scholarly journals Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion

2021 ◽  
Vol 12 ◽  
Author(s):  
Ines Krohn ◽  
Lutgardis Bergmann ◽  
Minyue Qi ◽  
Daniela Indenbirken ◽  
Yuchen Han ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Microbiologically Influenced Corrosion ◽  
Rna Seq ◽  
Secretion Systems ◽  
Fuel Tanks ◽  
Number Of Genes ◽  
Associated Proteins ◽  
Metagenome Sequencing ◽  
Bacteria And Fungi ◽  
Cultured Bacteria

Microbial contamination of fuels, associated with a wide variety of bacteria and fungi, leads to decreased product quality and can compromise equipment performance by biofouling or microbiologically influenced corrosion. Detection and quantification of microorganisms are critical in monitoring fuel systems for an early detection of microbial contaminations. To address these challenges, we have analyzed six metagenomes, one transcriptome, and more than 1,200 fluid and swab samples taken from fuel tanks or kerosene. Our deep metagenome sequencing and binning approaches in combination with RNA-seq data and qPCR methods implied a metabolic symbiosis between fungi and bacteria. The most abundant bacteria were affiliated with α-, β-, and γ-Proteobacteria and the filamentous fungi Amorphotheca. We identified a high number of genes, which are related to kerosene degradation and biofilm formation. Surprisingly, a large number of genes coded enzymes involved in polymer degradation and potential bio-corrosion processes. Thereby, the transcriptionally most active microorganisms were affiliated with the genera Methylobacteria, Pseudomonas, Kocuria, Amorpotheka, Aspergillus, Fusarium, and Penicillium. Many not yet cultured bacteria and fungi appeared to contribute to the biofilm transcriptional activities. The largest numbers of transcripts were observed for dehydrogenase, oxygenase, and exopolysaccharide production, attachment and pili/flagella-associated proteins, efflux pumps, and secretion systems as well as lipase and esterase activity.

scholarly journals Putative transmembrane transporter modulates higher-level aggression in Drosophila

2017 ◽  
Vol 114 (9) ◽  
pp. 2373-2378 ◽  
Author(s):  
Budhaditya Chowdhury ◽  
Yick-Bun Chan ◽  
Edward A. Kravitz
Keyword(s):  
Causal Effect ◽  
Nerve Terminals ◽  
Rna Seq ◽  
Wild Type ◽  
Temperature Dependent ◽  
Number Of Genes ◽  
Interesting Family ◽  
Solute Carrier ◽  
Transmembrane Transporter ◽  
Selection Of

By selection of winners of dyadic fights for 35 generations, we have generated a hyperaggressive Bully line of flies that almost always win fights against the parental wild-type Canton-S stock. Maintenance of the Bully phenotype is temperature dependent during development, with the phenotype lost when flies are reared at 19 °C. No similar effect is seen with the parent line. This difference allowed us to carry out RNA-seq experiments and identify a limited number of genes that are differentially expressed by twofold or greater in the Bullies; one of these was a putative transmembrane transporter, CG13646, which showed consistent and reproducible twofold down-regulation in Bullies. We examined the causal effect of this gene on the phenotype with a mutant line for CG13646, and with an RNAi approach. In all cases, reduction in expression of CG13646 by approximately half led to a hyperaggressive phenotype partially resembling that seen in the Bully flies. This gene is a member of a very interesting family of solute carrier proteins (SLCs), some of which have been suggested as being involved in glutamine/glutamate and GABA cycles of metabolism in excitatory and inhibitory nerve terminals in mammalian systems.

scholarly journals Role of DegQ in differential stability of flagellin subunits in Vibrio vulnificus

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
You-Chul Jung ◽  
Mi-Ae Lee ◽  
Han-Shin Kim ◽  
Kyu-Ho Lee
Keyword(s):  
Life Cycle ◽  
Biofilm Formation ◽  
Vibrio Vulnificus ◽  
Differential Regulation ◽  
Specific Manner ◽  
Associated Proteins ◽  
Differential Stability ◽  
Methionine Residues

