scholarly journals The Investigation of Promoter Sequences of Marseilleviruses Highlights a Remarkable Abundance of the AAATATTT Motif in Intergenic Regions

2017 ◽  
Vol 91 (21) ◽  
Author(s):  
Graziele Pereira Oliveira ◽  
Maurício Teixeira Lima ◽  
Thalita Souza Arantes ◽  
Felipe Lopes Assis ◽  
Rodrigo Araújo Lima Rodrigues ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Promoter Sequence ◽  
Content Type ◽  
Promoter Sequences ◽  
Promoter Motif ◽  
Wide Range ◽  
Multiple Copies ◽  
Intergenic Regions ◽  
Foreign Genes

ABSTRACT Viruses display a wide range of genomic profiles and, consequently, a variety of gene expression strategies. Specific sequences associated with transcriptional processes have been described in viruses, and putative promoter motifs have been elucidated for some nucleocytoplasmic large DNA viruses (NCLDV). Among NCLDV, the Marseilleviridae is a well-recognized family because of its genomic mosaicism. The marseilleviruses have an ability to incorporate foreign genes, especially from sympatric organisms inhabiting Acanthamoeba, its main known host. Here, we identified for the first time an eight-nucleotide A/T-rich promoter sequence (AAATATTT) associated with 55% of marseillevirus genes that is conserved in all marseilleviruses lineages, a higher level of conservation than that of any giant virus described to date. We instigated our prediction about the promoter motif by biological assays and by evaluating how single mutations in this octamer can impact gene expression. The investigation of sequences that regulate the expression of genes relative to lateral transfer revealed that the promoter motifs do not appear to be incorporated by marseilleviruses from donor organisms. Indeed, analyses of the intergenic regions that regulate lateral gene transfer-related genes have revealed an independent origin of the marseillevirus intergenic regions that does not match gene-donor organisms. About 50% of AAATATTT motifs spread throughout intergenic regions of the marseilleviruses are present as multiple copies. We believe that such multiple motifs are associated with increased expression of a given gene or are related to incorporation of foreign genes into the mosaic genome of marseilleviruses. IMPORTANCE The marseilleviruses draw attention because of the peculiar features of their genomes; however, little is known about their gene expression patterns or the factors that regulate those expression patterns. The limited published research on the expression patterns of the marseilleviruses and their unique genomes has led us to study the promoter motif sequences in the intergenic regions of the marseilleviruses. This work is the first to analyze promoter sequences in the genomes of the marseilleviruses. We also suggest a strong capacity to acquire foreign genes and to express those genes mediated by multiple copies of the promoter motifs available in intergenic regions. These findings contribute to an understanding of genomic expansion and plasticity observed in these giant viruses.

scholarly journals Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jorge A. Ramírez-Tejero ◽  
Jaime Jiménez-Ruiz ◽  
Alicia Serrano ◽  
Angjelina Belaj ◽  
Lorenzo León ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Growth And Development ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Expression Level ◽  
Resistant Cultivars ◽  
Pathogen Invasion ◽  
Wide Range ◽  
Olive Cultivars

