Identification and Characterization of Secondary Wall-Associated NAC Genes and Their Involvement in Hormonal Responses in Tobacco (Nicotiana tabacum)

Secondary wall-associated NAC (SWN) genes are a subgroup of NAC (NAM, ATAF, and CUC) transcription factors (TF) that play a key role in regulating secondary cell wall biosynthesis in plants. However, this gene family has not been systematically characterized, and their potential roles in response to hormones are unknown in Nicotiana tabacum. In this study, a total of 40 SWN genes, of which 12 from Nicotiana tomentosiformis, 13 from Nicotiana sylvestris, and 15 from Nicotiana tabacum, were successfully identified. The 15 SWNs from Nicotiana tabacum were further classified into three groups, namely, vascular-related NAC domain genes (NtVNDs), NAC secondary wall thickening promoting factor genes (NtNSTs), and secondary wall-associated NAC domain genes (NtSNDs). The protein characteristic, gene structure, and chromosomal location of 15 NtSWNs (also named Nt1 to Nt15) were also analyzed. The NtVND and NtNST group genes had five conserved subdomains in their N-terminal regions and a motif (LP[Q/x] L[E/x] S[P/A]) in their diverged C- terminal regions. Some hormones, dark and low-temperature related cis-acting elements, were significantly enriched in the promoters of NtSWN genes. A comprehensive expression profile analysis revealed that Nt4 and Nt12 might play a role in vein development. Others might be important for stem development. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that in the NtNST group, genes such as Nt7, Nt8, and Nt13 were more sensitive than the genes in NtVND and NtSND groups under abiotic stress conditions. A transactivation assay further suggested that Nt7, Nt8, and Nt13 showed a significant transactivation activity. Overall, SWN genes were finally identified and characterized in diploid and tetraploid tobacco, revealing new insights into their evolution, variation, and homology relationships. Transcriptome, cis-acting element, qRT-PCR, and transactivation assay analysis indicated the roles in hormonal and stress responses, which provided further resources in molecular mechanism and genetic improvement.

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Initial Characterization and Expression Pattern Analysis of Tobacco (Nicotiana Tabacum) HMGS Gene

E3S Web of Conferences ◽

10.1051/e3sconf/202129203094 ◽

2021 ◽

Vol 292 ◽

pp. 03094

Author(s):

Meiwei Zhao ◽

Tao Zhang ◽

Lei Yang ◽

Hongtao Feng ◽

Zhengxiong Zhao

Keyword(s):

Nicotiana Tabacum ◽

Withania Somnifera ◽

Profile Analysis ◽

Nicotiana Sylvestris ◽

Tissue Expression ◽

Nicotiana Attenuata ◽

Reading Frame ◽

Expression Profile Analysis ◽

Tissue Expression Profile ◽

Rapid Amplification

3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGS) is a member of condensing enzymes that catalyze a Claisen-like condensation reaction.The tobacco (nicotiana tabacum) HMGS gene was firstly characterized using the rapid amplification of cDNA ends methods based on one tobacco EST. The full-length tobacco HMGS gene mRNA was 1,773bp containing a 1389 bp open reading frame, which encodes a protein of 462 amino acids. Sequence analysis revealed that the HMGS of tobacco shares high homology with the HMGS of nicotiana tomentosiformis (96%), nicotiana attenuata (95%), Nicotiana sylvestris (95%), nicotiana benthamiana(94%), solanum lycopersicum(94%), solanum tuberosum(93%) and withania somnifera(93%). Results also showed that tobacco HMGS gene has a closer genetic relationship with the HMGS gene of withania somnifera. Tissue expression profile analysis revealed that the tobacco HMGS gene was highly expressed in flower, but moderately expressed in leaf and stem, and weakly expressed in root. Our experiment established the foundation for further research on this tobacco gene.