AbstractBiofilm formation of Vibrio vulnificus is initiated by adherence of flagellated cells to surfaces, and then flagellum-driven motility is not necessary during biofilm maturation. Once matured biofilms are constructed, cells become flagellated and swim to disperse from biofilms. As a consequence, timely regulations of the flagellar components’ expression are crucial to complete a biofilm life-cycle. In this study, we demonstrated that flagellins’ production is regulated in a biofilm stage-specific manner, via activities of a protease DegQ and a chaperone FlaJ. Among four flagellin subunits for V. vulnificus filament, FlaC had the highest affinities to hook-associated proteins, and is critical for maturating flagellum, showed the least susceptibility to DegQ due to the presence of methionine residues in its DegQ-sensitive domains, ND1 and CD0. Therefore, differential regulation by DegQ and FlaJ controls the cytoplasmic stability of flagellins, which further determines the motility-dependent, stage-specific development of biofilms.

scholarly journals Near-atomic resolution analysis of BipD, a component of the type III secretion system ofBurkholderia pseudomallei

2010 ◽  
Vol 66 (9) ◽  
pp. 990-993 ◽  
Author(s):  
M. Pal ◽  
P. T. Erskine ◽  
R. S. Gill ◽  
S. P. Wood ◽  
J. B. Cooper
Keyword(s):  
Crystal Form ◽  
Target Cells ◽  
X Rays ◽  
Secretion Systems ◽  
Monoclinic Crystal ◽  
Major Function ◽  
Type Iii ◽  
Associated Proteins ◽  
Target Cell Membrane ◽  
Type Iii Protein Secretion

Burkholderia pseudomallei, the causative agent of melioidosis, possesses a type III protein secretion apparatus that is similar to those found inSalmonellaandShigella. A major function of these secretion systems is to inject virulence-associated proteins into target cells of the host organism. ThebipDgene ofB. pseudomalleiencodes a secreted virulence factor that is similar in sequence and is most likely to be functionally analogous to IpaD fromShigellaand SipD fromSalmonella. Proteins in this family are thought to act as extracellular chaperones at the tip of the secretion needle to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and may also link the translocon pore with the secretion needle. BipD has been crystallized in a monoclinic crystal form that diffracted X-rays to 1.5 Å resolution and the structure was refined to anRfactor of 16.1% and anRfreeof 19.8% at this resolution. The putative dimer interface that was observed in previous crystal structures was retained and a larger surface area was buried in the new crystal form.

scholarly journals Usnic Acid, a Natural Antimicrobial Agent Able To Inhibit Bacterial Biofilm Formation on Polymer Surfaces

2004 ◽  
Vol 48 (11) ◽  
pp. 4360-4365 ◽  
Author(s):  
I. Francolini ◽  
P. Norris ◽  
A. Piozzi ◽  
G. Donelli ◽  
P. Stoodley
Keyword(s):  
Biofilm Formation ◽  
Usnic Acid ◽  
Modern Medicine ◽  
The Body ◽  
Bacterial Biofilm ◽  
Polymer Surfaces ◽  
Gram Positive Bacteria ◽  
The Status ◽  
Bacteria And Fungi ◽  
Systemic Infections

ABSTRACT In modern medicine, artificial devices are used for repair or replacement of damaged parts of the body, delivery of drugs, and monitoring the status of critically ill patients. However, artificial surfaces are often susceptible to colonization by bacteria and fungi. Once microorganisms have adhered to the surface, they can form biofilms, resulting in highly resistant local or systemic infections. At this time, the evidence suggests that (+)-usnic acid, a secondary lichen metabolite, possesses antimicrobial activity against a number of planktonic gram-positive bacteria, including Staphylococcus aureus, Enterococcus faecalis, and Enterococcus faecium. Since lichens are surface-attached communities that produce antibiotics, including usnic acid, to protect themselves from colonization by other bacteria, we hypothesized that the mode of action of usnic acid may be utilized in the control of medical biofilms. We loaded (+)-usnic acid into modified polyurethane and quantitatively assessed the capacity of (+)-usnic acid to control biofilm formation by either S. aureus or Pseudomonas aeruginosa under laminar flow conditions by using image analysis. (+)-Usnic acid-loaded polymers did not inhibit the initial attachment of S. aureus cells, but killing the attached cells resulted in the inhibition of biofilm. Interestingly, although P. aeruginosa biofilms did form on the surface of (+)-usnic acid-loaded polymer, the morphology of the biofilm was altered, possibly indicating that (+)-usnic acid interfered with signaling pathways.

