Transcriptome expression analysis of the gene regulation mechanism of bacterial mineralization tolerance to high concentrations of Cd2+

2021 ◽  
pp. 150911
Author(s):  
Shanshan Huang ◽  
Renlu Liu ◽  
Menglin Sun ◽  
Xiaofang Li ◽  
Yong Guan ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Expression Analysis ◽  
Regulation Mechanism ◽  
High Concentrations ◽  
Transcriptome Expression

scholarly journals Identification and Expression Analysis of the CsMYB Gene Family in Root Knot Nematode-Resistant and Susceptible Cucumbers

2020 ◽  
Vol 11 ◽  
Author(s):  
Chunyan Cheng ◽  
Qingrong Li ◽  
Xing Wang ◽  
Ying Li ◽  
Chuntao Qian ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Lipid Transfer Protein ◽  
Major Gene ◽  
Regulation Mechanism ◽  
Lipid Transfer ◽  
Biotic And Abiotic Stress ◽  
Root Knot Nematode ◽  
Element Analysis ◽  
Resistance Response

MYB (myeloblastosis) transcription factors (TFs) play important roles in controlling various physiological processes in plants, such as responses to biotic and abiotic stress, metabolism, and defense. A previous study identified a gene, Csa6G410090, encoding a plant lipid transfer protein (LTP), as a possible regulator in cucumber (Cucumis sativus L.) of the resistance response to root-knot nematode (RKN) [Meloidogyne incognita Kofoid and White (Chitwood)]. Myb-type DNA-binding TFs were presumed to regulate downstream genes expression, including LTPs, however, the regulation mechanism remained unclear. To elucidate whether and which MYB TFs may be involved in regulation of the resistance response, this study identified 112 genes as candidate members of the CsMYB gene family by combining CDD and SMART databases, using the Hidden Markov Model (HMM) and manual calibration. Within this group, ten phylogenetic subgroups were resolved according to sequence-based classification, consistent with results from comprehensive investigation of gene structure, conserved motifs, chromosome locations, and cis-element analysis. Distribution and collinearity analysis indicated that amplification of the CsMYB gene family in cucumber has occurred mainly through tandem repeat events. Spatial gene expression analysis showed that 8 CsMYB genes were highly expressed at differing levels in ten different tissues or organs. The roots of RKN-resistant and susceptible cucumbers were inoculated with M. incognita, finding that CsMYB (Csa6G538700, Csa1G021940, and Csa5G641610) genes showed up-regulation coincident with upregulation of the “hub” gene LTP (Csa6G410090) previously implicated as a major gene in the resistance response to RKN in cucumber. Results of this study suggest hypotheses regarding the elements and regulation of the resistant response as well as possible RKN resistance-enhancing strategies in cucumber and perhaps more broadly in plants.

scholarly journals Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xinyi Wan ◽  
Filipe Pinto ◽  
Luyang Yu ◽  
Baojun Wang
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Protein Binding ◽  
Gene Networks ◽  
Dynamic Range ◽  
Gene Expression Regulation ◽  
Single Layer ◽  
Regulation Mechanism ◽  
Gene Circuits ◽  
Synthetic Dna

AbstractVersatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

scholarly journals Whole transcriptome expression analysis and comparison of two different strains of Plasmodium falciparum using RNA-Seq

Genomics Data ◽  
2016 ◽  
Vol 8 ◽  
pp. 110-112 ◽  
Author(s):  
Hiasindh Ashmi Antony ◽  
Vrushali Pathak ◽  
Subhash Chandra Parija ◽  
Kanjaksha Ghosh ◽  
Amrita Bhattacherjee
Keyword(s):  
Plasmodium Falciparum ◽  
Expression Analysis ◽  
Rna Seq ◽  
Transcriptome Expression ◽  
Different Strains ◽  
Whole Transcriptome

Sa1672 - Apc Gene Regulation by Mir-135A and Mir-135B in Sporadic Colorectal Cancer: In Silico Approach and Expression Analysis

2018 ◽  
Vol 154 (6) ◽  
pp. S-349
Author(s):  
Mumtaz Anwar ◽  
Rakesh Kochhar ◽  
Deepak Kaul ◽  
Alka Bhatia ◽  
Safrun Mahmood
Keyword(s):  
Colorectal Cancer ◽  
Gene Regulation ◽  
Expression Analysis ◽  
In Silico ◽  
Apc Gene ◽  
Sporadic Colorectal Cancer

PREDICTING CANCEROUS GENES BASED ON REGULATION TRUTH TABLES

2006 ◽  
Vol 15 (05) ◽  
pp. 753-765
Author(s):  
RONG-MING CHEN ◽  
KUEI-CHUNG SHIH ◽  
ROUH-MEI HU ◽  
JEFFREY J. P. TSAI
Keyword(s):  
Gene Regulation ◽  
Rapid Development ◽  
Biological Research ◽  
Regulation Mechanism ◽  
Human Beings ◽  
Gene Expressions ◽  
Normal Tissues ◽  
Interactive Regulation ◽  
Living Organisms ◽  
And Behavior

