Identification and characterisation of barley (Hordeum vulgare) respiratory burst oxidase homologue family members

2008 ◽  
Vol 35 (5) ◽  
pp. 347 ◽  
Author(s):  
Damien J. Lightfoot ◽  
Annette Boettcher ◽  
Alan Little ◽  
Neil Shirley ◽  
Amanda J. Able
Keyword(s):  
Hordeum Vulgare ◽  
Respiratory Burst ◽  
Cellular Response ◽  
Expression Profiles ◽  
Genomic Structure ◽  
Expression Patterns ◽  
Family Members ◽  
Hordeum Vulgare L ◽  
Pathogen Invasion ◽  
Respiratory Burst Oxidase

Respiratory burst oxidase homologues (RBOHs) of the human phagocyte gp91phox gene have been isolated from several plant species and the proteins that they encode have been shown to play important roles in the cellular response to biotic stress via the production of superoxide. In this study we have identified and preliminarily characterised six RBOHs from barley (Hordeum vulgare L.). Conservation of the genomic structure and conceptual protein sequence was observed between all six barley RBOH genes when compared with Arabidopsis and rice RBOH gene family members. Four of the six barley RBOH transcripts had wide-spread constitutive spatial expression patterns. The inducible expression profiles of HvRBOHF1 and HvRBOHF2 in response to infection by the necrotrophic fungal pathogens Pyrenophora teres f. teres Drechsler and Rhynchosporium secalis (Oudem) J. Davis were further characterised by quantitative real-time PCR (qPCR). Increased expression of both transcripts was observed in leaf epidermal tissue in response to infection, which is in keeping with a suggested role for both transcripts in the early oxidative burst during the plant response to pathogen invasion. This research provides a basis for further analysis and establishment of the roles of this RBOH family in various reactive oxygen species dependent processes in barley.

scholarly journals Genome Wide Identification of Respiratory Burst Oxidase Homolog (Rboh) Genes in Citrus sinensis and Functional Analysis of CsRbohD in Cold Tolerance

2022 ◽  
Vol 23 (2) ◽  
pp. 648
Author(s):  
Yueliang Zhang ◽  
Yiwu Zhang ◽  
Li Luo ◽  
Chunyi Lu ◽  
Weiwen Kong ◽  
...  
Keyword(s):  
Cold Stress ◽  
Respiratory Burst ◽  
Citrus Sinensis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Microrna Target ◽  
Specific Expression ◽  
Cis Acting ◽  
Functional Studies ◽  
Respiratory Burst Oxidase

Respiratory burst oxidase homologs (Rbohs) are critical enzymes involved in the generation of reactive oxygen species (ROS) that play an important role in plant growth and development as well as various biotic and abiotic stresses in plants. Thus far, there have been few reports on the characterization of the Rboh gene family in Citrus. In this study, seven Rboh genes (CsRbohA~CsRbohG) were identified in the Citrus sinensis genome. The CsRboh proteins were predicted to localize to the cell membrane. Most CsRbohs contained four conserved domains, an EF-hand domain, and a transmembrane region. Phylogenetic analysis demonstrated that the CsRbohs were divided into five groups, suggesting potential distinct functions and evolution. The expression profiles revealed that these seven CsRboh genes displayed tissue-specific expression patterns, and five CsRboh genes were responsive to cold stress. Fourteen putative cis-acting elements related to stress response, hormone response, and development regulation were present within the promoters of CsRboh genes. The in-silico microRNA target transcript analyses indicated that CsRbohE might be targeted by csi-miR164. Further functional and physiological analyses showed that the knockdown of CsRbohD in trifoliate orange impaired resistance to cold stress. As a whole, our results provide valuable information for further functional studies of the CsRboh genes in response to cold stress.

scholarly journals RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics

2019 ◽  
Vol 20 (23) ◽  
pp. 6098 ◽  
Author(s):  
Amarinder Singh Thind ◽  
Kumar Parijat Tripathi ◽  
Mario Rosario Guarracino
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Web Application ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Differential Gene

The comparison of high throughput gene expression datasets obtained from different experimental conditions is a challenging task. It provides an opportunity to explore the cellular response to various biological events such as disease, environmental conditions, and drugs. There is a need for tools that allow the integration and analysis of such data. We developed the “RankerGUI pipeline”, a user-friendly web application for the biological community. It allows users to use various rank based statistical approaches for the comparison of full differential gene expression profiles between the same or different biological states obtained from different sources. The pipeline modules are an integration of various open-source packages, a few of which are modified for extended functionality. The main modules include rank rank hypergeometric overlap, enriched rank rank hypergeometric overlap and distance calculations. Additionally, preprocessing steps such as merging differential expression profiles of multiple independent studies can be added before running the main modules. Output plots show the strength, pattern, and trends among complete differential expression profiles. In this paper, we describe the various modules and functionalities of the developed pipeline. We also present a case study that demonstrates how the pipeline can be used for the comparison of differential expression profiles obtained from multiple platforms’ data of the Gene Expression Omnibus. Using these comparisons, we investigate gene expression patterns in kidney and lung cancers.