Abstract Background Olive orchards are threatened by a wide range of pathogens. Of these, Verticillium dahliae has been in the spotlight for its high incidence, the difficulty to control it and the few cultivars that has increased tolerance to the pathogen. Disease resistance not only depends on detection of pathogen invasion and induction of responses by the plant, but also on barriers to avoid the invasion and active resistance mechanisms constitutively expressed in the absence of the pathogen. In a previous work we found that two healthy non-infected plants from cultivars that differ in V. dahliae resistance such as ‘Frantoio’ (resistant) and ‘Picual’ (susceptible) had a different root morphology and gene expression pattern. In this work, we have addressed the issue of basal differences in the roots between Resistant and Susceptible cultivars. Results The gene expression pattern of roots from 29 olive cultivars with different degree of resistance/susceptibility to V. dahliae was analyzed by RNA-Seq. However, only the Highly Resistant and Extremely Susceptible cultivars showed significant differences in gene expression among various groups of cultivars. A set of 421 genes showing an inverse differential expression level between the Highly Resistant to Extremely Susceptible cultivars was found and analyzed. The main differences involved higher expression of a series of transcription factors and genes involved in processes of molecules importation to nucleus, plant defense genes and lower expression of root growth and development genes in Highly Resistant cultivars, while a reverse pattern in Moderately Susceptible and more pronounced in Extremely Susceptible cultivars were observed. Conclusion According to the different gene expression patterns, it seems that the roots of the Extremely Susceptible cultivars focus more on growth and development, while some other functions, such as defense against pathogens, have a higher expression level in roots of Highly Resistant cultivars. Therefore, it seems that there are constitutive differences in the roots between Resistant and Susceptible cultivars, and that susceptible roots seem to provide a more suitable environment for the pathogen than the resistant ones.

scholarly journals Endopeptidase PepO Regulates the SpeB Cysteine Protease and Is Essential for the Virulence of Invasive M1T1Streptococcus pyogenes

2018 ◽  
Vol 200 (8) ◽  
Author(s):  
Stephan Brouwer ◽  
Amanda J. Cork ◽  
Cheryl-Lynn Y. Ong ◽  
Timothy C. Barnett ◽  
Nicholas P. West ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Phase ◽  
Cysteine Protease ◽  
Genetic Regulation ◽  
Bacterial Pathogen ◽  
Targeted Mutagenesis ◽  
Human Neutrophils ◽  
Content Type ◽  
Wide Range ◽  
Human Infections

ABSTRACTStreptococcus pyogenes(group AStreptococcus[GAS]) causes a wide range of human infections. The pathogenesis of GAS infections is dependent on the temporal expression of numerous secreted and surface-associated virulence factors that interact with host proteins. Streptococcal pyrogenic exotoxin B (SpeB) is one of the most extensively studied toxins produced by GAS, and the coordinate growth phase-dependent regulation ofspeBexpression is linked to disease severity phenotypes. Here, we identified the endopeptidase PepO as a novel growth phase-dependent regulator of SpeB in the invasive GAS M1 serotype strain 5448. By using transcriptomics followed by quantitative reverse transcriptase PCR and Western blot analyses, we demonstrate through targeted mutagenesis that PepO influences growth phase-dependent induction ofspeBgene expression. Compared to wild-type and complemented mutant strains, we demonstrate that the 5448ΔpepOmutant strain is more susceptible to killing by human neutrophils and is attenuated in virulence in a murine model of invasive GAS infection. Our results expand the complex regulatory network that is operating in GAS to control SpeB production and suggest that PepO is a virulence requirement during GAS M1T1 strain 5448 infections.IMPORTANCEDespite the continuing susceptibility ofS. pyogenesto penicillin, this bacterial pathogen remains a leading infectious cause of global morbidity and mortality. A particular subclone of the M1 serotype (M1T1) has persisted globally for decades as the most frequently isolated serotype from patients with invasive and noninvasive diseases in Western countries. One of the key GAS pathogenicity factors is the potent broad-spectrum cysteine protease SpeB. Although there has been extensive research interest on the regulatory mechanisms that controlspeBgene expression, its genetic regulation is not fully understood. Here, we identify the endopeptidase PepO as a new regulator ofspeBgene expression in the globally disseminated M1T1 clone and as being essential for virulence.

scholarly journals Cumate-Inducible Gene Expression System for Sphingomonads and Other Alphaproteobacteria

2013 ◽  
Vol 79 (21) ◽  
pp. 6795-6802 ◽  
Author(s):  
Andreas Kaczmarczyk ◽  
Julia A. Vorholt ◽  
Anne Francez-Charlot
Keyword(s):  
Gene Expression ◽  
Caulobacter Crescentus ◽  
Paracoccus Denitrificans ◽  
Expression System ◽  
Model Organisms ◽  
Inducible Gene Expression ◽  
Gene Expression System ◽  
Content Type ◽  
Wide Range ◽  
Inducible Gene