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Genome-Wide Identification of Barley ABC Genes and Their Expression in Response to Abiotic Stress Treatment

Plants ◽

10.3390/plants9101281 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1281

Author(s):

Ziling Zhang ◽

Tao Tong ◽

Yunxia Fang ◽

Junjun Zheng ◽

Xian Zhang ◽

...

Keyword(s):

Abiotic Stress ◽

Amino Acid ◽

Stress Responses ◽

Transmembrane Domain ◽

Profile Analysis ◽

Tissue Expression ◽

Expression Profile Analysis ◽

Genome Wide ◽

Tissue Expression Profile ◽

Amino Acid Length

Adenosine triphosphate-binding cassette transporters (ABC transporters) participate in various plant growth and abiotic stress responses. In the present study, 131 ABC genes in barley were systematically identified using bioinformatics. Based on the classification method of the family in rice, these members were classified into eight subfamilies (ABCA–ABCG, ABCI). The conserved domain, amino acid composition, physicochemical properties, chromosome distribution, and tissue expression of these genes were predicted and analyzed. The results showed that the characteristic motifs of the barley ABC genes were highly conserved and there were great diversities in the homology of the transmembrane domain, the number of exons, amino acid length, and the molecular weight, whereas the span of the isoelectric point was small. Tissue expression profile analysis suggested that ABC genes possess non-tissue specificity. Ultimately, 15 differentially expressed genes exhibited diverse expression responses to stress treatments including drought, cadmium, and salt stress, indicating that the ABCB and ABCG subfamilies function in the response to abiotic stress in barley.

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Initial Characterization and Expression Pattern Analysis of Tobacco (Nicotiana Tabacum) 2-Hydroxyisoflavanone Dehydratasedase Gene

E3S Web of Conferences ◽

10.1051/e3sconf/202129203098 ◽

2021 ◽

Vol 292 ◽

pp. 03098

Author(s):

Meiwei Zhao ◽

Song Miao ◽

Jun Guo ◽

Yongyu Li ◽

Zhengxiong Zhao

Keyword(s):

Nicotiana Tabacum ◽

Profile Analysis ◽

Tissue Expression ◽

Reading Frame ◽

Lycopersicon Pennellii ◽

Nicotiana Tomentosiformis ◽

Expression Profile Analysis ◽

Tissue Expression Profile ◽

Rapid Amplification ◽

Single Exon Gene

The complete mRNA sequence of one tobacco (nicotiana tabacum) gene—2-hydroxyisoflavanone dehydratasedase, was amplified using the rapid amplification of cDNA ends methods based on one tobacco EST. The full-length tobacco 2-hydroxyisoflavanone dehydratasedase gene mRNA was 1,278bp containing a 966 bp open reading frame, which encodes a protein of 321 amino acids. Sequence analysis revealed that the 2-hydroxyisoflavanone dehydratasedase of tobacco shares high homology with the 2-hydroxyisoflavanone dehydratasedase of nicotiana tomentosiformis(99%), capsicum annuum(78%), potato(75%), lycopersicon pennellii(73%) and lycopersicon esculentum(72%). BLAST analysis within the tobacco high throughout genomic sequences database revealed that this gene has no intron and is a single exon gene. Results also showed that tobacco 2-hydroxyisoflavanone dehydratasedase gene has a closer genetic relationship with the 2-hydroxyisoflavanone dehydratasedase gene of nicotiana tomentosiformis. Tissue expression profile analysis revealed that the tobacco 2-hydroxyisoflavanone dehydratasedase gene was highly expressed in leaf and flower, but moderately expressed in root and stem. Our experiment established the foundation for further research on this tobacco gene.

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Genome-wide identification and evolution of HECT genes in wheat

PeerJ ◽

10.7717/peerj.10457 ◽

2020 ◽

Vol 8 ◽

pp. e10457

Author(s):

Xianwen Meng ◽

Ting Yang ◽

Jing Liu ◽

Mingde Zhao ◽

Jiuli Wang

Keyword(s):

Gene Family ◽

Stress Responses ◽

Segmental Duplication ◽

Profile Analysis ◽

Purifying Selection ◽

Expression Profile Analysis ◽

Genome Wide ◽

A Genome ◽

Ubiquitin Proteasome ◽

Proteasome Pathway

Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.