scholarly journals A comprehensive simulation study on classification of RNA-Seq data

2017 ◽  
Author(s):  
Gokmen Zararsiz ◽  
Dinçer Göksülük ◽  
Selçuk Korkmaz ◽  
Vahap Eldem ◽  
Gözde Ertürk Zararsız ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Sample Size ◽  
Linear Discriminant Analysis ◽  
Differential Expression ◽  
Simulation Study ◽  
Rna Seq ◽  
Linear Discriminant ◽  
Number Of Genes ◽  
Expression Rate

RNA sequencing (RNA-Seq) is a powerful technique for thegene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies.Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of geneexpression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption. Hence, these methods cannot be directly applied to RNA-Seq data since they violate both data structure and distributional assumptions. However, it is possible to apply these algorithms with appropriate modifications to RNA-Seq data. One way is to develop count-based classifiers, such as Poisson linear discriminant analysis and negative binomial linear discriminant analysis. Another way is to bring the data hierarchically closer to microarrays and apply microarray-based classifiers.In this study, we compared several classifiers including PLDA with and without power transformation, NBLDA, single SVM, bagging SVM (bagSVM), classification and regression trees (CART), and random forests (RF). We also examined the effect of several parameters such asoverdispersion, sample size, number of genes, number of classes, differential-expression rate, andthe transformation method on model performances.A comprehensive simulation study is conducted and the results are compared with the results of two miRNA and two mRNA experimental datasets. The results revealed that increasing the sample size, differential-expression rate, and number of genes and decreasing the dispersion parameter and number of groups lead to an increase in classification accuracy. Similar with differential-expression studies, the classification of RNA-Seq data requires careful attention when handling data overdispersion. We conclude that, as a count-based classifier, the power transformed PLDA and, as a microarray-based classifier, vst or rlog transformed RF and SVM clas sifiers may be a good choice for classification. An R/BIOCONDUCTOR package, MLSeq, is freely available at https://www.bioconductor.org/packages/release/bioc/html/MLSeq.html .

scholarly journals Disruption of c-di-GMP signaling networks unlocks cryptic expression of secondary metabolites during biofilm growth in Burkholderia pseudomallei

2021 ◽  
Author(s):  
Grace I Borlee ◽  
Mihnea R. Mangalea ◽  
Kevin H. Martin ◽  
Brooke A. Plumley ◽  
Samuel J. Golon ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Biofilm Formation ◽  
Burkholderia Pseudomallei ◽  
Gene Clusters ◽  
Etiologic Agent ◽  
Regulatory Control ◽  
Colony Morphology ◽  
Secretion Systems ◽  
Biofilm Growth ◽  
Conditional Expression

The regulation and production of secondary metabolites during biofilm growth of Burkholderia spp. is not well understood. To learn more about the crucial role and regulatory control of cryptic molecules produced during biofilm growth, we disrupted c-di-GMP signaling in Burkholderia pseudomallei, a soil-borne bacterial saprophyte and the etiologic agent of melioidosis. Our approach to these studies combined transcriptional profiling with genetic deletions that targeted key c-di-GMP regulatory components to characterize responses to changes in temperature. Mutational analyses and conditional expression studies of c-di-GMP genes demonstrates their contribution to phenotypes such as biofilm formation, colony morphology, motility, and expression of secondary metabolite biosynthesis when grown as a biofilm at different temperatures. RNA-seq analysis was performed at varying temperatures in a ΔII2523 mutant background that is responsive to temperature alterations resulting in hypo- and hyper- biofilm forming phenotypes. Differential regulation of genes was observed for polysaccharide biosynthesis, secretion systems, and nonribosomal peptide and polyketide synthase (NRPS/PKS) clusters in response to temperature changes. Deletion mutations of biosynthetic gene clusters (BGCs) clusters 2, 11, 14 (syrbactin), and 15 (malleipeptin) in wild-type and ΔII2523 backgrounds also reveals the contribution of these BGCs to biofilm formation and colony morphology in addition to inhibition of Bacillus subtilis and Rhizoctonia solani. Our findings suggest that II2523 impacts the regulation of genes that contribute to biofilm formation and competition. Characterization of cryptic BGCs under differing environmental conditions will allow for a better understanding of the role of secondary metabolites in the context of biofilm formation and microbe-microbe interactions.

