scholarly journals Identification, expression analysis, and the regulating function on C/EBPs of KLF10 in Dalian purple sea urchin, Strongylocentrotus nudus

Genome ◽  
2017 ◽  
Vol 60 (10) ◽  
pp. 837-849 ◽  
Author(s):  
Kaikai Wu ◽  
Zhiying Jia ◽  
Qi’ai Wang ◽  
Zhenlin Wei ◽  
Zunchun Zhou ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Core Promoter ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Promoter Regions ◽  
Over Expression ◽  
Purple Sea Urchin ◽  
Strongylocentrotus Nudus ◽  
Cdna Fragments ◽  
Insight Into

Accumulating evidence indicates that Krüppel-like factors (KLFs) play important roles in fat biology via the regulation of CCAAT/enhancer binding proteins (C/EBPs). However, KLFs and C/EBPs have not been identified from Strongylocentrotus nudus, and their roles in this species are not clear. In this study, the full-length cDNA of S. nudus KLF10 (SnKLF10) and three cDNA fragments of S. nudus C/EBPs (SnC/EBPs) were obtained. Examination of tissue distribution and expression patterns during gonadal development implied that SnKLF10 and SnC/EBPs play important roles in gonadal lipogenesis. The presence of transcription factor-binding sites (TFBSs) for KLFs in SnC/EBPs, and the results of an over-expression assay, revealed that SnKLF10 negatively regulates the transcription of SnC/EBPs. In addition, the core promoter regions of SnC/EBPs were determined, and multiple TFBSs for transcription factor (TFs) were identified, which are potential regulators of SnC/EBP transcription. Taken together, these results suggest that SnC/EBP genes are potential targets of SnKLF10, and that SnKLF10 plays a role in lipogenesis by repressing the transcription of SnC/EBPs. These findings provide information for further studies of KLF10 in invertebrates and provide new insight into the regulatory mechanisms of C/EBP transcription.

scholarly journals In Silico Prediction of Transcription Factor Collaborations Underlying Phenotypic Sexual Dimorphism in Zebrafish (Danio rerio)

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 873
Author(s):  
Shahrbanou Hosseini ◽  
Armin Otto Schmitt ◽  
Jens Tetens ◽  
Bertram Brenig ◽  
Henner Simianer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Sexual Dimorphism ◽  
Sex Determination ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Colour Pattern ◽  
Promoter Regions ◽  
Dimorphic Gene Expression

The transcriptional regulation of gene expression in higher organisms is essential for different cellular and biological processes. These processes are controlled by transcription factors and their combinatorial interplay, which are crucial for complex genetic programs and transcriptional machinery. The regulation of sex-biased gene expression plays a major role in phenotypic sexual dimorphism in many species, causing dimorphic gene expression patterns between two different sexes. The role of transcription factor (TF) in gene regulatory mechanisms so far has not been studied for sex determination and sex-associated colour patterning in zebrafish with respect to phenotypic sexual dimorphism. To address this open biological issue, we applied bioinformatics approaches for identifying the predicted TF pairs based on their binding sites for sex and colour genes in zebrafish. In this study, we identified 25 (e.g., STAT6-GATA4; JUN-GATA4; SOX9-JUN) and 14 (e.g., IRF-STAT6; SOX9-JUN; STAT6-GATA4) potentially cooperating TFs based on their binding patterns in promoter regions for sex determination and colour pattern genes in zebrafish, respectively. The comparison between identified TFs for sex and colour genes revealed several predicted TF pairs (e.g., STAT6-GATA4; JUN-SOX9) are common for both phenotypes, which may play a pivotal role in phenotypic sexual dimorphism in zebrafish.

scholarly journals A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila

PLoS Genetics ◽  
2021 ◽  
Vol 17 (6) ◽  
pp. e1009613
Author(s):  
Clara Poupault ◽  
Diane Choi ◽  
Khanh Lam-Kamath ◽  
Deepshe Dewett ◽  
Ansa Razzaq ◽  
...  
Keyword(s):  
Promoter Region ◽  
Core Promoter ◽  
Expression Patterns ◽  
Core Promoter Region ◽  
Promoter Regions ◽  
Specific Expression ◽  
General Activation ◽  
Different Color ◽  
Photoreceptor Neurons ◽  
Distal Promoter

