Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data.

Abstract:

:We introduce a manually constructed and curated regulatory network model that describes the current state of knowledge of transcriptional regulation of Bacillus subtilis. The model corresponds to an updated and enlarged version of the regulatory model of central metabolism originally proposed in 2008. We extended the original network to the whole genome by integration of information from DBTBS, a compendium of regulatory data that includes promoters, transcription factors (TFs), binding sites, motifs, and regulated operons. Additionally, we consolidated our network with all the information on regulation included in the SporeWeb and Subtiwiki community-curated resources on B. subtilis. Finally, we reconciled our network with data from RegPrecise, which recently released their own less comprehensive reconstruction of the regulatory network for B. subtilis. Our model describes 275 regulators and their target genes, representing 30 different mechanisms of regulation such as TFs, RNA switches, Riboswitches, and small regulatory RNAs. Overall, regulatory information is included in the model for ∼2500 of the ∼4200 genes in B. subtilis 168. In an effort to further expand our knowledge of B. subtilis regulation, we reconciled our model with expression data. For this process, we reconstructed the Atomic Regulons (ARs) for B. subtilis, which are the sets of genes that share the same "ON" and "OFF" gene expression profiles across multiple samples of experimental data. We show how ARs for B. subtilis are able to capture many sets of genes corresponding to regulated operons in our manually curated network. Additionally, we demonstrate how ARs can be used to help expand or validate the knowledge of the regulatory networks by looking at highly correlated genes in the ARs for which regulatory information is lacking. During this process, we were also able to infer novel stimuli for hypothetical genes by exploring the genome expression metadata relating to experimental conditions, gaining insights into novel biology.

journal_name

Front Microbiol

authors

Faria JP,Overbeek R,Taylor RC,Conrad N,Vonstein V,Goelzer A,Fromion V,Rocha M,Rocha I,Henry CS

doi

10.3389/fmicb.2016.00275

subject

Has Abstract

pub_date

2016-03-18 00:00:00

pages

275

issn

1664-302X

journal_volume

7

pub_type

杂志文章
  • A Novel qPCR Method for Simultaneous Detection and Quantification of Viable Pathogenic and Non-pathogenic Vibrio parahaemolyticus (tlh+ , tdh+ , and ureR + ).

    abstract::Pathogenic and non-pathogenic Vibrio parahaemolyticus strains were simultaneously detected and quantified using a novel viable multiplex real-time PCR (novel qPCR). We used a new PCR primer and probe, ureR, as a surrogate for detection of the toxin trh gene as the primer was better at identifying variant V. parahaemol...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.01747

    authors: Niu B,Hong B,Zhang Z,Mu L,Malakar PK,Liu H,Pan Y,Zhao Y

    更新日期:2018-08-02 00:00:00

  • Bovine Respiratory Syncytial Virus Enhances the Adherence of Pasteurella multocida to Bovine Lower Respiratory Tract Epithelial Cells by Upregulating the Platelet-Activating Factor Receptor.

    abstract::Coinfection by bovine respiratory syncytial virus (BRSV) and Pasteurella multocida (PM) frequently has been observed in cattle that develop severe pneumonia. We recently reported that BRSV infection significantly increased PM adherence to bovine lower respiratory tract epithelial cells. However, the molecular mechanis...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01676

    authors: Sudaryatma PE,Saito A,Mekata H,Kubo M,Fahkrajang W,Mazimpaka E,Okabayashi T

    更新日期:2020-07-31 00:00:00

  • Lower Termite Associations with Microbes: Synergy, Protection, and Interplay.

    abstract::Lower-termites are one of the best studied symbiotic systems in insects. Their ability to feed on a nitrogen-poor, wood-based diet with help from symbiotic microbes has been under investigation for almost a century. A unique microbial consortium living in the guts of lower termites is essential for wood-feeding. Host ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2016.00422

    authors: Peterson BF,Scharf ME

    更新日期:2016-04-08 00:00:00

  • Consumer Exposure to Antimicrobial Resistant Bacteria From Food at Swiss Retail Level.

    abstract::Background: Antimicrobial resistance (AMR) in bacteria is an increasing health concern. The spread of AMR bacteria (AMRB) between animals and humans via the food chain and the exchange of AMR genes requires holistic approaches for risk mitigation. The AMRB exposure of humans via food is currently only poorly understoo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00362

    authors: Jans C,Sarno E,Collineau L,Meile L,Stärk KDC,Stephan R

    更新日期:2018-03-06 00:00:00

  • Hyper-Osmotic Stress Elicits Membrane Depolarization and Decreased Permeability in Halotolerant Marine Debaryomyces hansenii Strains and in Saccharomyces cerevisiae.

