scholarly journals Genome sequencing of Aspergillus glaucus ‘CCHA’ provides insights into salt-stress adaptation

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8609
Author(s):  
Wenmin Qiu ◽  
Jingen Li ◽  
Yi Wei ◽  
Feiyu Fan ◽  
Jing Jiang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Redox State ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Natural Environments ◽  
Isolation And Identification ◽  
Microbial Genomes ◽  
Aspergillus Glaucus ◽  
Survey Analyses

Aspergillus, as a genus of filamentous fungi, has members that display a variety of different behavioural strategies, which are affected by various environmental factors. The decoded genomic sequences of many species vary greatly in their evolutionary similarities, encouraging studies on the functions and evolution of the Aspergillus genome in complex natural environments. Here, we present the 26 Mb de novo assembled high-quality reference genome of Aspergillus glaucus ‘China Changchun halophilic Aspergillus’ (CCHA), which was isolated from the surface of plants growing near a salt mine in Jilin, China, based on data from whole-genome shotgun sequencing using Illumina Solexa technology. The sequence, coupled with data from comprehensive transcriptomic survey analyses, indicated that the redox state and transmembrane transport might be critical molecular mechanisms for the adaptation of A. glaucus ‘CCHA’ to the high-salt environment of the saltern. The isolation of salt tolerance-related genes, such as CCHA-2114, and their overexpression in Escherichia coli demonstrated that A. glucus ‘CCHA’ is an excellent organism for the isolation and identification of salt tolerant-related genes. These data expand our understanding of the evolution and functions of fungal and microbial genomes, and offer multiple target genes for crop salt-tolerance improvement through genetic engineering.

scholarly journals Examination of the Transcriptional Response to LaMIR166a Overexpression in Larix kaempferi (Lamb.) Carr

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 576
Author(s):  
Yanru Fan ◽  
Wanfeng Li ◽  
Zhexin Li ◽  
Shaofei Dang ◽  
Suying Han ◽  
...  
Keyword(s):  
Cell Lines ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Pearson Correlation ◽  
Transcriptional Response ◽  
Correlation Coefficients ◽  
Embryonic Cell ◽  
Larix Kaempferi ◽  
Transgenic Cell

The study of somatic embryogenesis can provide insight into early plant development. We previously obtained LaMIR166a-overexpressing embryonic cell lines of Larix kaempferi (Lamb.) Carr. To further elucidate the molecular mechanisms associated with miR166 in this species, the transcriptional profiles of wild-type (WT) and three LaMIR166a-overexpressing transgenic cell lines were subjected to RNA sequencing using the Illumina NovaSeq 6000 system. In total, 203,256 unigenes were generated using Trinity de novo assembly, and 2467 differentially expressed genes were obtained by comparing transgenic and WT lines. In addition, we analyzed the cleaved degree of LaMIR166a target genes LaHDZ31–34 in different transgenic cell lines by detecting the expression pattern of LaHdZ31–34, and their cleaved degree in transgenic cell lines was higher than that in WT. The downstream genes of LaHDZ31–34 were identified using Pearson correlation coefficients. Yeast one-hybrid and dual-luciferase report assays revealed that the transcription factors LaHDZ31–34 could bind to the promoters of LaPAP, LaPP1, LaZFP5, and LaPHO1. This is the first report of gene expression changes caused by LaMIR166a overexpression in Japanese larch. These findings lay a foundation for future studies on the regulatory mechanism of miR166.

scholarly journals Prolactin independent rescue of mouse corpus luteum life span: identification of prolactin and luteinizing hormone target genes

2009 ◽  
Vol 297 (3) ◽  
pp. E676-E684 ◽  
Author(s):  
Anne Bachelot ◽  
Julie Beaufaron ◽  
Nathalie Servel ◽  
Cécile Kedzia ◽  
Philippe Monget ◽  
...  
Keyword(s):  
Luteinizing Hormone ◽  
Corpus Luteum ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Ovarian Function ◽  
De Novo ◽  
Embryo Implantation ◽  
Receptor Expression ◽  
Corpora Lutea ◽  
Mrna Expression Profiling

