scholarly journals An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA

2019 ◽  
Vol 7 (1) ◽  
pp. 9 ◽  
Author(s):  
Dae-Eun Cheong ◽  
So-Youn Park ◽  
Ho-Dong Lim ◽  
Geun-Joong Kim
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Expression System ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Single Element ◽  
Reading Frame ◽  
Cis Acting ◽  
Dna Libraries ◽  
Expression Module

Many integrated gene clusters beyond a single genetic element are commonly trapped as the result of promoter traps in (meta)genomic DNA libraries. Generally, a single element, which is mainly the promoter, is deduced from the resulting gene clusters and employed to construct a new expression vector. However, expression patterns of target proteins under the incorporated promoter are often inconsistent with those shown in clones harboring plasmids with gene clusters. These results suggest that the integrated set of gene clusters with diverse cis- and trans-acting elements is evolutionarily tuned as a complete set for gene expression, and is an expression module with all the components for the expression of a nested open reading frame (ORF). This possibility is further supported by truncation and/or serial deletion analysis of this module in which the expression of the nested ORF is highly fluctuated or reduced frequently, despite being supported by plentiful cis-acting elements in the spanning regions around the ORF such as the promoter, ribosome binding site (RBS), terminator, and 3′-/5′-UTRs for gene expression. Here, we examined whether an innate module with a naturally overexpressed gene could be considered as a scaffold for an expression system. For a proof-of-principle study, we mined a complete expression module with an innately overexpressed ORF in E. coli from a metagenomics DNA library, and incorporated it into a vector that had no regulatory element for expressing the insert. We obtained successful expression of several inserts such as MBP, GFPuv, β-glucosidase, and esterase using this simple construct without tuning and codon optimization of the target insert.

scholarly journals Development of cDNA normalization system and preliminary transcription analysis of KCS genes in apple tissues

2011 ◽  
Vol 59 (3) ◽  
pp. 9-12 ◽  
Author(s):  
Zsolt Albert ◽  
Cs. Deák ◽  
A. Miskó ◽  
M. Tóth ◽  
I. Papp
Keyword(s):  
Gene Expression ◽  
Expression System ◽  
Expression Patterns ◽  
Housekeeping Genes ◽  
Apple Fruit ◽  
Rt Pcr ◽  
Specific Primers ◽  
Specific Expression ◽  
Transcription Analysis ◽  
Tissue Specific

Wax production is an important aspect of apple (Malus domestica Borkh.) fruit development from both theoretical and practical point of views. The complex molecular mechanism that controls wax biosynthesis is still widely unknown but many studies focused on this topic. We aimed to develop further the experimental framework of these efforts with a description of an improved reference genes expression system. Results in the literature show that similarities exist among the expression of some housekeeping genes of different plant species. Based on these considerations and on gene expression data from Arabidopsis thaliana, some genes in apple were assigned for analysis. EST sequences of apple were used to design specific primers for RT-PCR experiments. Isolation of intact RNA from different apple tissues and performing RT-PCR reaction were also key point in obtaining expression patterns. To monitor DNA contamination of the RNA samples, specific primers were used that amplify intron-containing sequences from the cDNA. We found that actin primers can be used for the detection of intron containing genomic DNA, and tubulin primers are good internal controls in RT-PCR experiments. We were able to make a difference between tissue-specific and tissue-independent gene-expression, furthermore we found tissue specific differences between the expression patterns of candidate genes, that are potentially involved in wax-biosynthesis. Our results show that KCS1 and KCS4 are overexpressed in the skin tissue, this could mean that these genes have skin-specific expression in apple fruit.

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.

scholarly journals Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland

2019 ◽  
Vol 35 (20) ◽  
pp. 4206-4206
Author(s):  
Shahar Alon ◽  
Eli Eisenberg ◽  
Jasmine Jacob-Hirsch ◽  
Gideon Rechavi ◽  
Gad Vatine ◽  
...  
Keyword(s):  
Gene Expression ◽  
Pineal Gland ◽  
Regulatory Element ◽  
Cis Acting

scholarly journals A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

2019 ◽  
Author(s):  
Stewart TG Burgess ◽  
Edward J Marr ◽  
Kathryn Bartley ◽  
Francesca G Nunn ◽  
Rachel E Down ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Specific Gene ◽  
Multigene Families ◽  
Psoroptes Ovis ◽  
Specific Expression ◽  
Development Of Resistance

ABSTRACTPsoroptic mange, caused by infestation with the ectoparasitic mite,Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack ofP. ovistranscriptomic and genomic resources. Building on the recent publication of theP. ovisdraft genome, here we present a genomic analysis and transcriptomic atlas of gene expression inP. ovisrevealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3,075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis ofP. ovisallergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novelP. ovismultigene families including known allergens and novel genes with high levels of stage-specific expression. The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draftP. ovisgenome.