    abstract::The use of seawater and marine microorganisms can represent a sustainable alternative to avoid large consumption of freshwater performing industrial bioprocesses. Debaryomyces hansenii, which is a known halotolerant yeast, possess metabolic traits appealing for developing such processes. For this purpose, we studied s...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00064

    authors: Capusoni C,Arioli S,Donzella S,Guidi B,Serra I,Compagno C

    更新日期:2019-01-29 00:00:00

  • Inhibition of HTLV-1 Infection by HIV-1 First- and Second-Generation Integrase Strand Transfer Inhibitors.

    abstract::More than 10 million people worldwide are infected with the retrovirus human T-cell lymphotropic virus type 1 (HTLV-1). Infection phenotypes can range from asymptomatic to severe adult T-cell leukemia/lymphoma (ATLL) and HTLV-1-associated myelopathy. HTLV-1, like human immunodeficiency virus type 1 (HIV-1), is a blood...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01877

    authors: Barski MS,Minnell JJ,Maertens GN

    更新日期:2019-08-13 00:00:00

  • Meal Regularity Plays a Role in Shaping the Saliva Microbiota.

    abstract:Background:Diet may influence health directly or indirectly via the human microbiota, emphasizing the need to unravel these complex relationships for future health benefits. Associations between eating habits and gut microbiota have been shown, but less is known about the association between eating habits and saliva mi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00757

    authors: Viljakainen J,Raju SC,Viljakainen H,Figueiredo RAO,Roos E,Weiderpass E,Rounge TB

    更新日期:2020-04-24 00:00:00

  • Biophysical methods for the study of microbial surfaces.

    abstract::The challenge in studying the surface architecture of different microbial pathogens is to integrate the most current biochemical, spectroscopic, microscopic, and processing techniques. Individually these methods have insufficient sensitivity to reveal complex structures, such as branched, large, viscous polymers with ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2011.00207

    authors: Frases S,Viana NB,Casadevall A

    更新日期:2011-10-10 00:00:00

  • A Trypsin Inhibitor from Tecoma stans Leaves Inhibits Growth and Promotes ATP Depletion and Lipid Peroxidation in Candida albicans and Candida krusei.

    abstract::Tecoma stans (yellow elder) has shown medicinal properties and antimicrobial activity. Previous reports on antifungal activity of T. stans preparations and presence of trypsin inhibitor activity from T. stans leaves stimulated the investigation reported here. In this work, we proceeded to the purification and characte...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00611

    authors: Patriota LL,Procópio TF,de Souza MF,de Oliveira AP,Carvalho LV,Pitta MG,Rego MJ,Paiva PM,Pontual EV,Napoleão TH

    更新日期:2016-04-27 00:00:00

  • Fungal ITS1 Deep-Sequencing Strategies to Reconstruct the Composition of a 26-Species Community and Evaluation of the Gut Mycobiota of Healthy Japanese Individuals.

    abstract::The study of mycobiota remains relatively unexplored due to the lack of sufficient available reference strains and databases compared to those of bacterial microbiome studies. Deep sequencing of Internal Transcribed Spacer (ITS) regions is the de facto standard for fungal diversity analysis. However, results are often...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00238

    authors: Motooka D,Fujimoto K,Tanaka R,Yaguchi T,Gotoh K,Maeda Y,Furuta Y,Kurakawa T,Goto N,Yasunaga T,Narazaki M,Kumanogoh A,Horii T,Iida T,Takeda K,Nakamura S

    更新日期:2017-02-15 00:00:00

  • Porcine Epidemic Diarrhea Virus Shedding and Antibody Response in Swine Farms: A Longitudinal Study.

    abstract::The porcine epidemic diarrhea virus (PEDV) causes an acute and highly contagious enteric disease characterized by severe enteritis, vomiting, watery diarrhea, and a high mortality rate in seronegative neonatal piglets. In the last few years, PED had a large economic impact on the swine industries in Asia and the US, a...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.02009

    authors: Bertasio C,Giacomini E,Lazzaro M,Perulli S,Papetti A,Lavazza A,Lelli D,Alborali G,Boniotti MB

    更新日期:2016-12-15 00:00:00

  • Prokaryotic Genome Expansion Is Facilitated by Phages and Plasmids but Impaired by CRISPR.

