scholarly journals From the first touch to biofilm establishment by the human pathogen Candida glabrata: a genome-wide to nanoscale view

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mafalda Cavalheiro ◽  
Diana Pereira ◽  
Cécile Formosa-Dague ◽  
Carolina Leitão ◽  
Pedro Pais ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Biofilm Formation ◽  
Candida Glabrata ◽  
Opportunistic Pathogen ◽  
Adhesive Properties ◽  
Persistent Infections ◽  
Abiotic Surfaces ◽  
Genome Wide ◽  
A Genome ◽  
Cell Force

AbstractCandida glabrata is an opportunistic pathogen that adheres to human epithelial mucosa and forms biofilm to cause persistent infections. In this work, Single-cell Force Spectroscopy (SCFS) was used to glimpse at the adhesive properties of C. glabrata as it interacts with clinically relevant surfaces, the first step towards biofilm formation. Following a genetic screening, RNA-sequencing revealed that half of the entire transcriptome of C. glabrata is remodeled upon biofilm formation, around 40% of which under the control of the transcription factors CgEfg1 and CgTec1. Using SCFS, it was possible to observe that CgEfg1, but not CgTec1, is necessary for the initial interaction of C. glabrata cells with both abiotic surfaces and epithelial cells, while both transcription factors orchestrate biofilm maturation. Overall, this study characterizes the network of transcription factors controlling massive transcriptional remodelling occurring from the initial cell-surface interaction to mature biofilm formation.

scholarly journals Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

2021 ◽  
Author(s):  
Xiaoping Huang ◽  
Hongyu Zhang ◽  
Qiang Wang ◽  
Rong Guo ◽  
Lingxia Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Flag Leaf ◽  
Reduction Process ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse

2009 ◽  
Vol 20 (4) ◽  
pp. 236-246 ◽  
Author(s):  
X. Zheng ◽  
Y. Wang ◽  
Q. Yao ◽  
Z. Yang ◽  
K. Chen
Keyword(s):  
Transcription Factors ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

scholarly journals Increased Intracellular Cyclic di-AMP Levels Sensitize Streptococcus gallolyticus subsp. gallolyticus to Osmotic Stress and Reduce Biofilm Formation and Adherence on Intestinal Cells

2019 ◽  
Vol 201 (6) ◽  
Author(s):  
Wooi Keong Teh ◽  
Shaynoor Dramsi ◽  
Tim Tolker-Nielsen ◽  
Liang Yang ◽  
Michael Givskov
Keyword(s):  
Osmotic Stress ◽  
Biofilm Formation ◽  
Cell Aggregation ◽  
The Elderly ◽  
Opportunistic Pathogen ◽  
Intestinal Cells ◽  
Content Type ◽  
Streptococcus Gallolyticus ◽  
Abiotic Surfaces ◽  
Human Intestinal Cells

ABSTRACT Cyclic di-AMP is a recently identified second messenger exploited by a number of Gram-positive bacteria to regulate important biological processes. Here, we studied the phenotypic alterations induced by the increased intracellular c-di-AMP levels in Streptococcus gallolyticus, an opportunistic pathogen responsible for septicemia and endocarditis in the elderly. We report that an S. gallolyticus c-di-AMP phosphodiesterase gdpP knockout mutant, which displays a 1.5-fold higher intracellular c-di-AMP levels than the parental strain UCN34, is more sensitive to osmotic stress and is morphologically smaller than the parental strain. Unexpectedly, we found that a higher level of c-di-AMP reduced biofilm formation of S. gallolyticus on abiotic surfaces and reduced adherence and cell aggregation on human intestinal cells. A genome-wide transcriptomic analysis indicated that c-di-AMP regulates many biological processes in S. gallolyticus, including the expression of various ABC transporters and disease-associated genes encoding bacteriocin and Pil3 pilus. Complementation of the gdpP in-frame deletion mutant with a plasmid carrying gdpP in trans from its native promoter restored bacterial morphology, tolerance to osmotic stress, biofilm formation, adherence to intestinal cells, bacteriocin production, and Pil3 pilus expression. Our results indicate that c-di-AMP is a pleiotropic signaling molecule in S. gallolyticus that may be important for S. gallolyticus pathogenesis. IMPORTANCE Streptococcus gallolyticus is an opportunistic pathogen responsible for septicemia and endocarditis in the elderly and is also strongly associated with colorectal cancer. S. gallolyticus can form biofilms, express specific pili to colonize the host tissues, and produce a specific bacteriocin allowing killing of commensal bacteria in the murine colon. Nevertheless, how the expression of these colonization factors is regulated remains largely unknown. Here, we show that c-di-AMP plays pleiotropic roles in S. gallolyticus, controlling the tolerance to osmotic stress, cell size, biofilm formation on abiotic surfaces, adherence and cell aggregation on human intestinal cells, expression of Pil3 pilus, and production of bacteriocin. This study indicates that c-di-AMP may constitute a key regulatory molecule for S. gallolyticus host colonization and pathogenesis.