scholarly journals Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut (A. monticola)

2022 ◽  
Author(s):  
Nian Liu ◽  
Manish Pandey ◽  
Bei Wu ◽  
Li Huang ◽  
Huaiyong Luo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factors ◽  
Arachis Hypogaea ◽  
Oil Content ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Oil Accumulation ◽  
Species Specific ◽  
Wild Peanut

Abstract The wild allotetraploid peanut Arachis monticola contains higher oil content than cultivated allotetraploid Arachis hypogaea. To investigate its molecular mechanism controlling oil accumulation, we performed comparative transcriptomics from developing seeds between three Arachis monticola and five Arachis hypogaea varieties. The analysis not only showed species-specific grouping based on transcriptional profiles but also detected two gene clusters with divergent expression patterns enriched in lipid metabolism. Further, the differential expression gene analysis also indicated expression alteration in wild peanut leading to enhanced activity of oil biogenesis and limiting the rate of lipid degradation. We also constructed a regulatory network of lipid metabolic DEGs with co-expressed transcription factors. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. Genome-wide DNA methylation was found antagonistically correlated with gene expression during seed development. The results indicated that CG and CHG contexts methylation may negatively regulate specific lipid metabolic genes and transcription factors to subtly affect the difference of oil accumulation. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.

Epigenetic Remodeling in Innate Immunity and Inflammation

2021 ◽  
Vol 39 (1) ◽  
Author(s):  
Qian Zhang ◽  
Xuetao Cao
Keyword(s):  
Gene Expression ◽  
Innate Immunity ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Innate Immune ◽  
Annual Review ◽  
Specific Gene ◽  
Publication Date ◽  
Specific Expression ◽  
Epigenetic Remodeling

The innate immune response is a rapid response to pathogens or danger signals. It is precisely activated not only to efficiently eliminate pathogens but also to avoid excessive inflammation and tissue damage. cis-Regulatory element–associated chromatin architecture shaped by epigenetic factors, which we define as the epiregulome, endows innate immune cells with specialized phenotypes and unique functions by establishing cell-specific gene expression patterns, and it also contributes to resolution of the inflammatory response. In this review, we focus on two aspects: ( a) how niche signals during lineage commitment or following infection and pathogenic stress program epiregulomes by regulating gene expression levels, enzymatic activities, or gene-specific targeting of chromatin modifiers and ( b) how the programed epiregulomes in turn mediate regulation of gene-specific expression, which contributes to controlling the development of innate cells, or the response to infection and inflammation, in a timely manner. We also discuss the effects of innate immunometabolic rewiring on epiregulomes and speculate on several future challenges to be encountered during the exploration of the master regulators of epiregulomes in innate immunity and inflammation. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Transcriptional Characterizations of Differences between Eutopic and Ectopic Endometrium

Endocrinology ◽  
2006 ◽  
Vol 147 (1) ◽  
pp. 232-246 ◽  
Author(s):  
Yan Wu ◽  
André Kajdacsy-Balla ◽  
Estil Strawn ◽  
Zainab Basir ◽  
Gloria Halverson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Uterine Cavity ◽  
Gene Clusters ◽  
Mapk Signaling ◽  
Menstrual Phase ◽  
Expression Analysis Systematic Explorer ◽  
Genetic Mechanisms ◽  
Gynecological Disease

Endometriosis, defined as the presence of endometrial glandular and stromal cells outside the uterine cavity, is a common gynecological disease with poorly understood pathogenesis. Using laser capture microdissection and a cDNA microarray with 9600 genes/expressed sequence tags (ESTs), we have conducted a comprehensive profiling of gene expression differences between the ectopic and eutopic endometrium taken from 12 women with endometriosis adjusted for menstrual phase and the location of the lesions. With dye-swapping and replicated arrays, we found 904 genes/ESTs that are differentially expressed. We validated the gene expression using real-time RT-PCR. We found that the expression patterns of these genes/ESTs correctly classified the 12 patients into ovarian and nonovarian endometriosis. We identified gene clusters that are location-specific. In addition, we identified several biological themes using Expression Analysis Systematic Explorer. Finally, we identified 79 pathways with over 100 genes with known functions, which include oxidative stress, focal adhesion, Wnt signaling, and MAPK signaling. The identification of these genes and their associated pathways provides new insight. Our findings will stimulate future investigations on molecular genetic mechanisms underlying the pathogenesis of endometriosis.

scholarly journals Global Transcriptome Analysis of Shewanella oneidensis MR-1 Exposed to Different Terminal Electron Acceptors