The corpus luteum (CL) plays a central role in the maintenance of pregnancy in rodents, mainly by secreting progesterone. Female mice lacking prolactin (PRL) receptor (R) are sterile due to a failure of embryo implantation, which is a consequence of decreased luteinizing hormone (LH) receptor expression in the CL and inadequate levels of progesterone. We attempted to treat PRLR−/− females with human chorionic gonadotropin (hCG) and showed a de novo expression of LHR mRNA in the corpora lutea. Binding analysis confirmed that the LHR in hCG-treated PRLR−/− animals was functional. This was accompanied with increased expression of steroidogenic enzymes involved in progesterone synthesis. Despite these effects, no embryo implantation was observed because of high expression of 20α-hydroxysteroid dehydrogenase. To better appreciate the molecular mechanisms underlying maintenance of the CL, a series of mRNA expression-profiling experiments was performed on isolated corpora lutea of PRLR−/− and hCG-treated PRLR−/− mice. This approach revealed several novel candidate genes with potentially pivotal roles in ovarian function, among them, p27, VE-cadherin, Pten, and sFRP-4, a member of the Wnt/frizzled family. This study showed the differential role of PRL and LH in CL function and identified new targets of these hormones in luteal cells.

scholarly journals Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 157 ◽  
Author(s):  
Cristiano Piasecki ◽  
Yongil Yang ◽  
Daiane P. Benemann ◽  
Frederico S. Kremer ◽  
Vanessa Galli ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Glyphosate Resistance ◽  
Target Site ◽  
Differentially Expressed ◽  
Irreversible Damage ◽  
Conyza Bonariensis

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might ‘rescue’ resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

Balancing salinity stress responses in halophytes and non-halophytes: a comparison between Thellungiella and Arabidopsis thaliana

2013 ◽  
Vol 40 (9) ◽  
pp. 819 ◽  
Author(s):  
Dorothea Bartels ◽  
Challabathula Dinakar
Keyword(s):  
Arabidopsis Thaliana ◽  
Salt Tolerance ◽  
Salinity Tolerance ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Light Stress ◽  
Stress Factors ◽  
Natural Environments ◽  
Terrestrial Plants ◽  
Abiotic Stress Factors

Salinity is one of the major abiotic stress factors that drastically reduces agricultural productivity. In natural environments salinity often occurs together with other stresses such as dehydration, light stress or high temperature. Plants cope with ionic stress, dehydration and osmotic stress caused by high salinity through a variety of mechanisms at different levels involving physiological, biochemical and molecular processes. Halophytic plants exist successfully in stressful saline environments, but most of the terrestrial plants including all crop plants are glycophytes with varying levels of salt tolerance. An array of physiological, structural and biochemical adaptations in halophytes make them suitable models to study the molecular mechanisms associated with salinity tolerance. Comparative analysis of plants that differ in their abilities to tolerate salinity will aid in better understanding the phenomenon of salinity tolerance. The halophyte Thellungiella salsuginea has been used as a model for studying plant salt tolerance. In this review, T. salsuginea and the glycophyte Arabidopsis thaliana are compared with regards to their biochemical, physiological and molecular responses to salinity. In addition recent developments are presented for improvement of salinity tolerance in glycophytic plants using genes from halophytes.

scholarly journals De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5681 ◽  
Author(s):  
Li Li ◽  
Mimi Li ◽  
Xiwu Qi ◽  
Xingli Tang ◽  
Yifeng Zhou
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rna Sequencing ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Biosynthetic Pathways ◽  
Salt Stress Response ◽  
Glehnia Littoralis ◽  
Plant Signal Transduction

Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.

scholarly journals Identification and Characterization of Long Non-Coding RNA in Tomato Roots under Salt Stress

2021 ◽  
Author(s):  
Ning Li ◽  
Zhongyu Wang ◽  
Baike Wang ◽  
Juan Wang ◽  
Ruiqiang Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Differentially Expressed ◽  
Vegetable Crops ◽  
Tomato Roots ◽  
Non Coding Rnas