Color vision in Drosophila melanogaster is based on the expression of five different color-sensing Rhodopsin proteins in distinct subtypes of photoreceptor neurons. Promoter regions of less than 300 base pairs are sufficient to reproduce the unique, photoreceptor subtype-specific rhodopsin expression patterns. The underlying cis-regulatory logic remains poorly understood, but it has been proposed that the rhodopsin promoters have a bipartite structure: the distal promoter region directs the highly restricted expression in a specific photoreceptor subtype, while the proximal core promoter region provides general activation in all photoreceptors. Here, we investigate whether the rhodopsin promoters exhibit a strict specialization of their distal (subtype specificity) and proximal (general activation) promoter regions, or if both promoter regions contribute to generating the photoreceptor subtype-specific expression pattern. To distinguish between these two models, we analyze the expression patterns of a set of hybrid promoters that combine the distal promoter region of one rhodopsin with the proximal core promoter region of another rhodopsin. We find that the function of the proximal core promoter regions extends beyond providing general activation: these regions play a previously underappreciated role in generating the non-overlapping expression patterns of the different rhodopsins. Therefore, cis-regulatory motifs in both the distal and the proximal core promoter regions recruit transcription factors that generate the unique rhodopsin patterns in a combinatorial manner. We compare this combinatorial regulatory logic to the regulatory logic of olfactory receptor genes and discuss potential implications for the evolution of rhodopsins.

Isolation and Expression Analysis of Two DOPA Dioxygenases in Phytolacca americana

2009 ◽  
Vol 64 (7-8) ◽  
pp. 564-573 ◽  
Author(s):  
Kana Takahashi ◽  
Eri Takamura ◽  
Masaaki Sakuta
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Binding Sites ◽  
Biosynthetic Pathway ◽  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Inverse Pcr ◽  
Phytolacca Americana ◽  
Rt Pcr ◽  
Promoter Regions

Betacyanins and anthocyanins, two main red fl ower pigments, never occur together in the same plant. Although the anthocyanin biosynthetic pathway has been well analyzed, the biosynthetic genes and the regulatory mechanism of the betacyanin biosynthesis are still obscure. We cloned two cDNAs of DOPA dioxygenase from Phytolacca americana, PaDOD1 and PaDOD2, that may be involved in the betalain biosynthesis. The deduced amino acid sequence of PaDOD1 and PaDOD2 showed approximately 80% homology to each other. The promoter regions of PaDOD1 and PaDOD2 were isolated by inverse PCR and analyzed using PLACE database. Some putative MYB, bHLH, and environmental stress-responsive transcription factor binding sites were detected in the PaDOD1 and PaDOD2 promoter regions. Expression patterns of PaDOD1 and PaDOD2 in suspension cultures of P. americana were investigated by semiquantitative RT-PCR. The transcripts of PaDODs were found in both betacyanin-producing red cells and non-betacyanin-producing white cells, suggesting that not only the expression of DOD, but also the supplementation of DOPA might be a regulatory step for the betalain biosynthesis in P. americana.

scholarly journals Conservation and discreteness of the atromentin gene cluster in fungi

2020 ◽  
Author(s):  
James P. Tauber ◽  
John Hintze
Keyword(s):  
Transcription Factor ◽  
Gene Cluster ◽  
Gene Structure ◽  
Transcriptional Control ◽  
Parallel Evolution ◽  
Promoter Regions ◽  
Promoter Motif ◽  
Paraphyletic Group ◽  
Future Work ◽  
Insight Into

