scholarly journals Functional characterization of genes with circadian expression patterns in common wheat

2021 ◽  
Keyword(s):  
Common Wheat ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Circadian Expression

scholarly journals Genome-wide identification, phylogeny, and expression profile of the sucrose transporter multigene family in tobacco

2019 ◽  
Vol 99 (3) ◽  
pp. 312-323
Author(s):  
Shanshan Wang ◽  
Jun Yang ◽  
Xiaodong Xie ◽  
Feng Li ◽  
Mingzhu Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Nicotiana Sylvestris ◽  
Multiple Roles ◽  
Functional Conservation ◽  
Sucrose Transporters ◽  
Genome Wide ◽  
Pi Starvation ◽  
Profiling Analysis

The transportation and distribution of sucrose in plants is mediated by sucrose transporters (SUTs), which also participate in various plant developmental and resistance processes. However, no such study of the tobacco SUT family has been reported yet. In the present study, 11, 5, and 4 SUT genes were identified from the genomes of Nicotiana tabacum, Nicotiana sylvestris, and Nicotiana tomentosiformis, respectively. The exon–intron structures of the tobacco SUT genes were highly conserved in the three tobacco species. Gene loss, duplication, and chromosome exchange occurred in the NtSUT family during the formation of allotetraploid common tobacco. Expression profiling analysis revealed that the expression patterns of the NtSUT genes in common tobacco were closer to those in N. sylvestris plants. The NtSUT2s and NtSUT4 genes were ubiquitously expressed in various tobacco tissues, while the NtSUT1s gene was highly expressed in the maturing leaves, indicating their functional conservation and differentiation. The transcriptions of the NtSUT2t, NtSUT3s, NtSUT4, and NtSUT5s genes in tobacco plants were dramatically induced under Pi starvation, drought, and salinity stresses, but their highest expression levels occurred in different tissues, suggesting the multiple roles of NtSUTs in plant resistance to various abiotic stresses. This study provides useful information for the further functional characterization of SUT genes in tobacco.

scholarly journals Genome-Wide Identification and Expression Analysis of Sucrose Nonfermenting-1-Related Protein Kinase (SnRK) Genes in Triticum aestivum in Response to Abiotic Stress

2021 ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Plant Stress ◽  
Protein Motif ◽  
Genome Wide

The SnRK gene family is a key regulator playing an important role in plant stress response by phosphorylating the target protein to regulate the signalling pathways. The function of SnRK gene family has been reported in many species but is limited to Triticum asetivum. In this study, SnRK gene family in the wheat genome was identified and its structural characteristics were described. One hundred forty-seven SnRK genes distributed across 21 chromosomes were identified in the Triticum aestivum genome and categorised into three subgroups (SnRK1/2/3) based on phylogenetic analyses and domain types. The gene intron-exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication between the wheat, Arabidopsis, rice and barley genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. SnRK genes showed differential expression patterns in leaves, roots, spike, and grains. Redundant stress-related cis-elements were also found in the promoters of 129 SnRK genes and their expression levels varied widely following drought, ABA and light regulated elements. In particular, TaSnRK2.11 had higher and increased expression under the abiotic stresses and can be a candidate gene for the abiotc stress tolerance. The findings will aid in the functional characterization of TaSnRK genes for further research.

Design and Characterization of a Fluorescent Reporter Enabling Live-cell Monitoring of MCT8 Expression

2021 ◽  
Author(s):  
Adina Sophie Graffunder ◽  
Sarah Paisdzior ◽  
Robert Opitz ◽  
Kostja Renko ◽  
Peter Kühnen ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Live Cell ◽  
Monocarboxylate Transporter ◽  
Start Codon ◽  
Future Application ◽  
Gene Assay ◽  
Cell Monitoring