scholarly journals RicetissueTFDB: A Genome‐Wide Identification of Tissue‐Specific Transcription Factors in Rice

2019 ◽  
Vol 12 (1) ◽  
pp. 170081 ◽  
Author(s):  
Weiying Chen ◽  
Zhenyong Chen ◽  
Fuyan Luo ◽  
Mingli Liao ◽  
Shuhong Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Tissue Specific ◽  
Genome Wide ◽  
A Genome

Identifying biofilm regulators as novel targets for antimicrobial drug design

2020 ◽  
Author(s):  
Melanie Dostert ◽  
Corrie R Belanger ◽  
Travis M Blimkie ◽  
Reza Falsafi ◽  
Bhavjinder K Dhillon ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Immunocompromised Patients ◽  
Nosocomial Pathogen ◽  
Burn Wound ◽  
Antibiotic Resistant ◽  
Metabolic Genes ◽  
Genome Wide ◽  
A Genome ◽  
Novel Targets ◽  
Hypothetical Genes

<p>Antibiotic treatment regularly fails to cure patients suffering from infections caused by adaptively resistant microbial communities, referred to as biofilms. Even though at least two thirds of all clinical infections are associated with biofilms, there are no biofilm-specific therapies on the market or in clinical trials. <em>Pseudomonas aeruginosa</em> is a remarkably antibiotic resistant, nosocomial pathogen and biofilm-former that causes morbidity and mortality especially in cystic fibrosis and immunocompromised patients. This project aims to identify regulatory genes associated with drug resistance in <em>P. aeruginosa</em> biofilms to provide novel biofilm-specific targets for the design of potent drugs. A genome-wide screen of <em>P. aeruginosa</em> burn wound isolate UCBPP-PA14 identified 362 genes involved in biofilm formation, including dozens of regulatory and hypothetical genes. I will discuss regulatory as well as metabolic genes corresponding to the known resistome of antimicrobials.</p>

Directly Measuring the Adhesive and Elastic Properties of Bacteria using a Surface Force Apparatus: Effect of Desiccation

2006 ◽  
Vol 925 ◽  
Author(s):  
Cheol Ho Heo ◽  
Raina M Maier ◽  
Joan E Curry
Keyword(s):  
Elastic Properties ◽  
Material Properties ◽  
Biofilm Formation ◽  
Surface Force ◽  
Opportunistic Pathogen ◽  
Film Material ◽  
Surface Forces Apparatus ◽  
Adhesive Properties ◽  
Force Profile ◽  
Dry Conditions

ABSTRACTBacterial adhesion is the first step in biofilm formation which impacts numerous environmental, industrial and medical processes. Examples of undesirable consequences of biofilm formation include metal rust, sewage sludge and bacteria-related diseases. Desirable consequences are biofiltration and bioremediation. Bacteria are resilient and can survive in harsh environments. A severe stress is desiccation since dehydration can damage DNA and change the properties of proteins. Some bacteria protect against dehydration by accumulating sugars such as sucrose and trehalose while others undergo a transformation from an active to a dormant state. Evaporative deposition of bacteria on a surface shows that some bacteria aggregate to form two dimensional patterns which may be important for nutrient sharing and survival in dry conditions. Since bacteria are increasingly being employed as components in biosensors and biofilm reactors, it is important to understand the material properties of bacteria in dry conditions for these applications. For a decade, Atomic Force Microscopy (AFM) has been the primary tool used to study the adhesion and elastic properties of individual bacteria. In this work we show it is possible to use a Surface Forces Apparatus (SFA) to measure elastic and adhesive properties of small collections of surface bound bacteria. The measurements are conducted with incomplete, patterned bacterial films and we have developed a protocol to image the contact area with AFM after the experiment. Using the SFA, we measured the force profile between aPseudomonas aeruginosaPAO1 film and a bare mica surface.P. aeruginosaPAO1 is a ubiquitous gram-negative soil bacterium and is also an opportunistic pathogen. We repeated the measurement in the same contact position for six days to determine the effect of desiccation on the film material properties.

scholarly journals Natural selection driven by DNA binding proteins shapes genome-wide motif statistics

2016 ◽  
Author(s):  
Long Qian ◽  
Edo Kussell
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Large Collection ◽  
Functional Sites ◽  
Genome Wide ◽  
A Genome ◽  
Global Selection

AbstractEctopic DNA binding by transcription factors and other DNA binding proteins can be detrimental to cellular functions and ultimately to organismal fitness. The frequency of protein-DNA binding at non-functional sites depends on the global composition of a genome with respect to all possible short motifs, or k-mer words. To determine whether weak yet ubiquitous protein-DNA interactions could exert significant evolutionary pressures on genomes, we correlate in vitro measurements of binding strengths on all 8-mer words from a large collection of transcription factors, in several different species, against their relative genomic frequencies. Our analysis reveals a clear signal of purifying selection to reduce the large number of weak binding sites genome-wide. This evolutionary process, which we call global selection, has a detectable hallmark in that similar words experience similar evolutionary pressure, a consequence of the biophysics of protein-DNA binding. By analyzing a large collection of genomes, we show that global selection exists in all domains of life, and operates through tiny selective steps, maintaining genomic binding landscapes over long evolutionary timescales.