ABSTRACTTunable promoters represent a pivotal genetic tool for a wide range of applications. Here we present such a system for sphingomonads, a phylogenetically diverse group of bacteria that have gained much interest for their potential in bioremediation and their use in industry and for which no dedicated inducible gene expression system has been described so far. A strong, constitutive synthetic promoter was first identified through a genetic screen and subsequently combined with the repressor and the operator sites of thePseudomonas putidaF1cym/cmtsystem. The resulting promoter, termed PQ5, responds rapidly to the inducer cumate and shows a maximal induction ratio of 2 to 3 orders of magnitude in the different sphingomonads tested. Moreover, it was also functional in otherAlphaproteobacteria, such as the model organismsCaulobacter crescentus,Paracoccus denitrificans, andMethylobacterium extorquens. In the noninduced state, expression from PQ5is low enough to allow gene depletion analysis, as demonstrated with the essential genephyPofSphingomonassp. strain Fr1. A set of PQ5-based plasmids has been constructed allowing fusions to affinity tags or fluorescent proteins.

scholarly journals Construction and Characterization of a Gradually Inducible Expression Vector for Halobacterium salinarum, Based on thekdpPromoter

2012 ◽  
Vol 78 (7) ◽  
pp. 2100-2105 ◽  
Author(s):  
Dorthe Kixmüller ◽  
Jörg-Christian Greie
Keyword(s):  
Gene Expression ◽  
Expression Vector ◽  
Expression System ◽  
Expression Patterns ◽  
Inducible Expression ◽  
Halobacterium Salinarum ◽  
Expression Vectors ◽  
Content Type ◽  
Inducible Expression System

ABSTRACTGradually inducible expression vectors which are governed by variations of growth conditions are powerful tools for gene expression of conditionally lethal mutants. Furthermore, controlled expression allows monitoring of overproduction of proteins at various stages in their expressing hosts. ForHalobacterium salinarum, which is often used as a paradigm for halophilic archaea, such an inducible expression system is not available to date. Here we show that thekdppromoter (Pkdp), which facilitates gene expression upon K+limitation, can be used to establish such a system for molecular applications. Pkdpfeatures a rather high expression rate, with an approximately 50-fold increase that can be easily varied by K+concentrations in the growth medium. Besides the construction of an expression vector, our work describes the characterization of expression patterns and, thus, offers a gradually inducible expression system to the scientific community.

CURVE-BASED CLUSTERING OF TIME COURSE GENE EXPRESSION DATA USING SELF-ORGANIZING MAPS

2009 ◽  
Vol 07 (04) ◽  
pp. 645-661 ◽  
Author(s):  
XIN CHEN
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Regulatory Networks ◽  
Time Course ◽  
Clustering Algorithm ◽  
Expression Patterns ◽  
Self Organizing Map ◽  
Expression Data ◽  
Wide Range ◽  
Self Organizing

There is an increasing interest in clustering time course gene expression data to investigate a wide range of biological processes. However, developing a clustering algorithm ideal for time course gene express data is still challenging. As timing is an important factor in defining true clusters, a clustering algorithm shall explore expression correlations between time points in order to achieve a high clustering accuracy. Moreover, inter-cluster gene relationships are often desired in order to facilitate the computational inference of biological pathways and regulatory networks. In this paper, a new clustering algorithm called CurveSOM is developed to offer both features above. It first presents each gene by a cubic smoothing spline fitted to the time course expression profile, and then groups genes into clusters by applying a self-organizing map-based clustering on the resulting splines. CurveSOM has been tested on three well-studied yeast cell cycle datasets, and compared with four popular programs including Cluster 3.0, GENECLUSTER, MCLUST, and SSClust. The results show that CurveSOM is a very promising tool for the exploratory analysis of time course expression data, as it is not only able to group genes into clusters with high accuracy but also able to find true time-shifted correlations of expression patterns across clusters.