scholarly journals Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

2021 ◽  
Vol 23 (1) ◽  
pp. 469
Author(s):  
Kai Tong ◽  
Xinyang Wu ◽  
Long He ◽  
Shiyou Qiu ◽  
Shuang Liu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Expression Profiles ◽  
Stomatal Closure ◽  
Expression Patterns ◽  
Family Members ◽  
Triticum Aestivum L ◽  
Free Calcium ◽  
Cis Acting ◽  
Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

scholarly journals The Association between TIF1 Family Members and Cancer Stemness in Solid Tumors

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1528
Author(s):  
Patrycja Czerwinska ◽  
Nikola Agata Wlodarczyk ◽  
Anna Maria Jaworska ◽  
Andrzej Adam Mackiewicz
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Solid Tumors ◽  
Cancer Progression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Family Members ◽  
The Cancer Genome Atlas ◽  
Tumor Type ◽  
Cancer Stemness

Cancer progression entails a gradual loss of a differentiated phenotype in parallel with the acquisition of stem cell-like features. Cancer de-differentiation and the acquisition of stemness features are mediated by the transcriptional and epigenetic dysregulation of cancer cells. Here, using publicly available data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and harnessing several bioinformatic tools, we characterized the association between Transcriptional Intermediary Factor 1 (TIF1) family members and cancer stemness in 27 distinct types of solid tumors. We aimed to define the prognostic value for TIF1 members in predicting a stem cell-like cancer phenotype and patient outcome. Our results demonstrate that high expression of only one member of the TIF1 family, namely TIF1β (also known as Tripartite Motif protein 28, TRIM28) is consequently associated with enriched cancer stemness across the tested solid tumor types, resulting in a worse prognosis for cancer patients. TRIM28 is highly expressed in higher grade tumors that exhibit stem cell-like traits. In contrast to other TIF1 members, only TIF1β/TRIM28-associated gene expression profiles were robustly enriched with stemness markers regardless of the tumor type. Our work demonstrates that TIF1 family members exhibit distinct expression patterns in stem cell-like tumors, despite their structural and functional similarity. Among other TIF1 members, only TRIM28 might serve as a marker of cancer stemness features.

scholarly journals African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors associated with immunologic functions and environmental exposures

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Urminder Singh ◽  
Kyle M. Hernandez ◽  
Bruce J. Aronow ◽  
Eve Syrkin Wurtele
Keyword(s):  
Gene Expression ◽  
African American ◽  
African Americans ◽  
Environmental Factors ◽  
Cellular Response ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Reactive Oxygen ◽  
Mitigation Strategies ◽  
European Americans

AbstractThe COVID-19 pandemic has affected African American populations disproportionately with respect to prevalence, and mortality. Expression profiles represent snapshots of combined genetic, socio-environmental (including socioeconomic and environmental factors), and physiological effects on the molecular phenotype. As such, they have potential to improve biological understanding of differences among populations, and provide therapeutic biomarkers and environmental mitigation strategies. Here, we undertook a large-scale assessment of patterns of gene expression between African Americans and European Americans, mining RNA-Seq data from 25 non-diseased and diseased (tumor) tissue-types. We observed the widespread enrichment of pathways implicated in COVID-19 and integral to inflammation and reactive oxygen stress. Chemokine CCL3L3 expression is up-regulated in African Americans. GSTM1, encoding a glutathione S-transferase that metabolizes reactive oxygen species and xenobiotics, is upregulated. The little-studied F8A2 gene is up to 40-fold more highly expressed in African Americans; F8A2 encodes HAP40 protein, which mediates endosome movement, potentially altering the cellular response to SARS-CoV-2. African American expression signatures, superimposed on single cell-RNA reference data, reveal increased number or activity of esophageal glandular cells and lung ACE2-positive basal keratinocytes. Our findings establish basal prognostic signatures that can be used to refine approaches to minimize risk of severe infection and improve precision treatment of COVID-19 for African Americans. To enable dissection of causes of divergent molecular phenotypes, we advocate routine inclusion of metadata on genomic and socio-environmental factors for human RNA-sequencing studies.

scholarly journals Re-examination of the APETALA2/Ethylene-Responsive Factor Gene Family in Barley (Hordeum vulgare L.) Indicates a Role in the Regulation of Starch Synthesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinjin Ding ◽  
Hassan Karim ◽  
Yulong Li ◽  
Wendy Harwood ◽  
Carlos Guzmán ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Hordeum Vulgare ◽  
Gene Family ◽  
Expression Patterns ◽  
Starch Synthesis ◽  
Luciferase Reporter ◽  
Rice Starch ◽  
Hordeum Vulgare L ◽  
Genome Database ◽  
New Genes