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Temporal genomewide expression profiling of DSS colitis reveals novel inflammatory and angiogenesis genes similar to ulcerative colitis

Physiological Genomics ◽

10.1152/physiolgenomics.00138.2010 ◽

2011 ◽

Vol 43 (1) ◽

pp. 43-56 ◽

Cited By ~ 46

Author(s):

Kai Fang ◽

Megan Bruce ◽

Christopher B. Pattillo ◽

Songlin Zhang ◽

Randolph Stone ◽

...

Keyword(s):

Gene Expression ◽

Ulcerative Colitis ◽

Expression Profiling ◽

Profile Analysis ◽

Whole Genome ◽

Qrt Pcr ◽

Dss Colitis ◽

Genome Expression ◽

Expression Profile Analysis ◽

Whole Genome Expression

Dextran sodium sulfate (DSS)-induced colitis is widely used to study pathological mechanisms and potential treatments of inflammatory bowel disease. Because temporal changes in genome expression profiles remain unknown in this model, we performed whole genome expression profile analysis during the development of DSS colitis in comparison with ulcerative colitis (UC) specimens to identify novel and common responses during disease. Colon tissue from DSS-treated mice was collected at days 0, 2, 4, and 6. Half of each specimen was used for histopathological analysis and half for Affymetrix whole genome expression profiling and qRT-PCR validation. Genesifter and Ingenuity software analysis was used to identify differentially expressed genes and perform interactive network analysis. Identified DSS-associated genes in mice were also compared with UC patient data. We identified 1,609 genes that were significantly altered during DSS colitis; the majority were functionally related to inflammation, angiogenesis, metabolism, biological adhesion, cellular growth and proliferation, and cell-to-cell signaling responses. Five hundred and one genes were progressively upregulated, while one hundred seventy-three genes were progressively downregulated. Changes in gene expression were validated in a subset of 33 genes by qRT-PCR, with r2 = 0.925. Ingenuity gene interaction network analysis revealed novel relationships among antigen presentation, cell morphology, and other biological functions in the DSS mouse. Finally, DSS colitis gene array data were compared with UC patient array data: 152 genes were similarly upregulated, and 22 genes were downregulated. Temporal genomewide expression profile analysis of DSS-induced colitis revealed novel associations with various immune responses and tissue remodeling events such as angiogenesis similar to those in UC patients. This study provides a comprehensive view of DSS colitis changes in colon gene expression and identifies common molecules with clinical specimens that are interesting targets for further investigation.

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Expression profile analysis of circular RNAs in essential hypertension by microarray and bioinformatics

10.1101/376178 ◽

2018 ◽

Author(s):

Xingjie-Bao ◽

Xin-He ◽

Shuying-Zheng ◽

Yizhe-Luo ◽

Tianlun-Gu ◽

...

Keyword(s):

Essential Hypertension ◽

Expression Profile ◽

Microarray Data ◽

Profile Analysis ◽

Circular Rnas ◽

Healthy Controls ◽

Biological Functions ◽

Qrt Pcr ◽

Expression Profile Analysis ◽

Public Data

AbstractCircular RNAs (circRNAs), widely found in human cells, are involved in disease and play an important role in progression. To determine whether circRNAs are related in essential hypertension (EH), we analyzed the expression profile of circRNAs and miRNAs in 5 EH and 5 healthy controls cases which were screened by microarray. Through microarray data and public data analysis, differently expressed transcripts were divided into modules, and circRNAs were functionally annotated by miRNAs. The expression of two circRNAs, has_circ_0037909 and has_circ_0105015, were validated in EH by qRT-PCR, which may be associated with EH. Further analysis showed that two circRNAs might through immune system by up-regulation circRNAs and down-regulation expression. These circRNAs biological functions need to be further validated.