    abstract::Viruses and plasmids can introduce novel DNA into bacterial cells, thereby creating an opportunity for genome expansion; conversely, CRISPR, the prokaryotic adaptive immune system, which targets and eliminates foreign DNAs, may impair genome expansions. Recent studies presented conflicting results over the impact of C...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02254

    authors: Gao NL,Chen J,Wang T,Lercher MJ,Chen WH

    更新日期:2019-10-16 00:00:00

  • Evaluation of the biodegradation of Alaska North Slope oil in microcosms using the biodegradation model BIOB.

    abstract::We present the details of a numerical model, BIOB that is capable of simulating the biodegradation of oil entrapped in the sediment. The model uses Monod kinetics to simulate the growth of bacteria in the presence of nutrients and the subsequent consumption of hydrocarbons. The model was used to simulate experimental ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2014.00212

    authors: Torlapati J,Boufadel MC

    更新日期:2014-05-14 00:00:00

  • Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes.

    abstract::Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01002

    authors: Kulik T,Brankovics B,van Diepeningen AD,Bilska K,Żelechowski M,Myszczyński K,Molcan T,Stakheev A,Stenglein S,Beyer M,Pasquali M,Sawicki J,Wyrȩbek J,Baturo-Cieśniewska A

    更新日期:2020-05-25 00:00:00

  • Biomethanation of Syngas Using Anaerobic Sludge: Shift in the Catabolic Routes with the CO Partial Pressure Increase.

    abstract::Syngas generated by thermal gasification of biomass or coal can be steam reformed and purified into methane, which could be used locally for energy needs, or re-injected in the natural gas grid. As an alternative to chemical catalysis, the main components of the syngas (CO, CO2, and H2) can be used as substrates by a ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01188

    authors: Sancho Navarro S,Cimpoia R,Bruant G,Guiot SR

    更新日期:2016-08-03 00:00:00

  • Antimicrobial Potential of Epiphytic Bacteria Associated With Seaweeds of Little Andaman, India.

    abstract::Seaweeds of the intertidal regions are a rich source of surface associated bacteria and are potential source of antimicrobial molecules. In the present study, 77 epiphytic isolates from eight different algae collected from Little Andaman were enumerated. On testing for their antimicrobial activities against certain pa...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.00611

    authors: Karthick P,Mohanraju R

    更新日期:2018-04-04 00:00:00

  • Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability.

    abstract::Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10-11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01471

    authors: Mensch B,Neulinger SC,Künzel S,Wahl M,Schmitz RA

    更新日期:2020-06-26 00:00:00

  • Fecal Microbiota Characterization of Seychelles Giant Tortoises (Aldabrachelys gigantea) Living in Both Wild and Controlled Environments.

    abstract::A microbiome is defined as a complex collection of microorganisms and their genetic material. Studies regarding gut microbiomes of different animals have provided ecological and evolutionary information showing a strong link between health and disease. Very few studies have compared the gut microbiota of animals house...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.569249

    authors: Sandri C,Correa F,Spiezio C,Trevisi P,Luise D,Modesto M,Remy S,Muzungaile MM,Checcucci A,Zaborra CA,Mattarelli P

    更新日期:2020-10-20 00:00:00

  • Mycobacterium smegmatis PhoU Proteins Have Overlapping Functions in Phosphate Signaling and Are Essential.

    abstract::Many bacteria regulate gene expression in response to phosphate availability using a two-component signal transduction system, the activity of which is controlled by interaction with the Pst phosphate specific transporter and a cytoplasmic protein PhoU. Mycobacterium tuberculosis, the causative agent of tuberculosis, ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02523

    authors: Brokaw AM,Eide BJ,Muradian M,Boster JM,Tischler AD

    更新日期:2017-12-18 00:00:00

  • Arbuscular Mycorrhizal Fungi for the Biocontrol of Plant-Parasitic Nematodes: A Review of the Mechanisms Involved.

    abstract::Arbuscular mycorrhizal fungi (AMF) are obligate root symbionts that can protect their host plant against biotic stress factors such as plant-parasitic nematode (PPN) infection. PPN consist of a wide range of species with different life styles that can cause major damage in many important crops worldwide. Various mecha...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2015.01280

    authors: Schouteden N,De Waele D,Panis B,Vos CM

    更新日期:2015-11-17 00:00:00

  • Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012.

    abstract::Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Sal...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01317

    authors: Yousfi K,Usongo V,Berry C,Khan RH,Tremblay DM,Moineau S,Mulvey MR,Doualla-Bell F,Fournier E,Nadon C,Goodridge L,Bekal S

    更新日期:2020-06-17 00:00:00

  • Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1.

    abstract::The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.03130

    authors: Gregson BH,Metodieva G,Metodiev MV,Golyshin PN,McKew BA

    更新日期:2018-12-17 00:00:00

  • Ascertaining the relationship between Salmonella Typhimurium and Salmonella 4,[5],12:i:- by MLVA and inferring the sources of human salmonellosis due to the two serovars in Italy.