Several of ten thousands functional genes control the growth, genetics, and behavior of living organisms by regulating different gene expressions. The genes in a normal cell control the process of cell growth, differentiation, reproduction, and apoptosis via multiple steps of interactive regulation mechanism. The mechanism of gene regulation is a very important process in human beings. If there is something wrong in the gene regulation mechanism, it may cause some diseases such as cancer. It is very difficult to identify the regulatory relations among genes in human genome. Traditional biological research methods consume huge amount of time and man strength to do this work. In recent years, with the rapid development of microarray technologies, cDNA can be used to analyze the changes of gene expressions in different cells in a high throughput manner. In this paper, we propose a novel bioinformatics approach to predict possible cancerous genes based on a so-called regulation truth table (RTT) of genes. The RTT of two genes is constructed using the differential expressions of cDNA microarray data for tumor and normal tissues. The differences in regulatory relations of genes for tumor and normal tissues are adopted to identify possible cancerous genes.

scholarly journals Chromosomal Arrangement of AHL-Driven Quorum Sensing Circuits in Pseudomonas

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Zsolt Gelencsér ◽  
Borisz Galbáts ◽  
Juan F. Gonzalez ◽  
K. Sonal Choudhary ◽  
Sanjarbek Hudaiberdiev ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Quorum Sensing ◽  
Homoserine Lactone ◽  
Regulation Mechanism ◽  
Acyl Homoserine Lactone ◽  
Negative Regulators ◽  
Bacterial Genomes ◽  
Systematic Overview ◽  
Chromosomal Arrangement ◽  
Genomic Arrangement

Pseudomonas spp. are able to colonize a large variety of environments due to their wide adaptability which is also associated with an N-acyl homoserine lactone (AHL) gene regulation mechanism called quorum sensing (QS). In this article we present a systematic overview of the genomic arrangement patterns of quorum sensing genes found in Pseudomonas and compare the topologies with those found in other bacterial genomes. We find that the topological arrangement of QS genes is more variable than previously thought but there are a few unifying features that occur in many of the topological arrangements. We hypothesize that the negative regulators of QS that are often found between the canonical luxR/ and luxI-family genes may be crucial for stabilizing the output of QS circuits.

scholarly journals Complex Regulation Pathways of AmpC-Mediated β-Lactam Resistance in Enterobacter cloacae Complex

2015 ◽  
Vol 59 (12) ◽  
pp. 7753-7761 ◽  
Author(s):  
François Guérin ◽  
Christophe Isnard ◽  
Vincent Cattoir ◽  
Jean Christophe Giard
Keyword(s):  
Drug Targets ◽  
Genetic Regulation ◽  
Enterobacter Cloacae ◽  
Opportunistic Pathogen ◽  
Regulation Mechanism ◽  
Content Type ◽  
Genes Encoding ◽  
High Concentrations ◽  
High Level

ABSTRACTEnterobacter cloacaecomplex (ECC), an opportunistic pathogen causing numerous infections in hospitalized patients worldwide, is able to resist β-lactams mainly by producing the AmpC β-lactamase enzyme. AmpC expression is highly inducible in the presence of some β-lactams, but the underlying genetic regulation, which is intricately linked to peptidoglycan recycling, is still poorly understood. In this study, we constructed different mutant strains that were affected in genes encoding enzymes suspected to be involved in this pathway. As expected, the inactivation ofampC,ampR(which encodes the regulator protein ofampC), andampG(encoding a permease) abolished β-lactam resistance. Reverse transcription-quantitative PCR (qRT-PCR) experiments combined with phenotypic studies showed that cefotaxime (at high concentrations) and cefoxitin induced the expression ofampCin different ways: one involving NagZ (aN-acetyl-β-d-glucosaminidase) and another independent of NagZ. Unlike the model established forPseudomonas aeruginosa, inactivation of DacB (also known as PBP4) was not responsible for a constitutiveampCoverexpression in ECC, whereas it caused AmpC-mediated high-level β-lactam resistance, suggesting a post-transcriptional regulation mechanism. Global transcriptomic analysis by transcriptome sequencing (RNA-seq) of adacBdeletion mutant confirmed these results. Lastly, analysis of 37 ECC clinical isolates showed that amino acid changes in the AmpD sequence were likely the most crucial event involved in the development of high-level β-lactam resistancein vivoas opposed toP. aeruginosawheredacBmutations have been commonly found. These findings bring new elements for a better understanding of β-lactam resistance in ECC, which is essential for the identification of novel potential drug targets.

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