Autism spectrum mixed neurodevelopmental disorder associated with 6q27 deletion and multiple copies within 20q11.23: a case study

2014 ◽  
Vol 8 (3) ◽  
pp. 210-215
Author(s):  
Stephen Hopkins ◽  
Jeremy Turk ◽  
Adeniyi Daramola ◽  
Marinos Kyriakopoulos
Keyword(s):  
Neurodevelopmental Disorder ◽  
Autism Spectrum ◽  
Copy Number Variations ◽  
Comparative Genomic Hybridisation ◽  
Comparative Genomic ◽  
Content Type ◽  
Effective Strategies ◽  
Wide Range ◽  
Multiple Copies

Purpose – Copy Number Variations (CNVs) are not infrequently observed in aberrant neurodevelopment. CNVs can alter gene expression and have been linked to a wide range of neuropsychiatric disorders. The purpose of this case study is to report the association of CNVs with a mixed neurodevelopmental disorder. Design/methodology/approach – Array-Comparative Genomic Hybridisation analysis was carried out in a case of an eight-year-old boy presenting with a mixed neurodevelopmental disorder including autism spectrum disorder, intellectual disability, tic disorder, anxiety and severe aggression. The child's parents also underwent the same investigation. Findings – A 6q27 deletion and multiple copies within 20q11.23 were identified. The boy's father shared the 6q27 deletion and his mother also had multiple copies within 20q11.23. Originality/value – This is the first report linking the combination of 6p27 and 20q11 CNVs with a mixed neurodevelopmental presentation. Identifying CNVs that may underlie aberrant neurodevelopment is likely to assist in unravelling the aetiology of neurodevelopmental and psychiatric disorders and lead to more effective strategies for their characterisation and management.

scholarly journals RNA Expression Analysis Using an AntisenseBacillus subtilis Genome Array

2001 ◽  
Vol 183 (24) ◽  
pp. 7371-7380 ◽  
Author(s):  
Jian-Ming Lee ◽  
Shehui Zhang ◽  
Soumitra Saha ◽  
Sonia Santa Anna ◽  
Can Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dynamic Range ◽  
Expression Patterns ◽  
Transcript Level ◽  
Open Reading Frames ◽  
Biosynthetic Genes ◽  
Coding Regions ◽  
Intergenic Regions ◽  
Differential Gene ◽  
Novel Transcripts

ABSTRACT We have developed an antisense oligonucleotide microarray for the study of gene expression and regulation in Bacillus subtilis by using Affymetrix technology. Quality control tests of the B. subtilis GeneChip were performed to ascertain the quality of the array. These tests included optimization of the labeling and hybridization conditions, determination of the linear dynamic range of gene expression levels, and assessment of differential gene expression patterns of known vitamin biosynthetic genes. In minimal medium, we detected transcripts for approximately 70% of the known open reading frames (ORFs). In addition, we were able to monitor the transcript level of known biosynthetic genes regulated by riboflavin, biotin, or thiamine. Moreover, novel transcripts were also detected within intergenic regions and on the opposite coding strand of known ORFs. Several of these novel transcripts were subsequently correlated to new coding regions.

scholarly journals A Hybrid Approach for Biomarker Discovery from Microarray Gene Expression Data for Cancer Classification

2006 ◽  
Vol 2 ◽  
pp. 117693510600200 ◽  
Author(s):  
Yanxiong Peng ◽  
Wenyuan Li ◽  
Ying Liu
Keyword(s):  
Gene Expression ◽  
Biomarker Discovery ◽  
Expression Patterns ◽  
Hybrid Approach ◽  
Microarray Gene Expression Data ◽  
Small Subset ◽  
Microarray Gene Expression ◽  
Simple Method ◽  
Filter Methods ◽  
Wide Range

