T-cell leukemia virus Human T-cell leukemia virus (HTLV) type 1 infection in the country. This study aims to estimate the rate of HTLV infection and the geographical distribution of this virus in this state. Methods:All HTL...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01002

    authors: Pereira FM,de Almeida MDCC,Santos FLN,Carreiro RP,Regis-Silva CG,Galvão-Castro B,Grassi MFR

    更新日期:2019-05-14 00:00:00

  • Rhizosphere Protists Change Metabolite Profiles in Zea mays.

    abstract::Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrient...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00857

    authors: Kuppardt A,Fester T,Härtig C,Chatzinotas A

    更新日期:2018-05-03 00:00:00

  • Evidence for horizontal gene transfer of anaerobic carbon monoxide dehydrogenases.

    abstract::Carbon monoxide (CO) is commonly known as a toxic gas, yet both cultivation studies and emerging genome sequences of bacteria and archaea establish that CO is a widely utilized microbial growth substrate. In this study, we determined the prevalence of anaerobic carbon monoxide dehydrogenases ([Ni,Fe]-CODHs) in current...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2012.00132

    authors: Techtmann SM,Lebedinsky AV,Colman AS,Sokolova TG,Woyke T,Goodwin L,Robb FT

    更新日期:2012-04-17 00:00:00

  • Rhizosphere Bacterial Community Response to Continuous Cropping of Tibetan Barley.

    abstract::Long-term continuous cropping influences the nutrient of soil and microbiome of the rhizosphere, resulting in the yield decrease of crops. Tibetan barley is a dominant cereal crop cultivated at high altitudes in Tibet. Its growth and yield are negatively affected by continuous cropping; however, the response of the rh...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.551444

    authors: Yao Y,Yao X,An L,Bai Y,Xie D,Wu K

    更新日期:2020-11-30 00:00:00

  • Repetitive Short-Term Stimuli Imposed in Poor Mixing Zones Induce Long-Term Adaptation of E. coli Cultures in Large-Scale Bioreactors: Experimental Evidence and Mathematical Model.

    abstract::Rapidly changing concentrations of substrates frequently occur during large-scale microbial cultivations. These changing conditions, caused by large mixing times, result in a heterogeneous population distribution. Here, we present a powerful and efficient modeling approach to predict the influence of varying substrate...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01195

    authors: Nieß A,Löffler M,Simen JD,Takors R

    更新日期:2017-06-28 00:00:00

  • Mathematical Modeling Approaches for Assessing the Joint Toxicity of Chemical Mixtures Based on Luminescent Bacteria: A Systematic Review.

    abstract::Developments in industrial applications inevitably accelerate the discharge of enormous substances into the environment, whereas multi-component mixtures commonly cause joint toxicity which is distinct from the simple sum of independent effect. Thus, ecotoxicological assessment, by luminescent bioassays has recently b...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2020.01651

    authors: Wang D,Wang S,Bai L,Nasir MS,Li S,Yan W

    更新日期:2020-07-31 00:00:00

  • Antimicrobial Protection of Marsupial Pouch Young.

    abstract::Marsupials diverged from eutherian mammals about 148 million years ago and represent a unique lineage of mammals with distinctive morphological and reproductive characteristics. Marsupials have significantly shorter gestation periods than eutherians. Pregnancy typically ranges from 15 to 35 days, with young being born...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2017.00354

    authors: Cheng Y,Belov K

    更新日期:2017-03-07 00:00:00

  • Corrigendum: Azole-Resistance in Aspergillus terreus and Related Species: An Emerging Problem or a Rare Phenomenon?

    abstract::[This corrects the article DOI: 10.3389/fmicb.2018.00516.]. ...

    journal_title:Frontiers in microbiology

    pub_type: 已发布勘误

    doi:10.3389/fmicb.2018.03245

    authors: Zoran T,Sartori B,Sappl L,Aigner M,Sánchez-Reus F,Rezusta A,Chowdhary A,Taj-Aldeen SJ,Arendrup MC,Oliveri S,Kontoyiannis DP,Alastruey-Izquierdo A,Lagrou K,Lo Cascio G,Meis JF,Buzina W,Farina C,Drogari-Apiranthitou M,G

    更新日期:2019-01-14 00:00:00

  • Chromium Hyper-Tolerant Bacillus sp. MH778713 Assists Phytoremediation of Heavy Metals by Mesquite Trees (Prosopis laevigata).