scholarly journals Identification of Genes Regulating Cell Death inStaphylococcus aureus

2019 ◽  
Author(s):  
Rebecca Yee ◽  
Jie Feng ◽  
Jiou Wang ◽  
Jiazhen Chen ◽  
Ying Zhang
Keyword(s):  
Cell Death ◽  
Acetic Acid ◽  
Drug Targets ◽  
Opportunistic Pathogen ◽  
Infection Model ◽  
Chronic Infections ◽  
Bacterial Cell Death ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms

AbstractStaphylococcus aureusis an opportunistic pathogen that causes acute and chronic infections. Due toS. aureus’ s highly resistant and persistent nature, it is paramount to identify better drug targets in order to eradicateS. aureusinfections. Despite the efforts in understanding bacterial cell death, the genes and pathways ofS. aureuscell death remain elusive. Here, we performed a genome-wide screen using a transposon mutant library to study the genetic mechanisms involved inS. aureuscell death. Using a precisely controlled heat-ramp and acetic acid exposure assays, mutations in 27 core genes (hsdR1, hslO, nsaS, sspA, folD, mfd, vraF, kdpB, USA300HOU_2684, 0868, 0369, 0420, 1154, 0142, 0930, 2590, 0997, 2559, 0044, 2004, 1209, 0152, 2455, 0154, 2386, 0232, 0350 involved in transporters, transcription, metabolism, peptidases, kinases, transferases, SOS response, nucleic acid and protein synthesis) caused the bacteria to be more death-resistant. In addition, we identified mutations in core 10 genes (capA, gltT, mnhG1,USA300HOU_1780, 2496, 0200, 2029, 0336, 0329, 2386, involved in transporters, metabolism, transcription, cell wall synthesis) from heat-ramp and acetic acid that caused the bacteria to be more death-sensitive or with defect in persistence. Interestingly, death-resistant mutants were more virulent than the parental strain USA300 and caused increased mortality in aCaenorhabditis elegansinfection model. Conversely, death-sensitive mutants were less persistent and formed less persister cells upon exposure to different classes of antibiotics. These findings provide new insights into the mechanisms ofS. aureuscell death and offer new therapeutic targets for developing more effective treatments caused byS. aureus.

scholarly journals Function of BriC Peptide in the Pneumococcal Competence and Virulence Portfolio

2018 ◽  
Author(s):  
Surya D. Aggarwal ◽  
Rory Eutsey ◽  
Jacob West-Roberts ◽  
Arnau Domenech ◽  
Wenjie Xu ◽  
...  
Keyword(s):  
Murine Model ◽  
Biofilm Formation ◽  
Opportunistic Pathogen ◽  
Nasopharyngeal Colonization ◽  
Point Of Entry ◽  
Abiotic Surfaces ◽  
Biofilm Development

AbstractStreptococcus pneumoniae (pneumococcus) is an opportunistic pathogen that causes otitis media, sinusitis, pneumonia, meningitis and sepsis. The progression to this pathogenic lifestyle is preceded by asymptomatic colonization of the nasopharynx. This colonization is associated with biofilm formation; the competence pathway influences the structure and stability of biofilms. However, the molecules that link the competence pathway to biofilm formation are unknown. Here, we describe a new competence-induced gene, called briC, and demonstrate that its product promotes biofilm development and stimulates colonization in a murine model. We show that expression of briC is induced by the master regulator of competence, ComE. Whereas briC does not substantially influence early biofilm development on abiotic surfaces, it significantly impacts later stages of biofilm development. Specifically, briC expression leads to increases in biofilm biomass and thickness at 72h. Consistent with the role of biofilms in colonization, briC promotes nasopharyngeal colonization in the murine model. The function of BriC appears to be conserved across pneumococci, as comparative genomics reveal that briC is widespread across isolates. Surprisingly, many isolates, including strains from clinically important PMEN1 and PMEN14 lineages, which are widely associated with colonization, encode a long briC promoter. This long form captures an instance of genomic plasticity and functions as a competence-independent expression enhancer that may serve as a precocious point of entry into this otherwise competence-regulated pathway. Moreover, overexpression of briC by the long promoter fully rescues the comE-deletion induced biofilm defect in vitro, and partially in vivo. These findings indicate that BriC may bypass the influence of competence in biofilm development and that such a pathway may be active in a subset of pneumococcal lineages. In conclusion, BriC is a part of the complex molecular network that connects signaling of the competence pathway to biofilm development and colonization.

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