2005 ◽  
Vol 187 (20) ◽  
pp. 7138-7145 ◽  
Author(s):  
A. S. Beliaev ◽  
D. M. Klingeman ◽  
J. A. Klappenbach ◽  
L. Wu ◽  
M. F. Romine ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metal Ion ◽  
Expression Patterns ◽  
Complex Structure ◽  
Shewanella Oneidensis ◽  
Gene Clusters ◽  
Electron Acceptors ◽  
Reducing Conditions ◽  
Wide Range ◽  
Metal Electron

ABSTRACT To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. Several groups of genes exhibited elevated expression levels in the presence of metals, including those encoding putative multidrug efflux transporters, detoxification proteins, extracytoplasmic sigma factors and PAS-domain regulators. Only one of the 42 predicted c-type cytochromes in MR-1, SO3300, displayed significantly elevated transcript levels across all metal-reducing conditions. Genes encoding decaheme cytochromes MtrC and MtrA that were previously linked to the reduction of different forms of Fe(III) and Mn(IV), exhibited only slight decreases in relative mRNA abundances under metal-reducing conditions. In contrast, specific transcriptome responses were displayed to individual non-metal electron acceptors resulting in the identification of unique groups of nitrate-, thiosulfate- and TMAO-induced genes including previously uncharacterized multi-cytochrome gene clusters. Collectively, the gene expression results reflect the fundamental differences between metal and non-metal respiratory pathways of S. oneidensis MR-1, where the coordinate induction of detoxification and stress response genes play a key role in adaptation of this organism under metal-reducing conditions. Moreover, the relative paucity and/or the constitutive nature of genes involved in electron transfer to metals is likely due to the low-specificity and the opportunistic nature of the metal-reducing electron transport pathways.

Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium

2004 ◽  
Vol 20 (1) ◽  
pp. 117-130 ◽  
Author(s):  
Rafaela da Silva ◽  
Eliana Lucchinetti ◽  
Thomas Pasch ◽  
Marcus C. Schaub ◽  
Michael Zaugg
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Ischemia Reperfusion ◽  
Expression Patterns ◽  
Principal Component ◽  
Gene Clusters ◽  
Stable Gene ◽  
Transcriptional Responses ◽  
Rat Hearts

Pharmacological (PPC) and ischemic preconditioning (IschPC) provide comparable protection against ischemia in the heart. However, the genomic phenotype may depend on the type of preconditioning. Isolated perfused rat hearts were used to evaluate transcriptional responses to PPC and IschPC in the presence (mediator/effector response) or absence (trigger response) of 40 min of test ischemia using oligonucleotide microarrays. IschPC was induced by 3 cycles of 5 min of ischemia, and PPC by 15 min of 2.1 vol% isoflurane. Unsupervised analysis methods were used to identify gene expression patterns. PPC and IschPC were accompanied by marked alterations in gene expression. PPC and IschPC shared only ∼25% of significantly up- and downregulated genes after triggering. The two types of preconditioning induced a more uniform genomic response after ischemia/reperfusion. Numerous genes separated preconditioned from unprotected ischemic hearts. Three stable gene clusters were identified in the trigger response to preconditioning, while eight stable clusters related to cytoprotection, inflammation, remodeling, and long interspersed nucleotide elements (LINEs) were delineated after prolonged ischemia. A single stable sample cluster emerged from cluster analysis for both IschPC and unprotected myocardium, indicating a close molecular relationship between these two treatments. Principal component analysis revealed differences between PPC vs. IschPC, and trigger vs. mediator/effector responses in transcripts predominantly related to biosynthesis and apoptosis. IschPC and PPC similarly but distinctly reprogram the genetic response to ischemic injury. IschPC elicits a postischemic gene expression profile closer to unprotected myocardium than PPC, which may be therefore more advantageous as therapeutic strategy in cardioprotection.

scholarly journals Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fei Xu ◽  
Ferdinand Marlétaz ◽  
Daria Gavriouchkina ◽  
Xiao Liu ◽  
Tatjana Sauka-Spengler ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Homeobox Gene ◽  
Gene Interaction ◽  
Binding Interaction ◽  
Upstream Regulatory Element ◽  
A Cell ◽  
Insulin Gene Expression ◽  
Cell Culture Assay

AbstractHox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. Here, we report evidence indicating that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is a likely direct target of Pdx in Pacific oyster adults. We show that one insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue. Transcriptomic comparison suggests that this tissue plays a similar role to the vertebrate pancreas. Using ATAC-seq and ChIP, we identify an upstream regulatory element of the cgILP gene which shows binding interaction with cgPdx protein in oyster hepatopancreas and demonstrate, using a cell culture assay, that the oyster Pdx can act as a transcriptional activator through this site, possibly in synergy with NeuroD. These data argue that a classic homeodomain-target gene interaction dates back to the origin of Bilateria.

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