    abstract::Heavy metal accumulation in mesquite trees (Prosopis laevigata) growing in aluminum, titanium, chromium and zirconium-polluted soils of a semi-arid region in Mexico was investigated using wavelength dispersive X-ray fluorescence analysis. The results showed that P. laevigata trees can hyper accumulate up to 4100 mg/kg...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01833

    authors: Ramírez V,Baez A,López P,Bustillos R,Villalobos MÁ,Carreño R,Contreras JL,Muñoz-Rojas J,Fuentes LE,Martínez J,Munive JA

    更新日期:2019-08-13 00:00:00

  • Exposure to Arsenic Alters the Microbiome of Larval Zebrafish.

    abstract::Exposure to environmental toxins such as heavy metals can perturb the development and stability of microbial communities associated with human or animal hosts. Widespread arsenic contamination in rivers and riparian habitats therefore presents environmental and health concerns for populations living near sources of co...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01323

    authors: Dahan D,Jude BA,Lamendella R,Keesing F,Perron GG

    更新日期:2018-06-21 00:00:00

  • Chemosensitization as a means to augment commercial antifungal agents.

    abstract::Antimycotic chemosensitization and its mode of action are of growing interest. Currently, use of antifungal agents in agriculture and medicine has a number of obstacles. Foremost of these is development of resistance or cross-resistance to one or more antifungal agents. The generally high expense and negative impact, ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2012.00079

    authors: Campbell BC,Chan KL,Kim JH

    更新日期:2012-02-29 00:00:00

  • Dynamics Relationship of Phyllosphere and Rhizosphere Bacterial Communities During the Development of Bothriochloa ischaemum in Copper Tailings.

    abstract::Copper mining and the byproducts associated with the industry have led to serious pollution in the Loess Plateau of China. There is a potential in improving the ecological restoration efficiency of such degraded land through combining microbial and plant remediation approaches. However, the community structure and fun...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00869

    authors: Jia T,Yao Y,Wang R,Wu T,Chai B

    更新日期:2020-05-28 00:00:00

  • First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna.

    abstract::Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain e...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01343

    authors: Perez MF,Kurth D,Farías ME,Soria MN,Castillo Villamizar GA,Poehlein A,Daniel R,Dib JR

    更新日期:2020-06-23 00:00:00

  • Automated quantification of the phagocytosis of Aspergillus fumigatus conidia by a novel image analysis algorithm.

    abstract::Studying the pathobiology of the fungus Aspergillus fumigatus has gained a lot of attention in recent years. This is due to the fact that this fungus is a human pathogen that can cause severe diseases, like invasive pulmonary aspergillosis in immunocompromised patients. Because alveolar macrophages belong to the first...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00549

    authors: Kraibooj K,Schoeler H,Svensson CM,Brakhage AA,Figge MT

    更新日期:2015-06-09 00:00:00

  • Strong Inference in Mathematical Modeling: A Method for Robust Science in the Twenty-First Century.

    abstract::While there are many opinions on what mathematical modeling in biology is, in essence, modeling is a mathematical tool, like a microscope, which allows consequences to logically follow from a set of assumptions. Only when this tool is applied appropriately, as microscope is used to look at small items, it may allow to...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01131

    authors: Ganusov VV

    更新日期:2016-07-22 00:00:00

  • PMQR genes oqxAB and aac(6')Ib-cr accelerate the development of fluoroquinolone resistance in Salmonella typhimurium.

    abstract::Emergence of multidrug-resistant Salmonella typhimurium strains, especially the ACSSuT and nalidixic acid R types, has significantly compromised the effectiveness of current strategies to control Salmonella infections, resulting in increased morbidity and mortality. Clinical S. typhimurium isolates recovered in Hong K...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2014.00521

    authors: Wong MH,Chan EW,Liu LZ,Chen S

    更新日期:2014-10-02 00:00:00

  • Genetic Platforms of blaCTX-M in Carbapenemase-Producing Strains of K. pneumoniae Isolated in Chile.

    abstract::Objective: To elucidate whether the genetic platforms of blaCTX-M contribute to the phenotypes of multi-drug-resistance (MDR) in the first carbapenemase-producing K. pneumoniae strains isolated in Chile. Method: Twenty-two carbapenemase-producing K. pneumoniae strains isolated from different Chilean patients and hospi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00324

    authors: Carrasco-Anabalón S,Vera-Leiva A,Quezada-Aguiluz M,Morales-Rivera MF,Lima CA,Fernández J,Ulloa S,Domínguez M,González-Rocha G,Bello-Toledo H