    abstract::The current picture of human salmonellosis shows Salmonella Typhimurium and S. 4,[5],12:i:- as the most common serovars in Italy. The aims of this study were to investigate the genetic relationship between these serovars, as well as to test the possibility of inferring sources of human salmonellosis due to S. Typhimur...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00301

    authors: Barco L,Barrucci F,Cortini E,Ramon E,Olsen JE,Luzzi I,Lettini AA,Ricci A

    更新日期:2015-04-27 00:00:00

  • Sex Modulates Lactobacillus johnsonii N6.2 and Phytophenol Effectiveness in Reducing High Fat Diet Induced mTOR Activation in Sprague-Dawley Rats.

    abstract::Metabolic syndrome (MetS) is the underlying cause of some devastating diseases, including type 2 diabetes and cardiovascular disease. These diseases have been associated with over-activation of the mechanistic Target of Rapamycin (mTOR) pathway. This study utilizes a high fat diet (HFD) to induce MetS and to dissect t...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02649

    authors: Kling DN,DeBose-Scarlett EM,Teixeira LD,Gezan SA,Lorca GL,Gonzalez CF

    更新日期:2018-11-06 00:00:00

  • Mechanism and In Vivo Evaluation: Photodynamic Antibacterial Chemotherapy of Lysine-Porphyrin Conjugate.

    abstract::Lysine-porphyrin conjugate 4i has potent photosensitive antibacterial effect on clinical isolated bacterial strains such as Methicillin-resistant Staphylococcus aureus (MRSA), Escherichia coli, and Pseudomonas aeruginosa. The mechanism of photodynamic antibacterial chemotherapy of 4i (4i-PACT) in vitro and the treatme...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00242

    authors: Xu Z,Gao Y,Meng S,Yang B,Pang L,Wang C,Liu T

    更新日期:2016-03-02 00:00:00

  • Effect of Bifidobacterium breve in Combination With Different Antibiotics on Clostridium difficile.

    abstract::While combinations of probiotics with antibiotics have exhibited beneficial and adverse effects in the treatment of Clostridium difficile infection (CDI), no substantive explanation has been provided for these effects. In this study, C. difficile ATCC 9689 (CD) was treated with Bifidobacterium breve (YH68) in combinat...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02953

    authors: Yang J,Yang H

    更新日期:2018-12-04 00:00:00

  • Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing.

    abstract::LuxR solos are unexplored in Archaea, despite their vital role in the bacterial regulatory network. They assist bacteria in perceiving acyl homoserine lactones (AHLs) and/or non-AHLs signaling molecules for establishing intraspecies, interspecies, and interkingdom communication. In this study, we explored the potentia...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00798

    authors: Rajput A,Kumar M

    更新日期:2017-05-03 00:00:00

  • Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera.

    abstract::Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01169

    authors: Chronopoulou PM,Salonen I,Bird C,Reichart GJ,Koho KA

    更新日期:2019-05-28 00:00:00

  • Pre-cultivation with Selected Prebiotics Enhances the Survival and the Stress Response of Lactobacillus rhamnosus Strains in Simulated Gastrointestinal Transit.

    abstract::In our study, we dwelled upon combinations of lactobacilli/prebiotics, considering four different strains belonging to the Lactobacillus rhamnosus species, including Lactobacillus rhamnosus GG (LGG), and different prebiotics often found in commercial synbiotic products, such as inulin, lactulose and polyols mannitol a...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01067

    authors: Succi M,Tremonte P,Pannella G,Tipaldi L,Cozzolino A,Romaniello R,Sorrentino E,Coppola R

    更新日期:2017-06-14 00:00:00

  • Responses to Hydric Stress in the Seed-Borne Necrotrophic Fungus Alternaria brassicicola.

    abstract::Alternaria brassicicola is a necrotrophic fungus causing black spot disease and is an economically important seed-borne pathogen of cultivated brassicas. Seed transmission is a crucial component of its parasitic cycle as it promotes long-term survival and dispersal. Recent studies, conducted with the Arabidopsis thali...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.01969

    authors: N'Guyen GQ,Raulo R,Marchi M,Agustí-Brisach C,Iacomi B,Pelletier S,Renou JP,Bataillé-Simoneau N,Campion C,Bastide F,Hamon B,Mouchès C,Porcheron B,Lemoine R,Kwasiborski A,Simoneau P,Guillemette T

    更新日期:2019-08-30 00:00:00