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Initial Characterization and Expression Pattern Analysis of Tobacco (Nicotiana Tabacum) Sucrose Synthase Gene

E3S Web of Conferences ◽

10.1051/e3sconf/202129203101 ◽

2021 ◽

Vol 292 ◽

pp. 03101

Author(s):

Meiwei Zhao ◽

Juan Zou ◽

Sixuan Leng ◽

Ying Tao ◽

Zhengxiong Zhao

Keyword(s):

Nicotiana Tabacum ◽

Sucrose Synthase ◽

Dna Analysis ◽

Pattern Analysis ◽

Profile Analysis ◽

Expression Pattern Analysis ◽

Expression Profile Analysis ◽

Initial Characterization ◽

Rapid Amplification ◽

Gene Mrna

A novel tobacco(nicotiana tabacum) sucrose synthase genewas characterized using the rapid amplification of cDNA ends methods based on one tobacco EST. Thissucrose synthase gene mRNA was 2,954bp in length containing a 2,418bp open reading framewhich encodes a protein of 805 amino acids. Sequence analysis revealed that thissucrose synthase of tobacco shares high homology with the sucrose synthase of Nicotianaattenuata(98%), Nicotianasylvestris(98%), Nicotianatomentosiformis(98%), Capsicumannuum(95%), Capsicumbaccatum(95%), Solanumtuberosum(94%), Solanumlycopersicum(94%) and Solanumpennellii(94%). Results also showed that tobacco sucrose synthase gene has a closer genetic relationship with the sucrose synthase gene of Capsicumannuum.Genomic DNA analysis indicated that tobacco sucrose synthase gene is structured in 13 exons and 12 introns.Tissue expression profile analysis revealed that this tobacco sucrose synthase gene was highly expressed in leaf, but moderately expressed in root, stemand flower. These established the foundation for further research on the tobacco sucrose synthase gene.

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Expression Profile Analysis of Differentially Expressed Circular RNAs in Steroid-Induced Osteonecrosis of the Femoral Head

Disease Markers ◽

10.1155/2019/8759642 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Zhongxin Zhu ◽

Wenxi Du ◽

Huan Yu ◽

Hongting Jin ◽

Peijian Tong

Keyword(s):

Femoral Head ◽

Bioinformatics Analysis ◽

Profile Analysis ◽

Circular Rnas ◽

Healthy Individuals ◽

Bioinformatics Analyses ◽

Diagnostic Biomarkers ◽

Qrt Pcr ◽

Expression Profile Analysis

Background. A growing number of studies have suggested that circular RNAs (circRNAs) serve as potential diagnostic biomarkers in many diseases. However, the role of circRNAs in steroid-induced osteonecrosis of the femoral head (SONFH) has not been reported. Methods. Secondary sequencing was performed to profile circRNA expression in peripheral blood samples from three SONFH patients and three healthy individuals. We confirmed our preliminary findings by qRT-PCR. Bioinformatics analysis was conducted to predict their functions. Results. The result showed 345 dysregulated circRNAs. qRT-PCR of eight selected circRNAs preliminarily confirmed the results, which were consistent with RNA sequencing. Bioinformatics analyses were performed to predict the functions of circRNAs to target the genes of miRNAs and the networks of circRNA-miRNA-mRNA interactions. Conclusions. This study provides a new and fundamental circRNA profile of SONFH and a theoretical basis for further studies on the functions of circRNAs in SONFH.

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Genomic Survey, Characterization, and Expression Profile Analysis of the SBP Genes in Pineapple (Ananas comosus L.)

International Journal of Genomics ◽

10.1155/2017/1032846 ◽

2017 ◽

Vol 2017 ◽

pp. 1-14 ◽

Cited By ~ 7

Author(s):

Hina Ali ◽

Yanhui Liu ◽

Syed Muhammad Azam ◽

Zia ur Rahman ◽

S. V. G. N. Priyadarshani ◽

...