AbstractThe atromentin synthetase gene cluster is responsible for catalyzing the precursor pigment atromentin, which is further catalyzed into hundreds of different pigments that span different taxa in the Basidiomycota and is a distinguished feature of Boletales. Previous work identified co-transcription of the two essential clustered atromentin genes (the atromentin synthetase (NPS) and the aminotransferase) by inducible pigment conditions and also conserved genetic elements in the promoter regions (motifs). For this work, we found that the NPS and its promoter motif appeared to follow the same evolutionary path as the mushrooms’. The NPS appears to predate Boletales and originate in Agaricomycetes, and with convergent/parallel evolution that allowed ascomycetes to produce atromentin. Additionally, a consensus of the intron-exon gene structure for basidiomycetous, atromentin-catalyzing NPSs was identified whereby a significant deviation occurred in the paraphyletic group, Paxillaceae. This gene structure was not present in NPSs in Aspergilli. Lastly, we found a putative TATA box adjacent to the palindromic motif of NPS, indicating (co-)transcriptional control by a TATA(-like) binding transcription factor. Combined with previous decades’ worth of research, our results support that not only can atromentin derivatives be used for chemo-taxonomy, but also atromentin’s genetic basis. Future work using the putative promoter motif will provide new insight into which (co-)transcription factor may be responsible for the transcriptional control of atromentin synthetases.

Genome-wide identification of the AP2/ERF transcription factor family in pepper (Capsicum annuum L.)

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 663-674 ◽  
Author(s):  
Jing-Hao Jin ◽  
Min Wang ◽  
Huai-Xia Zhang ◽  
Abid Khan ◽  
Ai-Min Wei ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Differential Expression ◽  
Expression Profiles ◽  
Phytophthora Capsici ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Promoter Regions ◽  
Genome Database ◽  
Cis Acting ◽  
Biotic Stresses

The AP2/ERF family is one of the largest transcription factor families in the plant kingdom. AP2/ERF genes contributing to various processes including plant growth, development, and response to various stresses have been identified. In this study, 175 putative AP2/ERF genes were identified in the latest pepper genome database and classified into AP2, RAV, ERF, and Soloist subfamilies. Their chromosomal localization, gene structure, conserved motif, cis-acting elements within the promoter region, and subcellular locations were analyzed. Transient expression of CaAP2/ERF proteins in tobacco revealed that CaAP2/ERF064, CaAP2/ERF109, and CaAP2/ERF127 were located in the nucleus, while CaAP2/ERF171 was located in the nucleus and cytoplasm. Most of the CaAP2/ERF genes contained cis-elements within their promoter regions that responded to various stresses (HSE, LTR, MBS, Box-W1/W-box, and TC-rich repeats) and phytohormones (ABRE, CGTCA-motif, and TCA-element). Furthermore, RNA-seq analysis revealed that CaAP2/ERF genes showed differential expression profiles in various tissues as well as under biotic stresses. Moreover, qRT-PCR analysis of eight selected CaAP2/ERF genes also showed differential expression patterns in response to infection with Phytophthora capsici (HX-9) and in response to phytohormones (SA, MeJA, and ETH). This study will provide basic insights for further studies of the CaAP2/ERF genes involved in the interaction between pepper and P. capsici.

scholarly journals Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
Author(s):  
John S Reece-Hoyes ◽  
Jane Shingles ◽  
Denis Dupuy ◽  
Christian A Grove ◽  
Albertha JM Walhout ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Caenorhabditis Elegans ◽  
Gene Duplication ◽  
Expression Patterns ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Insight Into

scholarly journals Genome-Wide Identification of the B-BOX Genes that Respond to Multiple Ripening Related Signals in Sweet Cherry Fruit

2021 ◽  
Vol 22 (4) ◽  
pp. 1622
Author(s):  
Yanyan Wang ◽  
Zefeng Zhai ◽  
Yueting Sun ◽  
Chen Feng ◽  
Xiang Peng ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Stress Responses ◽  
Fruit Development ◽  
Sweet Cherry ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Light Induction ◽  
Promoter Regions ◽  
Genome Database ◽  
Gene Structures