AbstractThe monocarboxylate transporter 8 (MCT8) is a specific thyroid hormone transporter and plays an essential role in fetal development. Inactivating mutations in the MCT8 encoding gene SLC16A2 (solute carrier family 16, member 2) lead to the Allan-Herndon-Dudley syndrome, a condition presenting with severe endocrinological and neurological phenotypes. However, the cellular distribution pattern and dynamic expression profile are still not well known for early human neural development. Objective Development and characterization of fluorescent MCT8 reporters that would permit live-cell monitoring of MCT8 protein expression in vitro in human induced pluripotent stem cell (hiPSC)-derived cell culture models. Methods A tetracysteine (TC) motif was introduced into the human MCT8 sequence at four different positions as binding sites for fluorescent biarsenical dyes. Human Embryonic Kidney 293 cells were transfected and stained with fluorescein-arsenical hairpin-binder (FlAsH). Counterstaining with specific MCT8 antibody was performed. Triiodothyronine (T3) uptake was indirectly measured with a T3 responsive luciferase-based reporter gene assay in Madin-Darby Canine Kidney 1 cells for functional characterization. Results FlAsH staining and antibody counterstaining of all four constructs showed cell membrane expression of all MCT8 constructs. The construct with the tag after the first start codon demonstrated comparable T3 uptake to the MCT8 wildtype. Conclusion Our data indicate that introduction of a TC-tag directly after the first start codon generates a MCT8 reporter with suitable characteristics for live-cell monitoring of MCT8 expression. One promising future application will be generation of stable hiPSC MCT8 reporter lines to characterize MCT8 expression patterns during in vitro neuronal development.

Anterior neurectoderm is progressively induced during gastrulation: the role of the Xenopus homeobox gene orthodenticle

Development ◽  
1995 ◽  
Vol 121 (4) ◽  
pp. 993-1004 ◽  
Author(s):  
I.L. Blitz ◽  
K.W. Cho
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Ectopic Expression ◽  
Homeobox Gene ◽  
Neural Induction ◽  
Cement Gland ◽  
Spemann's Organizer ◽  
Vertical Contact

In order to study the regional specification of neural tissue we isolated Xotx2, a Xenopus homolog of the Drosophila orthodenticle gene. Xotx2 is initially expressed in Spemann's organizer and its expression is absent in the ectoderm of early gastrulae. As gastrulation proceeds, Xotx2 expression is induced in the overlying ectoderm and this domain of expression moves anteriorly in register with underlying anterior mesoderm throughout the remainder of gastrulation. The expression pattern of Xotx2 suggests that a wave of Xotx2 expression (marking anterior neurectoderm) travels through the ectoderm of the gastrula with the movement of underlying anterior (prechordal plate) mesoderm. This expression of Xotx2 is reminiscent of the Eyal-Giladi model for neural induction. According to this model, anterior neural-inducing signals emanating from underlying anterior mesoderm transiently induce anterior neural tissues after vertical contact with the overlying ectoderm. Further patterning is achieved when the ectoderm receives caudalizing signals as it comes in contact with more posterior mesoderm during subsequent gastrulation movements. Functional characterization of the Xotx2 protein has revealed its involvement in differentiation of the anterior-most tissue, the cement gland. Ectopic expression of Xotx2 in embryos induces extra cement glands in the skin as well as inducing a cement gland marker (XAG1) in isolated animal cap ectoderm. Microinjection of RNA encoding the organizer-specific homeo-domain protein goosecoid into the ventral marginal zone results in induction of the Xotx2 gene. This result, taken in combination with the indistinguishable expression patterns of Xotx2 and goosecoid in the anterior mesoderm suggests that Xotx2 is a target of goosecoid regulation.

scholarly journals Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Cuiling Yuan ◽  
Chunjuan Li ◽  
Xiaodong Lu ◽  
Xiaobo Zhao ◽  
Caixia Yan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drought Stress ◽  
Stress Responses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Nac Transcription Factor ◽  
Rna Seq ◽  
A Genome ◽  
Salt And Drought Stress

Abstract Background Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. Results We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. Conclusion Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.

scholarly journals Genome-wide identification and characterization of the ALOG gene family in Petunia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Feng Chen ◽  
Qin Zhou ◽  
Lan Wu ◽  
Fei Li ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Genome Wide ◽  
Domain Of Unknown Function ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

scholarly journals Genome-wide identification and characterization of SnRK family genes in Brassica napus