scholarly journals Functionally non-redundant paralogs spe-47 and spe-50 encode FB-MO associated proteins and interact with him-8

2020 ◽  
Author(s):  
Jessica N. Clark ◽  
Gaurav Prajapati ◽  
Fermina Aldaco ◽  
Thomas J. Sokolich ◽  
Steven Keung ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Chromatin Remodeling ◽  
Duplication Event ◽  
Sperm Function ◽  
C Elegans ◽  
Conserved Sequence ◽  
Long Period ◽  
Normal Sperm ◽  
Number Of Genes ◽  
Associated Proteins

AbstractThe activation of C. elegans spermatids to crawling spermatozoa is affected by a number of genes including spe-47. Here, we investigate a paralog to spe-47: spe-50, which has a highly conserved sequence and expression, but which is not functionally redundant to spe-47. Phylogenetic analysis indicates that the duplication event that produced the paralogs occurred prior to the radiation of the Caenorhabditis species included in the analysis, allowing a long period for the paralogs to diverge in function. Furthermore, we observed that knockout mutations in both genes, either alone or together, have little effect on sperm function. However, hermaphrodites harboring both knockout mutations combined with a third mutation in the him-8 gene are nearly self-sterile due to a sperm defect, even though they have numerous apparently normal sperm within their spermathecae. We suggest that the sperm in these triple mutants are defective in fusing with oocytes, and that the effect of the him-8 mutation is due to its role in chromatin remodeling.

scholarly journals YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 155 ◽  
Author(s):  
Sandeep Chakraborty ◽  
Monica Britton ◽  
Jill Wegrzyn ◽  
Timothy Butterfield ◽  
Pedro José Martínez-García ◽  
...  
Keyword(s):  
Transition Zone ◽  
Transcript Abundance ◽  
Black Walnut ◽  
Open Reading Frames ◽  
Rna Seq ◽  
Reading Frame ◽  
Homologous Genes ◽  
Associated Proteins ◽  
Molecular Components ◽  
Reading Frames

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.

scholarly journals Topological and Metagenomic Evidence For Intensified Bacterial-Fungal Interactions in Mangrove Root Interior

2021 ◽  
Author(s):  
Zhengyuan Zhou ◽  
Ruiwen Hu ◽  
Yanmei Ni ◽  
Wei Zhuang ◽  
Zhiwen Luo ◽  
...  
Keyword(s):  
Plant Performance ◽  
Sequencing Technologies ◽  
Mangrove Root ◽  
Domain Interactions ◽  
Network Topologies ◽  
Mangrove Roots ◽  
Metagenome Sequencing ◽  
Underlying Mechanisms ◽  
Bacteria And Fungi ◽  
Fungal Interactions

Abstract Background: Plant roots host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, potential interactions and underlying mechanisms remain largely unknown in root-associated microbial communities at a continuous fine-scale. Results: We analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment with more intensive interactions in bacterial-fungal network than in bacterial or fungal network, which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain interactions with fungi and stimulate biofilm formation. Also, high abundances of genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH and lasR) and aerobic cobamide biosynthesis (cobG, cobF and cobA) were detected in the endosphere.Conclusions: Our results reveal intensified inter-domain interactions of endophytes in the mangrove roots, creating a distinct micro-environment to promote a biofilm life-style.

Sign in / Sign up

Export Citation Format

Share Document