B-BOX proteins are zinc finger transcription factors that play important roles in plant growth, development, and abiotic stress responses. In this study, we identified 15 PavBBX genes in the genome database of sweet cherry. We systematically analyzed the gene structures, clustering characteristics, and expression patterns of these genes during fruit development and in response to light and various hormones. The PavBBX genes were divided into five subgroups. The promoter regions of the PavBBX genes contain cis-acting elements related to plant development, hormones, and stress. qRT-PCR revealed five upregulated and eight downregulated PavBBX genes during fruit development. In addition, PavBBX6, PavBBX9, and PavBBX11 were upregulated in response to light induction. We also found that ABA, BR, and GA3 contents significantly increased in response to light induction. Furthermore, the expression of several PavBBX genes was highly correlated with the expression of anthocyanin biosynthesis genes, light-responsive genes, and genes that function in multiple hormone signaling pathways. Some PavBBX genes were strongly induced by ABA, GA, and BR treatment. Notably, PavBBX6 and PavBBX9 responded to all three hormones. Taken together, BBX proteins likely play major roles in regulating anthocyanin biosynthesis in sweet cherry fruit by integrating light, ABA, GA, and BR signaling pathways.

scholarly journals The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Kuo Yang ◽  
Jian-Ping An ◽  
Chong-Yang Li ◽  
Xue-Na Shen ◽  
Ya-Jing Liu ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Transcription Factor ◽  
Liquid Chromatography ◽  
Zinc Finger ◽  
Leaf Senescence ◽  
Transcriptional Activity ◽  
Molecular Mechanisms ◽  
Liquid Chromatography Mass Spectrometry ◽  
Zinc Finger Transcription Factor ◽  
Insight Into

AbstractJasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.

scholarly journals Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam]

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fuyun Hou ◽  
Taifeng Du ◽  
Zhen Qin ◽  
Tao Xu ◽  
Aixian Li ◽  
...  
Keyword(s):  
Plant Development ◽  
Stress Responses ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Glycosyl Hydrolase ◽  
Expression Patterns ◽  
Human Beings ◽  
Promoter Regions ◽  
Cell Wall Modification ◽  
Biotic Stresses

Abstract Background Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear. Results In this study, 17 β-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analysis. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. Conclusions Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding.

scholarly journals The Coordinated Upregulated Expression of Genes Involved in MEP, Chlorophyll, Carotenoid and Tocopherol Pathways, Mirrored the Corresponding Metabolite Contents in Rice Leaves during De-Etiolation

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1456
Author(s):  
Xin Jin ◽  
Can Baysal ◽  
Margit Drapal ◽  
Yanmin Sheng ◽  
Xin Huang ◽  
...  
Keyword(s):  
Higher Plants ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Isoprenoid Biosynthesis ◽  
Promoter Regions ◽  
Expression Of Genes ◽  
Coordinated Expression ◽  
Rice Leaves ◽  
Mechanistic Basis ◽  
Phosphate Synthase

Light is an essential regulator of many developmental processes in higher plants. We investigated the effect of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1/2 genes (OsHDR1/2) and isopentenyl diphosphate isomerase 1/2 genes (OsIPPI1/2) on the biosynthesis of chlorophylls, carotenoids, and phytosterols in 14-day-old etiolated rice (Oyza sativa L.) leaves during de-etiolation. However, little is known about the effect of isoprenoid biosynthesis genes on the corresponding metabolites during the de-etiolation of etiolated rice leaves. The results showed that the levels of α-tocopherol were significantly increased in de-etiolated rice leaves. Similar to 1-deoxy-D-xylulose-5-phosphate synthase 3 gene (OsDXS3), both OsDXS1 and OsDXS2 genes encode functional 1-deoxy-D-xylulose-5-phosphate synthase (DXS) activities. Their expression patterns and the synthesis of chlorophyll, carotenoid, and tocopherol metabolites suggested that OsDXS1 is responsible for the biosynthesis of plastidial isoprenoids in de-etiolated rice leaves. The expression analysis of isoprenoid biosynthesis genes revealed that the coordinated expression of the MEP (2-C-methyl-D-erythritol 4-phosphate) pathway, chlorophyll, carotenoid, and tocopherol pathway genes mirrored the changes in the levels of the corresponding metabolites during de-etiolation. The underpinning mechanistic basis of coordinated light-upregulated gene expression was elucidated during the de-etiolation process, specifically the role of light-responsive cis-regulatory motifs in the promoter region of these genes. In silico promoter analysis showed that the light-responsive cis-regulatory elements presented in all the promoter regions of each light-upregulated gene, providing an important link between observed phenotype during de-etiolation and the molecular machinery controlling expression of these genes.

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