    更新日期:2018-03-06 00:00:00

  • Drosophila melanogaster as a High-Throughput Model for Host-Microbiota Interactions.

    abstract::Microbiota research often assumes that differences in abundance and identity of microorganisms have unique influences on host physiology. To test this concept mechanistically, germ-free mice are colonized with microbial communities to assess causation. Due to the cost, infrastructure challenges, and time-consuming nat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00751

    authors: Trinder M,Daisley BA,Dube JS,Reid G

    更新日期:2017-04-28 00:00:00

  • Effects of Intravenous Infusion With Sodium Butyrate on Colonic Microbiota, Intestinal Development- and Mucosal Immune-Related Gene Expression in Normal Growing Pigs.

    abstract::This study aimed to investigate effects of intravenous infusion with sodium butyrate (SB) on colonic microbiota, intestinal mucosal immune and intestinal development in normal growing pigs. Twelve crossbred barrows (Duroc × Landrace × Large White) fitted with a medical polyethylene cannula via internal jugular vein we...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01652

    authors: Chen X,Xu J,Su Y,Zhu W

    更新日期:2018-07-20 00:00:00

  • Enhanced Potency of a Broad H7N9-Neutralizing Antibody HNIgGA6 Through Structure-Based Design.

    abstract::H7N9 influenza virus was first isolated in 2013 and has caused five epidemic waves among humans to date. Treatment opinions are currently limited. Previously, we characterized a human neutralizing antibody, HNIgGA6, by isolating rearranged heavy- and light-chain genes from convalescent patients. The mAb disrupts viral...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01313

    authors: Chen C,Liu Z,Liu L,Wang J,Jin Q

    更新日期:2020-06-19 00:00:00

  • Spontaneously Occurring Small-Colony Variants of Staphylococcus aureus Show Enhanced Clearance by THP-1 Macrophages.

    abstract::Staphylococcus aureus is a common cause of chronic and relapsing infection, especially when the ability of the immune system to sterilize a focus of infection is compromised (e.g., because of a foreign body or in the cystic fibrosis lung). Chronic infections are associated with slow-growing colony phenotypes of S. aur...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01300

    authors: Stoneham SM,Cantillon DM,Waddell SJ,Llewelyn MJ

    更新日期:2020-06-12 00:00:00

  • A novel assay for the detection of bioactive volatiles evaluated by screening of lichen-associated bacteria.

    abstract::Volatile organic compounds (VOCs) produced by microorganisms are known both for their effect on pathogens and their role as mediators in various interactions and communications. Previous studies have demonstrated the importance of VOCs for ecosystem functioning as well as their biotechnological potential, but screenin...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00398

    authors: Cernava T,Aschenbrenner IA,Grube M,Liebminger S,Berg G

    更新日期:2015-05-01 00:00:00

  • Land Management and Microbial Seed Load Effect on Rhizosphere and Endosphere Bacterial Community Assembly in Wheat.

    abstract::Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of la...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02625

    authors: Kavamura VN,Robinson RJ,Hayat R,Clark IM,Hughes D,Rossmann M,Hirsch PR,Mendes R,Mauchline TH

    更新日期:2019-11-15 00:00:00

  • Corrigendum: Shifts in metabolic hydrogen sinks in the methanogenesis-inhibited ruminal fermentation: a meta-analysis.

    abstract::[This corrects the article on p. 37 in vol. 6, PMID: 25699029.]. ...

    journal_title:Frontiers in microbiology

    pub_type: 已发布勘误

    doi:10.3389/fmicb.2015.00538

    authors: Ungerfeld EM

    更新日期:2015-06-02 00:00:00

  • Protein Kinase Ime2 Is Required for Mycelial Growth, Conidiation, Osmoregulation, and Pathogenicity in Nematode-Trapping Fungus Arthrobotrys oligospora.

    abstract::Inducer of meiosis 2 (Ime2), a protein kinase that has been identified in diverse fungal species, functions in the regulation of various cellular processes, such as ascospore formation, pseudohyphal growth, and sexual reproduction. In this study, AoIme2, an ortholog of Saccharomyces cerevisiae Ime2, was characterized ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.03065

    authors: Xie M,Bai N,Yang J,Jiang K,Zhou D,Zhao Y,Li D,Niu X,Zhang KQ,Yang J

    更新日期:2020-01-14 00:00:00