Microarrays allow researchers to monitor the gene expression patterns for tens of thousands of genes across a wide range of cellular responses, phenotype and conditions. Selecting a small subset of discriminate genes from thousands of genes is important for accurate classification of diseases and phenotypes. Many methods have been proposed to find subsets of genes with maximum relevance and minimum redundancy, which can distinguish accurately between samples with different labels. To find the minimum subset of relevant genes is often referred as biomarker discovery. Two main approaches, filter and wrapper techniques, have been applied to biomarker discovery. In this paper, we conducted a comparative study of different biomarker discovery methods, including six filter methods and three wrapper methods. We then proposed a hybrid approach, FR-Wrapper, for biomarker discovery. The aim of this approach is to find an optimum balance between the precision of the biomarker discovery and the computation cost, by taking advantages of both filter method's efficiency and wrapper method's high accuracy. Our hybrid approach applies Fisher's ratio, a simple method easy to understand and implement, to filter out most of the irrelevant genes, then a wrapper method is employed to reduce the redundancy. The performance of FR-Wrapper approach is evaluated over four widely used microarray datasets. Analysis of experimental results reveals that the hybrid approach can achieve the goal of maximum relevance with minimum redundancy.

scholarly journals In VivoProgrammed Gene Expression Based on Artificial Quorum Networks

2015 ◽  
Vol 81 (15) ◽  
pp. 4984-4992 ◽  
Author(s):  
Teng Chu ◽  
Yajun Huang ◽  
Mingyu Hou ◽  
Qiyao Wang ◽  
Jingfan Xiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quorum Sensing ◽  
Cell Density ◽  
Protective Antigen ◽  
Expression System ◽  
Edwardsiella Tarda ◽  
Content Type ◽  
Genetic Components ◽  
Wide Range

ABSTRACTThe quorum sensing (QS) system, as a well-functioning population-dependent gene switch, has been widely applied in many gene circuits in synthetic biology. In our work, an efficient cell density-controlled expression system (QS) was established via engineering of theVibrio fischeri luxI-luxRquorum sensing system. In order to achievein vivoprogrammed gene expression, a synthetic binary regulation circuit (araQS) was constructed by assembling multiple genetic components, including the quorum quenching protein AiiA and the arabinose promoter ParaBAD, into the QS system.In vitroexpression assays verified that the araQS system was initiated only in the absence of arabinose in the medium at a high cell density.In vivoexpression assays confirmed that the araQS system presented anin vivo-triggered and cell density-dependent expression pattern. Furthermore, the araQS system was demonstrated to function well in different bacteria, indicating a wide range of bacterial hosts for use. To explore its potential applicationsin vivo, the araQS system was used to control the production of a heterologous protective antigen in an attenuatedEdwardsiella tardastrain, which successfully evoked efficient immune protection in a fish model. This work suggested that the araQS system could program bacterial expressionin vivoand might have potential uses, including, but not limited to, bacterial vector vaccines.

scholarly journals Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

2016 ◽  
Vol 82 (14) ◽  
pp. 4387-4400 ◽  
Author(s):  
Oleksandr Skyba ◽  
Dan Cullen ◽  
Carl J. Douglas ◽  
Shawn D. Mansfield
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
White Rot Fungi ◽  
Wood Decay ◽  
White Rot ◽  
Decay Fungi ◽  
Content Type ◽  
Postia Placenta ◽  
Substrate Composition ◽  
Wood Decay Fungi

ABSTRACTIdentification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi,Rhodonia placenta(formerlyPostia placenta) andPhanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-oldPopulus trichocarpa(poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold,P< 0.05) inP. chrysosporiumandP. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold,P< 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles ofP. chrysosporiumandP. placentaare influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode “proteins of unknown function,” and determining their role in lignocellulose degradation presents opportunities and challenges for future research.IMPORTANCEThis study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.

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