The APETALA2/Ethylene-Responsive factor (AP2/ERF) gene family is a large plant-specific transcription factor family, which plays important roles in regulating plant growth and development. A role in starch synthesis is among the multiple functions of this family of transcription factors. Barley (Hordeum vulgare L.) is one of the most important cereals for starch production. However, there are limited data on the contribution of AP2 transcription factors in barley. In this study, we used the recently published barley genome database (Morex) to identify 185 genes of the HvAP2/ERF family. Compared with previous work, we identified 64 new genes in the HvAP2/ERF gene family and corrected some previously misannotated and duplicated genes. After phylogenetic analysis, HvAP2/ERF genes were classified into four subfamilies and 18 subgroups. Expression profiling showed different patterns of spatial and temporal expression for HvAP2/ERF genes. Most of the 12 HvAP2/ERF genes analyzed using quantitative reverse transcription–polymerase chain reaction had similar expression patterns when compared with those of starch synthase genes in barley, except for HvAP2-18 and HvERF-73. HvAP2-18 is homologous to OsRSR1, which negatively regulates the synthesis of rice starch. Luciferase reporter gene, and yeast one-hybrid assays showed that HvAP2-18 bound the promoter of AGP-S and SBE1 in vitro. Thus, HvAP2-18 might be an interesting candidate gene to further explore the mechanisms involved in the regulation of starch synthesis in barley.

scholarly journals Genome-wide Identification, Evolutionary and Functional Analyses of Kfb Family Members in Potato

2022 ◽  
Author(s):  
Ruimin Tang ◽  
Haitao Dong ◽  
Liheng He ◽  
Peng Li ◽  
Yuanrui Shi ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Family Members ◽  
Structure Evolution ◽  
Duplicated Genes ◽  
Physiological Processes ◽  
Localization Analysis ◽  
And Function ◽  
Functional Mechanisms

Abstract Background: Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but this family members have not been systematically identified and analyzed in potato. Results: Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the KFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups according to their structural and phylogenetic features. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes. Among these genes, two pairs of genes (StKFB15/16 and StKFB40/41) were predicted to be tandemly duplicated genes, and one pair of genes (StKFB15/29) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses. Transcriptomic and qRT-PCR analyses of StKFBs deciphered that multiple StKFB genes were differentially expressed in three colored potato tubers. Genes that were highly expressed in yellow fleshed tubers (Jin-16) and were lowly expressed in the red- (Red Rose-2) or purple-fleshed (Xisen-8) tubers, such as StKFB07, StKFB15, StKFB23, StKFB29 and StKFB44, may negatively regulate anthocyanin biosynthesis.Conclusions: This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings set the stage for further study of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.

scholarly journals De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

2021 ◽  
Author(s):  
Satoshi Okubo ◽  
Kaede Terauchi ◽  
Shinji Okada ◽  
Takao Yamaura ◽  
Takumi Misaka ◽  
...  
Keyword(s):  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
3D Structure ◽  
Family Members ◽  
Rna Seq ◽  
High Similarity ◽  
Perennial Plant ◽  
Mannose Binding ◽  
Galanthus Nivalis

Abstract Background Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar to snowdrop (Galanthus nivalis) agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family members was unclear. Results Through de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and detailed analysis of the expression patterns of neoculin and neoculin-like genes in both species, we assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata, encoding both the basic and acidic subunits of neoculin in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in the two species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes differed considerably between the two species: the transcripts per million (TPM) values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. Conclusions The genetic diversity of neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in their expression profiles between C. latifolia and C. capitulata may be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level.

scholarly journals De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Satoshi Okubo ◽  
Kaede Terauchi ◽  
Shinji Okada ◽  
Yoshikazu Saito ◽  
Takao Yamaura ◽  
...  
Keyword(s):  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
3D Structure ◽  
Family Members ◽  
Rna Seq ◽  
High Similarity ◽  
Perennial Plant ◽  
Mannose Binding ◽  
Galanthus Nivalis

Abstract Background Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar to snowdrop (Galanthus nivalis) agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family members was unclear. Results Through de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and detailed analysis of the expression patterns of neoculin and neoculin-like genes in both species, we assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata, encoding both the basic and acidic subunits of neoculin in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in the two species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes differed considerably between the two species: the transcripts per million (TPM) values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. Conclusions The genetic diversity of neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in their expression profiles between C. latifolia and C. capitulata may be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level.

Sign in / Sign up

Export Citation Format

Share Document