2020 ◽  
Author(s):  
Weizhuo Zhu ◽  
Dezhi Wu ◽  
Lixi Jiang ◽  
Lingzhen Ye
Keyword(s):  
Brassica Napus ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Composition Analysis ◽  
Distribution Analysis ◽  
Element Analysis ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background: Sucrose non-fermenting 1 related protein kinases (SnRK) play crucial roles in responding to biotic and abiotic stresses through activating protein phosphorylation pathways. However, little information of SnRK genes was available in Brassica napus, one of important oil crops. Recently, the released sequences of the reference genome of B.napus provide a good chance to perform genome-wide identification and characterization of BnSnRK gene family in the rapeseed.Results: Totally 114 SnRK genes distributed on 19 chromosomes were identified in the genome of B.napus and classified into three subfamilies on the basis of phylogenetic analysis and the domain types. According to gene structure and motif composition analysis, the BnSnRK sequences showed obvious divergence among three subfamilies. Gene duplication and synteny between the genomes of the rapeseed and Arabidopsis were also analyzed to provide insights into the evolutionary characteristics of BnSnRK family genes. Cis-element analysis revealed that BnSnRKs may response to diverse environmental stresses. Moreover, the expression patterns of BnSnRKs in various tissues and under diverse abiotic stresses were distinct difference. Besides, Single Nucleotide Polymorphisms (SNP) distribution analysis suggests the function disparity of BnSnRK family genes in different genotypes of the rapeseed.Conclusion: We examined genomic structures, evolution features, expression patterns and SNP distribution of 114 BnSnRKs. The results provide valuable information for functional characterization of BnSnRK genes in future studies.

scholarly journals Circadian expression and functional characterization of PEA ‐15 within the mouse suprachiasmatic nucleus

2018 ◽  
Vol 47 (7) ◽  
pp. 845-857 ◽  
Author(s):  
Kelin Wheaton ◽  
Sydney Aten ◽  
Lucas Sales Queiroz ◽  
Kyle Sullivan ◽  
John Oberdick ◽  
...  
Keyword(s):  
Suprachiasmatic Nucleus ◽  
Functional Characterization ◽  
Circadian Expression

scholarly journals Functional characterization of the ABF gene family in upland cotton (Gossypium hirsutum L.)

2017 ◽  
Author(s):  
Tyson C. C. Kerr ◽  
Haggag Abdel-Mageed ◽  
MiYoung Kang ◽  
Dakota Cryer ◽  
Randy D. Allen
Keyword(s):  
Abscisic Acid ◽  
Abiotic Stress ◽  
Gossypium Hirsutum ◽  
Water Deficit ◽  
Upland Cotton ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Ectopic Expression ◽  
Differentially Expressed

AbstractThe AREB/ABF bZIP transcription factors play a pivotal role in abscisic acid-dependent abiotic stress-responsive gene expression. Despite the perennial damage and reduced productivity that result from water-deficit and unpredictable early season temperature fluctuations, these critical genes have not been previously examined in upland cotton (Gossypium hirsutum). Here, we report the isolation of the G. hirsutum ABF homologs, characterization of their expression patterns in response to abiotic stress treatments, and examination of their functions through heterologous ectopic expression in Arabidopsis. As expected for an allotetraploid, G. hirsutum ABF homologs are present in the genome as homeologous pairs. These genes are differentially expressed, both among the homologs and within the homeologous pairs, in response to exogenous abscisic acid (ABA) application, dehydration, and chilling temperatures. Furthermore, heterologous ectopic expression of many of the G. hirsutum ABF genes in Arabidopsis conferred increased tolerance to water deficit and osmotic stress, as well as cold tolerance, in a gene specific manner. These results indicate the G. hirsutum ABF homologs are functional in Arabidopsis and, as in other species, are likely to play an essential role in the abiotic stress response.HighlightThe Gossypium hirsutum ABF homeologs are differentially expressed in response to abiotic stress, and their ectopic expression in Arabidopsis can confer increased water deficit tolerance.

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