As one of the most important vegetable crops in the world, the production of tomatoes was restricted by salt stress. Therefore, it is of great interest to analyze the salt stress tolerance genes. As the non-coding RNAs (ncRNAs) with a length of more than 200 nucleotides, long non-coding RNAs (lncRNAs) lack the ability of protein-coding, but they can play crucial roles in plant development and response to abiotic stresses by regulating gene expression. Nevertheless, there are few studies on the roles of salt-induced lncRNAs in tomatoes. Therefore, we selected wild tomato Solanum pennellii (S. pennellii) and cultivated tomato M82 to be materials. By high-throughput sequencing, 1044 putative lncRNAs were identified here. Among them, 154 and 137 lncRNAs were differentially expressed in M82 and S. pennellii, respectively. Through functional analysis of target genes of differentially expressed lncRNAs (DE-lncRNAs), some genes were found to respond positively to salt stress by participating in Abscisic Acid (ABA) signaling pathway, brassinosteroid (BR) signaling pathway, ethylene (ETH) signaling pathway and anti-oxidation process. We also construct a salt-induced lncRNA-mRNA co-expression network to dissect the putative mechanisms of high salt tolerance in S. pennellii. We analyze the function of salt-induced lncRNAs in tomato roots at the genome-wide levels for the first time. These results will contribute to understanding the molecular mechanisms of salt tolerance in tomatoes from the perspective of lncRNAs.

scholarly journals Pathological LSD1 mutations cause HDAC-mediated aberrant gene repression during early cell differentiation

2021 ◽  
Author(s):  
Daria Bunina ◽  
Pierre-Luc Germain ◽  
Alejandro Lopez Tobon ◽  
Nadine Fernandez-Novel Marx ◽  
Christian Arnold ◽  
...  
Keyword(s):  
Stem Cells ◽  
Protein Function ◽  
Histone Deacetylases ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Neurodevelopmental Disorder ◽  
Differentiated Cells ◽  
Lineage Differentiation ◽  
Lysine Specific Demethylase

Lysine-specific demethylase 1 (LSD1/KDM1A) removes methylation of histone and non-histone substrates, and recruits a repressive chromatin complex. De novo LSD1 mutations impairing protein function lead to a rare neurodevelopmental disorder, but the molecular mechanisms of the pathology are unclear. Using patient-derived fibroblasts, reprogrammed pluripotent stem cells, and differentiated cells, we found over 4000 differentially expressed genes and 68 transcription factors (TFs) whose motif accessibilities changed upon LSD1 mutation. An enhancer-mediated gene regulatory network approach identified impaired transcriptional repressor activity in fibroblast and stem cells, leading to erroneous activation of their target genes. Furthermore, our analysis revealed overall decreases in TF target genes specifically during early lineage differentiation of LSD1 mutant stem cells, likely caused by increased activity of repressive co-factors of LSD1 - histone deacetylases (HDACs). Consistently, HDAC inhibitor restored changes in gene expression including downregulation phenotype. Our findings provide insights into pathogenesis of LSD1 mutations and targets for further therapeutic studies.

scholarly journals A regulatory cascade involving retinoic acid, Cbfa1, and matrix metalloproteinases is coupled to the development of a process of perichondrial invasion and osteogenic differentiation during bone formation

2001 ◽  
Vol 155 (7) ◽  
pp. 1333-1344 ◽  
Author(s):  
Maria J.G. Jiménez ◽  
Milagros Balbín ◽  
Jesús Alvarez ◽  
Toshihisa Komori ◽  
Paolo Bianco ◽  
...  
Keyword(s):  
Retinoic Acid ◽  
Bone Formation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
De Novo ◽  
Bone Matrix ◽  
Type Ii Collagen ◽  
Mitogen Activated Protein Kinase ◽  
Regulatory Cascade ◽  
The Matrix