Keyword(s):

Plant Architecture ◽

Profile Analysis ◽

Expression Profiles ◽

Ananas Comosus ◽

Rna Seq ◽

Qrt Pcr ◽

Expression Profile Analysis ◽

Expression Studies ◽

Flower And Fruit Development ◽

Regulatory Functions

Gene expression is regulated by transcription factors, which play many significant developmental processes. SQUAMOSA promoter-binding proteins (SBP) perform a variety of regulatory functions in leaf, flower, and fruit development, plant architecture, and sporogenesis. 16 SBP genes were identified in pineapple and were divided into four groups on basis of phylogenetic analysis. Five paralogs in pineapple for SBP genes were identified with Ka/Ks ratio varied from 0.20 for AcSBP14 and AcSBP15 to 0.36 for AcSBP6 and AcSBP16, respectively. 16 SBP genes were located on 12 chromosomes out of 25 pineapple chromosomes with highly conserved protein sequence structures. The isoionic points of SBP ranged from 6.05 to 9.57, while molecular weight varied from 22.7 to 121.9 kD. Expression profiles of SBP genes revealed that AcSBP7 and AcSBP15 (leaf), AcSBP13, AcSBP12, AcSBP8, AcSBP16, AcSBP9, and AcSBP11 (sepal), AcSBP6, AcSBP4, and AcSBP10 (stamen), AcSBP14, AcSBP1, and AcSBP5 (fruit) while the rest of genes showed low expression in studied tissues. Four genes, that is, AcSBP11, AcSBP6, AcSBP4, and AcSBP12, were highly expressed at 4°C, while AcSBP16 were upregulated at 45°C. RNA-Seq was validated through qRT-PCR for some genes. Salt stress-induced expression of two genes, that is, AcSBP7 and AcSBP14, while in drought stress, AcSBP12 and AcSBP15 were highly expressed. Our study lays a foundation for further gene function and expression studies of SBP genes in pineapple.

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Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

BMC Genomics ◽

10.1186/s12864-021-08000-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Kuiyin Li ◽

Lili Duan ◽

Yubo Zhang ◽

Miaoxiao Shi ◽

Songshu Chen ◽

...

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Stress Responses ◽

Gene Evolution ◽

Profile Analysis ◽

Stress Conditions ◽

Expression Profile Analysis ◽

Genome Wide ◽

Breeding Programmes ◽

Sorghum Breeding

Abstract Background Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically studied in some dicots and monocots, including Arabidopsis, tomato, chrysanthemum, soybean, wheat, corn, rice, and buckwheat. However, there are no related studies on sorghum. Results In this study, a total of 40 sorghum trihelix (SbTH) genes were identified based on the sorghum genome, among which 34 were located in the nucleus, 5 in the chloroplast, 1 (SbTH38) in the cytoplasm, and 1 (SbTH23) in the extracellular membrane. Phylogenetic analysis of the SbTH genes and Arabidopsis and rice trihelix genes indicated that the genes were clustered into seven subfamilies: SIP1, GTγ, GT1, GT2, SH4, GTSb8, and orphan genes. The SbTH genes were located in nine chromosomes and none on chromosome 10. One pair of tandem duplication gene and seven pairs of segmental duplication genes were identified in the SbTH gene family. By qPCR, the expression of 14 SbTH members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. Except for the leaves in which the genes were upregulated after only 2 h exposure to high temperature, the 12 SbTH genes were significantly upregulated in the stems of sorghum seedlings after 24 h under the other abiotic stress conditions. Among the selected genes, SbTH10/37/39 were significantly upregulated, whereas SbTH32 was significantly downregulated under different stress conditions. Conclusions In this study, we identified 40 trihelix genes in sorghum and found that gene duplication was the main force driving trihelix gene evolution in sorghum. The findings of our study serve as a basis for further investigation of the functions of SbTH genes and providing candidate genes for stress-resistant sorghum breeding programmes and increasing sorghum yield.

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