Tissue-remodeling processes are largely mediated by members of the matrix metalloproteinase (MMP) family of endopeptidases whose expression is strictly controlled both spatially and temporally. In this article, we have examined the molecular mechanisms that could contribute to modulate the expression of MMPs like collagenase-3 and MT1-MMP during bone formation. We have found that all-trans retinoic acid (RA), which usually downregulates MMPs, strongly induces collagenase-3 expression in cultures of embryonic metatarsal cartilage rudiments and in chondrocytic cells. This effect is dose and time dependent, requires the de novo synthesis of proteins, and is mediated by RAR-RXR heterodimers. Analysis of the signal transduction mechanisms underlying the upregulating effect of RA on collagenase-3 expression demonstrated that this factor acts through a signaling pathway involving p38 mitogen-activated protein kinase. RA treatment of chondrocytic cells also induces the production of MT1-MMP, a membrane-bound metalloproteinase essential for skeletal formation, which participates in a proteolytic cascade with collagenase-3. The production of these MMPs is concomitant with the development of an RA-induced differentiation program characterized by formation of a mineralized bone matrix, downregulation of chondrocyte markers like type II collagen, and upregulation of osteoblastic markers such as osteocalcin. These effects are attenuated in metatarsal rudiments in which RA induces the invasion of perichondrial osteogenic cells from the perichondrium into the cartilage rudiment. RA treatment also resulted in the upregulation of Cbfa1, a transcription factor responsible for collagenase-3 and osteocalcin induction in osteoblastic cells. The dynamics of Cbfa1, MMPs, and osteocalcin expression is consistent with the fact that these genes could be part of a regulatory cascade initiated by RA and leading to the induction of Cbfa1, which in turn would upregulate the expression of some of their target genes like collagenase-3 and osteocalcin.

scholarly journals Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 466 ◽  
Author(s):  
Erick Amombo ◽  
Xiaoning Li ◽  
Guangyang Wang ◽  
Shao An ◽  
Wei Wang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Dna Sequences ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Interaction Analysis ◽  
Quantitative Polymerase Chain Reaction ◽  
Future Research ◽  
Salt Treatment ◽  
Gene Expressions

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

scholarly journals The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury

2020 ◽  
Vol 31 (4) ◽  
pp. 716-730 ◽  
Author(s):  
Marc Johnsen ◽  
Torsten Kubacki ◽  
Assa Yeroslaviz ◽  
Martin Richard Späth ◽  
Jannis Mörsdorf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reperfusion Injury ◽  
Caloric Restriction ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Hypoxic Preconditioning ◽  
Preventive Strategies ◽  
Gene Expression Signatures

BackgroundAlthough AKI lacks effective therapeutic approaches, preventive strategies using preconditioning protocols, including caloric restriction and hypoxic preconditioning, have been shown to prevent injury in animal models. A better understanding of the molecular mechanisms that underlie the enhanced resistance to AKI conferred by such approaches is needed to facilitate clinical use. We hypothesized that these preconditioning strategies use similar pathways to augment cellular stress resistance.MethodsTo identify genes and pathways shared by caloric restriction and hypoxic preconditioning, we used RNA-sequencing transcriptome profiling to compare the transcriptional response with both modes of preconditioning in mice before and after renal ischemia-reperfusion injury.ResultsThe gene expression signatures induced by both preconditioning strategies involve distinct common genes and pathways that overlap significantly with the transcriptional changes observed after ischemia-reperfusion injury. These changes primarily affect oxidation-reduction processes and have a major effect on mitochondrial processes. We found that 16 of the genes differentially regulated by both modes of preconditioning were strongly correlated with clinical outcome; most of these genes had not previously been directly linked to AKI.ConclusionsThis comparative analysis of the gene expression signatures in preconditioning strategies shows overlapping patterns in caloric restriction and hypoxic preconditioning, pointing toward common molecular mechanisms. Our analysis identified a limited set of target genes not previously known to be associated with AKI; further study of their potential to provide the basis for novel preventive strategies is warranted. To allow for optimal interactive usability of the data by the kidney research community, we provide an online interface for user-defined interrogation of the gene expression datasets (http://shiny.cecad.uni-koeln.de:3838/IRaP/).

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